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Title:
RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function | Genome Biology
Description:
Background Vertebrate early embryogenesis is initially directed by a set of maternal RNAs and proteins, yet the mechanisms controlling this program remain largely unknown. Recent transcriptome-wide studies on RNA structure have revealed its pervasive and crucial roles in RNA processing and functions, but whether and how RNA structure regulates the fate of the maternal transcriptome have yet to be determined. Results Here we establish the global map of four nucleotide-based mRNA structures by icSHAPE during zebrafish early embryogenesis. Strikingly, we observe that RNA structurally variable regions are enriched in the 3β² UTR and contain cis-regulatory elements important for maternal-to-zygotic transition (MZT). We find that the RNA-binding protein Elavl1a stabilizes maternal mRNAs by binding to the cis-elements. Conversely, RNA structure formation suppresses Elavl1aβs binding leading to the decay of its maternal targets. Conclusions Our study finds that RNA structurally variable regions are enriched in mRNA 3β² UTRs and contain cis-regulatory elements during zebrafish early embryogenesis. We reveal that Elavl1a regulates maternal RNA stability in an RNA structure-dependent fashion. Overall, our findings reveal a broad and fundamental role of RNA structure-based regulation in vertebrate early embryogenesis.
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Keywords {π}
rna, elavla, binding, pubmed, fig, hpf, additional, article, file, zebrafish, regions, cas, maternal, variable, google, scholar, structurally, structural, mrna, sites, structure, icshape, early, test, zhang, genes, central, motif, analysis, embryogenesis, cell, utr, embryos, gene, protein, transcripts, reactivity, sequence, buffer, stability, performed, yang, values, transcriptome, set, vivo, significance, control, data, calculated,
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headline:RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function
description:Vertebrate early embryogenesis is initially directed by a set of maternal RNAs and proteins, yet the mechanisms controlling this program remain largely unknown. Recent transcriptome-wide studies on RNA structure have revealed its pervasive and crucial roles in RNA processing and functions, but whether and how RNA structure regulates the fate of the maternal transcriptome have yet to be determined. Here we establish the global map of four nucleotide-based mRNA structures by icSHAPE during zebrafish early embryogenesis. Strikingly, we observe that RNA structurally variable regions are enriched in the 3β² UTR and contain cis-regulatory elements important for maternal-to-zygotic transition (MZT). We find that the RNA-binding protein Elavl1a stabilizes maternal mRNAs by binding to the cis-elements. Conversely, RNA structure formation suppresses Elavl1aβs binding leading to the decay of its maternal targets. Our study finds that RNA structurally variable regions are enriched in mRNA 3β² UTRs and contain cis-regulatory elements during zebrafish early embryogenesis. We reveal that Elavl1a regulates maternal RNA stability in an RNA structure-dependent fashion. Overall, our findings reveal a broad and fundamental role of RNA structure-based regulation in vertebrate early embryogenesis.
datePublished:2020-05-18T00:00:00Z
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RNA structure
Zebrafish early embryogenesis
Structure-based regulome
Elavl1a
Animal Genetics and Genomics
Human Genetics
Plant Genetics and Genomics
Microbial Genetics and Genomics
Bioinformatics
Evolutionary Biology
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headline:RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function
description:Vertebrate early embryogenesis is initially directed by a set of maternal RNAs and proteins, yet the mechanisms controlling this program remain largely unknown. Recent transcriptome-wide studies on RNA structure have revealed its pervasive and crucial roles in RNA processing and functions, but whether and how RNA structure regulates the fate of the maternal transcriptome have yet to be determined. Here we establish the global map of four nucleotide-based mRNA structures by icSHAPE during zebrafish early embryogenesis. Strikingly, we observe that RNA structurally variable regions are enriched in the 3β² UTR and contain cis-regulatory elements important for maternal-to-zygotic transition (MZT). We find that the RNA-binding protein Elavl1a stabilizes maternal mRNAs by binding to the cis-elements. Conversely, RNA structure formation suppresses Elavl1aβs binding leading to the decay of its maternal targets. Our study finds that RNA structurally variable regions are enriched in mRNA 3β² UTRs and contain cis-regulatory elements during zebrafish early embryogenesis. We reveal that Elavl1a regulates maternal RNA stability in an RNA structure-dependent fashion. Overall, our findings reveal a broad and fundamental role of RNA structure-based regulation in vertebrate early embryogenesis.
