Neofunctionalization of a polyploidization-activated cotton long intergenic non-coding RNA DAN1 during drought stress regulation.
Neofunctionalization of a polyploidization-activated cotton long intergenic non-coding RNA DAN1 during drought stress regulation.
复制标题
干旱胁迫调节过程中多倍体化激活的棉花长基因间非编码RNA DAN1的新功能化
DOI：
10.1093/plphys/kiab179
复制
发表时间：
2021-08-03
期刊：
影响因子：
7.4
通讯作者：
Guan X
中科院分区：
文献类型：
--
作者：
Tao X;Li M;Zhao T;Feng S;Zhang H;Wang L;Han J;Gao M;Lu K;Chen Q;Zhou B;Guan X
全基因组复制（WGD）和杂交的基因组休克为编码和非编码基因的转录组引入了巨大的变异。改变的转录组为在新物种进化过程中改善适应性提供了分子基础。异源四倍体棉花与假定的二倍体祖先物种一起构成了研究基因组休克后快速基因新功能化的良好模型。在这里，我们报告了干旱相关非编码基因1（DAN 1），这是一种长基因间非编码RNA（lincRNA），它在棉花进化过程中杂交和WGD事件后从棉花祖先A-二倍体基因组中产生。异源四倍体高地棉（Gossypium hirsutum）中的DAN 1是主要在核质中表达的干旱响应lincRNA。通过RNA纯化分析和电泳迁移率变动分析的染色质分离表明，GhDAN 1 RNA可以与含有AAAG基序的DNA片段结合，类似于DNA与一个锌指转录因子结合序列的结合。GhDAN 1的抑制主要调节生长素反应途径中具有AAAG基序的基因，这些基因与干旱胁迫调节相关。因此，GhDAN 1沉默的植物表现出对干旱胁迫的耐受性提高。该表型类似于具有不可检测的DAN 1表达的A-二倍体棉花祖先物种的耐旱表型。DAN 1在棉花进化和耐旱性调控中的作用表明，种间杂交和WGD的基因组冲击刺激了自然进化过程中非编码基因的新功能化。一种杂交和多倍化激活的lncRNA，通过形成主要在生长素反应途径中靶向基因的RNA-DNA三链体，新功能化为干旱反应的调节因子。
The genomic shock of whole-genome duplication (WGD) and hybridization introduces great variation into transcriptomes, for both coding and noncoding genes. An altered transcriptome provides a molecular basis for improving adaptation during the evolution of new species. The allotetraploid cotton, together with the putative diploid ancestor species compose a fine model for study the rapid gene neofunctionalization over the genome shock. Here we report on Drought-Associated Non-coding gene 1 (DAN1), a long intergenic noncoding RNA (lincRNA) that arose from the cotton progenitor A-diploid genome after hybridization and WGD events during cotton evolution. DAN1 in allotetraploid upland cotton (Gossypium hirsutum) is a drought-responsive lincRNA predominantly expressed in the nucleoplasm. Chromatin isolation by RNA purification profiling and electrophoretic mobility shift assay analysis demonstrated that GhDAN1 RNA can bind with DNA fragments containing AAAG motifs, similar to DNA binding with one zinc finger transcription factor binding sequences. The suppression of GhDAN1 mainly regulates genes with AAAG motifs in auxin-response pathways, which are associated with drought stress regulation. As a result, GhDAN1-silenced plants exhibit improved tolerance to drought stress. This phenotype resembles the drought-tolerant phenotype of the A-diploid cotton ancestor species, which has an undetectable expression of DAN1. The role of DAN1 in cotton evolution and drought tolerance regulation suggests that the genomic shock of interspecific hybridization and WGD stimulated neofunctionalization of non-coding genes during the natural evolutionary process. A hybridization- and polyploidization-activated lncRNA neofunctionalized into a regulator of drought responses by forming RNA–DNA triplexes targeting genes mainly in the auxin response pathway.
登录
查看更多内容
DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
5.6
作者：
Du H;Liu H;Xiong L
通讯作者：
Xiong L
影响因子：
7
作者：
Buske FA;Bauer DC;Mattick JS;Bailey TL
通讯作者：
Bailey TL
DOI：
10.1073/pnas.1608827113
发表时间：
2016-11-29
影响因子：
11.1
作者：
Fedak, Halina;Palusinska, Malgorzata;Swiezewski, Szymon
通讯作者：
Swiezewski, Szymon
模因套件：用于发现和搜索的工具。
影响因子：
14.9
作者：
Bailey TL;Boden M;Buske FA;Frith M;Grant CE;Clementi L;Ren J;Li WW;Noble WS
通讯作者：
Noble WS