TY - JOUR

T1 - Nucleosome positioning around transcription start site correlates with gene expression only for active chromatin state in drosophila interphase chromosomes

AU - Levitsky, Victor G.

AU - Zykova, Tatyana Yu

AU - Moshkin, Yuri M.

AU - Zhimulev, Igor F.

N1 - Funding Information: Funding: The present study was supported by the Russian Science Foundation on the project # 19-14-00051 in analysis of chromatin types and gene transcripts; by the State Budget Projects # 0310-2019-0003 in nucleosome data analysis; by the Russian Science Foundation Project # 20-14-00140 in RNA-seq data analysis. Publisher Copyright: © 2020 by the authors. Licensee MDPI, Basel, Switzerland. Copyright: Copyright 2020 Elsevier B.V., All rights reserved.

PY - 2020/12/1

Y1 - 2020/12/1

N2 - We analyzed the whole-genome experimental maps of nucleosomes in Drosophila melanogaster and classified genes by the expression level in S2 cells (RPKM value, reads per kilobase million) as well as the number of tissues in which a gene was expressed (breadth of expression, BoE). Chromatin in 5′-regions of genes we classified on four states according to the hidden Markov model (4HMM). Only the Aquamarine chromatin state we considered as Active, while the rest three states we defined as Non-Active. Surprisingly, about 20/40% of genes with 5′-regions mapped to Active/Non-Active chromatin possessed the minimal/at least modest RPKM and BoE. We found that regardless of RPKM/BoE the genes of Active chromatin possessed the regular nucleosome arrangement in 5′-regions, while genes of Non-Active chromatin did not show respective specificity. Only for genes of Active chromatin the RPKM/BoE positively correlates with the number of nucleosome sites upstream/around TSS and negatively with that downstream TSS. We propose that for genes of Active chromatin, regardless of RPKM value and BoE the nucleosome arrangement in 5′-regions potentiates transcription, while for genes of Non-Active chromatin, the transcription machinery does not require the substantial support from nucleosome arrangement to influence gene expression.

AB - We analyzed the whole-genome experimental maps of nucleosomes in Drosophila melanogaster and classified genes by the expression level in S2 cells (RPKM value, reads per kilobase million) as well as the number of tissues in which a gene was expressed (breadth of expression, BoE). Chromatin in 5′-regions of genes we classified on four states according to the hidden Markov model (4HMM). Only the Aquamarine chromatin state we considered as Active, while the rest three states we defined as Non-Active. Surprisingly, about 20/40% of genes with 5′-regions mapped to Active/Non-Active chromatin possessed the minimal/at least modest RPKM and BoE. We found that regardless of RPKM/BoE the genes of Active chromatin possessed the regular nucleosome arrangement in 5′-regions, while genes of Non-Active chromatin did not show respective specificity. Only for genes of Active chromatin the RPKM/BoE positively correlates with the number of nucleosome sites upstream/around TSS and negatively with that downstream TSS. We propose that for genes of Active chromatin, regardless of RPKM value and BoE the nucleosome arrangement in 5′-regions potentiates transcription, while for genes of Non-Active chromatin, the transcription machinery does not require the substantial support from nucleosome arrangement to influence gene expression.

KW - 5-regulatory region

KW - Breadth of expression

KW - Chromatin landscape

KW - Expression level

KW - Housekeeping and widely expressed genes

KW - Nucleosome arrangement

KW - Tissue-specific and silent genes

UR - http://www.scopus.com/inward/record.url?scp=85097418957&partnerID=8YFLogxK

U2 - 10.3390/ijms21239282

DO - 10.3390/ijms21239282

M3 - Article

C2 - 33291385

AN - SCOPUS:85097418957

VL - 21

SP - 1

EP - 10

JO - International Journal of Molecular Sciences

JF - International Journal of Molecular Sciences

SN - 1661-6596

IS - 23

M1 - 9282

ER -