Unknown,Transcriptomics,Genomics,Proteomics

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ChIP-seq analyses of Hap4 and Hap5 genome-wide binding patterns in the pathogenic yeast Candida glabrata

ABSTRACT: We analyzed the DNA binding pattern of the Hap5 and Hap4 transcription factors by ChIP-seq in Candida glabrata. Myc-tagged versions of the two transcription factors were used. The mock IP was performed with an untagged, otherwise isogenic, strain. IP and Input DNA were sequenced on a Nextseq illumina machine. All cells were grown in rich media containing glycerol as the sole carbon source. Peak calling was performed using the bpeaks software, with the input and the IP used as references.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Candida glabrata

SUBMITTER: Frederic Devaux

PROVIDER: E-MTAB-10675 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Trimethylation of histone H3 lysine 27 (H3K27me3) plays a critical role in regulating gene expression during plant and animal development. We characterized the genome-wide distribution of H3K27me3 in five developmentally distinct tissues in maize plants of two genetic backgrounds, B73 and Mo17, representatives of two distinct heterotic groups. There are numerous differences in the distribution of H3K27me3 among tissues. In contrast, we found the distribution of H3K27me3 among the two genetic backgrounds to be quite similar. The tissue-specific patterns of H3K27me3 are often associated with differences in gene expression among the tissues and most of the imprinted genes that are expressed solely from the paternal allele in endosperm are targets of H3K27me3. Many maize genes with important developmental roles, including numerous genes encoding putative transcription factors, are modified with H3K27me3 in at least one of the tissues that were profiled. A comparison of the H3K27me3 targets in rice, maize, and Arabidopsis provided evidence for conservation of the H3K27me3 targets among plant species. However, there was limited evidence for conserved targeting of H3K27me3 in the two maize subgenomes derived from whole genome duplication. Genomic profiling of H3K27me3 in loss-of-function mutant stocks for Mez2 and Mez3, two of the three putative H3K27me3 methyltranferases present in the maize genome, suggests partial redundancy of this gene family for maintaining H3K27me3 patterns. Only a portion of the targets of H3K27me3 requires Mez2 and/or Mez3 and there was limited evidence for functional consequences of H3K27me3 at these targets. This study provides a catalogue of 6,337 genes that are marked by H3K27me3 in five maize tissues. B73 tissues for h3k27 analysis: Samples are replicated in triplicate with antibody pulldown (IP) and control genomic DNA (input) channels. histone modification mutants for h3k27 analysis: Samples are replicated in triplicate with antibody pulldown (IP) and control genomic DNA (input) channels. Mo17 tissues for h3k27 analysis: Samples contain antibody pulldown (IP) and control genomic DNA (input) channels.

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ChIP-seq analyses of Hap4 and Hap5 genome-wide binding patterns in the pathogenic yeast Candida glabrata

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