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Homo sapiens

ABSTRACT: Connected gene communities underlie transcriptional changes in Cornelia de Lange Syndrome

PROVIDER: PRJNA359791 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5139370.fastq.gz	Fastqsanger.gz
	SRR5139371.fastq.gz	Fastqsanger.gz
	SRR5139372.fastq.gz	Fastqsanger.gz
	SRR5139373.fastq.gz	Fastqsanger.gz
	SRR5139374.fastq.gz	Fastqsanger.gz

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Connected gene communities underlie transcriptional changes in Cornelia de Lange Syndrome

Project description:Cornelia de Lange syndrome (CdLS) is a complex multisystem developmental disorder caused by mutations in cohesin subunits and regulators. While the precise molecular mechanisms are not well defined, they point toward a global deregulation of the transcriptional gene expression program. Indeed, cohesin is associated with the boundaries of chromosome domains in addition to enhancers and promoters connecting the 3D genome organization with transcriptional control and gene expression. Here we show that connected gene communities, built with noncoding regulatory elements and genes physically interacting in the 3D chromosomal space, provide a molecular explanation for the pathoetiology of CdLS. Indeed, NIPBL and cohesin are important constituents of connected gene communities, both being centrally positioned at active noncoding regulatory elements. Interestingly, mutations in SMC1A and NIPBL lead to coordinated gene expression changes in connected communities. Our findings suggest a model where CdLS is explained by coordinated modulation of connected gene communities.

2017-07-13 | GSE93080 | GEO

Transcriptome comparison between CHOPS syndrome and Cornelia de Lange syndrome

2015-01-27 | GSE64034 | GEO

Transcriptome comparison between CHOPS syndrome and Cornelia de Lange syndrome

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

Cornelia-de-Lange syndrome associated mutations cause a DNA damage signalling and repair defect

Project description:Cornelia de Lange Syndrome is a multisystem developmental disorder typically caused by mutations in the gene encoding the cohesin loader NIPBL. The associated phenotype is generally assumed to be the consequence of aberrant transcriptional regulation. Recently, we identified a residue substitution in BRD4 associated with a Cornelia de Lange-like Syndrome, that reduces BRD4 binding to acetylated histones. Here we show that, although this mutation reduces BRD4-enhancer interaction in mouse embryonic stem cells, it does not affect transcription. Rather it delays the cell cycle, increased DNA damage signalling, and perturbs regulation of DNA repair in mutant cells. This uncovers a new role for BRD4 in DNA repair pathway choice. Furthermore, we find evidence of a similar increase in DNA damage signalling in cells derived from NIPBL-deficient individuals, suggesting that defective DNA damage signalling and repair is also a feature of typical Cornelia de Lange Syndrome.

2021-03-09 | GSE130659 | GEO

Affymetrix SNP array data for a pediatric acute lymphoblastic leukemia samples

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

Homo sapiens

Project description:Transcriptome comparison between CHOPS syndrome and Cornelia de Lange syndrome

| PRJNA269921 | ENA

Homo sapiens

Project description:SMC2: a candidate gene associated with Cornelia de Lange Syndrome

| PRJNA236306 | ENA

Homo sapiens

Project description:Genome wide DNA Methylation Study in Cornelia de Lange Syndrome

| PRJNA118177 | ENA

SMC2: a candidate gene associated with Cornelia de Lange Syndrome

Project description:whole-genome aCGH analysis also showed us that the patient carried a 12.01-1M Mb deletion region at chromosome bands 9q31.1-q32 (105,190,105-117,195,154). The deleted region encompasses 22 genes including SMC2 Two-condition Samples, Cornelia de Lange Syndrome vs. Normal cells.

2015-01-23 | E-GEOD-54354 | biostudies-arrayexpress

Nuclear SLIC-CAGE of human cortical neurons from Cornelia de Lange Syndrome patients and control individuals

Project description:We used SLIC-CAGE to map transcriptional start sites in cortical neurons from Cornelia de Lange Syndrome (CdLS) patients and control individuals. SLIC-CAGE was performed using nuclear RNA isolated from pre-frontal cortical grey matter. Usage of nuclear RNA allows enrichment of unstable RNAs, such as RNA originating from enhancer transcription. We characterised promoter-level gene expression in cortical neurons from CdLS patients and found deregulation of hundreds of genes enriched for neuronal functions.

2021-02-27 | E-MTAB-9045 | biostudies-arrayexpress

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