Junk DNA
by Owen Borville
July 31, 2024
Biology, Biosciences
“Junk DNA,” also known as non-functional DNA, refers to segments of DNA that established scientists believe or once believed lack a relevant biological function. Some of this "Junk DNA" is DNA in which the purpose is unknown, and therefore have been given this informal name.
While most organisms harbor some of this unknown DNA, or "junk DNA," which is often pseudogenes and fragments of transposons and viruses—there’s ongoing debate among scientists about whether certain organisms might possess substantial amounts of it.
Historically, scientists believed that only a small fraction of the human genome contained functional DNA elements (genes) that could be affected by mutations. This view emerged in the late 1940s, with predictions by population geneticist J.B.S. Haldane and Nobel laureate Hermann Muller. They suggested that if a significant portion of mutations were harmful, the human species couldn’t survive such a genetic load. Muller even estimated that the human genome could contain around 30,000 genes.
However, subsequent discoveries revealed that genome size variations weren’t directly tied to species complexity. The “C-value paradox” arose when closely related species exhibited vastly different genome sizes. Repetitive DNA sequences were identified as a major contributor to these differences. Some scientists speculated that repetitive DNA regulated gene expression, while others considered it nonfunctional.
In recent years, our understanding of "junk DNA" has changed. Noncoding DNA, once dismissed as “junk,” is now recognized as having diverse roles in gene regulation and cell biology. In other words, this "junk DNA" is not always useless or passive. Researchers continue to uncover the complexities of this genomic dark matter, challenging the notion that it’s entirely nonfunctional.
A Stanford Medicine-led study has clarified how ‘junk DNA’ influences gene expression. Changes to short, repetitive sequences in the genome have been linked to diseases like autism and schizophrenia. New revelations about how such changes increase and decrease gene expression may provide insight into these and other disorders.
A new study led by researchers at University of California, Berkeley, and Washington University explored the function of one component of this junk DNA, transposons, which are selfish DNA sequences able to invade their host genome. The study shows that at least one family of transposons — ancient viruses that have invaded our genome by the millions — plays a critical role in viability in the mouse, and perhaps in all mammals. When the researchers knocked out a specific transposon in mice, half their mouse pups died before birth.
In 2012, a research program called the ENCODE project concluded that around three quarters of the noncoding DNA (junk DNA) in the human genome did undergo transcription and that almost 50% of the genome was available to the proteins involved in genetic regulation such as transcription factors.
Cells use some of their noncoding DNA to create a diverse menagerie of RNA molecules that regulate or assist with protein production in various ways.
Only about 1 percent of DNA is made up of protein-coding genes; the other 99 percent is noncoding. Noncoding DNA does not provide instructions for making proteins. Scientists once thought noncoding DNA was “junk,” with no known purpose. However, it is becoming clear that at least some of it is integral to the function of cells, particularly the control of gene activity. For example, noncoding DNA contains sequences that act as regulatory elements, determining when and where genes are turned on and off. Such elements provide sites for specialized proteins (called transcription factors) to attach (bind) and either activate or repress the process by which the information from genes is turned into proteins (transcription). Noncoding DNA contains many types of regulatory elements:
Other regions of noncoding DNA provide instructions for the formation of certain kinds of RNA molecules. RNA is a chemical cousin of DNA. Examples of specialized RNA molecules produced from noncoding DNA include transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), which help assemble protein building blocks (amino acids) into a chain that forms a protein; microRNAs (miRNAs), which are short lengths of RNA that block the process of protein production; and long noncoding RNAs (lncRNAs), which are longer lengths of RNA that have diverse roles in regulating gene activity.
Some structural elements of chromosomes are also part of noncoding DNA. For example, repeated noncoding DNA sequences at the ends of chromosomes form telomeres. Telomeres protect the ends of chromosomes from being degraded during the copying of genetic material. Repetitive noncoding DNA sequences also form satellite DNA, which is a part of other structural elements. Satellite DNA is the basis of the centromere, which is the constriction point of the X-shaped chromosome pair. Satellite DNA also forms heterochromatin, which is densely packed DNA that is important for controlling gene activity and maintaining the structure of chromosomes.
Some noncoding DNA regions, called introns, are located within protein-coding genes but are removed before a protein is made. Regulatory elements, such as enhancers, can be located in introns. Other noncoding regions are found between genes and are known as intergenic regions.
The identity of regulatory elements and other functional regions in noncoding DNA is not completely understood. Researchers are working to understand the location and role of these genetic components.
So, while the term “junk DNA” persists, it’s essential to recognize that our understanding of these regions is still unfolding and under further research. A better term may be unknown DNA or uncoded DNA.
en.wikipedia.org
quantamagazine.org
news-medical.net
academic.oup.com
med.stanford.edu/news/all-news/2023/09/junk-dna-diseases.html
news.berkeley.edu/2021/10/18/so-called-junk-dna-plays-critical-role-in-mammalian-development/
news-medical.net/life-sciences/What-is-Junk-DNA.aspx
quantamagazine.org/the-complex-truth-about-junk-dna-20210901/
medlineplus.gov/genetics/understanding/basics/noncodingdna/
Maston GA, Evans SK, Green MR. Transcriptional regulatory elements in the human genome. Annu Rev Genomics Hum Genet. 2006;7:29-59. Review. PubMed: 16719718.
ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247. PubMed: 22955616; Free full text available from PubMed Central: PMC3439153.
