A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response.
A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response.
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DOI：
10.1101/gr.193763.115
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发表时间：
2016-02
期刊：
影响因子：
7
通讯作者：
Gaut BS
中科院分区：
文献类型：
--
作者：
Bousios A;Diez CM;Takuno S;Bystry V;Darzentas N;Gaut BS
转座因子（TE）在其宿主的基因组内增殖，宿主通过表观遗传学沉默它们来响应。关于植物中沉默的机制，特别是siRNA在指导DNA甲基化中的作用，已经知道很多。相比之下，很少有人知道siRNA的靶向模式沿着TE的长度，但这些信息可能提供关键的见解主机和TE之间的动态。通过关注玉米中6456个仔细注释的全长Sirevirus LTR逆转录转座子，我们表明它们的沉默与TE序列的潜在特征相关，并且还揭示了宿主-TE相互作用的三个特征。首先，siRNA定位在家族之间和元件之间变化，但特别是沿着元件的长度沿着变化。在LTR的顺式调节部分内，复杂的富含回文的区域充当siRNA匹配和序列进化的热点。这些模式在叶、雄穗和未成熟穗文库中是一致的，但特别强调花组织和21-至22-nt siRNA。其次，该区域具有形成发夹的能力，使其成为产生miRNA样发夹衍生的小RNA的潜在模板。第三，siRNAs靶向Sireviruses作为其年龄的递减函数，但最古老的元件仍然高度靶向，部分是由siRNAs交叉映射到最年轻的元件。我们表明，老Sireviruses的目标反映了他们保守的回文。总之，我们假设回文酶有助于活性元件的沉默，并影响转座潜力、siRNA靶向水平，最终影响基因组内元件的命运。
Transposable elements (TEs) proliferate within the genome of their host, which responds by silencing them epigenetically. Much is known about the mechanisms of silencing in plants, particularly the role of siRNAs in guiding DNA methylation. In contrast, little is known about siRNA targeting patterns along the length of TEs, yet this information may provide crucial insights into the dynamics between hosts and TEs. By focusing on 6456 carefully annotated, full-length Sirevirus LTR retrotransposons in maize, we show that their silencing associates with underlying characteristics of the TE sequence and also uncover three features of the host–TE interaction. First, siRNA mapping varies among families and among elements, but particularly along the length of elements. Within the cis-regulatory portion of the LTRs, a complex palindrome-rich region acts as a hotspot of both siRNA matching and sequence evolution. These patterns are consistent across leaf, tassel, and immature ear libraries, but particularly emphasized for floral tissues and 21- to 22-nt siRNAs. Second, this region has the ability to form hairpins, making it a potential template for the production of miRNA-like, hairpin-derived small RNAs. Third, Sireviruses are targeted by siRNAs as a decreasing function of their age, but the oldest elements remain highly targeted, partially by siRNAs that cross-map to the youngest elements. We show that the targeting of older Sireviruses reflects their conserved palindromes. Altogether, we hypothesize that the palindromes aid the silencing of active elements and influence transposition potential, siRNA targeting levels, and ultimately the fate of an element within the genome.