PUF60-activated exons uncover altered 3' splice-site selection by germline missense mutations in a single RRM.
PUF60-activated exons uncover altered 3' splice-site selection by germline missense mutations in a single RRM.
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DOI：
10.1093/nar/gky389
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发表时间：
2018-07-06
影响因子：
14.9
通讯作者：
Vorechovský I
中科院分区：
文献类型：
--
作者：
Královicová J;Ševcíková I;Stejskalová E;Obuca M;Hiller M;Stanek D;Vorechovský I
PUF60是一种剪接因子，结合尿苷(U)丰富的束，促进U2小核核糖核蛋白与初级转录物的结合。PUF60缺乏症（PD）可导致发育迟缓，并发智力残疾和脊柱、心脏、眼和肾缺陷，但PD的发病机制尚不清楚。使用RNA-Seq，我们鉴定了人类PUF60调控的外显子，并表明PUF60优先作为它们的激活子。puf60激活的内部外显子在其3 ‘剪接位点（3 ’ s）上游富集，前面有更长的AG二核苷酸隔离区和更远的分支位点，与控制外显子相比，在典型分支位点位置上具有更高的不配对相互作用的可能性。相比之下，puf60抑制的外显子显示u耗尽，RNA单链性估计较低。我们还描述了PUF60调控的可选剪接异构体编码其他u结合剪接因子，包括PUF60伴侣，这表明它们在细胞中是共调控的，并鉴定了来自转置元件的PUF60调控外显子。pd相关的氨基酸替换，即使在单个RNA识别基序（RRM）中，也改变了PUF60依赖外显子竞争3 ' s和分支点的选择，并且3 ' s的选择也受到PUF60的选择性剪接的影响。最后，我们提出在缺乏PUF60和PUF60-平行RBM39的细胞中检测到的RNA加工步骤的差异分布是由于RBM39 RS结构域的相互作用。总之，这些结果为3 ' s组织对外显子使用的调控提供了新的见解，并揭示了RRMs的种系突变异质性可以在剪接位点和分支位点选择水平上增强表型变异性。
PUF60 is a splicing factor that binds uridine (U)-rich tracts and facilitates association of the U2 small nuclear ribonucleoprotein with primary transcripts. PUF60 deficiency (PD) causes a developmental delay coupled with intellectual disability and spinal, cardiac, ocular and renal defects, but PD pathogenesis is not understood. Using RNA-Seq, we identify human PUF60-regulated exons and show that PUF60 preferentially acts as their activator. PUF60-activated internal exons are enriched for Us upstream of their 3′ splice sites (3′ss), are preceded by longer AG dinucleotide exclusion zones and more distant branch sites, with a higher probability of unpaired interactions across a typical branch site location as compared to control exons. In contrast, PUF60-repressed exons show U-depletion with lower estimates of RNA single-strandedness. We also describe PUF60-regulated, alternatively spliced isoforms encoding other U-bound splicing factors, including PUF60 partners, suggesting that they are co-regulated in the cell, and identify PUF60-regulated exons derived from transposed elements. PD-associated amino-acid substitutions, even within a single RNA recognition motif (RRM), altered selection of competing 3′ss and branch points of a PUF60-dependent exon and the 3′ss choice was also influenced by alternative splicing of PUF60. Finally, we propose that differential distribution of RNA processing steps detected in cells lacking PUF60 and the PUF60-paralog RBM39 is due to the RBM39 RS domain interactions. Together, these results provide new insights into regulation of exon usage by the 3′ss organization and reveal that germline mutation heterogeneity in RRMs can enhance phenotypic variability at the level of splice-site and branch-site selection.
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影响因子：
11.4
作者：
Crichlow, Gregg V.;Zhou, Hongwen;Hsiao, Hsin-hao;Frederick, Kendra B.;Debrosse, Maxime;Yang, Yuande;Folta-Stogniew, Ewa J.;Chung, Hye-Jung;Fan, Chengpeng;De La Cruz, Enrique M.;Levens, David;Lolis, Elias;Braddock, Demetrios
通讯作者：
Braddock, Demetrios
影响因子：
16.8
作者：
Cisse, Ibrahim I.;Kim, Hajin;Ha, Taekjip
通讯作者：
Ha, Taekjip
影响因子：
4.3
作者：
Corvelo A;Hallegger M;Smith CW;Eyras E
通讯作者：
Eyras E
影响因子：
5.3
作者：
Cazalla, D;Newton, K;Cáceres, JF
通讯作者：
Cáceres, JF
影响因子：
15.9
作者：
Besse, Whitney;Dong, Ke;Somlo, Stefan
通讯作者：
Somlo, Stefan