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Pan-AcH3 ChIP-chip with Custom High Resolution Tiling Arrays on HUVECs and HuAoVSMCs

ABSTRACT: Differential EC enrichment of pan-AcH3 was assessed at 34 select genes, including 19 EC-enriched genes, 6 broadly expressed genes, and 9 EC-excluded genes, by pan-AcH3 (AcH3K9 and AcH3K14) ChIP-chip analysis on human umbilical vein endothelial cells (HUVECs) and human aortic vascular smooth muscle cells (HuAoVSMCs) with a high resolution tiling DNA microarray. Specifically, the tiling array analyzes the 50 kb genomic region upstream of transcription initiation, the intragenic regions, and 50 kb genomic region downstream of the last exon.

ORGANISM(S): Homo sapiens

PROVIDER: GSE93868 | GEO | 2018/01/19

REPOSITORIES: GEO

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Pan-AcH4 ChIP-chip with High Resolution Tiling Arrays on HUVECs and HuAoVSMCs

Project description:Differential EC enrichment of pan-AcH4 was assessed at 34 select genes, including 19 EC-enriched genes, 6 broadly expressed genes, and 9 EC-excluded genes, by pan-AcH4 (AcH4K5, AcH4K8, AcH4K12, and AcH4K16) ChIP-chip analysis on human umbilical vein endothelial cells (HUVECs) and human aortic vascular smooth muscle cells (HuAoVSMCs) with a high resolution tiling DNA microarray. Specifically, the tiling array analyzes the 50 kb genomic region upstream of transcription initiation, the intragenic regions , and 50 kb genomic region downstream of the last exon.

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Project description:Pan-AcH3 ChIP-chip with Custom High Resolution Tiling Arrays on HUVECs and HuAoVSMCs

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Custom MHC array analysis of lymphoblastoid cell lines

Project description:The human MHC is a paradigm for genomics, showing striking association with disease but functional variants remain largely unresolved. Using an original hybrid microarray (containing tiling and junction probes) for the MHC and accounting for known sequence diversity, we have drawn the first high-resolution, strand-specific transcriptional map of the MHC, defining differences in gene expression for three common haplotypes associated with autoimmune disease. In total, 6% of the MHC is transcribed with one transcript per 1.4kb, including previously unrecognized intergenic transcription. The distributions of differentially expressed probes and polymorphisms between haplotypes are significantly correlated, arguing for cis effects. Haplotype-specific transcription involved 96 differentially expressed genes, including ZFP57, which was validated in a cohort of healthy volunteers, while 526 exons show haplotypic differences. We also find splicing events are significantly more extensive in the MHC than in the rest of the genome. This study marks a new step in immunogenetics. The results files (.bedgraph and .gff) contain tiling data for both the shared-path and the alternate paths (shared and haplotype-specific) , defining transcriptional activity across the entire MHC region in each sample.

2011-05-23 | GSE22453 | GEO

ChIP to AIRE regulated genes in HEK 293 cells

Project description:The Autoimmune Regulator (AIRE) protein is expressed in thymic medullary epithelial cells, where it promotes the ectopic expression of tissue-restricted antigens needed for efficient negative selection of developing thymocytes. Mutations in AIRE cause APECED syndrome, which is characterized by a breakdown of self-tolerance. The molecular mechanism by which AIRE increases the expression of a variety of different genes remains unknown. Here, we studied AIRE-regulated genes using whole genome expression analysis and chromatin immunoprecipitation. We show that AIRE preferentially activates genes that are tissue-specific and characterized by low levels of initial expression in stably transfected HEK293 cell model and mouse thymic medullary epithelial cells. In addition, the AIRE-regulated genes lack active chromatin marks, such as histone H3 trimethylation (H3K4me3) and acetylation (AcH3), on their promoters. We also show that during activation by AIRE, the target genes acquire histone H3 modifications associated with transcription and RNA polymerase II. In conclusion, our data show that AIRE is able to promote ectopic gene expression from chromatin associated with histone modifications characteristic to inactive genes. We compared the gene expression profiles of HEK293 cell-lines expressing either YFP (NC) or AIRE (AIRE1) proteins using Illumina BeadChips (GSE16877). Based on these results we chose more than 50 genes that where upregulated in the presence of AIRE and used chromatin immunoprecipitation and custom made Nimblegen tiling arrays to study the regions of 200kb up-and downstream of the genes in HEK293 cells expressing either YFP or AIRE protein. The following antibodies where used in the ChIP experiments: H3K4me3, AcH3, H3K27me3, H3, PolII and AIRE.

2010-09-10 | E-GEOD-17216 | biostudies-arrayexpress

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Project description:We introduce the Multiplexed Editing Regulatory Assay (MERA), a high-throughput CRISPR/Cas9-based approach that analyzes the regulatory genome for function in its native context. By tiling thousands of mutations across ~40 kb of cis-regulatory genomic space and using knock-in GFP reporters to read out gene activity, we obtain quantitative information on the contribution of cis-regulatory regions to gene expression. In addition, we performed a deep-sequencing strategy to find basepair-resolution functional motifs involved in regulation of the gene by sequencing thousands of functional and non-functional genotypes at genomic locations perturbed by specific guide RNAs. Design of 3908 gRNAs to perturb regulatory regions associated with the genes Tdgf1,Nanog,Zfp42 and Rpp25 as well as 10 GFP-targetting positive controls. Also, deep-sequencing of genomic regions mutated by 6 selected gRNAs after sorting the electroporated cells into GFP-positive and GFP-negative populations.

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