The SINEB1 element in the long non-coding RNA Malat1 is necessary for TDP-43 proteostasis.

Abstract

Transposable elements (TEs) comprise a large proportion of long non-coding RNAs (lncRNAs). Here, we employed CRISPR to delete a short interspersed nuclear element (SINE) in Malat1, a cancer-associated lncRNA, to investigate its significance in cellular physiology. We show that Malat1 with a SINE deletion forms diffuse nuclear speckles and is frequently translocated to the cytoplasm. SINE-deleted cells exhibit an activated unfolded protein response and PKR and markedly increased DNA damage and apoptosis caused by dysregulation of TDP-43 localization and formation of cytotoxic inclusions. TDP-43 binds stronger to Malat1 without the SINE and is likely 'hijacked' by cytoplasmic Malat1 to the cytoplasm, resulting in the depletion of nuclear TDP-43 and redistribution of TDP-43 binding to repetitive element transcripts and mRNAs encoding mitotic and nuclear-cytoplasmic regulators. The SINE promotes Malat1 nuclear retention by facilitating Malat1 binding to HNRNPK, a protein that drives RNA nuclear retention, potentially through direct interactions of the SINE with KHDRBS1 and TRA2A, which bind to HNRNPK. Losing these RNA-protein interactions due to the SINE deletion likely creates more available TDP-43 binding sites on Malat1 and subsequent TDP-43 aggregation. These results highlight the significance of lncRNA TEs in TDP-43 proteostasis with potential implications in both cancer and neurodegenerative diseases.

• Authors: Tuan M Nguyen, Elena B Kabotyanski, Lucas C Reineke, Jiaofang Shao, Feng Xiong, Joo-Hyung Lee, Julien Dubrulle, Hannah Johnson, Fabio Stossi, Phoebe S Tsoi, Kyoung-Jae Choi, Alexander G Ellis, Na Zhao, Jin Cao, Oluwatoyosi Adewunmi, Josephine C Ferreon, Allan Chris M Ferreon, Joel R Neilson, Michael A Mancini, Xi Chen, Jongchan Kim, Li Ma, Wenbo Li, Jeffrey M Rosen
• Journal: Nucleic acids research (Nucleic Acids Res) Vol. 48 Issue 5 Pg. 2621-2642 (03 18 2020) ISSN: 1362-4962 [Electronic] England
• PMID: 31863590 (Publication Type: Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't)
• Copyright: © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

Chemical References

• DNA-Binding Proteins
• Heterogeneous-Nuclear Ribonucleoprotein K
• MALAT1 long non-coding RNA, human
• RNA, Long Noncoding
• RNA, Messenger
• TARDBP protein, human
• eIF-2 Kinase

Topics

• Apoptosis
• Cell Line
• Cytoplasm (metabolism)
• DNA Damage
• DNA-Binding Proteins (metabolism)
• Endoplasmic Reticulum Stress
• Enzyme Activation
• Gene Dosage
• Heterogeneous-Nuclear Ribonucleoprotein K (metabolism)
• Humans
• Mitosis
• Models, Biological
• Protein Transport
• Proteostasis (genetics)
• RNA, Long Noncoding (genetics)
• RNA, Messenger (genetics, metabolism)
• Sequence Deletion (genetics)
• Short Interspersed Nucleotide Elements (genetics)
• eIF-2 Kinase