X-chromosome target specificity diverged between dosage compensation mechanisms of two closely related Caenorhabditis species
- Howard Hughes Medical Institute, University of California, Berkeley, United States
- Ithaca College, United States
Abstract
An evolutionary perspective enhances our understanding of biological mechanisms. Comparison of sex determination and X-chromosome dosage compensation mechanisms between the closely related nematode species C. briggsae (Cbr) and C. elegans (Cel) revealed that the genetic regulatory hierarchy controlling both processes is conserved, but the X-chromosome target specificity and mode of binding for the specialized condensin dosage compensation complex (DCC) controlling X expression have diverged. We identified two motifs within Cbr DCC recruitment sites that are highly enriched on X: 13-bp MEX and 30-bp MEX II. Mutating either MEX or MEX II in an endogenous recruitment site with multiple copies of one or both motifs reduced binding, but only removing all motifs eliminated binding in vivo. Hence, DCC binding to Cbr recruitment sites appears additive. In contrast, DCC binding to Cel recruitment sites is synergistic: mutating even one motif in vivo eliminated binding. Although all X-chromosome motifs share the sequence CAGGG, they have otherwise diverged so that a motif from one species cannot function in the other. Functional divergence was demonstrated in vivo and in vitro. A single nucleotide position in Cbr MEX can determine whether Cel DCC binds. This rapid divergence of DCC target specificity could have been an important factor in establishing reproductive isolation between nematode species and contrasts dramatically with conservation of target specificity for X-chromosome dosage compensation across Drosophila species and for transcription factors controlling developmental processes such as body-plan specification from fruit flies to mice.
Data availability
GEO GSE214714 is the accession number for the ChIP-seq data reported in this manuscript.
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Caenorhabditis briggsae SDC-2 and DPY-27 ChIP-seqNCBI Gene Expression Omnibus, GSE214714.
Article and author information
Author details
Funding
Howard Hughes Medical Institute
- Barbara J Meyer
National Institutes of Health (R35 GM131845)
- Barbara J Meyer
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2023, Yang et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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X-chromosome target specificity diverged between dosage compensation mechanisms of two closely related Caenorhabditis species
eLife 12:e85413.
https://doi.org/10.7554/eLife.85413
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