Non-coding DNA: Difference between revisions

Revision as of 02:17, 18 March 2023

Revision as of 02:47, 18 March 2023

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===Noncoding genes===

{{furtherSee also|Non-coding RNA}}

There are [[Gene|two types of genes]]: protein coding genes and [[Non-coding RNA|noncoding genes]].<ref>{{cite book | vauthors = Kampourakis K | date = 2017 | title = Making sense of genes | publisher = Cambridge University Press | place = Cambridge UK | isbn = 978-1-107-12813-2}}{{page needed|date=June 2022}}</ref> Noncoding genes are an important part of non-coding DNA and they include genes for [[transfer RNA]] and [[ribosomal RNA]]. These genes were discovered in the 1960s. Prokaryotic genomes contain genes for a number of other noncoding RNAs but noncoding RNA genes are much more common in eukaryotes.

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===Promoters and regulatory elements===

{{furtherMain|Promoter (genetics)}}

[[promoter (biology)|Promoter]]s are DNA segments near the 5' end of the gene where transcription begins. They are the sites where [[RNA polymerase]] binds to initiate RNA synthesis. Every gene has a noncoding promoter.

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===Introns===

{{furtherMain|Intron}}

[[File:Pre-mRNA.svg|right|thumbnail|upright=1.35|Illustration of an unspliced pre-mRNA precursor, with five [[intron]]s and six [[exon]]s (top). After the introns have been removed via splicing, the mature mRNA sequence is ready for translation (bottom).]]

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===Untranslated regions===

{{furtherMain|Untranslated region}}

The standard biochemistry and molecular biology textbooks describe non-coding nucleotides in mRNA located between the 5' end of the gene and the translation initiation codon. These regions are called 5'-untranslated regions or 5'-UTRs. Similar regions called 3'-untranslated regions (3'-UTRs) are found at the end of the gene. The 5'-UTRs and 3'UTRs are very short in bacteria but they can be several hundred nucleotides in length in eukaryotes. They contain short elements that control the initiation of translation (5'-UTRs) and transcription termination (3'-UTRs) as well as regulatory elements that may control mRNA stability, processing, and targeting to different regions of the cell.<ref>{{cite book | vauthors = Alberts B, Bray D, Lewis J, Raff M, Roberts K, Watson JD | date = 1994 | title = Molecular Biology of the Cell, 3rd edition | publisher = Garland Publishing Inc. | place = London, UK}}{{page needed|date=June 2022}}</ref><ref>{{ cite book | vauthors = Lewin B | date = 2004 | title = Genes VIII | publisher = Pearson/Prentice Hall | place = Upper Saddle River, NJ, USA}}{{page needed|date=June 2022}}</ref><ref>{{ cite book | vauthors = Moran L, Horton HR, Scrimgeour KG, Perry MD | date = 2012 | title = Principles of Biochemistry Fifth Edition | publisher = Pearson | place = Upper Saddle River, NJ, USA}}{{page needed|date=June 2022}}</ref>

===Origins of replication===

{{furtherMain|Origin of replication}}

DNA synthesis begins at specific sites called [[Origin of replication|origins of replication]]. These are regions of the genome where the DNA replication machinery is assembled and the DNA is unwound to begin DNA synthesis. In most cases, replication proceeds in both directions from the replication origin.

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===Centromeres===

{{furtherMain|Centromere}}

[[File:Human karyotype with bands and sub-bands.png|thumb|Schematic [[karyotype|karyogram]] of a human, showing an overview of the [[human genome]] on [[G banding]], wherein non-coding DNA is present at the centromeres (shown as narrow segment of each chromosome), and also occurs to a greater extent in darker ([[GC-content|GC poor]]) regions.<ref name=Romiguier2017>{{cite journal | vauthors = Romiguier J, Roux C | title = Analytical Biases Associated with GC-Content in Molecular Evolution | journal = Frontiers in Genetics | volume = 8 | issue = | pages = 16 | year = 2017 | pmid = 28261263 | pmc = 5309256 | doi = 10.3389/fgene.2017.00016 }} </ref><br>{{further|Karyotype}}]]

