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Cheng Y, Saville L, Gollen B, Veronesi AA, Mohajerani M, Joseph JT, Zovoilis A. Increased Alu RNA processing in Alzheimer brains is linked to gene expression changes. EMBO Rep 2021; 22:e52255. [PMID: 33645898 PMCID: PMC8097388 DOI: 10.15252/embr.202052255] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/23/2021] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
Despite significant steps in our understanding of Alzheimer's disease (AD), many of the molecular processes underlying its pathogenesis remain largely unknown. Here, we focus on the role of non-coding RNAs produced by small interspersed nuclear elements (SINEs). RNAs from SINE B2 repeats in mouse and SINE Alu repeats in humans, long regarded as "junk" DNA, control gene expression by binding RNA polymerase II and suppressing transcription. They also possess self-cleaving activity that is accelerated through their interaction with certain proteins disabling this suppression. Here, we show that similar to mouse SINE RNAs, human Alu RNAs, are processed, and the processing rate is increased in brains of AD patients. This increased processing correlates with the activation of genes up-regulated in AD patients, while increased intact Alu RNA levels correlate with down-regulated gene expression in AD. In vitro assays show that processing of Alu RNAs is accelerated by HSF1. Overall, our data show that RNAs from SINE elements in the human brain show a similar pattern of deregulation during amyloid beta pathology as in mouse.
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Affiliation(s)
- Yubo Cheng
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, AB, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
| | - Luke Saville
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, AB, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
| | - Babita Gollen
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, AB, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
| | - Ana Alvarez Veronesi
- Departments of Pathology and Clinical Neurosciences and Calgary Brain Bank, University of Calgary, Calgary, AB, Canada
| | - Majid Mohajerani
- Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
| | - Jeffrey T Joseph
- Departments of Pathology and Clinical Neurosciences and Calgary Brain Bank, University of Calgary, Calgary, AB, Canada
| | - Athanasios Zovoilis
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, AB, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
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Cheng Y, Saville L, Gollen B, Isaac C, Belay A, Mehla J, Patel K, Thakor N, Mohajerani MH, Zovoilis A. Increased processing of SINE B2 ncRNAs unveils a novel type of transcriptome deregulation in amyloid beta neuropathology. eLife 2020; 9:61265. [PMID: 33191914 PMCID: PMC7717908 DOI: 10.7554/elife.61265] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/15/2020] [Indexed: 12/18/2022] Open
Abstract
The functional importance of many non-coding RNAs (ncRNAs) generated by repetitive elements and their connection with pathologic processes remains elusive. B2 RNAs, a class of ncRNAs of the B2 family of SINE repeats, mediate through their processing the transcriptional activation of various genes in response to stress. Here, we show that this response is dysfunctional during amyloid beta toxicity and pathology in the mouse hippocampus due to increased levels of B2 RNA processing, leading to constitutively elevated B2 RNA target gene expression and high Trp53 levels. Evidence indicates that Hsf1, a master regulator of stress response, mediates B2 RNA processing in hippocampal cells and is activated during amyloid toxicity, accelerating the processing of SINE RNAs and gene hyper-activation. Our study reveals that in mouse, SINE RNAs constitute a novel pathway deregulated in amyloid beta pathology, with potential implications for similar cases in the human brain, such as Alzheimer’s disease (AD).
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Affiliation(s)
- Yubo Cheng
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada.,Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Canada
| | - Luke Saville
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada.,Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Canada
| | - Babita Gollen
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada.,Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Canada
| | - Christopher Isaac
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada.,Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Canada
| | - Abel Belay
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada.,Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Canada
| | - Jogender Mehla
- Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada
| | - Kush Patel
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada
| | - Nehal Thakor
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada
| | - Majid H Mohajerani
- Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada
| | - Athanasios Zovoilis
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada.,Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Canada
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3
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Structural determinants of the SINE B2 element embedded in the long non-coding RNA activator of translation AS Uchl1. Sci Rep 2018; 8:3189. [PMID: 29453387 PMCID: PMC5816658 DOI: 10.1038/s41598-017-14908-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/18/2017] [Indexed: 12/22/2022] Open
Abstract
Pervasive transcription of mammalian genomes leads to a previously underestimated level of complexity in gene regulatory networks. Recently, we have identified a new functional class of natural and synthetic antisense long non-coding RNAs (lncRNA) that increases translation of partially overlapping sense mRNAs. These molecules were named SINEUPs, as they require an embedded inverted SINE B2 element for their UP-regulation of translation. Mouse AS Uchl1 is the representative member of natural SINEUPs. It was originally discovered for its role in increasing translation of Uchl1 mRNA, a gene associated with neurodegenerative diseases. Here we present the secondary structure of the SINE B2 Transposable Element (TE) embedded in AS Uchl1. We find that specific structural regions, containing a short hairpin, are required for the ability of AS Uchl1 RNA to increase translation of its target mRNA. We also provide a high-resolution structure of the relevant hairpin, based on NMR observables. Our results highlight the importance of structural determinants in embedded TEs for their activity as functional domains in lncRNAs.
