Study

A unidirectional histone code in bidirectional promoters across cell types

Study ID Alternative Stable ID Type
EGAS00001001656 Other

Study Description

Recent studies indicate that thousands of genes are expressed from bidirectional promoters (BDPs). Gene regulation at BDPs is poorly understood, in particular how the cell is able to regulate them differently. Here we investigate the effect of histone Modifications in BDP regulation. In this study, we model the gene activity using different gene expression assays, such as RNA-Seq, GRO-cap, and CAGE around the BDP transcription start sites (TSSs) using different histone modifications in various cell types. We develop a new statistical approach that links histone modifications to gene expression at BDPs. It improves over previous methods, because it is able to capture spatial dependencies of histone modifications along a promoter and leads to more interpretable results. We predict a general histone code that is independent of transcript orientation, cell type, and promoter configuration. The histone code at BDPs reveals that promoters are regulated unidirectionally, such that the majority of histone marks associated with gene expression occur downstream of the gene's TSS. By ... (Show More)

Study Datasets 2 datasets.

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Dataset ID Description Technology Samples
EGAD00001005953
part of the DEEP project results resulted in the publication of 'Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters', Epigenetics & Chromatin (2018), Fatemeh et al., DOI: 10.1186/s13072-018-0236-7, PMID: 30414612, PMCID: PMC6230222. This dataset contains the subset of DEEP data related to that study.
Illumina HiSeq 2500 1
EGAD00001005954
Additional histone modification data, not yet released as part of IHEC, for cell line 01_HepG2_LiHG_Ct1, H3K122ac.
Illumina HiSeq 2500 1

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