Transcriptional and post-transcriptional regulation of young genes in plants

RAXWAL, Vivek Kumar, Somya SINGH, Manu AGARWAL and Karel ŘÍHA. Transcriptional and post-transcriptional regulation of young genes in plants. BMC Biology. London: BMC, 2022, vol. 20, No 1, p. 134-140. ISSN 1741-7007. Available from: https://dx.doi.org/10.1186/s12915-022-01339-7.

Basic information

• Original name: Transcriptional and post-transcriptional regulation of young genes in plants
• Authors: RAXWAL, Vivek Kumar (356 India, belonging to the institution), Somya SINGH, Manu AGARWAL and Karel ŘÍHA (203 Czech Republic, guarantor, belonging to the institution).
• Edition: BMC Biology, London, BMC, 2022, 1741-7007.

Other information

• Original language: English
• Type of outcome: Article in a journal
• Field of Study: 10600 1.6 Biological sciences
• Country of publisher: United Kingdom of Great Britain and Northern Ireland
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• Impact factor: Impact factor: 5.400
• RIV identification code: RIV/00216224:14740/22:00128459
• Organization unit: Central European Institute of Technology
• Doi: http://dx.doi.org/10.1186/s12915-022-01339-7
• UT WoS: 000808328600001
• Keywords in English: Abiotic stress; Evolutionary capacitance; Nonsense-mediated RNA decay; Open chromatin; Orphan genes; Young genes
• Tags: rivok
• Tags: International impact, Reviewed

Abstract

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.

Links

• EF15_003/0000479, research and development project: Name: Regulace rostlinné meiózy