Transcriptional and post-transcriptional regulation of young
genes in plants

J 2022

Transcriptional and post-transcriptional regulation of young genes in plants

RAXWAL, Vivek Kumar, Somya SINGH, Manu AGARWAL a Karel ŘÍHA

Základní údaje

Originální název

Transcriptional and post-transcriptional regulation of young genes in plants

Autoři

RAXWAL, Vivek Kumar (356 Indie, domácí), Somya SINGH, Manu AGARWAL a Karel ŘÍHA (203 Česká republika, garant, domácí)

Vydání

BMC Biology, London, BMC, 2022, 1741-7007

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 5.400

Kód RIV

RIV/00216224:14740/22:00128459

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1186/s12915-022-01339-7

UT WoS

000808328600001

Klíčová slova anglicky

Abiotic stress; Evolutionary capacitance; Nonsense-mediated RNA decay; Open chromatin; Orphan genes; Young genes

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 31. 1. 2023 15:34, Mgr. Pavla Foltynová, Ph.D.

Anotace

V originále

Background New genes continuously emerge from non-coding DNA or by diverging from existing genes, but most of them are rapidly lost and only a few become fixed within the population. We hypothesized that young genes are subject to transcriptional and post-transcriptional regulation to limit their expression and minimize their exposure to purifying selection. Results We performed a protein-based homology search across the tree of life to determine the evolutionary age of protein-coding genes present in the rice genome. We found that young genes in rice have relatively low expression levels, which can be attributed to distal enhancers, and closed chromatin conformation at their transcription start sites (TSS). The chromatin in TSS regions can be re-modeled in response to abiotic stress, indicating conditional expression of young genes. Furthermore, transcripts of young genes in Arabidopsis tend to be targeted by nonsense-mediated RNA decay, presenting another layer of regulation limiting their expression. Conclusions These data suggest that transcriptional and post-transcriptional mechanisms contribute to the conditional expression of young genes, which may alleviate purging selection while providing an opportunity for phenotypic exposure and functionalization.

Návaznosti

EF15_003/0000479, projekt VaV

Název: Regulace rostlinné meiózy

Citovat

RAXWAL, Vivek Kumar, Somya SINGH, Manu AGARWAL a Karel ŘÍHA. Transcriptional and post-transcriptional regulation of young genes in plants. BMC Biology. London: BMC, 2022, roč. 20, č. 1, s. 134-140. ISSN 1741-7007. Dostupné z: https://dx.doi.org/10.1186/s12915-022-01339-7.

@article{2251546,
   author = {Raxwal, Vivek Kumar and Singh, Somya and Agarwal, Manu and Říha, Karel},
   article_location = {London},
   article_number = {1},
   doi = {http://dx.doi.org/10.1186/s12915-022-01339-7},
   keywords = {Abiotic stress; Evolutionary capacitance; Nonsense-mediated RNA decay; Open chromatin; Orphan genes; Young genes},
   language = {eng},
   issn = {1741-7007},
   journal = {BMC Biology},
   title = {Transcriptional and post-transcriptional regulation of young genes in plants},
   url = {https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-022-01339-7},
   volume = {20},
   year = {2022}
}

TY  - JOUR
ID  - 2251546
AU  - Raxwal, Vivek Kumar - Singh, Somya - Agarwal, Manu - Říha, Karel
PY  - 2022
TI  - Transcriptional and post-transcriptional regulation of young genes in plants
JF  - BMC Biology
VL  - 20
IS  - 1
SP  - 134
EP  - 134
PB  - BMC
SN  - 17417007
KW  - Abiotic stress
KW  - Evolutionary capacitance
KW  - Nonsense-mediated RNA decay
KW  - Open chromatin
KW  - Orphan genes
KW  - Young genes
UR  - https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-022-01339-7
N2  - Background New genes continuously emerge from non-coding DNA or by diverging from existing genes, but most of them are rapidly lost and only a few become fixed within the population. We hypothesized that young genes are subject to transcriptional and post-transcriptional regulation to limit their expression and minimize their exposure to purifying selection. Results We performed a protein-based homology search across the tree of life to determine the evolutionary age of protein-coding genes present in the rice genome. We found that young genes in rice have relatively low expression levels, which can be attributed to distal enhancers, and closed chromatin conformation at their transcription start sites (TSS). The chromatin in TSS regions can be re-modeled in response to abiotic stress, indicating conditional expression of young genes. Furthermore, transcripts of young genes in Arabidopsis tend to be targeted by nonsense-mediated RNA decay, presenting another layer of regulation limiting their expression. Conclusions These data suggest that transcriptional and post-transcriptional mechanisms contribute to the conditional expression of young genes, which may alleviate purging selection while providing an opportunity for phenotypic exposure and functionalization.
ER  -

RAXWAL, Vivek Kumar, Somya SINGH, Manu AGARWAL a Karel ŘÍHA. Transcriptional and post-transcriptional regulation of young genes in plants. \textit{BMC Biology}. London: BMC, 2022, roč.~20, č.~1, s.~134-140. ISSN~1741-7007. Dostupné z: https://dx.doi.org/10.1186/s12915-022-01339-7.

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