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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Mechanisms of PU.1 binding site selection in-vivo

ABSTRACT: The majority of sequence-specific transcription factors bind genomic DNA only at a fraction of their potential binding sites and the ‘rules’ for binding or not-binding are only partially understood. Here, we studied the binding properties of the myeloid and B-cell specific transcription factor PU.1 in-vivo and in-vitro to unveil basic features of occupied vs. non-occupied consensus sites. In addition to published PU.1 ChIP-seq data we mapped CTCF binding sites in monocytes and macrophages to determine chromatin domain boundaries and performed MCIp-seq in monocytes to reveal DNA methylation patterns across the genome. ChIP-seq of CTCF in human monocytes and human monocyte-derived macrophages as well as MCIp-seq in human monocytes

ORGANISM(S): Homo sapiens

SUBMITTER: Michael Rehli

PROVIDER: E-GEOD-43098 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU.1.

Pham Thu-Hang TH Minderjahn Julia J Schmidl Christian C Hoffmeister Helen H Schmidhofer Sandra S Chen Wei W Längst Gernot G Benner Christopher C Rehli Michael M

Nucleic acids research 20130508 13

The transcription factor PU.1 is crucial for the development of many hematopoietic lineages and its binding patterns significantly change during differentiation processes. However, the 'rules' for binding or not-binding of potential binding sites are only partially understood. To unveil basic characteristics of PU.1 binding site selection in different cell types, we studied the binding properties of PU.1 during human macrophage differentiation. Using in vivo and in vitro binding assays, as well ...[more]

PMID: 23658224

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Mechanisms of PU.1 binding site selection in-vivo

Project description:The majority of sequence-specific transcription factors bind genomic DNA only at a fraction of their potential binding sites and the ‘rules’ for binding or not-binding are only partially understood. Here, we studied the binding properties of the myeloid and B-cell specific transcription factor PU.1 in-vivo and in-vitro to unveil basic features of occupied vs. non-occupied consensus sites. In addition to published PU.1 ChIP-seq data we mapped CTCF binding sites in monocytes and macrophages to determine chromatin domain boundaries and performed MCIp-seq in monocytes to reveal DNA methylation patterns across the genome.

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Global, comparative analysis of tissue-specific promoter CpG methylation.

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2007-08-07 | E-GEOD-5548 | biostudies-arrayexpress

Detection of aberrant DNA methylation in AML cell lines compared to normal human monocytes

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Dynamic epigenetic enhancer signatures are predictive for key transcriptional regulators associated with cellular differentiation states

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