No Expression Divergence despite Transcriptional Interference between Nested Protein-Coding Genes in Mammals.
No Expression Divergence despite Transcriptional Interference between Nested Protein-Coding Genes in Mammals.
复制标题
尽管哺乳动物嵌套蛋白编码基因之间存在转录干扰，但没有表达差异。
DOI：
10.3390/genes12091381
复制
发表时间：
2021-09-01
期刊：
影响因子：
3.5
通讯作者：
Assis R
中科院分区：
文献类型：
--
作者：
Assis R
嵌套的蛋白质编码基因在后生动物的进化过程中不断积累，早期对人类和果蝇微阵列数据的分析表明，这种现象仅仅是由于大内含子的存在。然而，最近一项使用RNA-seq数据的研究发现了转录干扰驱动果蝇嵌套基因之间快速表达差异的证据，说明重叠基因的准确表达估计可以增强对其关系的检测。因此，在这里，我将类似的方法应用于来自人类和小鼠的链特异性RNA-seq数据，以重新审视转录干扰在哺乳动物嵌套基因进化中的作用。一项基因组调查显示，虽然哺乳动物的巢状基因确实在进化过程中积累，但它们保留的频率低于果蝇。虽然哺乳动物嵌套基因的几个特性与果蝇中的观察结果和转录干扰下的预期一致，但与两者相反，它们的表达差异与非嵌套基因之间的差异没有统计学差异，并且在嵌套后也没有增加。总之，这些结果支持的假设，较低的选择效率限制哺乳动物的基因表达进化的速度，导致他们的依赖立即根除有害的嵌套基因，以避免转录干扰。
Nested protein-coding genes accumulated throughout metazoan evolution, with early analyses of human and Drosophila microarray data indicating that this phenomenon was simply due to the presence of large introns. However, a recent study employing RNA-seq data uncovered evidence of transcriptional interference driving rapid expression divergence between Drosophila nested genes, illustrating that accurate expression estimation of overlapping genes can enhance detection of their relationships. Hence, here I apply an analogous approach to strand-specific RNA-seq data from human and mouse to revisit the role of transcriptional interference in the evolution of mammalian nested genes. A genomic survey reveals that whereas mammalian nested genes indeed accrued over evolutionary time, they are retained at lower frequencies than in Drosophila. Though several properties of mammalian nested genes align with observations in Drosophila and with expectations under transcriptional interference, contrary to both, their expression divergence is not statistically different from that between unnested genes, and also does not increase after nesting. Together, these results support the hypothesis that lower selection efficiencies limit rates of gene expression evolution in mammals, leading to their reliance on immediate eradication of deleterious nested genes to avoid transcriptional interference.
登录
查看更多内容
影响因子：
14.9
作者：
Howe KL;Achuthan P;Allen J;Allen J;Alvarez-Jarreta J;Amode MR;Armean IM;Azov AG;Bennett R;Bhai J;Billis K;Boddu S;Charkhchi M;Cummins C;Da Rin Fioretto L;Davidson C;Dodiya K;El Houdaigui B;Fatima R;Gall A;Garcia Giron C;Grego T;Guijarro-Clarke C;Haggerty L;Hemrom A;Hourlier T;Izuogu OG;Juettemann T;Kaikala V;Kay M;Lavidas I;Le T;Lemos D;Gonzalez Martinez J;Marugán JC;Maurel T;McMahon AC;Mohanan S;Moore B;Muffato M;Oheh DN;Paraschas D;Parker A;Parton A;Prosovetskaia I;Sakthivel MP;Salam AIA;Schmitt BM;Schuilenburg H;Sheppard D;Steed E;Szpak M;Szuba M;Taylor K;Thormann A;Threadgold G;Walts B;Winterbottom A;Chakiachvili M;Chaubal A;De Silva N;Flint B;Frankish A;Hunt SE;IIsley GR;Langridge N;Loveland JE;Martin FJ;Mudge JM;Morales J;Perry E;Ruffier M;Tate J;Thybert D;Trevanion SJ;Cunningham F;Yates AD;Zerbino DR;Flicek P
通讯作者：
Flicek P
影响因子：
9.2
作者：
Lipinski, Kendra J.;Farslow, James C.;Fitzpatrick, Kelly A.;Lynch, Michael;Katju, Vaishali;Bergthorsson, Ulfar
通讯作者：
Bergthorsson, Ulfar
影响因子：
7
作者：
Keith N;Tucker AE;Jackson CE;Sung W;Lucas Lledó JI;Schrider DR;Schaack S;Dudycha JL;Ackerman M;Younge AJ;Shaw JR;Lynch M
通讯作者：
Lynch M
影响因子：
3.4
作者：
Jiang, Xueyuan;Assis, Raquel
通讯作者：
Assis, Raquel
影响因子：
3.3
作者：
Pereira, Vini;Waxman, David;Eyre-Walker, Adam
通讯作者：
Eyre-Walker, Adam