What is Junk DNA?

Junk DNA refers to fragments of DNA that do not encode protein sequences.

Junk DNA

Ever since the genomes of the first eukaryotes, including nucleated organisms from yeast to humans, were deciphered, scientists have been wondering why most of the organism's DNA did not form useful genes. From mutation protection to structural support of chromosomes, there are many possible explanations for this so-called junk DNA. However, the results of completely consistent research on junk DNA from humans, mice, and rats indicate that this region may contain important regulatory mechanisms that can control basic biochemical reactions and developmental processes. Will help organisms evolve more complex organisms. The discovery that complex organisms have more genes that do not mutate than simple eukaryotes undoubtedly greatly enhances this finding.

In order to have a deeper understanding of this problem, a research team led by David Haussler, a computational biologist at the University of California, Santa Cruz (UCSC), studied five species of vertebrates-humans, mice, and rats. , Chicken, and puffer fish compared with the garbage DNA sequences of four insects, two worms, and seven yeasts. The researchers got an amazing pattern from the comparison results: the more complex the organism, the more important junk DNA seems.

The implicit possibility is that if different kinds of organisms have the same DNA, then these DNAs must be used to solve some key problems. Yeasts and vertebrates share a certain amount of DNA. After all, they both need to make proteins, but only 15% of the shared DNA has nothing to do with genes. The research team reported in the online edition of the journal Genome Research that they compared yeast to more complex worms, which are a multicellular organism, and found that 40% of the shared DNA was not encoded. The researchers then compared vertebrates to insects, which are more complex than worms, and found that more than 66% of the shared DNA contained unencoded DNA.

UCSC computational biologist Adam Siepel, who participated in the research, points out that the results of worm research need to be treated with caution because scientists have analyzed only two of the genomes. Nevertheless, Siepel believes that this finding strongly supports the theory that the increased biological complexity of vertebrates and insects is mainly due to the fine patterns of gene regulation.

Philip Green, a molecular biologist at the University of Washington in Seattle, agrees. "The results of this research are convincing," he said, but he also stressed that research on all unencoded DNA that is not shared by living organisms remains inconclusive.

References: From the United States & lt; Medical Research & gt;

Quiet Revolution: Recognizing "junk" DNA fragments

According to the British "New Scientist" magazine (August 7 edition) and the German News Agency reported on the 10th, recently, Australian astrobiologist Paul Davis published an amazing view in the latest issue of "New Scientist" magazine: Alien civilizations may have written their "history of rise and fall" and "welcome words" to human cells into the DNA of our cells. Only when human technology has developed to a certain stage can we understand those DNA from aliens. "Encrypted information" left by people! It is not possible for aliens to communicate with humans using optoelectronics for more than 40 years. Astronomers around the world have tirelessly searched the vast space with astronomical telescopes, hoping to capture the optoelectronic information sent by an alien civilization to the earth. Scientists in the US "SETI" research program even launched the "Phoenix Project", using astronomical telescopes to look for laser signals in outer space that might be emitted by aliens. So far, however, all searches have failed. Professor Paul Davis believes that this futile result is reasonable, because if there is an alien civilization in other galaxies, then alien technology is likely to be ahead of humans for millions or even hundreds of millions of years, and it is difficult to believe Alien intelligent creatures with such advanced civilizations use "primitive" radios or lasers to communicate with Earth people. Davis said, "Aliens may show their presence in another way, just like leaving an obelisk in the science-fiction movie 2001" A Space Odyssey. "Leaving their remains on Earth may become A more compelling approach. "

However, this is not all. In the past few years, molecular biologists have increasingly felt that the name of "junk DNA" is too sloppy, and even the definition of "gene" needs to be rewritten. Encoding proteins is not the full meaning of DNA. Some of those non-coding regions may not have obvious functions, as shown in the experiments above, but we do nt know more about them, so we ca nt throw them into garbage dumps in a preconceived manner. In fact, there are already some dazzling things in the pile of "trash", and this is just the tip of the iceberg.

For example, a completely useless pseudogene is not so "false" in theory. In 2003, a Japanese research team discovered the first functional pseudogene. Scientists have developed a genetically modified mouse with a gene called "sex-lethal". The terrible foreign gene with this name did not cause any negative effects in most mice, but in a certain strain, all the mice died at an early age. Studies have shown that in this line of mice, a foreign gene accidentally inserted into a pseudogene called makorin1-p1 and destroyed it. This pseudogene is a mutated version of the makorin1 gene, which is much shorter than the "original" and does not encode a protein. It should be useless according to traditional theory. However, the fact is that when it is damaged, the corresponding true gene no longer works.

Well, at least this example shows that genes that do nt encode proteins are also vital to survival. There is nothing fake, just work differently from traditional genes. But recent research shows that some RNAs can interact with other RNAs, DNA, proteins, and even small molecule chemicals, which directly affect physiological functions-that is, instead of playing the role of a whip, they can directly work as coolies. Some fragments of junk DNA that do not encode proteins, such as the pseudogenes in the experiments described above, may function by being transcribed into RNA. These fragments are not genes in the traditional sense, they can be called "RNA genes". They are often very short and difficult to identify, but they are very important. They regulate the expression of other genes, making them on, off, more active or less active.

