Title | Identifying and mapping cell-type-specific chromatin programming of gene expression. |
Publication Type | Journal Article |
Year of Publication | 2014 |
Authors | Marstrand, TT, Storey, JD |
Journal | Proc Natl Acad Sci U S A |
Volume | 111 |
Issue | 6 |
Pagination | E645-54 |
Date Published | 2014 Feb 11 |
Keywords | Chromatin, Deoxyribonuclease I, Gene Expression Profiling, Humans, Polymorphism, Single Nucleotide, Regulatory Elements, Transcriptional |
Abstract | A problem of substantial interest is to systematically map variation in chromatin structure to gene-expression regulation across conditions, environments, or differentiated cell types. We developed and applied a quantitative framework for determining the existence, strength, and type of relationship between high-resolution chromatin structure in terms of DNaseI hypersensitivity and genome-wide gene-expression levels in 20 diverse human cell types. We show that ∼25% of genes show cell-type-specific expression explained by alterations in chromatin structure. We find that distal regions of chromatin structure (e.g., ±200 kb) capture more genes with this relationship than local regions (e.g., ±2.5 kb), yet the local regions show a more pronounced effect. By exploiting variation across cell types, we were capable of pinpointing the most likely hypersensitive sites related to cell-type-specific expression, which we show have a range of contextual uses. This quantitative framework is likely applicable to other settings aimed at relating continuous genomic measurements to gene-expression variation. |
Alternate Journal | Proc. Natl. Acad. Sci. U.S.A. |