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RNA structure
Zebrafish early embryogenesis
Structure-based regulome
Elavl1a
Animal Genetics and Genomics
Human Genetics
Plant Genetics and Genomics
Microbial Genetics and Genomics
Bioinformatics
Evolutionary Biology
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affiliation:
name:Beijing Institute of Genomics, Chinese Academy of Sciences
address:
name:CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
type:PostalAddress
type:Organization
name:University of Chinese Academy of Sciences
address:
name:University of Chinese Academy of Sciences, Beijing, China
type:PostalAddress
type:Organization
name:Jinsong Zhang
affiliation:
name:Tsinghua University
address:
name:MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
type:PostalAddress
type:Organization
name:Jian Heng
affiliation:
name:University of Chinese Academy of Sciences
address:
name:University of Chinese Academy of Sciences, Beijing, China
type:PostalAddress
type:Organization
name:Institute of Zoology, Chinese Academy of Sciences
address:
name:State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
type:PostalAddress
type:Organization
name:Jing Gong
affiliation:
name:Tsinghua University
address:
name:MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
type:PostalAddress
type:Organization
name:Ting Zhang
affiliation:
name:Beijing Institute of Genomics, Chinese Academy of Sciences
address:
name:CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
type:PostalAddress
type:Organization
name:University of Chinese Academy of Sciences
address:
name:University of Chinese Academy of Sciences, Beijing, China
type:PostalAddress
type:Organization
name:Pan Li
affiliation:
name:Tsinghua University
address:
name:MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
type:PostalAddress
type:Organization
name:Bao-Fa Sun
affiliation:
name:Beijing Institute of Genomics, Chinese Academy of Sciences
address:
name:CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
type:PostalAddress
type:Organization
name:Institute of Stem Cell and Regeneration, Chinese Academy of Sciences
address:
name:Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
type:PostalAddress
type:Organization
name:Ying Yang
affiliation:
name:Beijing Institute of Genomics, Chinese Academy of Sciences
address:
name:CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
type:PostalAddress
type:Organization
name:Institute of Stem Cell and Regeneration, Chinese Academy of Sciences
address:
name:Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
type:PostalAddress
type:Organization
name:Ning Zhang
affiliation:
name:State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences
address:
name:State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
type:PostalAddress
type:Organization
name:Yong-Liang Zhao
affiliation:
name:Beijing Institute of Genomics, Chinese Academy of Sciences
address:
name:CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
type:PostalAddress
type:Organization
name:University of Chinese Academy of Sciences
address:
name:University of Chinese Academy of Sciences, Beijing, China
type:PostalAddress
type:Organization
name:Institute of Stem Cell and Regeneration, Chinese Academy of Sciences
address:
name:Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
type:PostalAddress
type:Organization
name:Hai-Lin Wang
affiliation:
name:University of Chinese Academy of Sciences
address:
name:University of Chinese Academy of Sciences, Beijing, China
type:PostalAddress
type:Organization
name:State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences
address:
name:State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
type:PostalAddress
type:Organization
name:Feng Liu
affiliation:
name:University of Chinese Academy of Sciences
address:
name:University of Chinese Academy of Sciences, Beijing, China
type:PostalAddress
type:Organization
name:Institute of Zoology, Chinese Academy of Sciences
address:
name:State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
type:PostalAddress
type:Organization
email:[email protected]
name:Qiangfeng Cliff Zhang
affiliation:
name:Tsinghua University
address:
name:MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
type:PostalAddress
type:Organization
email:[email protected]
name:Yun-Gui Yang
affiliation:
name:Beijing Institute of Genomics, Chinese Academy of Sciences
address:
name:CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
type:PostalAddress
type:Organization
name:University of Chinese Academy of Sciences
address:
name:University of Chinese Academy of Sciences, Beijing, China
type:PostalAddress
type:Organization
name:Institute of Stem Cell and Regeneration, Chinese Academy of Sciences
address:
name:Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
type:PostalAddress
type:Organization
email:[email protected]
PostalAddress:
name:CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
name:University of Chinese Academy of Sciences, Beijing, China
name:MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
name:University of Chinese Academy of Sciences, Beijing, China
name:State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
name:MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
name:CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
name:University of Chinese Academy of Sciences, Beijing, China
name:MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
name:CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
name:Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
name:CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
name:Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
name:State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
name:CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
name:University of Chinese Academy of Sciences, Beijing, China
name:Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
name:University of Chinese Academy of Sciences, Beijing, China
name:State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
name:University of Chinese Academy of Sciences, Beijing, China
name:State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
name:MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
name:CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
name:University of Chinese Academy of Sciences, Beijing, China
name:Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
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