There are also some non-coding DNAs. Even if we do not understand their function at all, we can conclude that they are not garbage and must have important functions. The ultra-conserved region (UCR) belongs to this kind. In 2004, a group of American scientists published a report in the journal Science. They compared the genomes of many species, including humans, rats, mice, chickens, dogs, and fish, and found that some of them were extremely similar or even identical. DNA sequence. These sequences are located in non-coding regions, with a total of 480, which are completely the same in humans, rats and mice, and the similarity with the corresponding sequences of dogs, chickens and fish is also far beyond the average similarity of the genomes of various species. However, these sequences were not found in ascidians and Drosophila. People don't know what these highly-reserved sequences do. Their versions on humans and mice are exactly the same, which means that there has been no change in these sequences in the 75 million years since the ancestors of the human and mouse separated. This is extremely incredible. .

To prevent accidents, the researchers checked sequences that were longer than 200 base pairs in length. Statistically speaking, it is basically impossible for such a long sequence to repeat three times due to independent accidental mutation. With 480 such sequences repeated 3 times, it is even more impossible. Many people simply suspect that this experiment is wrong, that human DNA has contaminated mouse DNA samples. In addition, the versions of these sequences in humans and fish differ little, that is, they have changed little in the 400 million years after the separation of human and fish ancestors. This shows that their stability is critical to vertebrates, and even small differences can have fatal consequences.

Scientists speculate that some highly retained sequences may affect the activity of important genes, while others control embryonic development. These sequences differ greatly from each other, and no clues related to their function can be seen. Scientists are considering cultivating transgenic mice lacking a highly retained sequence and observing how they grow and develop, thereby judging the role of the sequence. This discovery proves once again that DNA that does not encode proteins and is traditionally considered junk is definitely not real junk.

It was once suspected that the more complex organisms, the greater the number of genes, but this fact has been overturned. As mentioned earlier, the number of human genes is similar to that of chickens and puffer fish, while rice has almost twice as many genes as humans, and amoeba and onions prove that the overall size of the genome has nothing to do with biological complexity. What exactly determines the fundamental differences between species? It seems that traditional genes must be considered in conjunction with the "junk" that has recently proven to be a treasure.

Astronomers once thought that the stars and dust that shine in the various bands of the electromagnetic spectrum are everything in this universe. However, more and more evidence has made them realize that there are dark matter and dark energy in the universe that are invisible to humans, and in fact they account for the vast majority of the mass of the universe. a few. The ultimate fate of the universe-will it ever expand or collapse into a singularity? It depends more on the mysterious quality in these shadows. The study of dark matter and dark energy is a major advance in cosmology and a major challenge, because scientists have so far failed to give a reasonable explanation of their nature. Junk DNA can be said to be the dark side of the genome, and it will change the face of biology, just as dark matter and dark energy change the face of cosmology.

Is junk DNA really junk?

Before the implementation of the Human Genome Project, there was some controversy about what should be done on this unprecedented worldwide collaborative research project in human history. There is a school of thought that only those DNA sequences that encode proteins need to be determined, because for DNA sequences, we only care about the gene-related part, and the general definition of a gene is the DNA sequence used to encode a protein; another school of thought It is believed that since it is to be measured, all the DNA sequences in the human chromosome should be determined, whether it is related to the encoded protein or not. The difference between these two viewpoints is mainly due to the fact that in the complete DNA sequence contained in a chromosome, the portion encoding the protein only takes up a very, very small portion, and most of the DNA sequence does not actually participate in encoding the protein, so Some DNA sequences were called junk DNA from the beginning, expressing the basic judgment of people's existence value.

However, with the deepening of research work, more and more evidence shows that the so-called junk DNA essentially contains very important information, not "junk"! So looking back today, we have to be grateful that the person in charge of the Human Genome Project eventually prevailed cautiously and was able to determine the complete DNA sequence of humans, thereby avoiding potentially significant scientific losses.

To a species, its junk DNA is indeed like junk, because there is no firm evidence yet to show that it is useful: it can neither encode proteins, act as genes, nor encode RNA, nor can it find obvious Signs of interaction with other molecules such as proteins. Of course, it is entirely possible that it performs a certain function, but it is only performed in the "underground", and we have not been able to see its function.

Now that we don't have any clues on how to find the role of junk DNA, we can instead explore the value of it indirectly. A good way is to compare the DNA sequences of different species on the evolutionary lineage of species. According to the understanding of modern biology, DNA sequences record all heritable life information of a species, so the evolutionary relationship between species in different evolutionary positions should be able to be expressed through the inheritance and change relationship of their DNA sequences. It is conceivable that when a new species evolves from its original species, it is impossible to replace all the proteins. On the contrary, the new species of protein it can produce should be only a small amount, but for what it has In terms of the new form and function, it is crucial. Therefore, only the coding information of such a protein is not found in the DNA sequence of its original species. At the same time, most other proteins that perform similar functions should be based on inheritance.

Modern evolutionary studies based on DNA sequences have indeed confirmed this. Some proteins that are very basic to life, from E. coli to humans, are very similar, and of course the corresponding gene sequences are also very small. In fact, biologists take advantage of this in turn, by comparing the degree of genetic difference between different species of the same protein to measure their distance on the evolutionary lineage, and even irrelevant and stable mutations based on DNA base mutations The hypothesis of speed regards genetic variation as a scale of time, so that the relative evolutionary age between species can be determined based on this clock of evolution.

Conservative garbage

Now that the DNA sequence encoding a protein has such a deep meaning, what about junk DNA sequences? Biologists were inspired from this, so they also compared the junk DNA between different species, and the result was no better than no idea, a shock!

