Ontology highlight
ABSTRACT:
PROVIDER: PRJNA832590 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18936540.fastq.gz | Fastqsanger.gz | |||
| SRR18936541_1.fastq.gz | Fastqsanger.gz | |||
| SRR18936541_2.fastq.gz | Fastqsanger.gz | |||
| SRR18936542.fastq.gz | Fastqsanger.gz | |||
| SRR18936543.fastq.gz | Fastqsanger.gz |
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Project description: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.
2024-05-21 | GSE267962 | GEO
Project description:Mammalian sex differences are determined by the X and Y chromosomes. Ancestral homologous genes on the sex chromosomes, termed X-Y gene pairs, have been predicted to drive sex differences. However, among the five X-Y gene pairs conserved across eutherians, which pairs drive sex-biased gene expression have remained undefined. Here, we investigate the roles of the X-Y gene pair Kdm5c-Kdm5d in regulating sex-biased gene expression independently of sex hormones using pluripotent mouse embryonic stem cells (ESCs) as a model. Wild-type (WT) XX female and WT XY male ESCs significantly differ in the expression of approximately 4% of all expressed genes, classified as female- or male-biased. Loss of Kdm5c in female ESCs results in the downregulation of female-biased genes. In contrast, loss of either Kdm5c or Kdm5d in male ESCs results in the upregulation of female-biased genes and downregulation of male-biased genes, effectively neutralizing sex-biased gene expression. In male ESCs, most sex-biased genes change in expression in a similar direction upon loss of Kdm5c or Kdm5d. However, Kdm5c loss dysregulates a greater number of sex-biased genes relative to Kdm5d loss in male ESCs. Remarkably, in female ESCs ectopic Kdm5d expression is sufficient to drive a sex-biased gene expression pattern similar to that of WT male ESCs. Taken together, these results establish Kdm5c-Kdm5d as a critical X-Y gene pair in driving sex-biased gene expression in pluripotent cells.
2024-12-13 | GSE277494 | GEO
Project description:Proteomic sex estimation of human remains via liquid chromatography tandem mass spectrometry (LC- MS/MS) of sexually dimorphic amelogenin peptides in tooth enamel. The human remains analyzed in this study were recovered from two archaeological sites, Síi Túupentak (CA-ALA-565; ca. 200-600 cal BP) and Rummey Ta Kuččuwiš Tiprectak (CA-ALA-704/H; ca. 180-2240 cal. BP), Late Holocene ancestral Ohlone villages in Central California. The X and Y chromosomes code for distinctive isoforms of amelogenin proteins, AMELX_HUMAN and AMELY_HUMAN. Fragments of these proteins can be detected using shotgun liquid chromatography mass spectrometry and assigned to the AMELX or AMELY isoform. We use nano-liquid chromatography coupled with orbitrap tandem mass spectrometry (LC-orbitrap-MS/MS). Signals of all peptides that can be unambiguously attributed to either AMELY or AMELX isoforms are summed and normalized for sample weight. Confident detection of AMELY specific peptides provides an unambiguous indicator of a male sex chromosome.
2020-07-20 | PXD016076 | Pride
Project description:The ancestral regions of 8 mammalian Y chromosomes
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Project description:Sex chromosomes in Trichonephila senegalensis
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Project description:Annotation of Chicken Sex Chromosomes
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