RNA structure maps across mammalian cellular compartments.

Autor: Sun L; MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.; Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China.; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China.; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China., Fazal FM; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.; Department of Dermatology, Stanford University, Stanford, CA, USA.; Department of Genetics, Stanford University, Stanford, CA, USA., Li P; MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.; Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China.; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China.; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China., Broughton JP; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.; Department of Dermatology, Stanford University, Stanford, CA, USA.; Department of Genetics, Stanford University, Stanford, CA, USA., Lee B; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.; Department of Dermatology, Stanford University, Stanford, CA, USA.; Department of Genetics, Stanford University, Stanford, CA, USA., Tang L; MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.; Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China.; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China.; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China., Huang W; MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.; Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China.; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China.; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China., Kool ET; Department of Chemistry, Stanford University, Stanford, CA, USA., Chang HY; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.; Department of Dermatology, Stanford University, Stanford, CA, USA.; Department of Genetics, Stanford University, Stanford, CA, USA.; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA., Zhang QC; MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China. qczhang@tsinghua.edu.cn.; Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China. qczhang@tsinghua.edu.cn.; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China. qczhang@tsinghua.edu.cn.; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China. qczhang@tsinghua.edu.cn.
Jazyk: angličtina
Zdroj: Nature structural & molecular biology [Nat Struct Mol Biol] 2019 Apr; Vol. 26 (4), pp. 322-330. Date of Electronic Publication: 2019 Mar 18.
DOI: 10.1038/s41594-019-0200-7
Abstrakt: RNA structure is intimately connected to each step of gene expression. Recent advances have enabled transcriptome-wide maps of RNA secondary structure, called 'RNA structuromes'. However, previous whole-cell analyses lacked the resolution to unravel the landscape and also the regulatory mechanisms of RNA structural changes across subcellular compartments. Here we reveal the RNA structuromes in three compartments, chromatin, nucleoplasm and cytoplasm, in human and mouse cells. The cytotopic structuromes substantially expand RNA structural information and enable detailed investigation of the central role of RNA structure in linking transcription, translation and RNA decay. We develop a resource with which to visualize the interplay of RNA-protein interactions, RNA modifications and RNA structure and predict both direct and indirect reader proteins of RNA modifications. We also validate a novel role for the RNA-binding protein LIN28A as an N 6 -methyladenosine modification 'anti-reader'. Our results highlight the dynamic nature of RNA structures and its functional importance in gene regulation.
Databáze: MEDLINE
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