Some people made a preliminary comparison of the human and mouse genome sequences and found that in the so-called junk DNA, 5% of the sequences are actually very conservative, which means that they do not have much difference between humans and mice. Comparing the DNA sequences of proteins, the amount of sequences that have not changed much between humans and mice is 1 to 2 percentage points less than junk DNA. Of course, those conservative junk DNA contains a part that is already very conservative. The sequence that encodes the RNA, but that portion should be small.

Another group of scientists has conducted a more systematic study of this issue. They first compared conserved non-gene sequences (CNGs) on human chromosome 21 by comparing them with mice, and strictly excluded sequences that could encode known proteins and sequences encoding RNA. Then, 220 such conservative non-gene sequences were selected, and 12 species of mammals whose evolutionary relationships were far apart were identified, including platypus and monkeys. They used polymerase chain reaction to find the 220 conserved non-gene sequences from the DNA of these 12 mammals. As a result, most of the 220 conserved non-gene sequences were found in the DNA sequence of at least one mammal. More than 25% of the conserved non-gene sequences are found simultaneously in the DNA sequences of at least 10 mammals.

What is even more surprising is that the similarity of these conserved non-gene sequences that coexist in different mammalian DNA sequences is even stronger than homologous coding proteins or RNA coding genes. Conserved non-gene sequences that are found in at least 12 species at the same time are less than half the difference in the nucleotide arrangement of their protein coding sequences if they are compared! The most prominent example is a short sequence of DNA containing 100 nucleotides. It mutates only at the position of 6 nucleotides among all 13 mammals including humans, even this platypus Short sequences are exactly like people!

The more conservative the more important

This shows that this short sequence has been kept in the genetic information of mammals since the platypus. It has been stable and has not changed much after the occurrence of so many new species. In general, such a high degree of conservation is very significant for the DNA sequence encoding a protein, because if a protein has a basic common life activity function in all these species, then any small Mutations may have fatal consequences, so while evolution produces new species, it must be required that this sequence is inherited by the new species without substantial mutation. But since those conserved non-gene sequences do not assume the task of encoding proteins or RNA, why are they so highly conserved?

Because this question is very puzzling, some people will naturally wonder if this experiment is likely to be wrong. For example, when looking for the same sequence in the DNA of other species, is it possible that the species was not due to contamination of the sample Is the sequence mixed in? This is also the issue that the experimenters are most concerned about, so they have taken all the strictest measures to avoid such errors. In addition, there is external evidence that their amazing experimental results should be error-free, that is, in addition to the 12 mammals of their choice, another research institution has published a similar study of dogs that they independently completed. When comparing the dog's data, the conclusions reached are the same. In this way, you can basically eliminate the worry about the experiment itself.

Because the mammals they selected included very primitive monopods and the most advanced humans, this means that these sequences must have gone through about 300 million years without much variation, and this conservativeness suggests that they It must have a very important role for this species, otherwise, the random mutations that occur in these sequences must have accumulated in such a long history, but since this accumulation cannot be seen, it can only explain their Mutation has the potential to affect species' survival opportunities! The general estimate is that these DNA sequences, once regarded as garbage, have a regulatory control effect on gene expression. Of course, such guesses will need a lot of future experiments to reveal and verify.

Researchers further estimated that there are about 60,000 such conservative non-gene sequences in the entire human DNA sequence. In contrast, the number of genes that a human has, that is, the entire DNA sequence, encodes a sequence unit of a protein. Only about 30,000. Therefore, although people mainly focus on those 30,000 gene sequences, no one can dare to predict how much we will feel when those 60,000 conservative non-gene sequences break the silence and express their unnamed functions to us. Shocked! At least, more and more people believe that junk DNA is definitely not junk.

Is Junk DNA really "junk" DNA? Or gold in trash, oasis in the desert? In this regard, industry experts have long argued. These arguments are intensifying, let's take a look at their latest developments.

The eukaryotic genome contains a large amount of non-coding DNA, which even exceeds 97% in humans. This is considered to be the non-intelligent design of the creator, and it has also become evidence of random evolution. In the past, these sequences have been considered to be non-functional, just selfish DNA sequences that are keen to expand themselves. So called "junk" DNA, junk DNA. These "junk DNA" mainly include introns, simple repeats, mobile sequences and their relics. Of course, some scientists insist that "junk" DNA should be called "non-coding" DNA. Calling "junk" only means that we do not understand the function of this part of DNA.

In the West, two types of evolution have tried to explain why non-coding DNA exists. One theory is that non-coding DNA is "junk" and consists of randomly generated sequences that have lost their ability to encode, but just partially replicated genes without function. The second theory considers non-coding genes to be "selfish," which includes DNA that replicates preferentially and has a greater amount of coded DNA. Because it is parasitic, it is actually a harmful gene.

Why does the perfect creator create these defective DNAs, which are mainly composed of useless, non-coding regions? Are these "garbage" really garbage?

Most scientists speculate that junk DNA is by no means junk. Genomic biologists have found treasure in these non-coding sequences and believe that "junk" is a serious misnomer. Early research suggests that there is some design behind the "junk" DNA. Subsequent research found that many "junk" DNA contains palindromic structures to maintain symmetry between complementary strands. Analysis of these sequences in Drosophila and Bombyx mori shows that these transposed and scattered repeats are highly non-random patterns. These patterns reflect that these sequences are under cellular regulation, not useless or selfish junk DNA. Among species that are distantly related, such as large artiodactyl mammals and humans, these simple repetitive (gt) n (ga) m DNA sequences are found in the major histocompatibility complex MHC-DRB gene. If these sequences were really junk, they would not have been preserved during millions of years of evolution. Another study showed that DNA contains a wide range of unexplainable patterns. Dr Eugene Stanley reports that these patterns are not the result of random changes. It's incredible that a position on a gene will affect nucleotides beyond 1 million bases.

