Individual-specific and allele-specific chromatin signatures in diverse human populations
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Vishy Iyer
PROVIDER: E-GEOD-19622 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Heritable individual-specific and allele-specific chromatin signatures in humans.
McDaniell Ryan R Lee Bum-Kyu BK Song Lingyun L Liu Zheng Z Boyle Alan P AP Erdos Michael R MR Scott Laura J LJ Morken Mario A MA Kucera Katerina S KS Battenhouse Anna A Keefe Damian D Collins Francis S FS Willard Huntington F HF Lieb Jason D JD Furey Terrence S TS Crawford Gregory E GE Iyer Vishwanath R VR Birney Ewan E
Science (New York, N.Y.) 20100318 5975
The extent to which variation in chromatin structure and transcription factor binding may influence gene expression, and thus underlie or contribute to variation in phenotype, is unknown. To address this question, we cataloged both individual-to-individual variation and differences between homologous chromosomes within the same individual (allele-specific variation) in chromatin structure and transcription factor binding in lymphoblastoid cells derived from individuals of geographically diverse ...[more]
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Project description:This SuperSeries is composed of the following subset Series: GSE19622: Individual-specific and allele-specific chromatin signatures in diverse human populations GSE25416: High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells (ChIP-seq) GSE30226: Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity [ChIP_seq]. GSE32692: Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells [new ChIP-Seq samples] For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Refer to individual Series
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Project description:Using DNaseI hypersensitivity (HS) assays (Dnase-seq), high resolution DNaseI digestion profiles were generated genome-wide in diverse human cell types. We showed that within general regions of DNaseI HS that are known to identify locations of gene regulatory elements, DNaseI digestion patterns allowed us to identify locations of individual transcription factor binding sites that protected against the bound DNA against digestion. To measure the accuracy of these footprints, we also generated ChIP-seq data for the CTCF DNA binding factor in the same cell growths. We found that DNaseI footprints containing the CTCF canonical binding motif show significant ChIP-seq signal while CTCF binding motifs not in footprints show almost no signal providing one measure of valdation of the DNaseI footprints. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Six cell lines representing cervica carcinoma, chronic myeloid leukemia, human embryonic stem cells, lymphoblastoid cells, human epidermal keratinocytes and umbilical vein endothelial cells were analyzed using Dnase-seq.
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