The SINEB1 Element in the Long Non-Coding RNA Malat1 Is Necessary for TDP-43 Proteostasis

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

Publication Date

3-18-2020

Journal

Nucleic Acids Research

DOI

10.1093/nar/gkz1176

PMID

31863590

PMCID

PMC7049706

PubMedCentral® Posted Date

12-21-2019

PubMedCentral® Full Text Version

Post-print

Published Open-Access

yes

Keywords

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

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.