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Burenina OY, Oretskaya TS, Kubareva EA. Non-Coding RNAs As Transcriptional Regulators In Eukaryotes. Acta Naturae 2017; 9:13-25. [PMID: 29340213 PMCID: PMC5762824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Indexed: 10/31/2022] Open
Abstract
Non-coding RNAs up to 1,000 nucleotides in length are widespread in eukaryotes and fulfil various regulatory functions, in particular during chromatin remodeling and cell proliferation. These RNAs are not translated into proteins: thus, they are non-coding RNAs (ncRNAs). The present review describes the eukaryotic ncRNAs involved in transcription regulation, first and foremost, targeting RNA polymerase II (RNAP II) and/or its major proteinaceous transcription factors. The current state of knowledge concerning the regulatory functions of SRA and TAR RNA, 7SK and U1 snRNA, GAS5 and DHFR RNA is summarized herein. Special attention is given to murine B1 and B2 RNAs and human Alu RNA, due to their ability to bind the active site of RNAP II. Discovery of bacterial analogs of the eukaryotic small ncRNAs involved in transcription regulation, such as 6S RNAs, suggests that they possess a common evolutionary origin.
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Affiliation(s)
- O. Y. Burenina
- Skolkovo Institute of Science and Technology, Nobel Str. 3, Moscow, 143026, Russia
- Lomonosov Moscow State University, Chemistry Department, Leninskie Gory 1, bld. 3, Moscow, 119991 , Russia
| | - T. S. Oretskaya
- Lomonosov Moscow State University, Chemistry Department, Leninskie Gory 1, bld. 3, Moscow, 119991 , Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, bld. 40, Moscow, 119991, Russia
| | - E. A. Kubareva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, bld. 40, Moscow, 119991, Russia
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Zovoilis A, Cifuentes-Rojas C, Chu HP, Hernandez AJ, Lee JT. Destabilization of B2 RNA by EZH2 Activates the Stress Response. Cell 2017; 167:1788-1802.e13. [PMID: 27984727 DOI: 10.1016/j.cell.2016.11.041] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 10/03/2016] [Accepted: 11/22/2016] [Indexed: 12/12/2022]
Abstract
More than 98% of the mammalian genome is noncoding, and interspersed transposable elements account for ∼50% of noncoding space. Here, we demonstrate that a specific interaction between the polycomb protein EZH2 and RNA made from B2 SINE retrotransposons controls stress-responsive genes in mouse cells. In the heat-shock model, B2 RNA binds stress genes and suppresses their transcription. Upon stress, EZH2 is recruited and triggers cleavage of B2 RNA. B2 degradation in turn upregulates stress genes. Evidence indicates that B2 RNA operates as a "speed bump" against advancement of RNA polymerase II, and temperature stress releases the brakes on transcriptional elongation. These data attribute a new function to EZH2 that is independent of its histone methyltransferase activity and reconcile how EZH2 can be associated with both gene repression and activation. Our study reveals that EZH2 and B2 together control activation of a large network of genes involved in thermal stress.
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Affiliation(s)
- Athanasios Zovoilis
- Howard Hughes Medical Institute; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Catherine Cifuentes-Rojas
- Howard Hughes Medical Institute; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Hsueh-Ping Chu
- Howard Hughes Medical Institute; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Alfredo J Hernandez
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jeannie T Lee
- Howard Hughes Medical Institute; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA.
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Polyadenylation of RNA transcribed from mammalian SINEs by RNA polymerase III: Complex requirements for nucleotide sequences. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:355-65. [PMID: 26700565 DOI: 10.1016/j.bbagrm.2015.12.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 12/09/2015] [Accepted: 12/11/2015] [Indexed: 01/08/2023]
Abstract
It is generally accepted that only transcripts synthesized by RNA polymerase II (e.g., mRNA) were subject to AAUAAA-dependent polyadenylation. However, we previously showed that RNA transcribed by RNA polymerase III (pol III) from mouse B2 SINE could be polyadenylated in an AAUAAA-dependent manner. Many species of mammalian SINEs end with the pol III transcriptional terminator (TTTTT) and contain hexamers AATAAA in their A-rich tail. Such SINEs were united into Class T(+), whereas SINEs lacking the terminator and AATAAA sequences were classified as T(-). Here we studied the structural features of SINE pol III transcripts that are necessary for their polyadenylation. Eight and six SINE families from classes T(+) and T(-), respectively, were analyzed. The replacement of AATAAA with AACAAA in T(+) SINEs abolished the RNA polyadenylation. Interestingly, insertion of the polyadenylation signal (AATAAA) and pol III transcription terminator in T(-) SINEs did not result in polyadenylation. The detailed analysis of three T(+) SINEs (B2, DIP, and VES) revealed areas important for the polyadenylation of their pol III transcripts: the polyadenylation signal and terminator in A-rich tail, β region positioned immediately downstream of the box B of pol III promoter, and τ region located upstream of the tail. In DIP and VES (but not in B2), the τ region is a polypyrimidine motif which is also characteristic of many other T(+) SINEs. Most likely, SINEs of different mammals acquired these structural features independently as a result of parallel evolution.
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