Euchromatic subdomains in rice centromeres are associated with genes and transcription

Yufeng Wu, Shinji Kikuchi, Huihuang D Yan, Wenli Zhang, Heidi Rosenbaum, A. Leonardo Iniguez, Jiming Jiang

Research output: Contribution to journalArticle

29 Citations (Scopus)

Abstract

The presence of the centromere-specific histone H3 variant, CENH3, defines centromeric (CEN) chromatin, but poorly understood epigenetic mechanisms determine its establishment and maintenance. CEN chromatin is embedded within pericentromeric heterochromatin in most higher eukaryotes, but, interestingly, it can show euchromatic characteristics; for example, the euchromatic histone modification mark dimethylated H3 Lys 4 (H3K4me2) is uniquely associated with animal centromeres. To examine the histone marks and chromatin properties of plant centromeres, we developed a genomic tiling array for four fully sequenced rice (Oryza sativa) centromeres and used chromatin immunoprecipitation-chip to study the patterns of four euchromatic histone modification marks: H3K4me2, trimethylated H3 Lys 4, trimethylated H3 Lys 36, and acetylated H3 Lys 4, 9. The vast majority of the four histone marks were associated with genes located in the H3 subdomains within the centromere cores. We demonstrate that H3K4me2 is not a ubiquitous component of rice CEN chromatin, and the euchromatic characteristics of rice CEN chromatin are hallmarks of the transcribed sequences embedded in the centro-meric H3 subdomains. We propose that the transcribed sequences located in rice centromeres may provide a barrier preventing loading of CENH3 into the H3 subdomains. The separation of CENH3 and H3 subdomains in the centromere core may be favorable for the formation of three-dimensional centromere structure and for rice centromere function.

Original languageEnglish (US)
Pages (from-to)4054-4064
Number of pages11
JournalPlant Cell
Volume23
Issue number11
DOIs
StatePublished - Nov 2011
Externally publishedYes

Fingerprint

Centromere
centromeres
Histone Code
transcription (genetics)
rice
chromatin
histones
Chromatin
Genes
genes
Oryza
Heterochromatin
Chromatin Immunoprecipitation
heterochromatin
Eukaryota
Epigenomics
epigenetics
Histones
eukaryotic cells
Oryza sativa

ASJC Scopus subject areas

  • Plant Science
  • Cell Biology

Cite this

Wu, Y., Kikuchi, S., Yan, H. D., Zhang, W., Rosenbaum, H., Iniguez, A. L., & Jiang, J. (2011). Euchromatic subdomains in rice centromeres are associated with genes and transcription. Plant Cell, 23(11), 4054-4064. https://doi.org/10.1105/tpc.111.090043

Euchromatic subdomains in rice centromeres are associated with genes and transcription. / Wu, Yufeng; Kikuchi, Shinji; Yan, Huihuang D; Zhang, Wenli; Rosenbaum, Heidi; Iniguez, A. Leonardo; Jiang, Jiming.

In: Plant Cell, Vol. 23, No. 11, 11.2011, p. 4054-4064.

Research output: Contribution to journalArticle

Wu, Y, Kikuchi, S, Yan, HD, Zhang, W, Rosenbaum, H, Iniguez, AL & Jiang, J 2011, 'Euchromatic subdomains in rice centromeres are associated with genes and transcription', Plant Cell, vol. 23, no. 11, pp. 4054-4064. https://doi.org/10.1105/tpc.111.090043
Wu, Yufeng ; Kikuchi, Shinji ; Yan, Huihuang D ; Zhang, Wenli ; Rosenbaum, Heidi ; Iniguez, A. Leonardo ; Jiang, Jiming. / Euchromatic subdomains in rice centromeres are associated with genes and transcription. In: Plant Cell. 2011 ; Vol. 23, No. 11. pp. 4054-4064.
@article{cbf9b1aa24724e3896f7c5dd9fab110f,
title = "Euchromatic subdomains in rice centromeres are associated with genes and transcription",
abstract = "The presence of the centromere-specific histone H3 variant, CENH3, defines centromeric (CEN) chromatin, but poorly understood epigenetic mechanisms determine its establishment and maintenance. CEN chromatin is embedded within pericentromeric heterochromatin in most higher eukaryotes, but, interestingly, it can show euchromatic characteristics; for example, the euchromatic histone modification mark dimethylated H3 Lys 4 (H3K4me2) is uniquely associated with animal centromeres. To examine the histone marks and chromatin properties of plant centromeres, we developed a genomic tiling array for four fully sequenced rice (Oryza sativa) centromeres and used chromatin immunoprecipitation-chip to study the patterns of four euchromatic histone modification marks: H3K4me2, trimethylated H3 Lys 4, trimethylated H3 Lys 36, and acetylated H3 Lys 4, 9. The vast majority of the four histone marks were associated with genes located in the H3 subdomains within the centromere cores. We demonstrate that H3K4me2 is not a ubiquitous component of rice CEN chromatin, and the euchromatic characteristics of rice CEN chromatin are hallmarks of the transcribed sequences embedded in the centro-meric H3 subdomains. We propose that the transcribed sequences located in rice centromeres may provide a barrier preventing loading of CENH3 into the H3 subdomains. The separation of CENH3 and H3 subdomains in the centromere core may be favorable for the formation of three-dimensional centromere structure and for rice centromere function.",
author = "Yufeng Wu and Shinji Kikuchi and Yan, {Huihuang D} and Wenli Zhang and Heidi Rosenbaum and Iniguez, {A. Leonardo} and Jiming Jiang",
year = "2011",
month = "11",
doi = "10.1105/tpc.111.090043",
language = "English (US)",
volume = "23",
pages = "4054--4064",
journal = "Plant Cell",
issn = "1040-4651",
publisher = "American Society of Plant Biologists",
number = "11",