Anglo-American scientists compared mouse and human / T cell receptor sites (TCRAC / TCRDC) C and C regions adjacent DNA with about 100,000 base pairs of DNA sequences. Studies have shown that mouse and human T cell receptor genes have surprisingly similar sequences. They compared those coding parts that really control the receiver's constituent sequences, and also compared the intermediate non-coding sequences, and found that the non-coding sequences were about 71% similar. These non-coding sequences are parts of sequences that have moved and changed randomly during the evolution of humans and rodents separately for 60 million years. In November 2003, "Science" magazine reported the results of experiments by Dermitzakis et al. They tested a set of non-genetic regions on human chromosome 21 and found that in 14 mammals, these sequences were even more conserved than regions that encode proteins. The degree of conservatism suggests that these regions have not been identified as functional. These "junks" have played an important role in the evolution of the human genome.

On May 7, 2004, Natural Science published an article by Helen Pearson online: Although the function of these DNA fragments is unknown, for all vertebrates, these junk DNA may actually be more important than any conjecture. David Haussler's team at the University of California has compared the genome sequences of humans, mice and mice. It was surprising to find that more than 480 conserved regions were identical in the three species. Most of these species have sequences similar to those of chickens, dogs, and fish, but these fragments are not found in ascidians and fruit flies. This fact indicates that during the 400 million years that humans and fish advanced from a common ancestor, the change was small, indicating that these garbage DNAs are important to the offspring of these organisms. Researchers are also investigating the actual role these sequences play. There are exactly the same components in different animals, telling us that even small changes in the sequence of these fragments may be eliminated during evolution. In contrast, non-essential regions of DNA tend to accumulate mutations and therefore have different sequences in different species.

Haussler believes they may control the activity of essential genes. About 1/4 of the sequences overlap with the genes and may be converted into RNA, an intermediate molecule that encodes proteins. These sequences may splice the RNA into different forms. Another possibility is that these sequences control embryonic development, and the development from fish to human is very similar. In previous research, scientists have known that similar conserved sequence components are directly related to brain and limb development. Until now, some people think that human DNA has contaminated mouse samples, only to come to the conclusion that extremely conservative fragments of humans and mice are 100% identical.

Studies have shown that the DNA sequences of these unassembled genes play an important role in life activities. Most non-coding DNA plays an essential role in the effective activity of the gene to which it belongs. Scientists have concluded that DNA that was once considered to be useless and not part of a gene that was kept intact from generation to generation was actually highly preserved and used. Like genes, much of the precise control of proteins occurs in non-coding junk regions.

A certain "junk" area can serve as a repository for DNA changes, so that DNA changes and can be recombined into new models to push evolution forward. Moreover, other non-coding regions act as buffers for drastic changes, and they absorb the effects of genetic material and viruses that infiltrate into animal chromosomes without permission. Without these non-coding regions to absorb foreign interference factors, viruses or foreign genetic sequences may be inserted into important genes, thereby disrupting the normal function of important genes. Scientists speculate that this junk DNA is involved in the organization of chromosomes, or some conventional functions. In September 2002, Nature magazine reported that the junk DNA could promote cell division.

Harvard Medical School's Fred Winston research team has provided new evidence in a recent study that believes that junk DNA has an important role. They found a new gene in the junk DNA of the yeast genome. This new gene does not encode a protein or an enzyme, but when this gene is turned on, it can regulate the expression of neighboring genes. Professor Fred Winston, who led the research, said, "This doesn't explain all junk DNA. It shows the potential use of some junk DNA." "I can't imagine the existence of such a regulatory gene." It can use transcriptional RNA to shield or suppress the function of neighboring genes in the yeast genome. They believe that this gene should also be present in the genomes of other organisms, including humans, that work in the same way.

Prior to this, British scientists found that "junk DNA" could affect the severity of the disease. Some "junk DNA" contains DNA sequences that are repeated many times. This repetitive DNA can provoke a response that ultimately prevents specific genes from being turned on, interfering with the cell's "gene silencing" mechanism, and then affecting the disease. During the division and proliferation of human cells, all genetic information is copied and transmitted to the next generation of cells. Different cells have different functions. For example, muscle cells and blood cells function very differently. Cells need to turn on and "silence" specific genes to achieve specific functions. The "gene silencing" mechanism is very important for the normal function of the cell. If the "silencing" is improper, it will lead to disease.

In addition, junk DNA is the repairer of DNA damage. This study, jointly conducted by scientists from the University of Michigan Medical School and Louisiana State University, has shown for the first time in mammalian cells that a piece of junk DNA called the LINE-1 element can jump to the chromosome where the DNA strand breaks and slip in Repair DNA damage at breaks. Normally, L1 cuts DNA with an enzyme called an endonuclease, so they can insert themselves into the genome. Experiments have shown that there is another mechanism that does not require endonucleases, that is, jumping directly to the broken DNA, which provides another way for L1 to integrate into the DNA strand. Because L1 is so old, they sometimes carry gene fragments when they jump to new sites, so geneticist Moran believes that L1 has played an important role in human evolution-increasing genetic diversity.

