Project description:We used Solexa sequencing technology to probe the gene expression of dorsal skin tissues from three full-sib Rex rabbits of different colors. The number of expressed genes in each sample was approximately 14,700. Compared with the chinchilla Rex rabbit control sample, the numbers of genes that exhibited greater than a 2-fold change in expression with a false discovery rate of ≤0.001 in the black rabbit sample and white rabbit sample were 1,809 and 460, respectively, and the number of common differentially expressed genes was 257.Of the 257 genes, 32 genes that were upregulated in sample B and downregulated in sample W. The FABP7 gene was the only gene that was downregulated in the B sample and upregulated in the W sample
Project description:Inspection of Hi-C and ChIP-seq data suggests that condensin DC is an X-chromosome enriched loop extruder that stalls at rex sites. Insertion of rex site on X-chromosome suggests orientation independent barrier function of rex sites. Insertion of rex site on chromosome-II results in recruitment and spreading of condensin DC that coincides with TAD formation.
2022-06-14 | GSE206065 | GEO
Project description:Screening and Analysis of Response Genes of Rex Rabbit SLC7A11 in Melanocytes
Project description:ChIP-seq for the SDC-3 subunit of the dosage compensation complex in wild-type N2 C. elegans and Hi-C in C' elegans strains with deleted rex and extra rex sites
Project description:In embryos, DCC binding across the length of the ~17.7 Mb X chromosome initiates at a set of recruitment elements on the X (rex). Individual rex sites collectively contribute to recruitment and repression, thus deletion of one or few rex sites causes subtle changes, as measured by mRNA-seq in mixed-stage embryos. We previously constructed a strain deleting rex-1, located ~6 kb downstream of dpy-23 (https://doi.org/10.7554/eLife.23645). Here we performed mRNA-seq in rex-1 deletion embryos.
Project description:This study was undertaken in order to characterize the functions of Rex-1 and identify potential Rex-1 target genes.Both alleles of the Rex-1 gene were disrupted in J1 mouse embryonic stem cells. Gene expression levels in one of the resulting Rex-1 knockout cell lines was compared to that of J1 wild type cells. Keywords: cell type comparison
Project description:Mechanisms establishing higher-order chromosome structures and their roles in gene regulation are elusive. We analyzed chromosome architecture during nematode X-chromosome dosage compensation, which represses transcription via a dosage-compensation condensin complex (DCC) that binds hermaphrodite Xs and establishes megabase-size topologically associating domains (TADs). We show that DCC binding at high-occupancy sites (rex sites) defines eight TAD boundary locations. Single rex deletions disrupted boundaries, and single insertions created new boundaries, demonstrating one rex site is necessary and sufficient for DCC-dependent boundary formation. Deleting eight rex sites (8rexΔ) recapitulated TAD structure of DCC mutants, permitting analysis when chromosome-wide domain architecture was disrupted but most DCC binding remained. 8rexΔ animals exhibited no changes in X expression and lacked dosage-compensation mutant phenotypes. Hence, TAD boundaries are neither the cause nor consequence of gene repression during dosage compensation. Abrogating TAD structure did, however, reduce thermotolerance, accelerate aging, and shorten lifespan, implicating chromosome architecture in regulating stress responses and aging.
