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| Status |
Public on May 21, 2024 |
| Title |
SMC-mediated dosage compensation in C. elegans evolved in the presence of an ancestral nematode mechanism [Hi-C] |
| Organisms |
Pristionchus pacificus; Oscheius tipulae |
| Experiment type |
Other
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| Summary |
Mechanisms of X chromosome dosage compensation have been studied extensively in a few model species representing clades of shared sex chromosome ancestry. However, the diversity within each clade as a function of sex chromosome evolution is largely unknown. Here, we anchor ourselves to the nematode Caenorhabditis elegans, for which a well-studied mechanism of dosage compensation occurs through a specialized structural maintenance of chromosomes (SMC) complex, and explore the diversity of dosage compensation in the surrounding phylogeny of nematodes. Through phylogenetic analysis of the C. elegans dosage compensation complex and a survey of its epigenetic signatures, including X-specific topologically associating domains (TADs) and X-enrichment of H4K20me1, we found that the condensin-mediated mechanism evolved recently in the lineage leading to Caenorhabditis through an SMC-4 duplication. Intriguingly, an independent duplication of SMC-4 and the presence of X-specific TADs in Pristionchus pacificus suggest that condensin-mediated dosage compensation arose more than once. mRNA-seq analyses of gene expression in several nematode species indicate that dosage compensation itself is ancestral, as expected from the ancient XO sex determination system. Indicative of the ancestral mechanism, H4K20me1 is enriched on the X chromosomes in Oscheius tipulae, which does not contain X-specific TADs or SMC-4 paralogs. Together, our results indicate that the dosage compensation system in C. elegans is surprisingly new, and condensin may have been co-opted repeatedly in nematodes, suggesting that the process of evolving a chromosome-wide gene regulatory mechanism for dosage compensation is constrained.
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| Overall design |
To examine the 3D genome structure of autosomes and X chromosomes in the nematodes Pristionchus pacificus and Oscheius tipulae, we performed Hi-C sequencing on early stage larvae.
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| Contributor(s) |
Aharonoff A, Kim J, Ercan S |
| Citation missing |
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| Submission date |
May 21, 2024 |
| Last update date |
May 22, 2024 |
| Contact name |
Avrami Aharonoff |
| E-mail(s) |
avramiaharonoff@gmail.com
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| Organization name |
New York University
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| Department |
Biology
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| Lab |
Sevinç Ercan
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| Street address |
29 Washington Place
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10003 |
| Country |
USA |
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| Platforms (2) |
| GPL32681 |
Illumina NovaSeq 6000 (Oscheius tipulae) |
| GPL34494 |
Illumina NovaSeq 6000 (Pristionchus pacificus) |
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| Samples (4)
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| GSM8282555 |
HiC, CEW1, early stage synchronized larvae, rep 1 |
| GSM8282556 |
HiC, CEW1, early stage synchronized larvae, rep 2 |
| GSM8282557 |
HiC, PS312, J2, rep1 |
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| Relations |
| BioProject |
PRJNA1113945 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE267963_RAW.tar |
1.2 Gb |
(http)(custom) |
TAR (of HIC) |
SRA Run Selector |
| Raw data are available in SRA |
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