For eukaryotes, non-coding DNA is necessary for differential gene expression in differentiated cells. Studies have shown that non-coding DNA provides a structural basis for metaphase chromosome banding. CpG islands, DNA loops, and GR band-based substrate attachment sites reveal how non-coding DNA forms the basis of chromosomal structure. Another study showed that non-coding DNA of eukaryotes is functional as a structural element in the nucleus. The study examined the genome of the single-cell photosynthetic organism Crytomonads. Depending on the proportion of nuclei in the cell, the cell size of this organism varies greatly. Researchers have found that a large amount of non-coding DNA is proportional to the size of the nucleus, so they believe that large nuclear organisms need more non-coding DNA in structure.

Increasing evidence shows that non-coding DNA plays an important role in regulating gene expression during development. Gel retention assays have shown that these simple repeats bind to nucleoproteins and show unique DNA-protein interaction properties. The DNA-protein interaction function has not yet been determined. However, many other examples of DNA-protein interactions have shown the regulatory role of DNA transcription. These studies demonstrate that non-coding DNA regulates the development of photoreceptor cells, the reproductive system, and the central nervous system. Therefore, non-coding DNA plays an important role in regulating development and embryonic origin. These non-coding DNAs provide the appropriate structure for protein translation.

Many studies have confirmed that non-coding DNA enhances the transcription of neighboring genes. Eosinophil-derived neurotoxin, eosinophil cationic protein, variable region of IgM rearrangement gene, -globin gene, tubulin gene, 4-N-acetylgalactosyl aminotransferase, aldolase B Genes, acetaldehyde reductase genes, k-light chain genes, and so on, all have descriptions of enhancement within genes. Other studies have confirmed that non-coding DNA acts as a silencing gene and inhibits the transcription of neighboring genes. Osteogenin gene, 2-crystallin gene, CD4 gene, -globin gene, glial cell adhesion molecule, neuron-glia cell adhesion molecule, platelet-derived growth factor A chain gene, renin gene This is described in studies such as this.

The role of non-coding DNA is so numerous and widespread, and evolutionary researchers are focusing on the "co-evolutionary" model of these sequences. In fact, contrary to what evolutionists have stated, these non-coding DNAs are necessary for the function of the genome. "Junk" DNA is some surprising "junk", refuting the "selfish" and "junk" theories of non-coding DNA. Scientists are working to find out why the large amount of junk DNA exists and use them to find potential treatments for diseases.

However, the latest reports suggest that "junk" is still junk. Elizabeth Pennisi published an article in Science on June 11, 2004, reporting that such DNA sequences can be discarded after they are used up. Geneticist Marcelo N-brega of the Berkeley National Laboratory in California found that by removing millions of these bases from the mouse genome, mice behaved normally. Edward Rubin and colleagues found that some of the DNA sequences abandoned by human genes- The long non-coding DNA sequences between genes are almost the same as those abandoned in mice.

Having a common ancestor more than 80 million years ago, conservation of this species seems unlikely unless these areas serve the same purpose. The authors therefore assume that these regions must perform a certain function, that is, genetic regulation. N-brega and colleagues compared these conservative areas between fish and humans, and we know that fish and humans are more alienated. Most conserved sequences are not only functional but also help regulate genes. But the results of the rat-human comparison are different. They compared 15 abandoned sequences in 2 species and found that only one sequence was a regulatory region.

This is confusing, N-brega and colleagues decided to delete these abandoned junk DNA fragments from the mouse genome, hoping to learn what other functions these fragments have. Geneticist Yiwen Zhu knocked out two regions. One was about 2 million bases and the other was 100 bases. These two regions are conserved in humans and mice, but not in fish. After inserting the modified genome into mouse embryonic stem cells, Zhu inserted cells into the mouse embryo. They then looked for anomalies in the offspring of the test mice. But no difference was seen between genetically engineered mice and normal mice, and there were no obvious symptoms.

It's amazing that knocking out 2 million bases without any effect. Therefore, some people suspect that this is not true. They believe that these non-coding regions may actually be functional, but they have not been shown in N-brega's experiments.

As Rubin said, is the genome like a soap opera? Can I skip 100 episodes without any impact? Or is it like Hemingway's novel, you can't find clues without reading a page of stories? Or, as Australian astrobiologist Davis claims, human junk DNA may be hiding some valuable information about aliens? This issue will continue to attract a large number of scientists to conduct research on this issue, and we believe that we can draw accurate conclusions in the near future.

The curved, sticky, famous DNA molecule has been added with many noble metaphors: it is the book of life, the molecular director, and the blueprint of human life.

However, for researchers who focus on the entire molecule, not just individual genes arranged on chemical coils, a few other simple metaphors are better: DNA is like a grandmother's little loft, or a small, smart town Flea market.

Others believe that human DNA can be regarded as a tiny ecosystem, an invisible place of residence, filled with competing pieces of genetic material, often showing meekness. In fact, they are selfish. Parasites completely ignore the needs of the human host cells they parasite.

These analogies are derived from the study of a large number of double helix regions, which do not exist as a program for the production of proteins in the body. Their regions are often described with a scornful description: "junk DNA."

Of the 3 billion chemical units or base pairs that make up human DNA, only 3% to 5% exist as an effective region for coding: some produce hormones, collagen, hemoglobin, endorphin, and enzymes, and Genetic instructions for all other human proteins effective substances. The remaining DNA base pairs remain to be explained, and sentence-by-page, page-by-page, and scroll-by-scroll explanations of gene sequences seem to say nothing at first. Useless fillers, plastic foam, and all waste are squeezed into almost every nucleus of the body.

