title: Characterization of chromatin accessibility with a transposome hypersensitive sites sequencing (THS-seq) assay.
abstract: Chromatin accessibility captures in vivo protein-chromosome binding status, and is considered an informative proxy for protein-DNA interactions. DNase I and Tn5 transposase assays require thousands to millions of fresh cells for comprehensive chromatin mapping. Applying Tn5 tagmentation to hundreds of cells results in sparse chromatin maps. We present a transposome hypersensitive sites sequencing assay for highly sensitive characterization of chromatin accessibility. Linear amplification of accessible DNA ends with in vitro transcription, coupled with an engineered Tn5 super-mutant, demonstrates improved sensitivity on limited input materials, and accessibility of small regions near distal enhancers, compared with ATAC-seq.
authors: Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, USA.|Biomedical Sciences Graduate Program, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, USA.
authors: Brandon Chin
authors: BC
authors: Sos
authors: Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, USA.
authors: Ho-Lim
authors: HL
authors: Fung
authors: Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, USA.
authors: Derek Rui
authors: DR
authors: Gao
authors: Illumina Inc, 5200 Illumina Way, San Diego, CA, USA.
authors: Trina Faye
authors: TF
authors: Osothprarop
authors: Illumina Inc, 5200 Illumina Way, San Diego, CA, USA.
authors: Amirali
authors: A
authors: Kia
authors: Illumina Inc, 5200 Illumina Way, San Diego, CA, USA.
authors: Molly Min
authors: MM
authors: He
authors: Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, USA. kzhang@bioeng.ucsd.edu.|Biomedical Sciences Graduate Program, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, USA. kzhang@bioeng.ucsd.edu.
authors: Kun
authors: K
authors: Zhang
mesh_terms: D045744:Cell Line, Tumor; D002843:Chromatin / Q000235:genetics*; D004247:DNA / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics; D003850:Deoxyribonuclease I / Q000235:genetics; D006801:Humans; D017423:Sequence Analysis, RNA / Q000379:methods; D014158:Transcription, Genetic; D019895:Transposases / Q000235:genetics
chemical_list: D002843:Chromatin; D004251:DNA Transposable Elements; C473503:Tn5 transposase; D004247:DNA; D019895:Transposases; D003850:Deoxyribonuclease I