Non-coding DNA: Difference between revisions

Revision as of 12:00, 30 April 2022

Revision as of 18:13, 12 May 2022

Line 19:

{{Main|Conserved non-coding sequence}}

===Cis-Promoters and trans-regulatory elements===

[[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.

[[Cis-regulatory element]]s are sequences that control the [[Transcription (genetics)|transcription]] of a nearby gene. Many such elements are involved in the [[evolutionary developmental biology|evolution and control of development]].<ref name=Carroll_2008>{{cite journal | vauthors = Carroll SB | title = Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution | journal = Cell | volume = 134 | issue = 1 | pages = 25–36 | date = July 2008 | pmid = 18614008 | doi = 10.1016/j.cell.2008.06.030 | s2cid = 2513041 | author-link1 = Sean B. Carroll }}</ref> Cis-elements may be located in [[Directionality (molecular biology)#5′-end|5']] or [[Directionality (molecular biology)#3′-end|3']] [[untranslated region]]s or within [[intron]]s. [[Trans-regulatory element]]s control the [[Transcription (genetics)|transcription]] of a distant gene.

[[Cis-regulatory element| Regulatory elements]] are sites that control the [[Transcription (genetics)|transcription]] of a nearby gene. They are almost always sequences where [[transcription factor]]s bind to DNA and these transcription factors can either activate transcription (activators) or repress transcription (repressors). Regulatory elements were discoverd in the 1960s and their general characteristics were worked out in the 1970s by studying specific transcription factors in bacteria and bacteriophage.

[[promoter (biology)|Promoter]]s facilitate the transcription of a particular gene and are typically [[Upstream and downstream (DNA)|upstream]] of the coding region. [[Enhancer (genetics)|Enhancer]] sequences may also exert very distant effects on the transcription levels of genes.<ref>{{cite journal | vauthors = Visel A, Rubin EM, Pennacchio LA | title = Genomic views of distant-acting enhancers | journal = Nature | volume = 461 | issue = 7261 | pages = 199–205 | date = September 2009 | pmid = 19741700 | pmc = 2923221 | doi = 10.1038/nature08451 | author-link3 = Len A. Pennacchio | bibcode = 2009Natur.461..199V }}</ref>

Promoters and regulatory sequences represent an abundant class of noncoding DNA but they mostly consist of a collection of relatively short sequences so they don't take up a very large fraction of the genome. The exact amount of regulatory DNA in mammalian genome is unclear because it is difficult to distinguish between spurious transcription factor binding sites and those that are functional. The binding characteristics of typical [[DNA-binding protein]]s were characterized in the 1970s and the biochemical properties of transcription factors predict that in cells with large genomes the majority of binding sites will be fortuitous and not biologiacally functional.

Many regulatory sequences occur near the promoter, usually upstream of the transcription start site of the gene. Some occur within a gene and a few are located downstream of the transcription termination site. In eukaryotes, there are some regulatory ssequences that are located at a considerable distance from the promoter region. These distant regulatory sequences are often called [[Enhancer (genetics)|Enhancers]] but there is no rigorous definition of enhancer that distinguishes it from other transcription factor binding sites.<ref>{{cite journal | vauthors = Compe E, Egly J-M | title = The Long Road to Understanding RNAPII Transcription Initiation and Related Syndromes | journal = Annual Review of Biochemistry | volume = 90 | pages = 193-219 | date = 2021 | doi = 10.1146/annurev-biochem-090220-112253}}</ref><ref>{{cite journal | vauthors = Visel A, Rubin EM, Pennacchio LA | title = Genomic views of distant-acting enhancers | journal = Nature | volume = 461 | issue = 7261 | pages = 199–205 | date = September 2009 | pmid = 19741700 | pmc = 2923221 | doi = 10.1038/nature08451 | author-link3 = Len A. Pennacchio | bibcode = 2009Natur.461..199V }}</ref>.

===Introns===