TY - JOUR

T1 - Assessment of transcriptional importance of cell line-specific features based on GTRD and FANTOM5 data

AU - Sharipov, Ruslan N.

AU - Kondrakhin, Yury V.

AU - Ryabova, Anna S.

AU - Yevshin, Ivan S.

AU - Kolpakov, Fedor A.

N1 - Publisher Copyright: © 2020 Sharipov et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.

PY - 2020/12/21

Y1 - 2020/12/21

N2 - Creating a complete picture of the regulation of transcription seems to be an urgent task of modern biology. Regulation of transcription is a complex process carried out by transcription factors (TFs) and auxiliary proteins. Over the past decade, ChIP-Seq has become the most common experimental technology studying genome-wide interactions between TFs and DNA. We assessed the transcriptional significance of cell line-specific features using regression analysis of ChIP-Seq datasets from the GTRD database and transcriptional start site (TSS) activities from the FANTOM5 expression atlas. For this purpose, we initially generated a large number of features that were defined as the presence or absence of TFs in different promoter regions around TSSs. Using feature selection and regression analysis, we identified sets of the most important TFs that affect expression activity of TSSs in human cell lines such as HepG2, K562 and HEK293. We demonstrated that some TFs can be classified as repressors and activators depending on their location relative to TSS.

AB - Creating a complete picture of the regulation of transcription seems to be an urgent task of modern biology. Regulation of transcription is a complex process carried out by transcription factors (TFs) and auxiliary proteins. Over the past decade, ChIP-Seq has become the most common experimental technology studying genome-wide interactions between TFs and DNA. We assessed the transcriptional significance of cell line-specific features using regression analysis of ChIP-Seq datasets from the GTRD database and transcriptional start site (TSS) activities from the FANTOM5 expression atlas. For this purpose, we initially generated a large number of features that were defined as the presence or absence of TFs in different promoter regions around TSSs. Using feature selection and regression analysis, we identified sets of the most important TFs that affect expression activity of TSSs in human cell lines such as HepG2, K562 and HEK293. We demonstrated that some TFs can be classified as repressors and activators depending on their location relative to TSS.

KW - CHIP-SEQ

KW - INTEGRATIVE ANALYSIS

KW - BINDING-SITES

KW - COMPUTATION

KW - ENHANCERS

KW - ATLAS

UR - http://www.scopus.com/inward/record.url?scp=85098912106&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0243332

DO - 10.1371/journal.pone.0243332

M3 - Article

C2 - 33347457

AN - SCOPUS:85098912106

VL - 15

JO - PLoS ONE

JF - PLoS ONE

SN - 1932-6203

IS - 12

M1 - e0243332

ER -