Plank JL, Dean A. Enhancer function: mechanistic and genome-wide insights come together. Mol Cell. 2014 Jul 3;55(1):5-14. doi: 10.1016/j.molcel.2014.06.015. Review. PubMed: 24996062.
by Owen Borville
July 31, 2024
Biology, Biosciences
“Junk DNA,” also known as non-functional DNA, refers to segments of DNA that established scientists believe or once believed lack a relevant biological function. Some of this "Junk DNA" is DNA in which the purpose is unknown, and therefore have been given this informal name.
While most organisms harbor some of this unknown DNA, or "junk DNA," which is often pseudogenes and fragments of transposons and viruses—there’s ongoing debate among scientists about whether certain organisms might possess substantial amounts of it.
Historically, scientists believed that only a small fraction of the human genome contained functional DNA elements (genes) that could be affected by mutations. This view emerged in the late 1940s, with predictions by population geneticist J.B.S. Haldane and Nobel laureate Hermann Muller. They suggested that if a significant portion of mutations were harmful, the human species couldn’t survive such a genetic load. Muller even estimated that the human genome could contain around 30,000 genes.
However, subsequent discoveries revealed that genome size variations weren’t directly tied to species complexity. The “C-value paradox” arose when closely related species exhibited vastly different genome sizes. Repetitive DNA sequences were identified as a major contributor to these differences. Some scientists speculated that repetitive DNA regulated gene expression, while others considered it nonfunctional.
In recent years, our understanding of "junk DNA" has changed. Noncoding DNA, once dismissed as “junk,” is now recognized as having diverse roles in gene regulation and cell biology. In other words, this "junk DNA" is not always useless or passive. Researchers continue to uncover the complexities of this genomic dark matter, challenging the notion that it’s entirely nonfunctional.
A Stanford Medicine-led study has clarified how ‘junk DNA’ influences gene expression. Changes to short, repetitive sequences in the genome have been linked to diseases like autism and schizophrenia. New revelations about how such changes increase and decrease gene expression may provide insight into these and other disorders.
A new study led by researchers at University of California, Berkeley, and Washington University explored the function of one component of this junk DNA, transposons, which are selfish DNA sequences able to invade their host genome. The study shows that at least one family of transposons — ancient viruses that have invaded our genome by the millions — plays a critical role in viability in the mouse, and perhaps in all mammals. When the researchers knocked out a specific transposon in mice, half their mouse pups died before birth.
In 2012, a research program called the ENCODE project concluded that around three quarters of the noncoding DNA (junk DNA) in the human genome did undergo transcription and that almost 50% of the genome was available to the proteins involved in genetic regulation such as transcription factors.
Cells use some of their noncoding DNA to create a diverse menagerie of RNA molecules that regulate or assist with protein production in various ways.
Only about 1 percent of DNA is made up of protein-coding genes; the other 99 percent is noncoding. Noncoding DNA does not provide instructions for making proteins. Scientists once thought noncoding DNA was “junk,” with no known purpose. However, it is becoming clear that at least some of it is integral to the function of cells, particularly the control of gene activity. For example, noncoding DNA contains sequences that act as regulatory elements, determining when and where genes are turned on and off. Such elements provide sites for specialized proteins (called transcription factors) to attach (bind) and either activate or repress the process by which the information from genes is turned into proteins (transcription). Noncoding DNA contains many types of regulatory elements:
Other regions of noncoding DNA provide instructions for the formation of certain kinds of RNA molecules. RNA is a chemical cousin of DNA. Examples of specialized RNA molecules produced from noncoding DNA include transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), which help assemble protein building blocks (amino acids) into a chain that forms a protein; microRNAs (miRNAs), which are short lengths of RNA that block the process of protein production; and long noncoding RNAs (lncRNAs), which are longer lengths of RNA that have diverse roles in regulating gene activity.
Some structural elements of chromosomes are also part of noncoding DNA. For example, repeated noncoding DNA sequences at the ends of chromosomes form telomeres. Telomeres protect the ends of chromosomes from being degraded during the copying of genetic material. Repetitive noncoding DNA sequences also form satellite DNA, which is a part of other structural elements. Satellite DNA is the basis of the centromere, which is the constriction point of the X-shaped chromosome pair. Satellite DNA also forms heterochromatin, which is densely packed DNA that is important for controlling gene activity and maintaining the structure of chromosomes.
Some noncoding DNA regions, called introns, are located within protein-coding genes but are removed before a protein is made. Regulatory elements, such as enhancers, can be located in introns. Other noncoding regions are found between genes and are known as intergenic regions.
The identity of regulatory elements and other functional regions in noncoding DNA is not completely understood. Researchers are working to understand the location and role of these genetic components.
So, while the term “junk DNA” persists, it’s essential to recognize that our understanding of these regions is still unfolding and under further research. A better term may be unknown DNA or uncoded DNA.
en.wikipedia.org
quantamagazine.org
news-medical.net
academic.oup.com
med.stanford.edu/news/all-news/2023/09/junk-dna-diseases.html
news.berkeley.edu/2021/10/18/so-called-junk-dna-plays-critical-role-in-mammalian-development/
news-medical.net/life-sciences/What-is-Junk-DNA.aspx
quantamagazine.org/the-complex-truth-about-junk-dna-20210901/
medlineplus.gov/genetics/understanding/basics/noncodingdna/
Maston GA, Evans SK, Green MR. Transcriptional regulatory elements in the human genome. Annu Rev Genomics Hum Genet. 2006;7:29-59. Review. PubMed: 16719718.
ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247. PubMed: 22955616; Free full text available from PubMed Central: PMC3439153.
Plank JL, Dean A. Enhancer function: mechanistic and genome-wide insights come together. Mol Cell. 2014 Jul 3;55(1):5-14. doi: 10.1016/j.molcel.2014.06.015. Review. PubMed: 24996062.