Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA112861 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:CHOPS syndrome is caused by germline gain-of-function mutations of AFF4. Cornelia de Lange syndrome is caused by germline mutations of cohesin loading factors or cohesin complex genes such as NIPBL, SMC1A, SMC3 and HDAC8. There are many overlapping clinical features exist between CHOPS syndrome and Cornelia de Lange syndrome. To identified commonly dysregulated genes in CHOPS syndrome and Cornelia de Lange syndrome, we perfomred side-by-side transcriptome comparison between CHOPS syndrome and Cornelia de Lange syndrome.
2015-01-27 | GSE64034 | GEO
Project description:CHOPS syndrome is caused by germline gain-of-function mutations of AFF4. Cornelia de Lange syndrome is caused by germline mutations of cohesin loading factors or cohesin complex genes such as NIPBL, SMC1A, SMC3 and HDAC8. There are many overlapping clinical features exist between CHOPS syndrome and Cornelia de Lange syndrome. To identified commonly dysregulated genes in CHOPS syndrome and Cornelia de Lange syndrome, we perfomred side-by-side transcriptome comparison between CHOPS syndrome and Cornelia de Lange syndrome. In this transcriptome analysis, patient derived skin fibroblasts from two CHOPS syndrome probands, two Cornelia de Lange syndrome probands, and four age-gender-ethnicity matched healthy control subjects were used.The samples used for Human Gene 2.0 arrays are two CHOPs syndrome samples (CDL160 and CDL444), two Cornelia de Lange syndrome samples (CdL006: 7 year-old Caucasian female NIPBL 742_743delCT ;L248TfsX6 and CdL015: 10 year-old Caucasian male NIPBL 2969delG;G990DfsX2), and four age gender matched control samples (GM01652, GM01864, GM02036 and GM03348).
2015-01-27 | E-GEOD-64034 | biostudies-arrayexpress
Project description:First evidence of a Cornelia de Lange Syndrome patient with a novel cohesin mutation and Acute Lymphoblastic Leukemia
2019-11-23 | GSE122859 | GEO
Project description:The cohesin complex has crucial roles in many structural and functional aspects of chromosomes including sister chromatid cohesion, genome organization, gene transcription and DNA repair. Cohesin recruitment onto chromosomes requires nucleosome free DNA and a specialized cohesin loader complex comprised of the Scc2 and Scc4 subunits. The cohesin loader, in addition to stimulating cohesin ATP hydrolysis and facilitating topological loading onto DNA, leads cohesin to chromatin receptors such as the RSC chromatin remodeling complex. Here, we explore the cohesin loader-RSC interaction and show that its Scc4 subunit contacts a conserved RSC ATPase motor module. The cohesin loader enhances RSC chromatin remodeling activity in vitro, as well as promoter nucleosome eviction in vivo. These findings provide insight into how the cohesin loader recognizes, as well as influences, the chromatin landscape, with implications for our understanding of human developmental disorders including Cornelia de Lange and Coffin-Siris syndromes.
2022-11-29 | PXD033446 | Pride
Project description:Heterozygous mutations in the cohesin regulator, NIPBL, or cohesin structural components SMC1A, and SMC3, result in Cornelia de Lange Syndrome (CdLS). Genome-wide transcription assessment has identified unique profiles of genes dysregulated in CdLS that correlate with different clinical presentations. Cohesin binding analysis demonstrates a preference for intergenic regions suggesting a cis-regulatory function mimicking that of an insulator. However, the binding sites are enriched within the promoter regions of the dysregulated genes and are significantly decreased in CdLS probands, indicating an alternative role of cohesin as a classic transcription factor. Keywords: ChIP-chip
2009-05-28 | GSE12603 | GEO
Project description:Mutations in NIPBL are the major cause of Cornelia de Lange Syndrome (CdLS). NIPBL is the cohesin loading factor and has recently been associated with the BET (Bromodomains and Extra Terminal (ET) domain) proteins BRD2 and BRD4. Related to this, a CdLS-like phenotype has been described associated to BRD4 mutations. We have study the genomic occupancy of NIPBL in mouse P19 teratocarcinoma cells.