As scientists are willing to point out, one's rubbish is another's wealth. They gradually discovered that most of the non-coding DNA plays an essential role in the effective activities of the genes rooted in them. Scientists have concluded that the DNA that was once considered useless and was not part of the positive force that kept the genes intact from generation to generation was actually highly preserved and used. Just like genes, after undergoing tens of thousands of years and sometimes millions of years of evolution, their chemical properties are still intact, which means that what was once regarded as useless "junk" is for those who own them. Organs are essential.

In some cases, "junk" is seen as a subtle facilitator of genes, amplifying gene activity from whispering regulation to loud shouting. In other cases, when chromosomes are bent and wrinkled, the "junk" tells the chromosomes what their shape should be.

Certain "junk" areas can act as a repository for DNA changes, allowing DNA to become more easily mixed, mutated, and recombined into new patterns, pushing evolution forward. They are like antiques in the attic. They look strange today. Someone bumped into it. After polishing it, they dragged it into the downstairs room to admire everyone.

Moreover, some other non-coding regions act as buffers for drastic changes. They act as a protective coat, absorbing the effects of genetic material and viruses that infiltrate into animal chromosomes without permission. Without these additional non-coding regions to absorb foreign blows, viruses or foreign genetic sequences (jumps from one part of the chromosome to another, those mysterious ones called "transporters" or "jump genes" Genetic material) may have a small landing in the middle of important genes, thereby disrupting the normal function of important genes.

The new study confirms the feasibility of the claims of the "Human Genome Project" advocates, which are a federal plan to explore the entire composition of human DNA. Pragmatists have suggested focusing on areas of normal genes that contain 50,000 to 100,000 genes, while those obsessed with "junk" genes insist that all 3 billion gene blocks should be taken seriously. They envisioned that many interesting insights into human evolution would come from the work of studying the large amounts of material between and around genes.

"I don't believe that DNA is junk," said Dr. Walter Gilbert, a human genetics theorist at Harvard. Protein chemists are biased against DNA. "He added that coding regions may produce proteins that chemists value, but true biologists know that most of the precise control of these proteins occurs behind the scenes. , Exists in non-coded junk areas.

In an article published in the Journal of the National Academy of Natural Sciences, Roy Britton (PhD from California Institute of Technology, 26 years ago, he described "junk" DNA for the first time) said that there are some of our most known DNA trash has a reason to exist as a molecular guide. These sequences, called "Alu sequences", are short, repetitive, each with about 280 DNA base pairs, and they are widely distributed in all primates, including humans Among animal chromosomes. They have long been regarded as useless remnants of genetic events of the primitive era, and virus-like DNA fragments were embedded in the chromosomes of the ancient ape of South Africa and have never been removed because they have been harmless. In this way, the "Aru sequence" has been very lazy, and after tens of thousands of years of slow, gentle, and complex replication, it has become the DNA we see today.

However, Dr. Britton believes that, no matter what its origins, the "Aru sequence" has been selected by primate hosts to perform its duties, and may serve as a delicate regulator of nearby genes. He said that the "Aru Sequence" is so well preserved that we cannot interpret it as a useless tramp. Moreover, some of the preserved parts of the "Aru sequence" may, as predicted, provide a place of refuge for proteins that knock or raise genes.

Dr. Britton said in a telephone interview: It seems premature to conclude that the typical "junk" is under pressure of selection and may have certain functions. But I accept the general view that if something is universal, it will be used.

In the journal Nature Genes, Dr. Ben F. Cooper of Victoria University of British Columbia and Dr. Leroy Hood of Washington University in Seattle, USA, said they compared large pieces of human DNA with corresponding mouse DNA. . They studied 100,000 base pairs of genes responsible for producing the body's T cell receptors, a critical part of the immune system. They compared the coding parts of the sequences that really control the composition of the receptor. They also compared the middle parts, the so-called intragene regions (introns), which are producing a protein (such as many Chemical ubs and wells) were compiled in a complex process.

To their surprise, they confirmed a hypothesis of a gene that is important to the animal's immune system: not only are humans and mice giving very similar commands to recipients, but also the internal regions of the genes that are considered waste. It's very similar. These internal regions of the gene are exactly the parts of the sequence that have moved around and changed arbitrarily during the 60 million years of evolution that distinguished humans from rodents. That being the case, why should we bother to study those clumsy genetic disturbances that may not be useful for the final function of the recipient?

"When we discovered this genetic material, we had to think that the inner region of the gene was involved in the organization of the chromosome, or some regular function. The word 'junk' for me is' I don't know 'Euphemism.'

But Coub also said that there are significant differences between humans and rodents in other genes and non-coding regions, which seems to indicate that in some cases this inheritance is unnecessary. But the fact is the opposite: these areas may be places for mutation and evolution, and they are a safe experimental base, where new genetic information may be generated without destroying existing genes. Finally, these changes may be integrated into the animal's gene coding region through a sensitive mix of chromosomes, and a new protein may be produced.

"My point is that 'junk' DNA is absolutely necessary in the process of evolution and recombination," said Dr. J. Craig Want, of the Genomics Institute in Rockville, Maryland.

Dr. Want points out that there are good reasons for those who have long ignored "junk" DNA. After all, some creatures don't have these "junks" and are fully functional. The genes for variola virus, E. coli and other microorganisms are crowded one by one, with no "junk" or intragenic regions. There are even several higher organisms, such as puffer fish, with very little non-coding DNA. Dr. Sini Brugener of the Medical Research Council of Cambridge, UK, suggests that studying the pufferfish genome is a shortcut to understanding the chromosomes of all higher animals.

