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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Chromatin immunoprecipitation of key transcriptional regulators, RNA polymerase II and histone methylation in mouse and human liver to measure binding at regulatory regions of homologous genes

ABSTRACT: To identify experimentally both conserved and evolving aspects of transcriptional regulation, we have measured the binding of key transcriptional regulators, RNA polymerase II and histone methylation in mouse and human liver at regulatory regions of homologous genes. As expected, the set of genes for which regulator binding is conserved is enriched for known liver-specific genes, conserved binding events are associated with sequence motifs in both species, and target genes show conserved gene expression. Strikingly, a significant number of homlogous genes are bound in only one species, and expression of these genes is no more conserved than expected by chance.

ORGANISM(S): Homo sapiens

SUBMITTER: Duncan Odom

PROVIDER: E-TABM-144 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Chromatin immunoprecipitation of tissue-specific transcriptional regulators in mouse and human liver to measure binding at regulatory regions of homologous genes

Project description:To identify experimentally both conserved and evolving aspects of transcriptional regulation, we have measured the binding of key transcriptional regulators, RNA polymerase II and histone methylation in mouse and human liver at regulatory regions of homologous genes. As expected, the set of genes for which regulator binding is conserved is enriched for known liver-specific genes, conserved binding events are associated with sequence motifs in both species, and target genes show conserved gene expression. Strikingly, a significant number of homlogous genes are bound in only one species, and expression of these genes is no more conserved than expected by chance.

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2006-06-14 | E-WMIT-7 | biostudies-arrayexpress

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2008-06-11 | E-TABM-485 | biostudies-arrayexpress

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2009-01-22 | E-TABM-556 | biostudies-arrayexpress

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Project description:Understanding the transcriptional regulatory circuitry responsible for pluripotency and self-renewal in embryonic stem (ES) cells is fundamental to understanding human development and realizing the therapeutic potential of these cells. The transcription factor Oct4 and the chromatin-modifying Polycomb complex, key regulators of ES cell pluripotency and self-renewal, contribute to positive and negative control of a known set of protein-coding genes. MicroRNAs (miRNAs), non-coding transcripts that participate in post-transcriptional gene regulation are also important for normal pluripotency and self-renewal in ES cells, but there has been no systematic investigation of how miRNA expression is controlled by transcriptional regulators of ES cell identity. Here we identify promoters for miRNAs in the human and mouse genomes and describe the subset of these genes that are under the control of Oct4 and Polycomb in ES cells. We find that the majority of miRNAs that are uniquely or preferentially expressed in ES cells are bound by and dependent on Oct4. Oct4 also occupies a set of miRNA genes that are co-occupied by the Polycomb Group protein, Suz12. These miRNAs, repressed in ES cells, are later expressed in differentiated cells in a highly tissue-specific fashion, suggesting that they may contribute to cell-fate determinations. These data reveal how the core transcriptional regulatory circuitry of ES cells controls the miRNA expression program that contributes to pluripotency and self-renewal.

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