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The genome-scale DNA-binding profile of BarR

ABSTRACT: The genome-scale DNA-binding profile of BarR

PROVIDER: PRJEB13298 | ENA |

REPOSITORIES: ENA

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The genome-scale DNA-binding profile of BarR

Project description:The Leucine-responsive Regulatory Protein (Lrp) family is a widespread family of regulatory transcription factors in prokaryotes. BarR is an Lrp-like transcription factor in the model archaeon Sulfolobus acidocaldarius that activates the expression of a -alanine aminotransferase gene, which is involved in -alanine degradation. In contrast to classical Lrp-like transcription factors, BarR is not responsive to any of the -amino acids but interacts specifically with -alanine. Besides the juxtaposed -alanine aminotransferase gene, other regulatory targets of BarR have not yet been identified although -alanine is the precursor of coenzyme A and thus an important central metabolite. The aim of this study is to extend the knowledge of the DNA-binding characteristics of BarR and of its corresponding regulon from a local to a genome-wide perspective.

2016-04-15 | E-MTAB-4615 | biostudies-arrayexpress

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The genome-scale DNA-binding profile of BarR, a β-alanine responsive transcription factor in the archaeon Sulfolobus acidocaldarius.

Project description: Not available

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Genome-Wide Analysis of Host-Chromosome Binding Sites for Epstein-Barr Virus Nuclear Antigen 1 (EBNA1)

Project description:The Epstein-Barr Virus (EBV) Nuclear Antigen 1 (EBNA1) protein is required for the establishment of EBV latent infection in proliferating B-lymphocytes. EBNA1 is a multifunctional DNA-binding protein that stimulates DNA replication at the viral origin of plasmid replication (OriP), regulates transcription of viral and cellular genes, and tethers the viral episome to the cellular chromosome. EBNA1 also provides a survival function to B-lymphocytes, potentially through its ability to alter cellular gene expression. Chromatin-immunoprecipitation (ChIP) combined with massively parallel deep-sequencing (ChIP-Seq) was used to identify cellular sites bound by EBNA1. Sites identified by ChIP-Seq were validated by conventional real-time PCR, and ChIP-Seq provided quantitative, high-resolution detection of the known EBNA1 binding sites on the EBV genome at OriP and Qp. We identified at least one cluster of unusually high-affinity EBNA1 binding sites on chromosome 11, between the divergent FAM55D and FAM55B genes. A consensus for all cellular EBNA1 binding sites is distinct from those derived from the known viral binding sites, suggesting that some of these sites are indirectly bound by EBNA1. We conclude that EBNA1 can interact with a large number of cellular genes and chromosomal loci in latently infected cells, but that these sites are likely to represent a complex ensemble of direct and indirect EBNA1 binding sites. Study of Epstein-Barr virus (EBV)

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The genome-scale DNA-binding of FadR transcription factor in Sulfolobus acidocaldarius

Project description:The genome-scale DNA-binding of FadR transcription factor in Sulfolobus acidocaldarius

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Genome wide DNA binding profile of SOX3 in mouse testes

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