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RNA Structural Dynamics Regulates Early Embryogenesis Through Controlling Transcriptome Fate and Function

64 Pages Posted: 23 Aug 2019 Sneak Peek Status: Under Review

See all articles by Boyang Shi

Boyang Shi

Chinese Academy of Sciences (CAS) - CAS Key Laboratory of Genomic and Precision Medicine

Jinsong Zhang

Tsinghua University - MOE Key Laboratory of Bioinformatics

Jian Heng

Chinese Academy of Sciences (CAS) - State Key Laboratory of Membrane Biology

Jing Gong

Tsinghua University - MOE Key Laboratory of Bioinformatics

Ting Zhang

Chinese Academy of Sciences (CAS) - CAS Key Laboratory of Genomic and Precision Medicine

Pan Li

Tsinghua University - MOE Key Laboratory of Bioinformatics

Bao-Fa Sun

Chinese Academy of Sciences (CAS) - CAS Key Laboratory of Genomic and Precision Medicine

Ying Yang

Chinese Academy of Sciences (CAS) - CAS Key Laboratory of Genomic and Precision Medicine

Ning Zhang

Chinese Academy of Sciences (CAS) - State Key Laboratory of Environmental Chemistry and Ecotoxicology

Yong-Liang Zhao

Chinese Academy of Sciences (CAS) - CAS Key Laboratory of Genomic and Precision Medicine

Hai-Lin Wang

Chinese Academy of Sciences (CAS) - University of Chinese Academy of Sciences

Feng Liu

Chinese Academy of Sciences (CAS), Kunming Institute of Zoology, State Key Laboratory of Membrane Biology; Chinese Academy of Sciences (CAS) - Institute for Stem Cell and Regeneration; Chinese Academy of Sciences (CAS) - University of Chinese Academy of Sciences

Qiangfeng Cliff Zhang

Tsinghua University - MOE Key Laboratory of Bioinformatics

Yun-Gui Yang

Chinese Academy of Sciences (CAS) - CAS Key Laboratory of Genomic and Precision Medicine; Chinese Academy of Sciences (CAS) - University of Chinese Academy of Sciences; Chinese Academy of Sciences (CAS) - Institute for Stem Cell and Regeneration

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Abstract

Early embryogenesis in vertebrates is initially directed by 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. Here we established the first global map of four nucleotide-based mRNA structures during zebrafish early embryogenesis. Strikingly, we observed RNA structurally variable regions are enriched in the 3’ UTR, and contain cis-regulatory elements important for maternal-to-zygotic transition (MZT). We found that the RNA binding protein Elavl1a stabilized maternal mRNAs by binding to the cis-elements. Conversely, RNA structure formation suppressed Elavl1a’s binding leading to the decay of its maternal targets. Overall, our findings revealed a broad and fundamental role of RNA structure-based regulation in vertebrate early embryogenesis.

Keywords: RNA structure, zebrafish early embryogenesis, structure-based regulome, Elavl1a

Suggested Citation

Shi, Boyang and Zhang, Jinsong and Heng, Jian and Gong, Jing and Zhang, Ting and Li, Pan and Sun, Bao-Fa and Yang, Ying and Zhang, Ning and Zhao, Yong-Liang and Wang, Hai-Lin and Liu, Feng and Zhang, Qiangfeng Cliff and Yang, Yun-Gui, RNA Structural Dynamics Regulates Early Embryogenesis Through Controlling Transcriptome Fate and Function (August 21, 2019). DEVELOPMENTAL-CELL-D-19-00726. Available at SSRN: https://ssrn.com/abstract=3440907 or http://dx.doi.org/10.2139/ssrn.3440907
This is a paper under consideration at Cell Press and has not been peer-reviewed.

Boyang Shi

Chinese Academy of Sciences (CAS) - CAS Key Laboratory of Genomic and Precision Medicine ( email )

Beijing
China

Jinsong Zhang

Tsinghua University - MOE Key Laboratory of Bioinformatics

China

Jian Heng

Chinese Academy of Sciences (CAS) - State Key Laboratory of Membrane Biology

Beijing
China

Jing Gong

Tsinghua University - MOE Key Laboratory of Bioinformatics

China

Ting Zhang

Chinese Academy of Sciences (CAS) - CAS Key Laboratory of Genomic and Precision Medicine

Beijing
China

Pan Li

Tsinghua University - MOE Key Laboratory of Bioinformatics

China

Bao-Fa Sun

Chinese Academy of Sciences (CAS) - CAS Key Laboratory of Genomic and Precision Medicine

Beijing
China

Ying Yang

Chinese Academy of Sciences (CAS) - CAS Key Laboratory of Genomic and Precision Medicine

Beijing
China

Ning Zhang

Chinese Academy of Sciences (CAS) - State Key Laboratory of Environmental Chemistry and Ecotoxicology

52 Sanlihe Rd.
Datun Road, Anwai
Beijing, Xicheng District 100864
China

Yong-Liang Zhao

Chinese Academy of Sciences (CAS) - CAS Key Laboratory of Genomic and Precision Medicine

Beijing
China

Hai-Lin Wang

Chinese Academy of Sciences (CAS) - University of Chinese Academy of Sciences

Building 7, NO. 80 Zhongguancun Road
Beijing, Beijing 100190
China

Feng Liu

Chinese Academy of Sciences (CAS), Kunming Institute of Zoology, State Key Laboratory of Membrane Biology ( email )

Beijing
China

Chinese Academy of Sciences (CAS) - Institute for Stem Cell and Regeneration ( email )

Beijing
China

Chinese Academy of Sciences (CAS) - University of Chinese Academy of Sciences ( email )

Building 7, NO. 80 Zhongguancun Road
Beijing, Beijing 100190
China

Qiangfeng Cliff Zhang

Tsinghua University - MOE Key Laboratory of Bioinformatics

China

Yun-Gui Yang (Contact Author)

Chinese Academy of Sciences (CAS) - CAS Key Laboratory of Genomic and Precision Medicine ( email )

Beijing
China

Chinese Academy of Sciences (CAS) - University of Chinese Academy of Sciences ( email )

Building 7, NO. 80 Zhongguancun Road
Beijing, Beijing 100190
China

Chinese Academy of Sciences (CAS) - Institute for Stem Cell and Regeneration ( email )

Beijing
China

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