Antisense Transcription across Nucleotide Repeat Expansions in Neurodegenerative and Neuromuscular Diseases: Progress and Mysteries

Abstract

Unstable repeat expansions and insertions cause more than 30 neurodegenerative and neuromuscular diseases. Remarkably, bidirectional transcription of repeat expansions has been identified in at least 14 of these diseases. More remarkably, a growing number of studies has been showing that both sense and antisense repeat RNAs are able to dysregulate important cellular pathways, contributing together to the observed clinical phenotype. Notably, antisense repeat RNAs from spinocerebellar ataxia type 7, myotonic dystrophy type 1, Huntington's disease and frontotemporal dementia/amyotrophic lateral sclerosis associated genes have been implicated in transcriptional regulation of sense gene expression, acting either at a transcriptional or posttranscriptional level. The recent evidence that antisense repeat RNAs could modulate gene expression broadens our understanding of the pathogenic pathways and adds more complexity to the development of therapeutic strategies for these disorders. In this review, we cover the amazing progress made in the understanding of the pathogenic mechanisms associated with repeat expansion neurodegenerative and neuromuscular diseases with a focus on the impact of antisense repeat transcription in the development of efficient therapies.

Keywords: RNA foci; nuclear inclusions; splicing misregulation; trinucleotide repeats.

Figure 1

Repeat expansions and insertions causing neurodegenerative and neuromuscular diseases. Top: pathogenic repeat expansions spread over 5′ and 3′ UTRs, exons and introns; novel repeat insertions are highlighted in a blue box; bidirectional transcription is known for the disorders in orange. Bottom: in SCA12, a 5′UTR (CAG)_n expansion leads to gene upregulation, whereas expanded (CGG)_n leads to CpG hypermethylation with silencing of FMRP expression in FXS; coding transcripts containing the expanded (CAG)_n are able to (1) sequester RBPs such as MBNL1, forming nuclear RNA foci, which causes dysregulation of several cellular processes like (2) transcription, (3) mRNA splicing, (4) nucleocytoplasmic transport; in the cytoplasm, coding repeat expansions are (5) translated in proteins with expanded polyQ tracts leading to ubiquitin-positive (U) inclusions in neurons, or are (6) RAN-translated in polypeptides; in FRDA, a biallelic intronic (GAA)_n expansion leads to repressive chromatin with consequent gene silencing; in SCA10, the (ATTCT)_n is transcribed forming nuclear RNA foci with hnRNP K; in SCA31, nuclear RNA foci colocalize with TDP-43, FUS and hnRNP A2/B1 and pentapeptides are produced. PolyQ-polyglutamine; polyS-polyserine; polyA-polyalanine; polyWNGME-poly-tryptophan-asparagine-glycine-methionine-glutamic acid.

Figure 2

Toxicity mediated by microsatellite repeats bidirectionally transcribed in neurodegenerative and neuromuscular diseases. (a) The (CAG)_exp RNA from ATXN2 is translated into polyQ that abnormally interact with proteins in stress granules; the ATXN2-AS (CUG)_exp forms RNA foci with splicing factors leading to misplicing of other mRNAs; from the ATXN7 strand, the (CAG)_exp RNA is translated into toxic polyQ that form nuclear inclusions with RNA and DNA-binding proteins, dysregulating transcription and cellular mRNAs splicing; in ATXN7AS, the (CUG)_exp reduces CTCF-binding, causing SCAANT1 downregulation and consequent derepression of ATXN7 promoter, leading to ataxin-7 overexpression and global transcriptional dysregulation; from the ATXN8 strand, the (CAG)_exp RNA is translated into toxic polyQ that form ubiquitin-positive intranuclear inclusions; the ATXN8OS (CUG)_exp forms nuclear RNA foci causing misplicing or is RAN-translated. (b) In SCA36 and C9ORF72 FTD/ALS, sense and antisense strand RNAs aggregate in nuclear RNA foci or are translated into DRPs. (c) The FMR1 (GGC)_55–200 RNA forms nuclear foci or is RAN-translated into toxic peptides, which form intranuclear inclusions; from ASFMR1 strand, the (GCC)_55–200 RNA can be translated into toxic peptides, leading to intranuclear aggregation. (d) From the HTT strand, the (CAG)_exp RNA can aggregate in nuclear RNA foci or form hairpins posteriorly cleaved by DICER; the (CAG)_exp RNA is also translated into polyQ proteins, forming nuclear inclusions, or it is RAN-translated; in HTTAS orientation, the (CUG)_exp RNA regulates the HTT RNA on a RISC-dependent manner and can be RAN-translated into polypeptides. In HDL2, the (CAG)_exp RNA forms RNA foci, leading to splicing misregulation; polyQ can be generated from the antisense (CAG)_exp RNA, impairing the cellular transcriptional activity. (e) In DM2, both sense and antisense repeat RNAs form foci or are RAN-translated in polytetrapeptides; in DM1 DMPK orientation, the (CUG)_exp forms RNA foci with consequent misplicing of several cellular mRNAs. In congenital DM1, the (CTG)_>1000 reduces CTCF-binding and CpG methylation, downregulating antisense transcription; antisense transcription causes DMPK alternative promoter upregulation, leading to DMPK overexpression; DMPKAS CAGs also form RNA foci and are RAN-translated. DRP-dipeptide repeats; polyQ-polyglutamine; polyA-polyalanine; polyS-polyserine; polyL-polyleucine; polyC-polycysteine; polyP-polyproline; polyG-polyglycine; polyGP-poly-glycine-proline; polyPR-poly-proline-arginine; polyLPAC-poly-leucine-proline-alanine-cysteine; polyQAGR-poly-glutamine-alanine-glycine-arginine.

