Details

Autor(en) / Beteiligte

• Funk, Cory C.
• Casella, Alex M.
• Jung, Segun
• Richards, Matthew A.
• Rodriguez, Alex
• Shannon, Paul
• Donovan-Maiye, Rory
• Heavner, Ben
• Chard, Kyle
• Xiao, Yukai
• Glusman, Gustavo
• Ertekin-Taner, Nilufer
• Golde, Todd E.
• Toga, Arthur
• Hood, Leroy
• Van Horn, John D.
• Kesselman, Carl
• Foster, Ian
• Madduri, Ravi
• Price, Nathan D.
• Ament, Seth A.

Titel

Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types

Ist Teil von

• Cell reports (Cambridge), 2020-08, Vol.32 (7), p.108029-108029, Article 108029

Ort / Verlag

United States: Elsevier Inc

Erscheinungsjahr

2020

Link zum Volltext

Quelle

Alma/SFX Local Collection

Beschreibungen/Notizen

• Characterizing the tissue-specific binding sites of transcription factors (TFs) is essential to reconstruct gene regulatory networks and predict functions for non-coding genetic variation. DNase-seq footprinting enables the prediction of genome-wide binding sites for hundreds of TFs simultaneously. Despite the public availability of high-quality DNase-seq data from hundreds of samples, a comprehensive, up-to-date resource for the locations of genomic footprints is lacking. Here, we develop a scalable footprinting workflow using two state-of-the-art algorithms: Wellington and HINT. We apply our workflow to detect footprints in 192 ENCODE DNase-seq experiments and predict the genomic occupancy of 1,515 human TFs in 27 human tissues. We validate that these footprints overlap true-positive TF binding sites from ChIP-seq. We demonstrate that the locations, depth, and tissue specificity of footprints predict effects of genetic variants on gene expression and capture a substantial proportion of genetic risk for complex traits. [Display omitted] •Comprehensive map of TF occupancy in human tissues from DNase-seq footprints•Footprints contain genetic variants associated with changes in gene expression•Tissue-specific associations of footprints with genetic risk for complex traits DNase-seq footprinting provides a means to predict genome-wide binding sites for hundreds of transcription factors (TFs) simultaneously. Funk et al. analyze data from the ENCODE consortium to create a resource of footprints in 27 human tissues, demonstrating associations of tissue-specific TF occupancy with gene regulation and disease risk.