Profiling of cytosine DNA-methylation in the Arabidopsis CAF-1 mutant fas2

Chromatin Assembly Factor CAF-1 is a histone chaperone involved in nucleosome formation after replication. Here, cytosine DNA-methylation was profiled by bisulphite DNA sequencing in Arabidopsis wild type and the fas2 CAF-1 mutant. To test for transgenerational changes in DNA methylation, fas2 mutants of generation 1 and 6 were compared. Overall design: Characterisation of the transgenerational methylation changes in fas2-4 mutants using genome-wide bisulfite sequencing. The transgenerational effect was assessed by bisulphite sequencing the first homozygous generation segregated from a selfed heterozygous fas2-4 parental plant and the 6th selfed generation. Col-0 accession was used as a reference. The DNA was sequenced in 100 bp pair-end mode. To increase coverage, mates were mapped as independent single end reads: R1 as directional and R2 in a non-directional.

染色质组装因子CAF-1（Chromatin Assembly Factor CAF-1）是一类参与复制后核小体组装的组蛋白伴侣蛋白。本研究采用亚硫酸氢盐DNA测序（bisulphite DNA sequencing）技术，对拟南芥野生型及fas2 CAF-1突变体的胞嘧啶DNA甲基化水平开展图谱分析。为探究DNA甲基化的跨代变化情况，本研究对第1代与第6代fas2突变体进行了比较。

实验设计概述：通过全基因组亚硫酸氢盐测序（genome-wide bisulfite sequencing）对fas2-4突变体的跨代甲基化变化进行表征。本研究通过亚硫酸氢盐DNA测序，分别对自交杂合fas2-4亲本植株分离得到的首个纯合子代，以及第6代自交子代进行测序，以此评估DNA甲基化的跨代效应。本研究以Col-0生态型作为参考样本。测序采用100 bp双端测序模式。为提升测序覆盖度，将双端reads拆分为独立的单端reads进行比对：其中R1采用定向比对方式，R2采用非定向比对方式。