Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations

Olivera Grujic, Tanya N. Phung, Soo Bin Kwon, Adriana Arneson, Yuju Lee, Kirk E. Lohmueller and Jason Ernst ()
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Olivera Grujic: University of California, Los Angeles
Tanya N. Phung: University of California, Los Angeles
Soo Bin Kwon: University of California, Los Angeles
Adriana Arneson: University of California, Los Angeles
Yuju Lee: University of California, Los Angeles
Kirk E. Lohmueller: University of California, Los Angeles
Jason Ernst: University of California, Los Angeles

Nature Communications, 2020, vol. 11, issue 1, 1-16

Abstract: Abstract Annotations of evolutionary sequence constraint based on multi-species genome alignments and genome-wide maps of epigenomic marks and transcription factor binding provide important complementary information for understanding the human genome and genetic variation. Here we developed the Constrained Non-Exonic Predictor (CNEP) to quantify the evidence of each base in the genome being in an evolutionarily constrained non-exonic element from an input of over 60,000 epigenomic and transcription factor binding features. We find that the CNEP score outperforms baseline and related existing scores at predicting evolutionarily constrained non-exonic bases from such data. However, a subset of them are still not well predicted by CNEP. We developed a complementary Conservation Signature Score by CNEP (CSS-CNEP) that is predictive of those bases. We further characterize the nature of constrained non-exonic bases with low CNEP scores using additional types of information. CNEP and CSS-CNEP are resources for analyzing constrained non-exonic bases in the genome.

Date: 2020
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DOI: 10.1038/s41467-020-19962-9

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