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Homo sapiens

ABSTRACT: Genome-wide maps of chromatin state in Williams-Beuren (WBS), Williams-Beuren Region duplication (WBRdupS), Smith-Magenis (DGS), DiGeorge (DGS) lymphoblastoid cell lines

PROVIDER: PRJNA148607 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR365005.fastq.gz	Fastqsanger.gz
	SRR365006.fastq.gz	Fastqsanger.gz
	SRR365007.fastq.gz	Fastqsanger.gz
	SRR365008.fastq.gz	Fastqsanger.gz
	SRR365009.fastq.gz	Fastqsanger.gz

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Williams-Beuren syndrome: typical deletions versus atypical deletions of the 7q11.23 region

2010-09-09 | GSE18188 | GEO

Williams-Beuren syndrome: typical deletions versus atypical deletions of the 7q11.23 region

Project description:We have performed comparative transcriptome profile from lymphoblastoid cell lines from four Williams-Beuren syndrome patients and two patients with partial deletions of the region. The goal was to find deregulated genes specifically in WBS versus atypical deletions, and to determine the biological pathways affected in WBS patients. 6 samples were hybridized twice each: once labeled with Cy5 and once labeled with Cy3 (dye-swap). Each sample was hybridized against a pool of five controls of the same gender.

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Project description:Williams-Beuren Syndrome (WBS) is a neurodevelopmental disorder caused by aa 1.5 Mb microdeletion on human chromosome 7. Although the molecular cause of the disorder is well-established, little is known about the global impact of the deletion on gene expression. Here we profiled the transcriptomes of fibroblast cell lines from 8 young girls with WBS, and 9 sex- and age-matched control individuals Keywords: disease state analysis, gene expression profiling

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Cannabinoid signaling modulation through JZL184 restores key phenotypes of a mouse model for Williams- Beuren syndrome

Project description:JZL184 treatment restores neurological and cardiac phenotypes of a mouse model of Williams-Beuren syndrome

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Structural variation-induced changes of chromatin architecture and gene expression

Project description:Copy number variants (CNVs) influence the expression of genes that map not only within the rearrangement, but also to its flanks. To assess the possible mechanism(s) underlying this “neighboring effect”, we compared intrachromosomal interactions and histone modifications in cell lines of patients affected by genomic disorders and control individuals. Using chromosome conformation capture (4C-seq), we observed that a set of genes flanking the Williams-Beuren Syndrome critical region (WBSCR) were often looping together, possibly forming an interacting cluster with each other and the WBSCR. Deletion of the WBSCR disrupts the expression of this group of flanking genes, as well as long-range interactions between them and the rearranged interval. We also pinpointed concomitant changes in histone modifications between samples.We conclude that large genomic rearrangements can lead to chromatin conformation changes that extend far away from the structural variant, thereby possibly modulating expression globally and modifying the phenotype. For example, we determined that the chromatin conformation, histone marks and relative expression levels of the flanking AUTS2 gene, mutations of which are associated with autism and intellectual disabilities, are modified in cell lines from Williams-Beuren syndrome patients. Examination of 4C-seq interaction profile of seven different genes (of which three in duplicate) in 2 different cell lines.

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Expression data from Merm1/Wbscr22 knock-down tumor cells

Project description:Merm1/Wbscr22 is one of genes in chromosomal region deleted in Williams-Beuren syndrome, a multisystem developmental disorder. Wbscr22 contains a nuclear localization signal and an S-adenosyl-L-methionine-dependent methyltransferase fold, but its real function is completely unknown.　In this study, to examine the function, we compared the gene expression profiles between control and Merm1/Wbscr22 knock-downed tumor cells.

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Recurrent disruption of HIP1 identified in patients with epilepsy, learning difficulties, intellectual disability, and neurobehavioral abnormalities

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2010-08-28 | GSE23834 | GEO

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2010-08-28 | E-GEOD-23834 | biostudies-arrayexpress

RNA-seq of human iPSCs derived neural crest stem cells (NCSCs) upon knock-down of BAZ1B (WSTF), including 3 williams beuren syndrome lines, 1 atypical deletion line, and 3 individuals with 7q11.23 duplication syndrome. Each line has been infected with a scramble, or at least one of two short-hairpins (as described in the coupled paper).

Project description:In order to dissect the role of BAZ1B in the paradigmatic craniofacial dysmorphisms that characterize Williams Beuren Syndrome and the simmetrical genetically opposite 7q11.23 duplication syndrome(7dupASD), we selected a large cohort of NCSCs lines (4 from WBS patients, 3 from 7dupASD patients and 4 from control individuals) to perform transcriptomic profiling. These lines show a clear cranial identity signatures which is crucial to pinpoint the disease pathogenesis, We then knocked-down (KD) BAZ1B via RNA interference in all lines across the three genetic conditions, including also NCSCs derived from a particularly informative atypical WBS patient (atWBS) bearing a partial deletion of the region that spares BAZ1B and six additional genes (see paper). In order to establish a high-resolution gradient of BAZ1B dosages, we selected two distinct shRNA against BAZ1B (i.e., sh1 and sh2) along with a scrambled shRNA sequence (hereafter scr) as negative control, for a total of 32 NCSC lines. KD efficiency was evaluated both at the RNA level by quantitative PCR (qPCR), confirming the attainment of the desired gradient with an overall reduction of about 40% for sh1 and 70% for sh2, as well as reduction at the protein level, as detected by Western blot (see the coupled paper).

2020-02-29 | E-MTAB-8455 | biostudies-arrayexpress

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