Evolutionary origins of pseudogenes and their association with regulatory sequences in plants

First author: Jianbo Xie; Affiliations: Beijing Forestry University (北京林业大学): Beijing, China

Corresponding author: Deqiang Zhang

Pseudogenes (Ψs), non-functional relatives of functional genes, form by duplication or retrotransposition, and loss of gene function by disabling mutations. Evolutionary analysis provides clues to Ψ origins and effects on gene regulation. However, few systematic studies of plant Ψs have been conducted, hampering comparative analyses. Here, we examined the origin, evolution and expression patterns of Ψs and their relationships with noncoding sequences in seven plant species. We identified approximately 250,000 Ψs, most of which are more lineage specific than protein-coding genes. The distribution of Ψs on the chromosome indicates that genome recombination may contribute to Ψ elimination. Most Ψs evolve rapidly in terms of sequence and expression levels, showing tissue specific expression patterns. We found that a surprisingly large fraction of nonTE regulatory noncoding RNAs (microRNAs and long noncoding RNAs) originate from transcription of putative Ψ proximal upstream regions. We also found that transcription factor binding sites preferentially occur in putative Ψ proximal upstream regions compared with random intergenic regions, suggesting Ψs have conditioned genome evolution by providing transcription factor binding sites that serve as promoters and enhancers. We therefore propose that rapid rewiring of Ψ transcriptional regulatory regions is a major mechanism driving the origin of novel regulatory modules.

假基因是功能基因那些不具功能的同源物，由复制或反转录转座作用形成，并经历有害突变后丧失了原本的基因功能。演化分析有助于研究假基因的起源以及其在基因调控方面的作用。然而，很少有研究针对植物假基因进行系统地分析。本文，作者探索了七个植物物种中假基因的起源、演化和表达模式，同时还有这些假基因与非编码序列的关系。作者共鉴定了250000个假基因，分析发现这些假基因要比蛋白序列具有更多的谱系特异性。假基因在染色体上的分布显示基因组重组可能会作用于假基因的消除。大多数的假基因在序列和表达大水平上演化速度较快，并且具有组织特异性的表达模式。作者发现一大类包括microRNA和lncRNA在内的非TE调控非编码RNA起源于假基因上游近端区域的转录。作者还发现与随机的基因间隔区相比，转录因子结合位点优先富集在假基因上游近端区域，说明假基因通过提供转录因子结合位点发挥启动子和增强子的作用，以此来影响基因组的演化。因此，作者提出假基因转录调控区域的快速演变是驱动新的调控模块起源的一个主要机制。

通讯：张德强 (http://biology.bjfu.edu.cn/szdw/bqwrcgcgjjrx/269650.html)

个人简介：1999-2002年，北京林业大学生物学院，博士；2002-2004年，中国林业科学研究院林业所，博士后。

研究方向：分子遗传学、功能基因组学和基因辅助育种。

doi: https://doi.org/10.1105/tpc.18.00601

Journal: Plant Cell

First Published: February 13, 2019