Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Genome-wide distribution maps of histone variants H2A.Lap1 and H2A.Z in 30do mouse spermatids [ChIP_seq]

ABSTRACT: Chromatin performs numerous functions during cellular differentiation, and therefore it must be capable of adopting a multitude of different structures. How these various structures are established is poorly understood, but we propose that specific histone H2A variants will have a key role in remodelling chromatin during differentiation. Structurally, we show here that the gain of just a single acidic amino acid residue has generated a new mouse H2A.Bbd-like histone variant, H2A.Lap1, and that when incorporated into nucleosomal arrays imparts on them unique biophysical properties that are distinct from arrays containing either H2A or human H2A.Bbd. Functionally, we identify H2A.Lap1 as a novel chromatin component of active genes that are expressed during spermatogenesis, and in combination with H2A.Z create a unique chromatin landscape at the start site of transcription. During round spermatid differentiation, H2A.Lap1 dramatically loads onto the inactive X chromosome enabling a subset of its genes to be transcriptionally activated Examination of 2 different histone variants in mouse spermatids.

ORGANISM(S): Mus musculus

SUBMITTER: Rohan Williams

PROVIDER: E-GEOD-29913 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A unique H2A histone variant occupies the transcriptional start site of active genes.

Soboleva Tatiana A TA Nekrasov Maxim M Pahwa Anuj A Williams Rohan R Huttley Gavin A GA Tremethick David J DJ

Nature structural & molecular biology 20111204 1

Transcriptional activation is controlled by chromatin, which needs to be unfolded and remodeled to ensure access to the transcription start site (TSS). However, the mechanisms that yield such an 'open' chromatin structure, and how these processes are coordinately regulated during differentiation, are poorly understood. We identify the mouse (Mus musculus) H2A histone variant H2A.Lap1 as a previously undescribed component of the TSS of active genes expressed during specific stages of spermatogene ...[more]

PMID: 22139013

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Project description:Chromatin performs numerous functions during cellular differentiation, and therefore it must be capable of adopting a multitude of different structures. How these various structures are established is poorly understood, but we propose that specific histone H2A variants will have a key role in remodelling chromatin during differentiation. Structurally, we show here that the gain of just a single acidic amino acid residue has generated a new mouse M-bM-^@M-^XH2A.Bbd-likeM-bM-^@M-^Y histone variant, H2A.Lap1, and that when incorporated into nucleosomal arrays imparts on them unique biophysical properties that are distinct from arrays containing either H2A or human H2A.Bbd. Functionally, we identify H2A.Lap1 as a novel chromatin component of active genes that are expressed during spermatogenesis, and in combination with H2A.Z create a unique chromatin landscape at the start site of transcription. During round spermatid differentiation, H2A.Lap1 dramatically loads onto the inactive X chromosome enabling a subset of its genes to be transcriptionally activated. We used microarrays together with ChIP-seq data in order to see distribution of Lap1 and expression level of the Lap1 associated genes Total RNA was isolated using TRIzol (Invitrogen) and the RNeasy Mini Kit (Qiagen). Samples were DNase I treated (Roche) and reverse transcribed using Superscript II reverse transcriptase following the manufacturerM-bM-^@M-^Ys recommendations (Invitrogen). DNA was either analysed by semiM-bM-^@M-^Squantitative PCR, real-time qPCR using SYBR Green PCR master mix (Applied Biosystems), or subjected to DNA microarray analysis (in triplicate) using the GeneChip Mouse Gene 1.0 ST Array (Affymetrix). Robust Multichip Average (RMA) correction and probe set summaries were obtained using Affymetrix Power Tools software annotation (Affymetrix) based on the mm9 mouse genome. Unless otherwise stated, all subsequent expression analyses (see Supplementary Methods) were performed in the R statistical computing environment (version 2.11.1).

Dataset Information

Genome-wide distribution maps of histone variants H2A.Lap1 and H2A.Z in 30do mouse spermatids [ChIP_seq]

Publications

A unique H2A histone variant occupies the transcriptional start site of active genes.

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