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转座子变体及其对拟南芥基因表达的影响。

Transposon variants and their effects on gene expression in Arabidopsis.

机构信息

Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.

出版信息

PLoS Genet. 2013;9(2):e1003255. doi: 10.1371/journal.pgen.1003255. Epub 2013 Feb 7.

DOI:10.1371/journal.pgen.1003255
PMID:23408902
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3567156/
Abstract

Transposable elements (TEs) make up the majority of many plant genomes. Their transcription and transposition is controlled through siRNAs and epigenetic marks including DNA methylation. To dissect the interplay of siRNA-mediated regulation and TE evolution, and to examine how TE differences affect nearby gene expression, we investigated genome-wide differences in TEs, siRNAs, and gene expression among three Arabidopsis thaliana accessions. Both TE sequence polymorphisms and presence of linked TEs are positively correlated with intraspecific variation in gene expression. The expression of genes within 2 kb of conserved TEs is more stable than that of genes next to variant TEs harboring sequence polymorphisms. Polymorphism levels of TEs and closely linked adjacent genes are positively correlated as well. We also investigated the distribution of 24-nt-long siRNAs, which mediate TE repression. TEs targeted by uniquely mapping siRNAs are on average farther from coding genes, apparently because they more strongly suppress expression of adjacent genes. Furthermore, siRNAs, and especially uniquely mapping siRNAs, are enriched in TE regions missing in other accessions. Thus, targeting by uniquely mapping siRNAs appears to promote sequence deletions in TEs. Overall, our work indicates that siRNA-targeting of TEs may influence removal of sequences from the genome and hence evolution of gene expression in plants.

摘要

转座元件 (TEs) 在许多植物基因组中占很大比例。它们的转录和转座通过 siRNA 和表观遗传标记（包括 DNA 甲基化）来控制。为了剖析 siRNA 介导的调控与 TE 进化之间的相互作用，并研究 TE 差异如何影响附近基因的表达，我们研究了三个拟南芥品系之间的 TEs、siRNAs 和基因表达的全基因组差异。TE 序列多态性和连锁 TE 的存在与基因表达的种内变异呈正相关。保守 TE 附近的基因表达比携带序列多态性的变异 TE 附近的基因表达更稳定。TE 和紧密连锁的相邻基因的多态性水平也呈正相关。我们还研究了 24 个核苷酸长的 siRNAs 的分布，这些 siRNAs 介导了 TE 的抑制。由唯一映射 siRNAs 靶向的 TE 平均距离编码基因更远，显然是因为它们更强烈地抑制了相邻基因的表达。此外，siRNAs，尤其是唯一映射的 siRNAs，在其他品系缺失的 TE 区域富集。因此，唯一映射 siRNAs 的靶向似乎促进了 TE 中的序列缺失。总的来说，我们的工作表明，TE 的 siRNA 靶向可能影响基因组中序列的去除，从而影响植物中基因表达的进化。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1e1f/3567156/21ae185fc707/pgen.1003255.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1e1f/3567156/492e393a8ff5/pgen.1003255.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1e1f/3567156/64ea0c263db1/pgen.1003255.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1e1f/3567156/7d1ff6f5dfe4/pgen.1003255.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1e1f/3567156/40531d847f5c/pgen.1003255.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1e1f/3567156/33474a4f88d0/pgen.1003255.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1e1f/3567156/fe976d16cbe2/pgen.1003255.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1e1f/3567156/21ae185fc707/pgen.1003255.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1e1f/3567156/492e393a8ff5/pgen.1003255.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1e1f/3567156/64ea0c263db1/pgen.1003255.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1e1f/3567156/7d1ff6f5dfe4/pgen.1003255.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1e1f/3567156/40531d847f5c/pgen.1003255.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1e1f/3567156/33474a4f88d0/pgen.1003255.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1e1f/3567156/fe976d16cbe2/pgen.1003255.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1e1f/3567156/21ae185fc707/pgen.1003255.g007.jpg

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