ハクサイのヘテロシスを示すF1とその親系統を用いたゲノムワイドなヒストン修飾解析

概要

Brassica rapa L. encompasses commercially important cultivars of vegetables, oilseeds,
condiments, and fodder and is a crop closely related to Arabidopsis thaliana (Cheng et al. 2014,
Cheng et al. 2016a, Lv et al. 2020). In addition to its agronomic significance, B. rapa is also
important for genomic studies, because it has the first complete genome sequence to be
determined within the genus Brassica (Wang et al. 2011). B. rapa (AA genome) is one of the
ancestral species of the allotetraploid species, Brassica nigra L (AABB) and Brassica napus L
(AACC) (Chalhoub et al. 2014, Yang J et al. 2016b). The B. rapa genome has undergone a
whole-genome triplication after speciation between A. thaliana and B. rapa (Wang et al. 2011).
The whole-genome triplication results in multiple copies of paralogous genes and generates three
subgenomes, the least fractioned subgenome (LF) and two more fractionated subgenomes (MF1
and MF2) within the B. rapa genome (Wang et al. 2011). After the whole genome triplication,
subfunctionalization such as different expression levels or DNA methylation levels among three
subgenomes or paralogous genes has been observed (Parkin et al. 2014, Chen et al. 2015).
The basic unit of chromatin is the nucleosome, which consists of 147 bp of DNA
wrapped around a histone octamer containing two of each of H2A, H2B, H3, and H4 (Li et al.
2007). Chromatin structure is regulated by posttranslational modification of histone proteins
such as methylation, acetylation, phosphorylation, ubiquitylation, and sumoylation (Strahl and
Allis 2000, Jenuwein and Allis 2001, Li et al. 2007). Specific amino acid residues of the Nterminal tail of histone proteins are targets for posttranslational modifications that can impact
gene expression by altering the chromatin structure. In plants, tri-methylation of histone H3
lysine 4 (H3K4me3) and H3K36me3 are often associated with transcriptional activation and that
of H3K9me2 and H3K27me3 with transcriptional repression (Fuchs et al. 2006, Li et al. 2007,
Xiao et al. 2016). Histone modification is an epigenetic regulatory mechanism, which affects
transcriptional activity of chromatin without changing DNA sequence and is crucial for the
development and the adaptation of plants to changing environments (Fujimoto et al. 2012a,
Quadrana and Colot 2016).
The application of high-throughput sequencing technologies provides an opportunity to
identify the genome-wide profiles of histone modification by a combination of chromatin
immunoprecipitation (ChIP) and genome-wide sequencing (ChIP-seq). ...

この論文で使われている画像