TY  - JOUR
A1  - Ardakani, Fatemeh Behjati
A1  - Kattler, Kathrin
A1  - Nordström, Karl
A1  - Gasparoni, Nina
A1  - Gasparoni, Gilles
A1  - Fuchs, Sarah
A1  - Sinha, Anupam
A1  - Barann, Matthias
A1  - Ebert, Peter
A1  - Fischer, Jonas
A1  - Hutter, Barbara
A1  - Zipprich, Gideon
A1  - Imbusch, Charles D.
A1  - Felder, Bärbel
A1  - Eils, Jürgen
A1  - Brors, Benedikt
A1  - Lengauer, Thomas
A1  - Manke, Thomas
A1  - Rosenstiel, Philip
A1  - Walter, Jörn
A1  - Schulz, Marcel Holger
T1  - Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters
T2  - Epigenetics & chromatin
N2  - Background: Bidirectional promoters (BPs) are prevalent in eukaryotic genomes. However, it is poorly understood how the cell integrates different epigenomic information, such as transcription factor (TF) binding and chromatin marks, to drive gene expression at BPs. Single-cell sequencing technologies are revolutionizing the field of genome biology. Therefore, this study focuses on the integration of single-cell RNA-seq data with bulk ChIP-seq and other epigenetics data, for which single-cell technologies are not yet established, in the context of BPs.
Results: We performed integrative analyses of novel human single-cell RNA-seq (scRNA-seq) data with bulk ChIP-seq and other epigenetics data. scRNA-seq data revealed distinct transcription states of BPs that were previously not recognized. We find associations between these transcription states to distinct patterns in structural gene features, DNA accessibility, histone modification, DNA methylation and TF binding profiles.
Conclusions: Our results suggest that a complex interplay of all of these elements is required to achieve BP-specific transcriptional output in this specialized promoter configuration. Further, our study implies that novel statistical methods can be developed to deconvolute masked subpopulations of cells measured with different bulk epigenomic assays using scRNA-seq data.
KW  - Bidirectional genes
KW  - Single-cell RNA-seq
KW  - Epigenetics
Y1  - 2018
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/48457
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-484573
SN  - 1756-8935
N1  - Open Access: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
VL  - 11
IS  - 1, Art. 66
SP  - 1
EP  - 14
PB  - BioMed Central
CY  - London
ER  -