RT Journal Article
SR Electronic
T1 Tree Based Co-Clustering Identifies Variation in Chromatin Accessibility Across Hematopoietic Cell Types
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.05.07.443145
DO 10.1101/2021.05.07.443145
A1 Thomas B. George
A1 Nathaniel K. Strawn
A1 Sivan Leviyang
YR 2021
UL http://biorxiv.org/content/early/2021/05/08/2021.05.07.443145.abstract
AB Chromatin accessibility, as measured by ATACseq, varies between hematopoietic cell types in different branches of the hematopoietic differentiation tree, e.g. T cells vs B cells, but methods that relate variation in chromatin accessibility to the placement of a cell type on the differentiation tree are lacking. Using an ATACseq dataset recently published by the ImmGen consortium, we construct associations between chromatin accessibility and hematopoietic cell types using a novel co-clustering approach that accounts for the structure of the hematopoietic, differentiation tree. Under a model in which all loci and cell types within a co-cluster have a shared accessibility state, we show that roughly 80% of cell type associated accessibility variation can be captured through 12 cell type clusters and 20 genomic locus clusters. Using publicly available ChIPseq datasets, we show that our clustering reflects transcription factor binding patterns with implications for regulation across cell types. Our results provide a framework for analysis of chromatin state variation across cell types related by a tree or network.Competing Interest StatementThe authors have declared no competing interest.