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BMC genomics
01 26, 2018;19 (1): 97.

Rice nucleosome patterns undergo remodeling coincident with stress-induced gene expression.

Qi Zhang, Dong-Ha Oh, Sandra Feuer DiTusa, Mangu V RamanaRao, Niranjan Baisakh, Maheshi Dassanayake, Aaron P Smith
Author Information
  1. Qi Zhang: Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
  2. Dong-Ha Oh: Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
  3. Sandra Feuer DiTusa: Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
  4. Mangu V RamanaRao: School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA.
  5. Niranjan Baisakh: School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA.
  6. Maheshi Dassanayake: Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
  7. Aaron P Smith: Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA. apsmith@lsu.edu. ORCID
PMID: 29373953 DOI: 10.1186/s12864-017-4397-8

Abstract

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.

Keywords

Chromatin remodeling Differential gene expression MNase-seq Nucleosome patterns Phosphate starvation RNA-seq Rice

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Grants

  1. IOS-1127051/Directorate for Biological Sciences
  2. MCB-1616827/Directorate for Biological Sciences
  3. PJ011379/Rural Development Administration

MeSH Term

Chromatin Assembly and Disassembly
Gene Expression Regulation, Plant
Nucleosomes
Oryza
Sequence Analysis, RNA
Stress, Physiological
Transcription Factors

Chemicals

Nucleosomes
Transcription Factors
Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

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