Meiotically Stable Natural Epialleles of <em>Sadhu,</em> a Novel Arabidopsis Retroposon

Epigenetic variation is a potential source of genomic and phenotypic variation among different individuals in a population, and among different varieties within a species. We used a two-tiered approach to identify naturally occurring epigenetic alleles in the flowering plant Arabidopsis: a primary screen for transcript level polymorphisms among three strains (Col, Cvi, Ler), followed by a secondary screen for epigenetic alleles. Here, we describe the identification of stable, meiotically transmissible epigenetic alleles that correspond to one member of a previously uncharacterized non-LTR retroposon family, which we have designated Sadhu. The pericentromeric At2g10410 element is highly expressed in strain Col, but silenced in Ler and 18 other strains surveyed. Transcription of this locus is inversely correlated with cytosine methylation and both the expression and DNA methylation states map in a Mendelian manner to stable cis-acting variation. The silent Ler allele can be converted by the epigenetic modifier mutation ddm1 to a meiotically stable expressing allele with an identical primary nucleotide sequence, demonstrating that the variation responsible for transcript level polymorphism among Arabidopsis strains is epigenetic. We extended our characterization of the Sadhu family members and show that different elements are subject to both genetic and epigenetic variation in natural populations. These findings support the view that an important component of natural variation in retroelements is epigenetic.表观遗传变异（Epigenetic variation）是种群内不同个体间以及物种内不同变种间基因组与表型变异的潜在来源。我们采用双层级研究策略，在开花植物拟南芥（Arabidopsis）中鉴定自然存在的表观等位基因：首先对Col、Cvi、Ler三个菌株的转录水平多态性开展初筛，随后针对表观等位基因进行复筛。本文报道了一类稳定且可经减数分裂传递的表观等位基因的鉴定结果，该等位基因对应此前未被表征的非长末端重复序列（non-LTR）逆转座子家族的一个成员，我们将该家族命名为Sadhu。着丝粒旁区域的At2g10410元件在Col菌株中呈高表达状态，但在Ler及其他18个被检测的菌株中均发生基因沉默。该位点的转录水平与胞嘧啶甲基化（cytosine methylation）呈负相关，且其表达状态与DNA甲基化模式均以孟德尔式遗传方式定位至稳定的顺式作用变异区域。沉默的Ler等位基因可通过表观遗传修饰突变体ddm1转化为具有完全相同初级核苷酸序列的、减数分裂稳定的表达型等位基因，这证明拟南芥菌株间转录水平多态性的成因是表观遗传变异。我们进一步对Sadhu家族的成员进行了表征分析，结果显示该家族的不同逆转座元件在自然种群中均存在遗传与表观遗传两类变异。上述研究结果支持了这一学术观点：逆转座元件的自然变异中，重要的组成部分是表观遗传变异。