2020-01-01 | GSE132784 | GEO
Project description:Vertebrates have two cohesin complexes that consist of Smc1, Smc3, Rad21/Scc1 and either SA1 or SA2, but their functional specificity is unclear. Mouse embryos lacking SA1 show developmental delay and die before birth. Comparison of the genome wide distribution of cohesin in wild-type and SA1-null cells reveals that SA1 is largely responsible for cohesin accumulation at promoters and at sites bound by the insulator protein CTCF. As a consequence, ablation of SA1 alters transcription of genes involved in biological processes related to Cornelia de Lange syndrome (CdLS), a genetic disorder linked to dysfunction of cohesin. We show that the presence of cohesin-SA1 at the promoter of myc and of protocadherin genes positively regulates their expression, a task that cannot be assumed by cohesin-SA2. Cohesin binding pattern along some gene clusters is also affected by the lack of SA1, leading to dysregulation of the genes within. We hypothesize that impaired cohesin-SA1 function in gene expression underlies the molecular etiology of CdLS. Examination of genome wide distribution of cohesin subunits in wildtype and SA1-null cells
2012-03-15 | E-GEOD-32319 | biostudies-arrayexpress
Project description:Vertebrates have two cohesin complexes that consist of Smc1, Smc3, Rad21/Scc1 and either SA1 or SA2, but their functional specificity is unclear. Mouse embryos lacking SA1 show developmental delay and die before birth. Comparison of the genome wide distribution of cohesin in wild-type and SA1-null cells reveals that SA1 is largely responsible for cohesin accumulation at promoters and at sites bound by the insulator protein CTCF. As a consequence, ablation of SA1 alters transcription of genes involved in biological processes related to Cornelia de Lange syndrome (CdLS), a genetic disorder linked to dysfunction of cohesin. We show that the presence of cohesin-SA1 at the promoter of myc and of protocadherin genes positively regulates their expression, a task that cannot be assumed by cohesin-SA2. Cohesin binding pattern along some gene clusters is also affected by the lack of SA1, leading to dysregulation of the genes within. We hypothesize that impaired cohesin-SA1 function in gene expression underlies the molecular etiology of CdLS. Two-condition experiment, SA1 KO vs. WT cells. 3 Biological replicates.
2012-03-15 | E-GEOD-32234 | biostudies-arrayexpress
Project description:The evolutionarily conserved cohesin complex is crucial for holding sister chromatids together from the time of DNA replication until their segregation during the metaphase to anaphase transition. Human diseases associated with with mutations in the cohesin network are termed "cohesinopathies". Scc2 is required for loading cohesin onto DNA prior to DNA replication. Cornelia de Lange syndrome (CdLS), a developmental disorder characterized by growth and intellectual impairment is caused by mutations in Scc2. How mutations in Scc2 gives rise to these developmental defects is currently unknown, as overt defects in chromosome segregation are not observed in CdLS patients.This has led to the hypothesis that developmental disorders in CdLS patients are a result of dysregulated gene expression. To examine the transcriptional program of Scc2 mutants called scc2-4, RNA sequencing was performed. Analysis of gene expression program shows upregulation of genes involved in ribosome biogenesis and downregulation of genes needed for oxidative phosphorylation. Studies are currently underway to investigate how scc2-4 mutation causes gene misregulation. The answer(s) could provide insight into the molecular etiology of CdLS. Examining gene expression in 3 biological replicates of scc2-4 relative to wt by Ilumina sequencing
2015-06-16 | E-GEOD-55316 | biostudies-arrayexpress
Project description:Mutations in NIPBL are the major cause of Cornelia de Lange Syndrome (CdLS). NIPBL is the cohesin loading factor and has recently been associated with the BET (Bromodomains and Extra Terminal (ET) domain) proteins BRD2 and BRD4. Related to this, a CdLS-like phenotype has been described associated to BRD4 mutations. To understand the relationship between NIPBL and BET proteins, we have performed RNA-Seq expression analysis following depletion of the different proteins in mouse P19 teratocarcinoma cells. Results indicate that genes regulated by NIPBL largely overlap with those regulated by BRD4 but not with those regulated by BRD2.
2020-01-01 | GSE132785 | GEO