TY - JOUR
T1 - HITS-CLIP and Integrative Modeling Define the Rbfox Splicing-Regulatory Network Linked to Brain Development and Autism
AU - Weyn-Vanhentenryck, Sebastien M.
AU - Mele, Aldo
AU - Yan, Qinghong
AU - Sun, Shuying
AU - Farny, Natalie
AU - Zhang, Zuo
AU - Xue, Chenghai
AU - Herre, Margaret
AU - Silver, Pamela A.
AU - Zhang, Michael Q.
AU - Krainer, Adrian R.
AU - Darnell, Robert B.
AU - Zhang, Chaolin
N1 - Funding Information:
The authors would like to thank Masato Yano for generating pRbfox3 plasmid, Joe Luna for methodological development assistance, Yuan Yuan and Michael Moore for helpful discussion, Scott Dewell for high-throughput sequencing, Melis Kayikci and Jernej Ule for ASPIRE analysis, Jinbiao Ma and Judith Kribelbauer for assistance with the interpretation of the Rbfox1-RNA complex structure data, and Judith Kribelbauer for assistance with the preparation of Figure 2 G. This work was supported by grants from the National Institutes of Health (GM74688 and HG001696 to M.Q.Z., GM42699 to A.R.K., NS81706 and NS34389 to R.B.D., and R00GM95713 to C.Z.) and Simons Foundation Autism Research Initiative (240432 to R.B.D. and 297990 to C.Z.). R.B.D. is a Howard Hughes Medical Institute Investigator.
PY - 2014/3/27
Y1 - 2014/3/27
N2 - The RNA binding proteins Rbfox1/2/3 regulate alternative splicing in the nervous system, and disruption of Rbfox1 has been implicated in autism. However, comprehensive identification of functional Rbfox targets has been challenging. Here, we perform HITS-CLIP for all three Rbfox family members in order to globally map, at a single-nucleotide resolution, their invivo RNA interaction sites in the mouse brain. We find that the two guanines in the Rbfox binding motif UGCAUG are critical for protein-RNA interactions and crosslinking. Using integrative modeling, these interaction sites, combined with additional datasets, define 1,059 direct Rbfox targetalternative splicing events. Over half of the quantifiable targets show dynamic changes during brain development. Of particular interest are 111 events from 48 candidate autism-susceptibility genes, including syndromic autism genes Shank3, Cacna1c, and Tsc2. Alteration of Rbfox targets in some autistic brains is correlated with downregulation of all three Rbfox proteins, supporting the potential clinical relevance of the splicing-regulatory network.
AB - The RNA binding proteins Rbfox1/2/3 regulate alternative splicing in the nervous system, and disruption of Rbfox1 has been implicated in autism. However, comprehensive identification of functional Rbfox targets has been challenging. Here, we perform HITS-CLIP for all three Rbfox family members in order to globally map, at a single-nucleotide resolution, their invivo RNA interaction sites in the mouse brain. We find that the two guanines in the Rbfox binding motif UGCAUG are critical for protein-RNA interactions and crosslinking. Using integrative modeling, these interaction sites, combined with additional datasets, define 1,059 direct Rbfox targetalternative splicing events. Over half of the quantifiable targets show dynamic changes during brain development. Of particular interest are 111 events from 48 candidate autism-susceptibility genes, including syndromic autism genes Shank3, Cacna1c, and Tsc2. Alteration of Rbfox targets in some autistic brains is correlated with downregulation of all three Rbfox proteins, supporting the potential clinical relevance of the splicing-regulatory network.
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U2 - 10.1016/j.celrep.2014.02.005
DO - 10.1016/j.celrep.2014.02.005
M3 - Article
C2 - 24613350
AN - SCOPUS:84897051164
SN - 2211-1247
VL - 6
SP - 1139
EP - 1152
JO - Cell Reports
JF - Cell Reports
IS - 6
ER -