Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere.
The centromere is the chromosomal site for assembly of the kinetochore where spindle fibers attach during cell division. In most multicellular eukaryotes, centromeres are composed of long tracts of satellite repeats that are recalcitrant to sequencing and fine-scale genetic mapping. Here, we report the genomic and genetic characterization of the complete centromere of rice (Oryza sativa) chromosome 3. Using a DNA fiber-fluorescence in situ hybridization approach, we demonstrated that the centromere of chromosome 3 (Cen3) contains approximately 441 kb of the centromeric satellite repeat CentO. Cen3 includes an approximately 1,881-kb domain associated with the centromeric histone CENH3. This CENH3-associated chromatin domain is embedded within a 3,113-kb region that lacks genetic recombination. Extensive transcription was detected within the CENH3 binding domain based on comprehensive annotation of protein-coding genes coupled with empirical measurements of mRNA levels using RT-PCR and massively parallel signature sequencing. Genes <10 kb from the CentO satellite array were expressed in several rice tissues and displayed histone modification patterns consistent with euchromatin, suggesting that rice centromeric chromatin accommodates normal gene expression. These results support the hypothesis that centromeres can evolve from gene-containing genomic regions.
Yan
Huihuang
H
Department of Horticulture, University of Wisconsin, Madison, 53706, USA.
Ito
Hidetaka
H
Nobuta
Kan
K
Ouyang
Shu
S
Jin
Weiwei
W
Tian
Shulan
S
Lu
Cheng
C
Venu
R C
RC
Wang
Guo-Liang
GL
Green
Pamela J
PJ
Wing
Rod A
RA
Buell
C Robin
CR
Meyers
Blake C
BC
Jiang
Jiming
J
D002503:Centromere; D047369:Chromatin Immunoprecipitation; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D004276:DNA, Satellite / Q000737:chemistry; D019143:Evolution, Molecular; D008040:Genetic Linkage; D023281:Genomics; D006657:Histones / Q000737:chemistry / Q000378:metabolism; D017404:In Situ Hybridization, Fluorescence; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017434:Protein Structure, Tertiary; D012333:RNA, Messenger / Q000378:metabolism; D034741:RNA, Small Interfering / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014158:Transcription, Genetic
D004276:DNA, Satellite; D006657:Histones; D010940:Plant Proteins; D012333:RNA, Messenger; D034741:RNA, Small Interfering