Rice nucleosome patterns undergo remodeling coincident with stress-induced gene expression
| Autor: | Maheshi Dassanayake, Sandra Feuer DiTusa, Niranjan Baisakh, Aaron P. Smith, Dong Ha Oh, Qi Zhang, Mangu Venkata Ramanarao |
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| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
lcsh:QH426-470 lcsh:Biotechnology Eukaryotic DNA replication Chromatin remodeling 03 medical and health sciences Transcription (biology) Gene Expression Regulation Plant Stress Physiological lcsh:TP248.13-248.65 Gene expression Nucleosome patterns Genetics Nucleosome MNase-seq Gene Phosphate starvation Differential gene expression 2. Zero hunger biology Sequence Analysis RNA food and beverages Oryza Chromatin Assembly and Disassembly Chromatin Cell biology Nucleosomes lcsh:Genetics 030104 developmental biology biology.protein Rice RNA-seq Biotechnology Micrococcal nuclease Transcription Factors Research Article |
| Zdroj: | BMC Genomics BMC Genomics, Vol 19, Iss 1, Pp 1-16 (2018) |
| ISSN: | 1471-2164 |
| Popis: | Background Formation of nucleosomes along eukaryotic DNA has an impact on transcription. Major transcriptional changes occur in response to low external phosphate (Pi) in plants, but the involvement of chromatin-level mechanisms in Pi starvation responses have not been investigated. Results We mapped nucleosomes along with transcriptional changes after 24-h of Pi starvation in rice (Oryza sativa) by deep sequencing of micrococcal nuclease digested chromatin and ribosome-depleted RNA. We demonstrated that nucleosome patterns at rice genes were affected by both cis- and trans-determinants, including GC content and transcription. Also, categorizing rice genes by nucleosome patterns across the transcription start site (TSS) revealed nucleosome patterns that correlated with distinct functional categories of genes. We further demonstrated that Pi starvation resulted in numerous dynamic nucleosomes, which were enhanced at genes differentially expressed in response to Pi starvation. Conclusions We demonstrate that rice nucleosome patterns are suggestive of gene functions, and reveal a link between chromatin remodeling and transcriptional changes in response to deficiency of a major macronutrient. Our findings help to enhance the understanding towards eukaryotic gene regulation at the chromatin level. Electronic supplementary material The online version of this article (10.1186/s12864-017-4397-8) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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