Figure 2

Toxicity mediated by microsatellite repeats bidirectionally transcribed in neurodegenerative and neuromuscular diseases. (a) The (CAG)_exp RNA from ATXN2 is translated into polyQ that abnormally interact with proteins in stress granules; the ATXN2-AS (CUG)_exp forms RNA foci with splicing factors leading to misplicing of other mRNAs; from the ATXN7 strand, the (CAG)_exp RNA is translated into toxic polyQ that form nuclear inclusions with RNA and DNA-binding proteins, dysregulating transcription and cellular mRNAs splicing; in ATXN7AS, the (CUG)_exp reduces CTCF-binding, causing SCAANT1 downregulation and consequent derepression of ATXN7 promoter, leading to ataxin-7 overexpression and global transcriptional dysregulation; from the ATXN8 strand, the (CAG)_exp RNA is translated into toxic polyQ that form ubiquitin-positive intranuclear inclusions; the ATXN8OS (CUG)_exp forms nuclear RNA foci causing misplicing or is RAN-translated. (b) In SCA36 and C9ORF72 FTD/ALS, sense and antisense strand RNAs aggregate in nuclear RNA foci or are translated into DRPs. (c) The FMR1 (GGC)_55–200 RNA forms nuclear foci or is RAN-translated into toxic peptides, which form intranuclear inclusions; from ASFMR1 strand, the (GCC)_55–200 RNA can be translated into toxic peptides, leading to intranuclear aggregation. (d) From the HTT strand, the (CAG)_exp RNA can aggregate in nuclear RNA foci or form hairpins posteriorly cleaved by DICER; the (CAG)_exp RNA is also translated into polyQ proteins, forming nuclear inclusions, or it is RAN-translated; in HTTAS orientation, the (CUG)_exp RNA regulates the HTT RNA on a RISC-dependent manner and can be RAN-translated into polypeptides. In HDL2, the (CAG)_exp RNA forms RNA foci, leading to splicing misregulation; polyQ can be generated from the antisense (CAG)_exp RNA, impairing the cellular transcriptional activity. (e) In DM2, both sense and antisense repeat RNAs form foci or are RAN-translated in polytetrapeptides; in DM1 DMPK orientation, the (CUG)_exp forms RNA foci with consequent misplicing of several cellular mRNAs. In congenital DM1, the (CTG)_>1000 reduces CTCF-binding and CpG methylation, downregulating antisense transcription; antisense transcription causes DMPK alternative promoter upregulation, leading to DMPK overexpression; DMPKAS CAGs also form RNA foci and are RAN-translated. DRP-dipeptide repeats; polyQ-polyglutamine; polyA-polyalanine; polyS-polyserine; polyL-polyleucine; polyC-polycysteine; polyP-polyproline; polyG-polyglycine; polyGP-poly-glycine-proline; polyPR-poly-proline-arginine; polyLPAC-poly-leucine-proline-alanine-cysteine; polyQAGR-poly-glutamine-alanine-glycine-arginine.