Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

Abstract

Gene regulation at functional elements (e.g., enhancers, promoters, insulators) is governed by an interplay of nucleosome remodeling, histone modifications, and transcription factor binding. To enhance our understanding of gene regulation, the ENCODE Consortium has generated a wealth of ChIP-seq data on DNA-binding proteins and histone modifications. We additionally generated nucleosome positioning data on two cell lines, K562 and GM12878, by MNase digestion and high-depth sequencing. Here we relate 14 chromatin signals (12 histone marks, DNase, and nucleosome positioning) to the binding sites of 119 DNA-binding proteins across a large number of cell lines. We developed a new method for unsupervised pattern discovery, the Clustered AGgregation Tool (CAGT), which accounts for the inherent heterogeneity in signal magnitude, shape, and implicit strand orientation of chromatin marks. We applied CAGT on a total of 5084 data set pairs to obtain an exhaustive catalog of high-resolution patterns of histone modifications and nucleosome positioning signals around bound transcription factors. Our analyses reveal extensive heterogeneity in how histone modifications are deposited, and how nucleosomes are positioned around binding sites. With the exception of the CTCF/cohesin complex, asymmetry of nucleosome positioning is predominant. Asymmetry of histone modifications is also widespread, for all types of chromatin marks examined, including promoter, enhancer, elongation, and repressive marks. The fine-resolution signal shapes discovered by CAGT unveiled novel correlation patterns between chromatin marks, nucleosome positioning, and sequence content. Meta-analyses of the signal profiles revealed a common vocabulary of chromatin signals shared across multiple cell lines and binding proteins.

The spring-loaded genome: Nucleosome redistributions are widespread, transient, and DNA-directed

“…This expectation has been unfulfilled as whole-genome studies reveal that nucleosome distributions are remarkably similar between different cell types (Supplemental Fig. 18; Gaffney et al 2012;Kundaje et al 2012;Teif et al 2012). Whole-genome studies have demonstrated that transcribing RNA polymerase is associated with lower nucleosomal occupancy and that conserved noncoding sequences may be sites of regulatory nucleosomes (Schones et al 2008).…”

An Efficient Method for Electroporation of Small Interfering RNAs into ENCODE Project Tier 1 GM12878 and K562 Cell Lines

“…[12][13][14][15][16][17][18][19][20] Yet, RNAi studies have not been routinely performed in this line as a result of technical difficulties with nucleic acid delivery by cationic lipid-mediated transfection. In this study, efforts were made to optimize the transfection conditions in GM12878 cells by use of electroporation for RNAi studies.…”

“…[12][13][14][15][16][17][18][19][20] Both GM12878 and K562 cells possess a relatively normal karyotype, unlike HEK293 and HeLa cells that have undergone extensive chromosomal aneuploidy. For this reason the GM12878 and K562 cell lines were chosen for use in the Tier 1 ENCODE Project, along with H1 human embryonic stem cells.…”

Chromatin computation: Epigenetic inheritance as a pattern reconstruction problem

“…towards the centromere) from the local chromatin structure. In reality, it appears that asymmetries are induced locally and thus are oriented relative to features such as promotors, insulators, or transcription factor binding sites (Kundaje et al, 2012). Such complex rewriting rules indeed seem to be common for eukaryotic systems, as histone-modifying enzymes are often part of large enzyme complexes with multiple protein domains, each of which having a particular function such as DNA sequence recognition or histone binding.…”