}

TY - JOUR

T1 - Euchromatic subdomains in rice centromeres are associated with genes and transcription

AU - Wu, Yufeng

AU - Kikuchi, Shinji

AU - Yan, Huihuang D

AU - Zhang, Wenli

AU - Rosenbaum, Heidi

AU - Iniguez, A. Leonardo

AU - Jiang, Jiming

PY - 2011/11

Y1 - 2011/11

N2 - The presence of the centromere-specific histone H3 variant, CENH3, defines centromeric (CEN) chromatin, but poorly understood epigenetic mechanisms determine its establishment and maintenance. CEN chromatin is embedded within pericentromeric heterochromatin in most higher eukaryotes, but, interestingly, it can show euchromatic characteristics; for example, the euchromatic histone modification mark dimethylated H3 Lys 4 (H3K4me2) is uniquely associated with animal centromeres. To examine the histone marks and chromatin properties of plant centromeres, we developed a genomic tiling array for four fully sequenced rice (Oryza sativa) centromeres and used chromatin immunoprecipitation-chip to study the patterns of four euchromatic histone modification marks: H3K4me2, trimethylated H3 Lys 4, trimethylated H3 Lys 36, and acetylated H3 Lys 4, 9. The vast majority of the four histone marks were associated with genes located in the H3 subdomains within the centromere cores. We demonstrate that H3K4me2 is not a ubiquitous component of rice CEN chromatin, and the euchromatic characteristics of rice CEN chromatin are hallmarks of the transcribed sequences embedded in the centro-meric H3 subdomains. We propose that the transcribed sequences located in rice centromeres may provide a barrier preventing loading of CENH3 into the H3 subdomains. The separation of CENH3 and H3 subdomains in the centromere core may be favorable for the formation of three-dimensional centromere structure and for rice centromere function.

AB - The presence of the centromere-specific histone H3 variant, CENH3, defines centromeric (CEN) chromatin, but poorly understood epigenetic mechanisms determine its establishment and maintenance. CEN chromatin is embedded within pericentromeric heterochromatin in most higher eukaryotes, but, interestingly, it can show euchromatic characteristics; for example, the euchromatic histone modification mark dimethylated H3 Lys 4 (H3K4me2) is uniquely associated with animal centromeres. To examine the histone marks and chromatin properties of plant centromeres, we developed a genomic tiling array for four fully sequenced rice (Oryza sativa) centromeres and used chromatin immunoprecipitation-chip to study the patterns of four euchromatic histone modification marks: H3K4me2, trimethylated H3 Lys 4, trimethylated H3 Lys 36, and acetylated H3 Lys 4, 9. The vast majority of the four histone marks were associated with genes located in the H3 subdomains within the centromere cores. We demonstrate that H3K4me2 is not a ubiquitous component of rice CEN chromatin, and the euchromatic characteristics of rice CEN chromatin are hallmarks of the transcribed sequences embedded in the centro-meric H3 subdomains. We propose that the transcribed sequences located in rice centromeres may provide a barrier preventing loading of CENH3 into the H3 subdomains. The separation of CENH3 and H3 subdomains in the centromere core may be favorable for the formation of three-dimensional centromere structure and for rice centromere function.

UR - http://www.scopus.com/inward/record.url?scp=84855168343&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84855168343&partnerID=8YFLogxK

U2 - 10.1105/tpc.111.090043

DO - 10.1105/tpc.111.090043

M3 - Article

VL - 23

SP - 4054

EP - 4064

JO - Plant Cell

JF - Plant Cell

SN - 1040-4651

IS - 11

ER -