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Structural imprints in vivo decode RNA regulatory mechanisms

Author

Listed:
  • Robert C. Spitale

    (Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine)

  • Ryan A. Flynn

    (Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine)

  • Qiangfeng Cliff Zhang

    (Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine)

  • Pete Crisalli

    (Stanford University)

  • Byron Lee

    (Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine)

  • Jong-Wha Jung

    (Stanford University)

  • Hannes Y. Kuchelmeister

    (Stanford University)

  • Pedro J. Batista

    (Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine)

  • Eduardo A. Torre

    (Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine)

  • Eric T. Kool

    (Stanford University)

  • Howard Y. Chang

    (Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine)

Abstract

The single-stranded nature of RNAs synthesized in the cell gives them great scope to form different structures, but current methods to measure RNA structure in vivo are limited; now, a new methodology allows researchers to examine all four nucleotides in mouse embryonic stem cells.

Suggested Citation

  • Robert C. Spitale & Ryan A. Flynn & Qiangfeng Cliff Zhang & Pete Crisalli & Byron Lee & Jong-Wha Jung & Hannes Y. Kuchelmeister & Pedro J. Batista & Eduardo A. Torre & Eric T. Kool & Howard Y. Chang, 2015. "Structural imprints in vivo decode RNA regulatory mechanisms," Nature, Nature, vol. 519(7544), pages 486-490, March.
    • Handle: RePEc:nat:nature:v:519:y:2015:i:7544:d:10.1038_nature14263
    DOI: 10.1038/nature14263
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    Cited by:

    1. Ainara González-Iglesias & Aida Arcas & Ana Domingo-Muelas & Estefania Mancini & Joan Galcerán & Juan Valcárcel & Isabel Fariñas & M. Angela Nieto, 2024. "Intron detention tightly regulates the stemness/differentiation switch in the adult neurogenic niche," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    2. Bo Yu & Pan Li & Qiangfeng Cliff Zhang & Lin Hou, 2022. "Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    3. Debjit Khan & Iyappan Ramachandiran & Kommireddy Vasu & Arnab China & Krishnendu Khan & Fabio Cumbo & Dalia Halawani & Fulvia Terenzi & Isaac Zin & Briana Long & Gregory Costain & Susan Blaser & Amand, 2024. "Homozygous EPRS1 missense variant causing hypomyelinating leukodystrophy-15 alters variant-distal mRNA m6A site accessibility," Nature Communications, Nature, vol. 15(1), pages 1-24, December.
    4. Tammy C. T. Lan & Matty F. Allan & Lauren E. Malsick & Jia Z. Woo & Chi Zhu & Fengrui Zhang & Stuti Khandwala & Sherry S. Y. Nyeo & Yu Sun & Junjie U. Guo & Mark Bathe & Anders Näär & Anthony Griffith, 2022. "Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    5. Sepideh Tavakoli & Mohammad Nabizadeh & Amr Makhamreh & Howard Gamper & Caroline A. McCormick & Neda K. Rezapour & Ya-Ming Hou & Meni Wanunu & Sara H. Rouhanifard, 2023. "Semi-quantitative detection of pseudouridine modifications and type I/II hypermodifications in human mRNAs using direct long-read sequencing," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    6. Gongwang Yu & Yao Liu & Zizhang Li & Shuyun Deng & Zhuoxing Wu & Xiaoyu Zhang & Wenbo Chen & Junnan Yang & Xiaoshu Chen & Jian-Rong Yang, 2023. "Genome-wide probing of eukaryotic nascent RNA structure elucidates cotranscriptional folding and its antimutagenic effect," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    7. Yuwei Zhang & Jieyu Zhao & Xiaona Chen & Yulong Qiao & Jinjin Kang & Xiaofan Guo & Feng Yang & Kaixin Lyu & Yiliang Ding & Yu Zhao & Hao Sun & Chun-Kit Kwok & Huating Wang, 2024. "DHX36 binding induces RNA structurome remodeling and regulates RNA abundance via m6A reader YTHDF1," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    8. Harshita Sharma & Matthew N. Z. Valentine & Naoko Toki & Hiromi Nishiyori Sueki & Stefano Gustincich & Hazuki Takahashi & Piero Carninci, 2024. "Decryption of sequence, structure, and functional features of SINE repeat elements in SINEUP non-coding RNA-mediated post-transcriptional gene regulation," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    9. Ryan Damme & Kongpan Li & Minjie Zhang & Jianhui Bai & Wilson H. Lee & Joseph D. Yesselman & Zhipeng Lu & Willem A. Velema, 2022. "Chemical reversible crosslinking enables measurement of RNA 3D distances and alternative conformations in cells," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    10. Haoran Zhu & Yuning Yang & Yunhe Wang & Fuzhou Wang & Yujian Huang & Yi Chang & Ka-chun Wong & Xiangtao Li, 2023. "Dynamic characterization and interpretation for protein-RNA interactions across diverse cellular conditions using HDRNet," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
    11. Shurong Liu & Junhong Huang & Jie Zhou & Siyan Chen & Wujian Zheng & Chang Liu & Qiao Lin & Ping Zhang & Di Wu & Simeng He & Jiayi Ye & Shun Liu & Keren Zhou & Bin Li & Lianghu Qu & Jianhua Yang, 2024. "NAP-seq reveals multiple classes of structured noncoding RNAs with regulatory functions," Nature Communications, Nature, vol. 15(1), pages 1-21, December.

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