However, as explained by Britton and others, the vast majority of complex organisms have complex genomes and many non-gene sequences. Two types of sequences: genetic and non-gene, are usually easily distinguished. Genes are often abundant in their sequences; that is, individual G, T, A, and C base pairs are programmed in fairly complex combinations. In contrast, junk sequences are often simpler and more redundant, consisting of one or two letters that are repeated countless times. However, this is just a general rule. Scientists are often misled by a concept. They just consider a gene to be garbage because it is single. Similarly, some non-coding regions often show considerable complexity.

Scientists have also discovered that there is a pattern followed by various types of advanced genomes. Most mammals, whether they are humans, voles, cats, moles, etc., have a genome of about 3 billion base pairs in length, which means that "junk" and genes have been involved in the long evolution of mammals. It's in some strange equilibrium. And, for reasons that are completely unclear, the genome of a plant is often longer than that of a mammal. For example, wheat's DNA is about 16 billion base pairs in length, while wild lilies are about 100 billion in length; most of the "junk" DNA is a lengthy, non-coding single form.

Dr. Gilbert pointed out that some microbes, such as variola virus and bacteria, have tiny, neat and unnecessary genomes. They multiply quickly, but cannot trigger any activity related to immediate replication. However, the life strategies and replication strategies of higher animals are not just as simple as double fission every 20 seconds. They can provide more complex and advanced genomes and can contribute to the long and tortuous evolution process.

Embryo development is a wonderful process, from an initial cell to an entire living body. There is no doubt that embryonic development is a strictly regulated process, and everything in this process must reach the right place at the right time. Development and cell biologists are exploring molecular clues as to why humans are in the study of embryonic development. During embryonic development, germ layer formation determines which cells become which organs. In the latest study, researchers at the Sanford-Burnham Institute found that microRNAs play a vital role in this process. They pointed out that microRNAs are powerful regulators of cell fate during embryonic development.

Mark Mercola, a professor at the Sanford-Burnham Institute who led the study, said that during the early stages of embryonic development, cells are distributed to form ectoderm, mesoderm, and endoderm, a process that is considered one of the most important developmental events. MicroRNAs play an important role in the localization of cells and germ layers.

microRNAs are relatively short and do not encode proteins. For many years, academia has regarded genomic regions encoding microRNAs as "junk".

However, according to the ENCODE project, a large amount of data in this academic community has shown that "junk" DNA is not junk. Although microRNA does not encode a protein, it can bind to mRNA and prevent the protein encoded by mRNA from being synthesized. In this way, microRNAs determine whether a protein is synthesized at a specific time, and thus play an important regulatory role. MicroRNAs are being considered an important part of normal cell function and human disease processes, and this latest study points out that microRNAs are also important for embryonic development.

To study the microRNAs that affect germ layer formation during early embryonic development, the researchers screened the entire genome microRNA library systematically to identify key molecules that control complex biological processes. Specifically, scientists studied approximately 900 microRNAs (mostly) in the human genome, testing the ability of microRNAs to direct embryonic stem cells to form mesoderm and endoderm. From this, they discovered that there are two microRNA families, let-7 and miR-18, that block endoderm formation and promote mesoderm and ectoderm formation.

To verify the findings, the researchers artificially blocked let-7's function. Studies have shown that let-7's loss of function greatly changes the fate of embryonic cells, and cells that should have formed mesoderm and ectoderm are transformed into endoderm, confirming the key role of microRNA in embryo development.

Subsequently, researchers conducted in-depth studies on the mechanism of action of let-7 and miR-18. They found that these microRNAs direct the formation of mesoderm and ectoderm by inhibiting the TGF signaling pathway. TGF affects many cellular behaviors, including cell proliferation and differentiation. let-7 and miR-18 regulate the activity of TGF, which determines the direction of cell differentiation. ^[2]

After collecting and studying IQ test data from 130 countries, Richard Lynn, an emeritus professor at the University of Ulster in the UK, came to a bold conclusion: Chinese, Japanese, and Koreans have the highest IQ in the world, on average The value is 105. As an East Asian, he is certainly willing to believe the results of Professor Lynn's research, but his conclusion has caused controversy on topics including racial discrimination.

Scientists at the University of Oxford have discovered a gene regulation mechanism that is closely related to cell division. This mechanism is related to an RNA in the nucleus. Its role was previously unknown. The discovery may provide inspiration for stopping cancer cells from expanding.

As we all know, RNA plays an important role in protein synthesis, but scientists have long known that not all kinds of RNA are directly related to protein synthesis. A study funded by the British Medical Research Council (MRC) and the Wellcome Foundation has shown that certain types of RNA play an important role in regulating genes. The findings were published online in Nature.

Human genome engineering has identified about 34,000 genes involved in protein production. The rest of the gene fragments-that is, most genes-are thought to consist of so-called non-functional "junk" DNA fragments. But research in recent years has found that these so-called "junk" DNAs produce about 500,000 RNAs, although the function of these RNAs has not yet been discovered.

"In the past few years, a revolution has been quietly happening in the biological world, and people have begun to recognise the role of RNA. Scientists are beginning to discover that These so-called "junk" DNA fragments are actually extremely important, and the number of RNA species they make is surprising, and their potential significance is extraordinary. "

Akoulitchevv's group is particularly interested in the fact that RNA is closely related to the regulation of a gene called dihydrofolate reductase (DHFR), which can determine the gene's opening and closing status. An enzyme produced by the DHFR gene controls thymine, which is important for rapidly dividing cells. Inhibition of the DHFR gene can effectively prevent the expansion of cancer cells.

