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Identifying Transcription Error-Enriched Genomic Loci Using Nuclear Run-on Circular-Sequencing Coupled with Background Error Modeling.

Abstract：

:RNA polymerase transcribes certain genomic loci with higher errors rates. These transcription error-enriched genomic loci (TEELs) have implications in disease. Current deep-sequencing methods cannot distinguish TEELs from post-transcriptional modifications, stochastic transcription errors, and technical noise, impeding efforts to elucidate the mechanisms linking TEELs to disease. Here, we describe background error model-coupled precision nuclear run-on circular-sequencing (EmPC-seq) to discern genomic regions enriched for transcription misincorporations. EmPC-seq innovatively combines a nuclear run-on assay for capturing nascent RNA before post-transcriptional modifications, a circular-sequencing step that sequences the same nascent RNA molecules multiple times to improve accuracy, and a statistical model for distinguishing error-enriched regions among stochastic polymerase errors. Applying EmPC-seq to the ribosomal RNA transcriptome, we show that TEELs of RNA polymerase I are not randomly distributed but clustered together, with higher error frequencies at nascent transcript 3' ends. Our study establishes a reliable method of identifying TEELs with nucleotide precision, which can help elucidate their molecular origins.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Cheung PP,Jiang B,Booth GT,Chong TH,Unarta IC,Wang Y,Suarez GD,Wang J,Lis JT,Huang X

doi

10.1016/j.jmb.2020.04.011

subject

Has Abstract

pub_date

2020-06-12 00:00:00

pages

3933-3949

issue

13

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(20)30284-9

journal_volume

432

pub_type

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