Non-coding Repeat Research Articles

Abstract 137: Epigenetic regulation of APOBEC3A mutagenesis and tumor evolution during targeted therapy in non-small cell lung cancer

Abstract Acquired drug resistance to even the most effective anti-cancer targeted therapies remains an unsolved clinical problem. Although many drivers of acquired drug resistance have been identified, the underlying molecular mechanisms shaping tumor evolution during treatment are incompletely understood. We recently demonstrated that lung cancer targeted therapies commonly used in the clinic induce the expression of cytidine deaminase APOBEC3A (A3A), leading to sustained mutagenesis in drug tolerant cancer cells persisting during therapy. Preventing therapy-induced A3A mutagenesis by gene deletion decreased the accumulation of chromosomal aberrations and delayed the emergence of drug resistance. Thus, we hypothesize that inhibition of A3A may represent a potential therapeutic strategy to halt the evolution of resistant clones and prevent acquired resistance to lung cancer targeted therapies. Understanding the molecular mechanism of A3A induction during targeted therapy is a crucial step to develop targeting A3A therapies.Using a targeted drug combination screen, we found that DNA methyltransferase (DNMT) inhibitors induce expression of APOBEC3A in non-small cell lung cancer cells, phenocopying the effects of targeted therapies. RNA-seq profiling revealed that both targeted therapies and DNMT inhibitors increase expression of non-coding repeat RNAs. Repeatome analysis identified distinct classes of non-codding RNAs including endogenous retrovirus elements (ERV) in drug tolerant persister cells. Activation of endogenous intracellular viral sensing pathways by exogenous nucleic acids mimicking viral infection induced APOBEC3A, and genetic perturbation of RIG-I or MAVS reduced APOBEC3A induced by targeted therapy. These findings suggest that epigenetic derepression of retroviral repeat elements may underly APOBEC3A mutagenic activity and tumor evolution during lung cancer targeted therapy. Citation Format: Hideko Isozaki, Ramin Sakhtemani, Naveed Nikpour, Susanna Monroe, Jessica Lin, Lecia Sequist, Zofia Piotrowska, Justin Gainor, Rémi Buisson, Michael Lawrence, Aaron Hata. Epigenetic regulation of APOBEC3A mutagenesis and tumor evolution during targeted therapy in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 137.

Synthesis and cloning of long repeat sequences using single-stranded circular DNA.

Non-coding repeat expansion causes several neurodegenerative diseases, such as fragile X syndrome, amyotrophic lateral sclerosis/frontotemporal dementia, and spinocerebellar ataxia (SCA31). Such repetitive sequences must be investigated to understand disease mechanisms and prevent them, using novel approaches. However, synthesizing repeat sequences from synthetic oligonucleotides is challenging as they are unstable, lack unique sequences, and exhibit propensity to make secondary structures. Synthesizing long repeat sequence using polymerase chain reaction is often difficult due to lack of unique sequence. Here, we employed a rolling circle amplification technique to obtain seamless long repeat sequences using tiny synthetic single-stranded circular DNA as template. We obtained 2.5-3kbp uninterrupted TGGAA repeats, which is observed in SCA31, and confirmed it using restriction digestion, Sanger and Nanopore sequencing. This cell-free, in vitro cloning method may be applicable for other repeat expansion diseases and be used to produce animal and cell culture models to study repeat expansion diseases in vivo and in vitro.

Deregulations of miR‐1 and its target Multiplexin promote dilated cardiomyopathy associated with myotonic dystrophy type 1

