Chemical reversible crosslinking enables measurement of RNA 3D distances and alternative conformations in cells
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DOI: 10.1038/s41467-022-28602-3
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- Yoichiro Sugimoto & Alessandra Vigilante & Elodie Darbo & Alexandra Zirra & Cristina Militti & Andrea D’Ambrogio & Nicholas M. Luscombe & Jernej Ule, 2015. "hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1," Nature, Nature, vol. 519(7544), pages 491-494, March.
- 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. "Erratum: Structural imprints in vivo decode RNA regulatory mechanisms," Nature, Nature, vol. 527(7577), pages 264-264, November.
- Elizabeth A. Dethoff & Jeetender Chugh & Anthony M. Mustoe & Hashim M. Al-Hashimi, 2012. "Functional complexity and regulation through RNA dynamics," Nature, Nature, vol. 482(7385), pages 322-330, February.
- Vincent V. Pham & Carolina Salguero & Shamsun Nahar Khan & Jennifer L. Meagher & W. Clay Brown & Nicolas Humbert & Hugues Rocquigny & Janet L. Smith & Victoria M. D’Souza, 2018. "HIV-1 Tat interactions with cellular 7SK and viral TAR RNAs identifies dual structural mimicry," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
- Zhiyuan Yang & Qingwei Zhu & Kunxin Luo & Qiang Zhou, 2001. "The 7SK small nuclear RNA inhibits the CDK9/cyclin T1 kinase to control transcription," Nature, Nature, vol. 414(6861), pages 317-322, November.
- Zhipeng Lu & Jimmy K. Guo & Yuning Wei & Diana R. Dou & Brian Zarnegar & Qing Ma & Rui Li & Yang Zhao & Fan Liu & Hani Choudhry & Paul A. Khavari & Howard Y. Chang, 2020. "Structural modularity of the XIST ribonucleoprotein complex," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
- Van Trung Nguyen & Tamás Kiss & Annemieke A. Michels & Olivier Bensaude, 2001. "7SK small nuclear RNA binds to and inhibits the activity of CDK9/cyclin T complexes," Nature, Nature, vol. 414(6861), pages 322-325, November.
- 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.
- Klemens Wild & Milan Aleksić & Karine Lapouge & Keven D. Juaire & Dirk Flemming & Stefan Pfeffer & Irmgard Sinning, 2020. "MetAP-like Ebp1 occupies the human ribosomal tunnel exit and recruits flexible rRNA expansion segments," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
- Tsang, Eric W. K., 2014. "Old and New," Management and Organization Review, Cambridge University Press, vol. 10(03), pages 390-390, November.
- Andreas M. Anger & Jean-Paul Armache & Otto Berninghausen & Michael Habeck & Marion Subklewe & Daniel N. Wilson & Roland Beckmann, 2013. "Structures of the human and Drosophila 80S ribosome," Nature, Nature, vol. 497(7447), pages 80-85, May.
- Silvi Rouskin & Meghan Zubradt & Stefan Washietl & Manolis Kellis & Jonathan S. Weissman, 2014. "Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo," Nature, Nature, vol. 505(7485), pages 701-705, January.
- Minjie Zhang & Kongpan Li & Jianhui Bai & Willem A. Velema & Chengqing Yu & Ryan van Damme & Wilson H. Lee & Maia L. Corpuz & Jian-Fu Chen & Zhipeng Lu, 2021. "Optimized photochemistry enables efficient analysis of dynamic RNA structuromes and interactomes in genetic and infectious diseases," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
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