Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

H4K12 acetylation in Human Spermatozoa

ABSTRACT: H4K12 acetylation mapped by chromatin Chromatin immunoprecipitation (ChIP) in human sperm. ChIP mapping of chromatin modification. Three biological replicates hybridized to each of two chips.

ORGANISM(S): Homo sapiens

SUBMITTER: Martin Brinkworth

PROVIDER: E-GEOD-13101 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

Endonuclease-sensitive regions of human spermatozoal chromatin are highly enriched in promoter and CTCF binding sequences.

Arpanahi Ali A Brinkworth Martin M Iles David D Krawetz Stephen A SA Paradowska Agnieszka A Platts Adrian E AE Saida Myriam M Steger Klaus K Tedder Philip P Miller David D

Genome research 20090707 8

During the haploid phase of mammalian spermatogenesis, nucleosomal chromatin is ultimately repackaged by small, highly basic protamines to generate an extremely compact, toroidal chromatin architecture that is critical to normal spermatozoal function. In common with several species, however, the human spermatozoon retains a small proportion of its chromatin packaged in nucleosomes. As nucleosomal chromatin in spermatozoa is structurally more open than protamine-packaged chromatin, we considered ...[more]

PMID: 19584098

Similar Datasets

Project description:we aimed to provide an objective roadmap for histone sample preparation wherein the most notable findings and most important metrics were highlighted. This roadmap included a Histone Coverage Tool that allows researchers to make a snapshot of public or in-house data in search of a protocol that suits their specific needs. However, despite the fact that the coverage provided by a sample preparation workflow is pivotal to answer specific research questions, it should be noted that other metrics such as enzyme specificity and workflow variability can be equally important. Moreover, when it comes to histone sample preparation there are multiple additional challenges and pitfalls compared to regular bottom-up proteomics workflows. First there is the abundance and unequal distribution of arginine and lysine cleavage sites, which makes it virtually impossible to cover the entire histone code with a single bottom-up workflow. The most widely spread workaround for the abundance of cleavage sites is derivatization of lysine residues used to block tryptic digest and create longer peptides. However, this also introduces chemical noise, which obscures biological PTMs, while lowering sensitivity due to diluted signal. The most obvious alternative is an arginine specific digest. However, on the one hand, derivatization of lysine residues not only increases peptide length but also increases retention on the LC-system, while decreasing charge state distribution of the precursor ions. The latter presumably reduces instrumental variation of the workflow, which is remarkable since this source of variation is generally assumed to be constant in the field of LC-MS/MS based proteomics. On the other hand, lysine derivatization also increases the singly charged precursor fraction, which is usually not fragmented in regular data dependent acquisitions, thus increasing the risk of losing annotations. It is clear that not one histone sample preparation workflow will fit all research questions. However, we hope that this manuscript will guide researchers in making informed decisions about the many pitfalls and trade-offs involved in optimizing or assessing histone sample preparation workflows.

Project description:Exposure of the budding Saccharomyces cerevisiae to an alkaline environment produces a robust transcriptional response involving hundreds of genes. Part of this response is triggered by an almost immediate burst of calcium that activates the Ser/Thr protein phosphatase calcineurin. Activated calcineurin dephosphorylates the transcription factor Crz1, which moves to the nucleus and binds to calcineurin/Crz1 responsive gene promoters. In this work we present a genome-wide study of the binding of Crz1 to gene promoters in response to high pH stress. Environmental alkalinization promoted a time-dependent recruitment of Crz1 to 152 intergenic regions, the vast majority between 1 to 5 min upon stress onset. Positional evaluation of the genomic coordinates combined with existing transcriptional studies allowed identifying 139 genes likely responsive to Crz1 regulation. Gene Ontology analysis confirmed the relevant impact of calcineurin/Crz1 on a set of genes involved in glucose utilization, and uncovered novel targets, such as genes responsible for trehalose metabolism. We also identified over a dozen of genes encoding transcription factors that are likely under the control of Crz1, suggesting a possible mechanism for amplification of the signal at the transcription level. Further analysis of the binding sites allowed refining the consensus sequence for Crz1 binding to gene promoters and the effect of chromatin accessibility in the timing of Crz1 recruitment to promoters. The present work defines at the genomic-wide level the kinetics of binding of Crz1 to gene promoters in response to alkaline stress, confirms diverse previously known Crz1 targets and identifies many putative novel ones. Because the relevance of calcineurin/Crz1 in signaling diverse stress conditions, our data will contribute to understand the transcriptional response in other circumstances that also involves calcium signaling, such as exposition to sexual pheromones or saline stress. ChIP-Seq from five time points after alkalinization (t=0, 1, 2, 5 and 20 min) was collected from two independent experiments (A and B) and the ratio Tx/T0 was calculated.

Dataset Information

H4K12 acetylation in Human Spermatozoa

Publications

Endonuclease-sensitive regions of human spermatozoal chromatin are highly enriched in promoter and CTCF binding sequences.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets