Editing Transcriptome (section)

==Types of RNA transcripts==

Almost all functional transcripts are derived from known genes. The only exceptions are a small number of transcripts that might play a direct role in regulating gene expression near the prompters of known genes. (See [[Enhancer RNA]].)

Gene occupy most of prokaryotic genomes so most of their genomes are transcribed. Many eukaryotic genomes are very large and known genes may take up only a fraction of the genome. In mammals, for example, known genes only account for 40-50% of the genome.<ref name="Francis&Wörheide2017">{{cite journal | vauthors = Francis WR, Wörheide G | title = Similar Ratios of Introns to Intergenic Sequence across Animal Genomes | journal = Genome Biology and Evolution | volume = 9 | issue = 6 | pages = 1582–1598 | date = June 2017 | pmid = 28633296 | pmc = 5534336 | doi = 10.1093/gbe/evx103 }}</ref> Nevertheless, identified transcripts often map to a much larger fraction of the genome suggesting that the transcriptome contains spurious transcripts that do not come from genes. Some of these transcripts are known to be non-functional because they map to transcribed pseudogenes or degenerative transposons and viruses. Others map to unidentified regions of the genome that may be junk DNA.

Spurious transcription is very common in eukaryotes, especially those with large genomes that might contain a lot of [[junk DNA]].<ref name = vanBakeletal2011>{{ cite journal | vauthors = van Bakel H, Nislow C, Blencowe BJ, and Hughes TR | date = 2011 | title = Response to "the reality of pervasive transcription | journal = PLOS Biology | volume = 9 | issue = 7 | pages = e1001102 |  doi = 10.1371/journal.pbio.1001102 | s2cid = 15680321 | pmc = 3134445 | doi-access = free }}</ref><ref name = Jensenetal2013>{{ cite journal | vauthors = Jensen TH, Jacquier A, and Libri D | date = 2013 | title = Dealing with pervasive transcription | journal = Molecular Cell | volume = 52 | issue = 4 | pages = 473–484 | doi = 10.1016/j.molcel.2013.10.032 | pmid = 24267449 | doi-access = free }}</ref><ref name = Sverdlov2017>{{ cite journal | last = Sverdlov | first = Eugene | date = 2017 | title = Transcribed Junk Remains Junk If It Does Not Acquire A Selected Function in Evolution | journal = BioEssays | volume = 39 | issue = 12 | pages = 1700164 | doi = 10.1002/bies.201700164 | pmid = 29071727 | s2cid = 35346807 }}</ref><ref name = Wade&Grainger2018>{{ cite journal | vauthors = Wade JT, and Grainger DC | date = 2018 | title =  Spurious transcription and its impact on cell function | journal = Transcription | volume = 9 | issue = 3 | pages = 182–189 | doi = 10.1080/21541264.2017.1381794 | pmid = 28980880 | pmc = 5927700 }}</ref> Some scientists claim that if a transcript has not been assigned to a known gene then the default assumption must be that it is junk RNA until it has been shown to be functional.<ref name=vanBakeletal2011/><ref name = Palazzo&Lee2015>{{ cite journal | vauthors = Palazzo AF, and Lee ES | date = 2015 | title = Non-coding RNA: what is functional and what is junk? | journal =  Frontiers in Genetics | volume = 6 | page = 2 | doi = 10.3389/fgene.2015.00002 | pmid = 25674102 | pmc = 4306305 | doi-access = free }}</ref> This would mean that much of the transcriptome in species with large genomes is probably junk RNA. (See [[Non-coding RNA]])

The transcriptome includes the transcripts of protein-coding genes (mRNA plus introns) as well as the transcripts of non-coding genes (functional RNAs plus introns).

*[[Ribosomal RNA]]/rRNA: Usually the most abundant RNA in the transcriptome.
*[[Long non-coding RNA]]/lncRNA: Non-coding RNA transcripts that are more than 200 nucleotides long. Members of this group comprise the largest fraction of the non-coding transcriptome other than introns. It is not known how many of these transcripts are functional and how many are junk RNA.
*[[transfer RNA]]/tRNA
*[[micro RNA]]/miRNA: 19-24 nucleotides (nt) long. Micro RNAs up- or downregulate expression levels of mRNAs by the process of [[RNA interference]] at the post-transcriptional level.<ref name="etymology" />
*[[small interfering RNA]]/siRNA: 20-24 nt
*[[small nucleolar RNA]]/snoRNA
*[[Piwi-interacting RNA]]/piRNA: 24-31 nt. They interact with [[Piwi protein]]s of the [[Argonaute]] family and have a function in targeting and cleaving [[transposon]]s.<ref name="cellerino12" />
*[[enhancer RNA]]/eRNA:<ref name="etymology" />