Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks
Regulation of gene expression is thought to play a major role in adaptation, but the relative importance of cis- and trans- regulatory mechanisms in the early stages of adaptive divergence is unclear. Using RNAseq of threespine stickleback fish gill tissue from four independent marine-freshwater eco...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2019-05-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/43785 |
| _version_ | 1828376259571220480 |
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| author | Jukka-Pekka Verta Felicity C Jones |
| author_facet | Jukka-Pekka Verta Felicity C Jones |
| author_sort | Jukka-Pekka Verta |
| collection | DOAJ |
| description | Regulation of gene expression is thought to play a major role in adaptation, but the relative importance of cis- and trans- regulatory mechanisms in the early stages of adaptive divergence is unclear. Using RNAseq of threespine stickleback fish gill tissue from four independent marine-freshwater ecotype pairs and their F1 hybrids, we show that cis-acting (allele-specific) regulation consistently predominates gene expression divergence. Genes showing parallel marine-freshwater expression divergence are found near to adaptive genomic regions, show signatures of natural selection around their transcription start sites and are enriched for cis-regulatory control. For genes with parallel increased expression among freshwater fish, the quantitative degree of cis- and trans-regulation is also highly correlated across populations, suggesting a shared genetic basis. Compared to other forms of regulation, cis-regulation tends to show greater additivity and stability across different genetic and environmental contexts, making it a fertile substrate for the early stages of adaptive evolution. |
| first_indexed | 2024-04-14T07:57:24Z |
| format | Article |
| id | doaj.art-547b651d2de1427abc0ba15c12fadc85 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-14T07:57:24Z |
| publishDate | 2019-05-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-547b651d2de1427abc0ba15c12fadc852022-12-22T02:04:59ZengeLife Sciences Publications LtdeLife2050-084X2019-05-01810.7554/eLife.43785Predominance of cis-regulatory changes in parallel expression divergence of sticklebacksJukka-Pekka Verta0https://orcid.org/0000-0003-1701-6124Felicity C Jones1https://orcid.org/0000-0002-5027-1031Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring, Tübingen, Germany; Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, FinlandFriedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring, Tübingen, GermanyRegulation of gene expression is thought to play a major role in adaptation, but the relative importance of cis- and trans- regulatory mechanisms in the early stages of adaptive divergence is unclear. Using RNAseq of threespine stickleback fish gill tissue from four independent marine-freshwater ecotype pairs and their F1 hybrids, we show that cis-acting (allele-specific) regulation consistently predominates gene expression divergence. Genes showing parallel marine-freshwater expression divergence are found near to adaptive genomic regions, show signatures of natural selection around their transcription start sites and are enriched for cis-regulatory control. For genes with parallel increased expression among freshwater fish, the quantitative degree of cis- and trans-regulation is also highly correlated across populations, suggesting a shared genetic basis. Compared to other forms of regulation, cis-regulation tends to show greater additivity and stability across different genetic and environmental contexts, making it a fertile substrate for the early stages of adaptive evolution.https://elifesciences.org/articles/43785gene regulationparallel evolutionselective sweepsgenetic assimilationHaldane's sievethreespine stickleback |
| spellingShingle | Jukka-Pekka Verta Felicity C Jones Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks eLife gene regulation parallel evolution selective sweeps genetic assimilation Haldane's sieve threespine stickleback |
| title | Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks |
| title_full | Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks |
| title_fullStr | Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks |
| title_full_unstemmed | Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks |
| title_short | Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks |
| title_sort | predominance of cis regulatory changes in parallel expression divergence of sticklebacks |
| topic | gene regulation parallel evolution selective sweeps genetic assimilation Haldane's sieve threespine stickleback |
| url | https://elifesciences.org/articles/43785 |
| work_keys_str_mv | AT jukkapekkaverta predominanceofcisregulatorychangesinparallelexpressiondivergenceofsticklebacks AT felicitycjones predominanceofcisregulatorychangesinparallelexpressiondivergenceofsticklebacks |