Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

Abstract

The human body contains thousands of unique cell types, each with specialized functions. Cell identity is governed in large part by gene transcription programs, which are determined by regulatory elements encoded in DNA. To identify regulatory elements active in seven cell lines representative of diverse human cell types, we used DNase-seq and FAIRE-seq (Formaldehyde Assisted Isolation of Regulatory Elements) to map ''open chromatin.'' Over 870,000 DNaseI or FAIRE sites, which correspond tightly to nucleosome-depleted regions, were identified across the seven cell lines, covering nearly 9% of the genome. The combination of DNaseI and FAIRE is more effective than either assay alone in identifying likely regulatory elements, as judged by coincidence with transcription factor binding locations determined in the same cells. Open chromatin common to all seven cell types tended to be at or near transcription start sites and to be coincident with CTCF binding sites, while open chromatin sites found in only one cell type were typically located away from transcription start sites and contained DNA motifs recognized by regulators of cell-type identity. We show that open chromatin regions bound by CTCF are potent insulators. We identified clusters of open regulatory elements (COREs) that were physically near each other and whose appearance was coordinated among one or more cell types. Gene expression and RNA Pol II binding data support the hypothesis that COREs control gene activity required for the maintenance of cell-type identity. This publicly available atlas of regulatory elements may prove valuable in identifying noncoding DNA sequence variants that are causally linked to human disease.

Uniform, optimal signal processing of mapped deep-sequencing data

“…2d). A similar result was obtained previously 3 , although in that case the two data types were integrated by first calling peaks individually and then combining the resulting P values using Fisher's combined probability test 3 . In our analysis, this two-step method was less successful than direct integrative analysis using DFilter (Fig.…”

“…The technology is now used to obtain genome-wide maps of histone modification, transcription factor binding, chromatin openness, gene expression, DNA methylation, replication origins and mRNA binding by microRNAs and ribosomes, to name but a few of the applications in a rapidly growing list [1][2][3] . At the same time, a plethora of bioinformatic tools has been developed for processing sequence-tag signals from the various assays.…”

“…DNase-seq and FAIRE-seq data from 'Tier 1' human cell lines of the ENCODE project (http://genome.ucsc.edu/encode/cellTypes.html) were used in this analysis 3 . As before, DFilter generated its own training set by scanning the genome for windows of high tag density.…”

“…For example, the two assays appear to differ in their sensitivity at promoter regions 3 . However, a direct quantitative comparison on a comprehensive benchmark data set has not been performed.…”

Apolipoprotein E region molecular signatures of Alzheimer's disease

“…Another study also reported that rs405509 regulates APOE promoter activity (Artiga et al., 1998). Rs387976 ( NECTIN2 ), located in an open chromatin region, seems to mediate transcription factor binding (Song et al., 2011). Ten functional variants were found to exist in active expression states in multiple cell lines, ranging from 1 (rs387976) to 63 (rs157580 [ TOMM40 ]) of 68 cell types with data available from Ensembl.…”