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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Chromatin state dynamics during blood formation (ChIP-Seq)

ABSTRACT: We develop a new ChIpseq method (iChIP) to profile chromatin states of low cell number samples. We use IChIP to profile the chromatin dynamics during hematopoiesis across 16 different cell types which include the principal hematopoietic progenitors Examination of 2 different histone modifications in 2 cell types.

ORGANISM(S): Mus musculus

SUBMITTER: Ido Amit

PROVIDER: E-GEOD-59636 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Immunogenetics. Chromatin state dynamics during blood formation.

Lara-Astiaso David D Weiner Assaf A Lorenzo-Vivas Erika E Zaretsky Irina I Jaitin Diego Adhemar DA David Eyal E Keren-Shaul Hadas H Mildner Alexander A Winter Deborah D Jung Steffen S Friedman Nir N Amit Ido I

Science (New York, N.Y.) 20140807 6199

Chromatin modifications are crucial for development, yet little is known about their dynamics during differentiation. Hematopoiesis provides a well-defined model to study chromatin state dynamics; however, technical limitations impede profiling of homogeneous differentiation intermediates. We developed a high-sensitivity indexing-first chromatin immunoprecipitation approach to profile the dynamics of four chromatin modifications across 16 stages of hematopoietic differentiation. We identify 48,4 ...[more]

PMID: 25103404

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Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

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A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin states (ChIP-Seq)

Project description:During hematopoiesis, cells originating from the same stem cell reservoir differentiate into distinct cell types. The mechanisms enabling common progenitors to differentiate into distinct cell fates are not fully understood. Here, we identify chromatin-regulating and cell-fate-determining transcription factors (TF) governing dendritic cell (DC) development by annotating the enhancer and promoter landscapes of the DC lineage. Combining these analyses with detailed over-expression, knockdown and ChIP-Seq studies, we show that Irf8 functions as a plasmacytoid DC epigenetic and fate-determining TF, regulating massive, cell-specific chromatin changes in thousands of pDC enhancers. Importantly, Irf8 forms a negative feedback loop with Cebpb, a monocyte-derived DC epigenetic fate-determining TF. We show that using this circuit logic, differential activity of TF can stably define epigenetic and transcriptional states, regardless of the microenvironment. More broadly, our study proposes a general paradigm that allows closely related cells with a similar set of signal-dependent factors to generate differential and persistent enhancer landscapes. Here analyzed 2 experiments, each one contains samples of moDC and pDC ex vivo cultured cells. The first experiment contains 32 samples of moDC and pDC following stimulation with various TLR stimulators. The second experiment contains 8 samples of moDC and pDC following perturbations; Cebpb and Irf8 knock down or over expression.

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| phs001704 | dbGaP

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