Maps of open chromatin highlight cell type–restricted patterns of regulatory sequence variation at hematological trait loci

Abstract

Nearly three-quarters of the 143 genetic signals associated with platelet and erythrocyte phenotypes identified by metaanalyses of genome-wide association (GWA) studies are located at non-protein-coding regions. Here, we assessed the role of candidate regulatory variants associated with cell type-restricted, closely related hematological quantitative traits in biologically relevant hematopoietic cell types. We used formaldehyde-assisted isolation of regulatory elements followed by next-generation sequencing (FAIRE-seq) to map regions of open chromatin in three primary human blood cells of the myeloid lineage. In the precursors of platelets and erythrocytes, as well as in monocytes, we found that open chromatin signatures reflect the corresponding hematopoietic lineages of the studied cell types and associate with the cell typespecific gene expression patterns. Dependent on their signal strength, open chromatin regions showed correlation with promoter and enhancer histone marks, distance to the transcription start site, and ontology classes of nearby genes. Cell type-restricted regions of open chromatin were enriched in sequence variants associated with hematological indices. The majority (63.6%) of such candidate functional variants at platelet quantitative trait loci (QTLs) coincided with binding sites of five transcription factors key in regulating megakaryopoiesis. We experimentally tested 13 candidate regulatory variants at 10 platelet QTLs and found that 10 (76.9%) affected protein binding, suggesting that this is a frequent mechanism by which regulatory variants influence quantitative trait levels. Our findings demonstrate that combining large-scale GWA data with open chromatin profiles of relevant cell types can be a powerful means of dissecting the genetic architecture of closely related quantitative traits.

Epigenetic Modification of Histone 3 Lysine 27

“…These data are consistent with the hypothesis that for CYP2C9 activation, cross-talk between CAR and HNF4␣ involves local changes in chromatin architecture in which the promoter adopts a looped conformation (37) that may, in part, rely on the differential histone modifications described previously. Future FAIRE-seq analyses of genome-wide FAIRE data will reveal regions of MED25 regulation in genes that are important for diverse cellular processes (57).…”

Disentangling effects of colocalizing genomic annotations to functionally prioritize non-coding variants within complex trait loci

“…We then compared the results of GoShifter to those of the more commonly used matching-based enrichment tests 2,5,[7][8][9][10]12,13,19,29,[31][32][33][34][35][36][37][38] (Table S1). These methods typically match SNPs on GEN, MAF, and TSS proximity.…”

“…[1][2][3][4][5][6][7][8][9][10][11][12] Profiles of such functional genomic annotations, including transcription factor binding sites and open chromatin regions from hundreds of cell types, are rapidly becoming available. [13][14][15] But, the most informative annotation is not always known.…”

Massively parallel sequencing: the new frontier of hematologic genomics

“…56 Already, systems such as molecular inversion probes are offering new ways to advance NGS capabilities and facilitate sequencing of the thousands of individuals required to pursue rare variant discoveries in human genetics. 57 The scale of massively parallel sequencing opens new avenues for all forms of biological analysis, including analysis of sequence variants (shown in Table 1 [58][59][60][61][62][63] ). 64 Variant discovery and RNA sequencing are the principal applications today for NGS.…”