Predictive model of transcriptional elongation control identifies trans regulatory factors from chromatin signatures

Abstract

Promoter-proximal Polymerase II (Pol II) pausing is a key rate limiting step for gene expression. DNA and RNA-binding trans-acting factors regulating the extent of pausing have been identified. However, we lack a quantitative model of how interactions of these factors determine pausing, therefore the relative importance of implicated factors is unknown. Moreover, previously unknown regulators might exist. Here we address this gap with a machine learning model that accurately predicts the extent of promoter proximal Pol II pausing from large scale genome and transcriptome binding maps, as well as gene annotation and sequence composition features. We demonstrate high accuracy and generalizability of the model by validation on an independent cell line which reveals the models cell line agnostic character. Model interpretation in light of prior knowledge about molecular functions of regulatory factors confirms the interconnection of pausing with other RNA processing steps. Harnessing underlying feature contributions we assess the relative importance of each factor, quantify their predictive effects and systematically identify previously unknown regulators of pausing. We additionally identify 16 previously unknown 7SK ncRNA interacting RNA-binding proteins predictive of pausing. Our work provides a framework to further our understanding of the regulation of the critical early steps in transcriptional elongation. Key Points: Please provide 3 bullet points summarizing the manuscripts contribution to the field- ML model that accurately predicts promoter proximal Pol II pausing from ChIP and eClip-seq data - Quantification of the interconnection of pausing and other steps of gene regulation - Identification of novel putative trans regulators of pausing GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/496993v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@1c7dfc3org.highwire.dtl.DTLVardef@133886eorg.highwire.dtl.DTLVardef@41f694org.highwire.dtl.DTLVardef@a396af_HPS_FORMAT_FIGEXP M_FIG C_FIG