{{further|Centromere}}

Centromeres are the sites where spindle fibers attach to newly replicated chromosomes in order to segregate them into daughter cells when the cell divides. Each eukaryotic chromosome has a single functional centromere that's seen as a constricted region in a condensed metaphase chromosome. Centromeric DNA consists of a number of repetitive DNA sequences that often take up a significant fraction of the genome because each centromere can be millions of base pairs in length. In humans, for example, the sequences of all 24 centromeres have been determined<ref>{{ cite journal | vauthors = Altemose N, Logsdon GA, Bzikadze AV, Sidhwani P, Langley SA, Caldas GV, et al. | title = Complete genomic and epigenetic maps of human centromeres | journal = Science | volume = 376 | pages = 56 | date = 2021 | issue = 6588 | doi = 10.1126/science.abl4178| pmid = 35357911 | pmc = 9233505 | s2cid = 247853627 }}</ref> and they account for about 6% of the genome. However, it's unlikely that all of this noncoding DNA is essential since there is considerable variation in the total amount of centromeric DNA in different individuals.<ref>{{cite journal | vauthors = Miga KH | title = Centromeric satellite DNAs: hidden sequence variation in the human population | journal = Genes | volume = 10 | pages = 353 | date = 2019 | issue = 5 | doi = 10.3390/genes10050352| pmid = 31072070 | pmc = 6562703 | doi-access = free }}</ref> Centromeres are another example of functional noncoding DNA sequences that have been known for almost half a century and it's likely that they are more abundant than coding DNA.

===Telomeres===

{{furtherMain|Telomere}}

Telomeres are regions of repetitive DNA at the end of a [[chromosome]], which provide protection from chromosomal deterioration during [[DNA replication]]. Recent studies have shown that telomeres function to aid in its own stability. Telomeric repeat-containing RNA (TERRA) are transcripts derived from telomeres. TERRA has been shown to maintain telomerase activity and lengthen the ends of chromosomes.<ref>{{cite journal | vauthors = Cusanelli E, Chartrand P | title = Telomeric noncoding RNA: telomeric repeat-containing RNA in telomere biology | journal = Wiley Interdisciplinary Reviews. RNA | volume = 5 | issue = 3 | pages = 407–419 | date = May 2014 | pmid = 24523222 | doi = 10.1002/wrna.1220 | s2cid = 36918311 }}</ref>

===Scaffold attachment regions===

{{furtherMain|Scaffold/matrix attachment region}}

Both prokaryotic and eukarotic genomes are organized into large loops of protein-bound DNA. In eukaryotes, the bases of the loops are called [[Scaffold/matrix attachment region|scaffold attachment regions]] (SARs) and they consist of stretches of DNA that bind an RNA/protein complex to stabilize the loop. There are about 100,000 loops in the human genome and each one consists of about 100 bp of DNA. The total amount of DNA devoted to SARs accounts for about 0.3% of the human genome.<ref>{{cite journal | vauthors = Mistreli T | date = 2020 | title = The self-organizing genome: Principles of genome architecture and function | journal = Cell | volume = 183 | issue = 1 | pages = 28–45 | doi = 10.1016/j.cell.2020.09.014 | pmid = 32976797 | pmc = 7541718 }}</ref>

===Pseudogenes===

{{furtherMain|Pseudogene}}

Pseudogenes are mostly former genes that have become non-functional due to mutation but the term also refers to inactive DNA sequences that are derived from RNAs produced by functional genes ([[Pseudogene|processed pseudogenes]]). Pseudogenes are only a small fraction of noncoding DNA in prokaryotic genomes because they are eliminated by negative selection. In some eukaryotes, however, pseudogenes can accumulate because selection isn't powerful enough to eliminate them (see [[Nearly neutral theory of molecular evolution]]).

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===Repeat sequences, transposons and viral elements===

{{furtherMain|Repeated sequence (DNA)}}

[[File:Bacterial mobile elements.svg|thumb|upright=1.35|[[Mobile genetic elements]] in the cell (left) and how they can be acquired (right)]]