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Autophagy regulation by RNA alternative splicing and implications in human diseases

Author

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  • Patricia González-Rodríguez

    (Karolinska Institutet
    University of Oslo)

  • Daniel J. Klionsky

    (University of Michigan)

  • Bertrand Joseph

    (Karolinska Institutet)

Abstract

Autophagy and RNA alternative splicing are two evolutionarily conserved processes involved in overlapping physiological and pathological processes. However, the extent of functional connection is not well defined. Here, we consider the role for alternative splicing and generation of autophagy-related gene isoforms in the regulation of autophagy in recent work. The impact of changes to the RNA alternative splicing machinery and production of alternative spliced isoforms on autophagy are reviewed with particular focus on disease relevance. The use of drugs targeting both alternative splicing and autophagy as well as the selective regulation of single autophagy-related protein isoforms, are considered as therapeutic strategies.

Suggested Citation

  • Patricia González-Rodríguez & Daniel J. Klionsky & Bertrand Joseph, 2022. "Autophagy regulation by RNA alternative splicing and implications in human diseases," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30433-1
    DOI: 10.1038/s41467-022-30433-1
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    References listed on IDEAS

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    1. Keisuke Mochida & Yu Oikawa & Yayoi Kimura & Hiromi Kirisako & Hisashi Hirano & Yoshinori Ohsumi & Hitoshi Nakatogawa, 2015. "Receptor-mediated selective autophagy degrades the endoplasmic reticulum and the nucleus," Nature, Nature, vol. 522(7556), pages 359-362, June.
    2. Eric T. Wang & Rickard Sandberg & Shujun Luo & Irina Khrebtukova & Lu Zhang & Christine Mayr & Stephen F. Kingsmore & Gary P. Schroth & Christopher B. Burge, 2008. "Alternative isoform regulation in human tissue transcriptomes," Nature, Nature, vol. 456(7221), pages 470-476, November.
    3. Charlotte Hubbert & Amaris Guardiola & Rong Shao & Yoshiharu Kawaguchi & Akihiro Ito & Andrew Nixon & Minoru Yoshida & Xiao-Fan Wang & Tso-Pang Yao, 2002. "HDAC6 is a microtubule-associated deacetylase," Nature, Nature, vol. 417(6887), pages 455-458, May.
    4. Jiajie Diao & Rong Liu & Yueguang Rong & Minglei Zhao & Jing Zhang & Ying Lai & Qiangjun Zhou & Livia M. Wilz & Jianxu Li & Sandro Vivona & Richard A. Pfuetzner & Axel T. Brunger & Qing Zhong, 2015. "ATG14 promotes membrane tethering and fusion of autophagosomes to endolysosomes," Nature, Nature, vol. 520(7548), pages 563-566, April.
    5. Kenichi Yoshida & Masashi Sanada & Yuichi Shiraishi & Daniel Nowak & Yasunobu Nagata & Ryo Yamamoto & Yusuke Sato & Aiko Sato-Otsubo & Ayana Kon & Masao Nagasaki & George Chalkidis & Yutaka Suzuki & M, 2011. "Frequent pathway mutations of splicing machinery in myelodysplasia," Nature, Nature, vol. 478(7367), pages 64-69, October.
    6. Joseph T. Glessner & Kai Wang & Guiqing Cai & Olena Korvatska & Cecilia E. Kim & Shawn Wood & Haitao Zhang & Annette Estes & Camille W. Brune & Jonathan P. Bradfield & Marcin Imielinski & Edward C. Fr, 2009. "Autism genome-wide copy number variation reveals ubiquitin and neuronal genes," Nature, Nature, vol. 459(7246), pages 569-573, May.
    7. Saikat Bhattacharya & Michaella J. Levy & Ning Zhang & Hua Li & Laurence Florens & Michael P. Washburn & Jerry L. Workman, 2021. "The methyltransferase SETD2 couples transcription and splicing by engaging mRNA processing factors through its SHI domain," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    8. Aliaksandr Khaminets & Theresa Heinrich & Muriel Mari & Paolo Grumati & Antje K. Huebner & Masato Akutsu & Lutz Liebmann & Alexandra Stolz & Sandor Nietzsche & Nicole Koch & Mario Mauthe & Istvan Kato, 2015. "Regulation of endoplasmic reticulum turnover by selective autophagy," Nature, Nature, vol. 522(7556), pages 354-358, June.
    9. Avraham Ashkenazi & Carla F. Bento & Thomas Ricketts & Mariella Vicinanza & Farah Siddiqi & Mariana Pavel & Ferdinando Squitieri & Maarten C. Hardenberg & Sara Imarisio & Fiona M. Menzies & David C. R, 2017. "Polyglutamine tracts regulate beclin 1-dependent autophagy," Nature, Nature, vol. 545(7652), pages 108-111, May.
    Full references (including those not matched with items on IDEAS)

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