التفاصيل البيبلوغرافية
| العنوان: |
XL-DNase-seq: improved footprinting of dynamic transcription factors. |
| المؤلفون: |
Oh, Kyu-Seon1 (AUTHOR), Ha, Jisu1 (AUTHOR), Baek, Songjoon2 (AUTHOR), Sung, Myong-Hee1 (AUTHOR) sungm@mail.nih.gov |
| المصدر: |
Epigenetics & Chromatin. 6/4/2019, Vol. 12 Issue 1, pN.PAG-N.PAG. 1p. |
| مصطلحات موضوعية: |
*TRANSCRIPTION factors, *GENE regulatory networks, *REGULATOR genes |
| مستخلص: |
Background: As the cost of high-throughput sequencing technologies decreases, genome-wide chromatin accessibility profiling methods such as the assay of transposase-accessible chromatin using sequencing (ATAC-seq) are employed widely, with data accumulating at an unprecedented rate. However, accurate inference of protein occupancy requires higher-resolution footprinting analysis where major hurdles exist, including the sequence bias of nucleases and the short-lived chromatin binding of many transcription factors (TFs) with consequent lack of footprints. Results: Here we introduce an assay termed cross-link (XL)-DNase-seq, designed to capture chromatin interactions of dynamic TFs. Mild cross-linking improved the detection of DNase-based footprints of dynamic TFs but interfered with ATAC-based footprinting of the same TFs. Conclusions: XL-DNase-seq may help extract novel gene regulatory circuits involving previously undetectable TFs. The DNase-seq and ATAC-seq data generated in our systematic comparison of various cross-linking conditions also represent an unprecedented-scale resource derived from activated mouse macrophage-like cells which share many features of inflammatory macrophages. [ABSTRACT FROM AUTHOR] |
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