Nucleosome Positioning around Transcription Start Site Correlates with Gene Expression Only for Active Chromatin State in Drosophila Interphase Chromosomes
| Autor: | Tatyana Yu Zykova, Igor F. Zhimulev, Yuri M. Moshkin, Victor G. Levitsky |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
0301 basic medicine chromatin landscape Transcription Genetic expression level 5′-regulatory region 01 natural sciences Catalysis Article Inorganic Chemistry lcsh:Chemistry 03 medical and health sciences Transcription (biology) Gene expression Nucleosome housekeeping and widely expressed genes Animals breadth of expression Physical and Theoretical Chemistry Promoter Regions Genetic Molecular Biology Gene lcsh:QH301-705.5 Interphase Spectroscopy biology Schneider 2 cells Organic Chemistry Chromosome Mapping General Medicine biology.organism_classification Chromatin Assembly and Disassembly Chromatin Computer Science Applications Cell biology Nucleosomes 030104 developmental biology tissue-specific and silent genes Drosophila melanogaster lcsh:Biology (General) lcsh:QD1-999 Gene Expression Regulation nucleosome arrangement Transcription Initiation Site 010606 plant biology & botany Transcription Factors |
| Zdroj: | International Journal of Molecular Sciences Volume 21 Issue 23 International Journal of Molecular Sciences, Vol 21, Iss 9282, p 9282 (2020) |
| ISSN: | 1422-0067 |
| Popis: | 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&prime 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&prime 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&prime 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&prime 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. |
| Databáze: | OpenAIRE |
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