RNA, Genome Output and Input
RNA, the transcriptional output of genomes, not only templates protein synthesis or directly engages in catalytic functions, but can feed back to the genome and serve as regulatory input for gene expression. Transcripts affecting the RNA abundance of other genes act by mechanisms similar to and in c...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2020-10-01
|
| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2020.589413/full |
| _version_ | 1818036415407063040 |
|---|---|
| author | Jörg Morf Srinjan Basu Paulo P. Amaral |
| author_facet | Jörg Morf Srinjan Basu Paulo P. Amaral |
| author_sort | Jörg Morf |
| collection | DOAJ |
| description | RNA, the transcriptional output of genomes, not only templates protein synthesis or directly engages in catalytic functions, but can feed back to the genome and serve as regulatory input for gene expression. Transcripts affecting the RNA abundance of other genes act by mechanisms similar to and in concert with protein factors that control transcription. Through recruitment or blocking of activating and silencing complexes to specific genomic loci, RNA and protein factors can favor transcription or lower the local gene expression potential. Most regulatory proteins enter nuclei from all directions to start the search for increased affinity to specific DNA sequences or to other proteins nearby genuine gene targets. In contrast, RNAs emerge from spatial point sources within nuclei, their encoding genes. A transcriptional burst can result in the local appearance of multiple nascent RNA copies at once, in turn increasing local nucleic acid density and RNA motif abundance before diffusion into the nuclear neighborhood. The confined initial localization of regulatory RNAs causing accumulation of protein co-factors raises the intriguing possibility that target specificity of non-coding, and probably coding, RNAs is achieved through gene/RNA positioning and spatial proximity to regulated genomic regions. Here we review examples of positional cis conservation of regulatory RNAs with respect to target genes, spatial proximity of enhancer RNAs to promoters through DNA looping and RNA-mediated formation of membrane-less structures to control chromatin structure and expression. We speculate that linear and spatial proximity between regulatory RNA-encoding genes and gene targets could possibly ease the evolutionary pressure on maintaining regulatory RNA sequence conservation. |
| first_indexed | 2024-12-10T07:10:35Z |
| format | Article |
| id | doaj.art-0b2a686236534de29079b15cdfc339d8 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-10T07:10:35Z |
| publishDate | 2020-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-0b2a686236534de29079b15cdfc339d82022-12-22T01:58:03ZengFrontiers Media S.A.Frontiers in Genetics1664-80212020-10-011110.3389/fgene.2020.589413589413RNA, Genome Output and InputJörg Morf0Srinjan Basu1Paulo P. Amaral2Jeffrey Cheah Biomedical Centre, Wellcome – Medical Research Council (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United KingdomJeffrey Cheah Biomedical Centre, Wellcome – Medical Research Council (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United KingdomJeffrey Cheah Biomedical Centre, The Milner Therapeutics Institute, University of Cambridge, Cambridge, United KingdomRNA, the transcriptional output of genomes, not only templates protein synthesis or directly engages in catalytic functions, but can feed back to the genome and serve as regulatory input for gene expression. Transcripts affecting the RNA abundance of other genes act by mechanisms similar to and in concert with protein factors that control transcription. Through recruitment or blocking of activating and silencing complexes to specific genomic loci, RNA and protein factors can favor transcription or lower the local gene expression potential. Most regulatory proteins enter nuclei from all directions to start the search for increased affinity to specific DNA sequences or to other proteins nearby genuine gene targets. In contrast, RNAs emerge from spatial point sources within nuclei, their encoding genes. A transcriptional burst can result in the local appearance of multiple nascent RNA copies at once, in turn increasing local nucleic acid density and RNA motif abundance before diffusion into the nuclear neighborhood. The confined initial localization of regulatory RNAs causing accumulation of protein co-factors raises the intriguing possibility that target specificity of non-coding, and probably coding, RNAs is achieved through gene/RNA positioning and spatial proximity to regulated genomic regions. Here we review examples of positional cis conservation of regulatory RNAs with respect to target genes, spatial proximity of enhancer RNAs to promoters through DNA looping and RNA-mediated formation of membrane-less structures to control chromatin structure and expression. We speculate that linear and spatial proximity between regulatory RNA-encoding genes and gene targets could possibly ease the evolutionary pressure on maintaining regulatory RNA sequence conservation.https://www.frontiersin.org/articles/10.3389/fgene.2020.589413/fullRNAlncRNAgene regulationchromosome conformationtranscriptional bursting |
| spellingShingle | Jörg Morf Srinjan Basu Paulo P. Amaral RNA, Genome Output and Input Frontiers in Genetics RNA lncRNA gene regulation chromosome conformation transcriptional bursting |
| title | RNA, Genome Output and Input |
| title_full | RNA, Genome Output and Input |
| title_fullStr | RNA, Genome Output and Input |
| title_full_unstemmed | RNA, Genome Output and Input |
| title_short | RNA, Genome Output and Input |
| title_sort | rna genome output and input |
| topic | RNA lncRNA gene regulation chromosome conformation transcriptional bursting |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2020.589413/full |
| work_keys_str_mv | AT jorgmorf rnagenomeoutputandinput AT srinjanbasu rnagenomeoutputandinput AT paulopamaral rnagenomeoutputandinput |