Biologists have been thinking for a long time that since almost all specific physiological functions are performed by proteins, DNA that does not encode proteins should be useless and can be called "junk DNA."

It has been 52 years since DNA double helix structures have been shown to humans. It seems that humans have mapped the genomes of many species, including themselves. However, the latest issue of "Science World" magazine pointed out that the "gene" that is usually flooded with academic papers and news media is just a few small paragraphs in the book of life. Most parts of the genome are still hidden in the shadows, and have been ignored as "trash" for a long time. Only a few rays of light are revealed, showing that this huge "junkyard" may contain treasures commensurate with its volume.

Junk DNA in the name of junk

After the sketching of the human genome is completed, common sense such as 23 pairs of chromosomes and 3 billion base pairs has become familiar to non-professionals, and human understanding of their own genetic map has been greatly supplemented and modified. Around 2000, scientists also estimated that there are about 100,000 genes in the human genome, but within five years this number has fallen to 20,000 to 40,000. A more popular saying is about 25,000. These genes contain only about 2% of the total human genome sequence. In other words, about 98% of the information in the blueprint of human life does not seem to belong to any gene and is useless garbage. However, what is genetic waste?

The vast majority of life on earth uses DNA as genetic material, and some viruses use RNA, and there is no other solution-why this is so, scientists do not know. They are eager to find extraterrestrial life, even if it is just bacteria. An important reason is to see whether the use of DNA by Earth's life is accidental or inevitable. DNA consists of 4 bases, or 4 "letters," called A, T, C, and G, respectively. In RNA, the letter T is replaced by U. The entire DNA double helix is like a very long, twisted ladder. Each side of the ladder is a band made up of many letters one by one. Each letter is combined with the corresponding position of the letter on the opposite band to form a step. Is "base pair". Among them, only A and T can be combined with each other, and C and G can be combined with each other, so the base sequence of one of the double strands of DNA is known, and the other one is determined, and the two strands are complementary.

Biological genetic information is the arrangement of these letters on the DNA strand. The process of turning a blueprint into an actual product is a process in which a piece of DNA synthesizes a corresponding RNA sequence (transcription) according to its base sequence, and then the RNA sequence information guides the process of amino acids joining together to form a protein (translation). The physiological functions of organisms are basically completed by proteins, such as transporting oxygen in the blood, performing metabolism, and so on. It can be said that DNA gives orders, RNA waves the whip, and protein is a horrible cow. The process from DNA to RNA to protein is the "central law" of biology.

Such a piece of DNA that can eventually form a protein or "encode a certain protein" is what we traditionally call a "gene." In humans and other organisms, such genes make up only a small part of the entire genome, and they sporadically fall into the dark wilderness like gems. Between each gene is a large piece of DNA sequence that cannot make a protein, that is, a "non-coding sequence".

Cemetery with junk DNA genes

An episode of a 50-minute TV series is split into several sections to be played. The ads inserted in the middle of it are more than half an hour in total. Has it made you intolerable? So what would you feel if you put a 98-minute commercial on a 2-minute serious program? Yes, it's too much! Why is life so wasteful? Except for sex cells, each cell in the human body has a complete set of DNA, and only about 2% of the content of each set of DNA is useful. In other mammals, the ratio is much the same. The genomes of some species are more "sophisticated" and less litter. For example, the genome of chickens is only 1/3 of that of humans and pufferfish is 1/10 of humans, but they have about the same number of genes as humans. Some are even more exaggerated. For example, the onion genome is 12 times the size of the human genome, and the amoeba's genome is more than 200 times larger than the human genome.

There are many explanations for the source of junk DNA, such as a part of the junk from viruses. Retroviruses are a class of viruses that use RNA as their genetic material, of which we are most familiar with HIV. When they invade a host cell, they convert their own RNA into DNA and insert it into the genome, hopping around and making a lot of copies. The process from DNA to RNA is called transcription, which in turn is called reverse transcription. This is also the name of this type of virus. Some retroviruses cause disease, cause AIDS or cancer, and some have no effect. In the course of evolution, many retroviral DNA remained in the human genome and became garbage.

Some junk DNA may be the remains of dead genes, known as "pseudogenes." Scientists believe that they were originally true genes encoding proteins, which lost their function due to mutation and were discarded. Their sequences are very similar to true genes, but there are subtle differences that make it impossible for pseudogenes to encode proteins. Removal of pseudogenes will not affect the function of the organism. Occasionally, a pseudogene will change and resurrect from death may cause trouble. Because the existence of pseudogenes does not increase or reduce the survival advantage of organisms, it is difficult for evolution to remove them from the genome. It is like throwing things into the trash can and no one takes the trash can to empty it. The more things accumulate in the house. There are a large number of pseudogenes in the biological genome, and there are about 20,000 in the human body, which is almost the same as the number of true genes.

There is evidence that at least part of the junk DNA is very much like real junk, because animals still live well after losing them. In October 2004, a group of American scientists reported in the journal Nature that they deleted more than one million base pairs of non-coding DNA in the mouse genome (about 1% of the mouse genome), but did not Perceived effects on development, lifespan and reproduction of these mice. Of the more than 100 tissue tests assessing gene activity, only two found differences. They also bred non-coding DNA mice that lost 3 million base pairs and found no apparent abnormalities.