Integrative epigenomic and functional characterization assay based annotation of regulatory activity across diverse human cell types

Tevfik Umut Dincer; Jason Ernst

doi:10.1101/2023.07.14.549056

Integrative epigenomic and functional characterization assay based annotation of regulatory activity across diverse human cell types

bioRxiv [Preprint]. 2023 Jul 15:2023.07.14.549056. doi: 10.1101/2023.07.14.549056.

Authors

Tevfik Umut Dincer^{1

2}, Jason Ernst^{1

2

3

4

5

6

7}

Affiliations

¹ Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, 90095, USA.
² Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA.
³ Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at University of California, Los Angeles, CA, 90095, USA.
⁴ Computer Science Department, University of California, Los Angeles, CA, 90095, USA.
⁵ Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, 90095, USA.
⁶ Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA.
⁷ Department of Computational Medicine, University of California, Los Angeles, CA, 90095, USA.

Abstract

We introduce ChromActivity, a computational framework for predicting and annotating regulatory activity across the genome through integration of multiple epigenomic maps and various functional characterization datasets. ChromActivity generates genomewide predictions of regulatory activity associated with each functional characterization dataset across many cell types based on available epigenomic data. It then for each cell type produces (1) ChromScoreHMM genome annotations based on the combinatorial and spatial patterns within these predictions and (2) ChromScore tracks of overall predicted regulatory activity. ChromActivity provides a resource for analyzing and interpreting the human regulatory genome across diverse cell types.

Keywords: CRISPR screens; epigenome; gene regulation; genome annotation; hidden markov model; machine learning; massively parallel reporter assays.

Publication types

Preprint

Grants and funding

US National Institutes of Health (DP1DA044371, U01MH130995, U01MH105578, UH3NS104095, U01HG012079); US National Science Foundation (1254200, 2125664); Rose Hills Innovator Award, and the UCLA Jonsson Comprehensive Cancer Center and Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research Ablon Scholars Program.