Myotonic dystrophy type 1 (DM1) is the most common muscular dystrophy in adults. It is caused by the excessive expansion of noncoding CTG repeats, which when transcribed affects the functions of RNA‐binding factors with adverse effects on alternative splicing, processing, and stability of a large set of muscular and cardiac transcripts. Among these effects, inefficient processing and down‐regulation of muscle‐ and heart‐specific miRNA, miR‐1, have been reported in DM1 patients, but the impact of reduced miR‐1 on DM1 pathogenesis has been unknown. Here, we use Drosophila DM1 models to explore the role of miR‐1 in cardiac dysfunction in DM1. We show that miR‐1 down‐regulation in the heart leads to dilated cardiomyopathy (DCM), a DM1‐associated phenotype. We combined in silico screening for miR‐1 targets with transcriptional profiling of DM1 cardiac cells to identify miR‐1 target genes with potential roles in DCM. We identify Multiplexin (Mp) as a new cardiac miR‐1 target involved in DM1. Mp encodes a collagen protein involved in cardiac tube formation in Drosophila. Mp and its human ortholog Col15A1 are both highly enriched in cardiac cells of DCM‐developing DM1 flies and in heart samples from DM1 patients with DCM, respectively. When overexpressed in the heart, Mp induces DCM, whereas its attenuation rescues the DCM phenotype of aged DM1 flies. Reduced levels of miR‐1 and consecutive up‐regulation of its target Mp/Col15A1 might be critical in DM1‐associated DCM.

Repeat-associated non-AUG translation in neuromuscular diseases: mechanisms and therapeutic insights.

Expanded short tandem repeats cause more than 50 monogenic diseases, which are mostly neuromuscular diseases. In the non-coding repeat expansion diseases, in which the expanded repeat sequence is located outside of the coding region, the toxicity of the transcribed repeat-containing RNAs had been the focus of research. However, recent studies have revealed that repeat RNAs can be translated into repeat polypeptides, despite the lack of an AUG initiation codon, by non-canonical repeat-associated non-AUG translation (RAN translation). RAN translated repeat polypeptides have actually been confirmed in patients' tissues. Moreover, various cellular and animal disease models have demonstrated the toxicity of these peptides, suggesting the pathogenic roles of RAN translation in the repeat expansion diseases. In this review, we will outline RAN translation, from the viewpoint of its molecular mechanisms to its potential as a therapeutic target for the repeat expansion diseases.

Tandem Repeat DNA Provides Many Cytological Markers for Hybrid Zone Analysis in Two Subspecies of the Grasshopper Chorthippus parallelus.

Recent advances in next generation sequencing (NGS) have greatly increased our understanding of non-coding tandem repeat (TR) DNA. Here we show how TR DNA can be useful for the study of hybrid zones (HZ), as it serves as a marker to identify introgression in areas where two biological entities come in contact. We used Illumina libraries to analyse two subspecies of the grasshopper Chorthippus parallelus, which currently form a HZ in the Pyrenees. We retrieved a total of 152 TR sequences, and used fluorescent in situ hybridization (FISH) to map 77 families in purebred individuals from both subspecies. Our analysis revealed 50 TR families that could serve as markers for analysis of this HZ, using FISH. Differential TR bands were unevenly distributed between chromosomes and subspecies. Some of these TR families yielded FISH bands in only one of the subspecies, suggesting the amplification of these TR families after the geographic separation of the subspecies in the Pleistocene. Our cytological analysis of two TR markers along a transect of the Pyrenean hybrid zone showed asymmetrical introgression of one subspecies into the other, consistent with previous findings using other markers. These results demonstrate the reliability of TR-band markers for hybrid zone studies.

Tell me more – telomere biology and understanding telomere defects

Telomeres are DNA-protein structures at the ends of chromosomes that maintain chromosome stability and protects them from damage during mitosis and prevents abnormal fusion with adjacent chromosomes. They are non-coding repeats of the (TTAGGG)n nucleotide sequence. Telomere length affects cell replication potential and cell senescence. There are numerous proteins and enzymes that protect and maintain telomere length. Telomere disorders are a heterogenous group of diseases caused by germline pathogenic variants in genes involved in telomere maintenance. The clinical features are variable but often include bone marrow failure, idiopathic pulmonary fibrosis (IPF), liver cirrhosis, premature greying of hair, and dysplastic nails. However, incomplete penetrance and variable expressivity influence the clinical phenotype in individuals, which results is underdiagnosis or late diagnosis for many patients. At birth, telomere length on average in white blood cells (WBCs) is estimated to be 10Kb and the rate of attrition ranges from 27–41 base pairs each year. There are many factors that affect telomere length but genetics plays a significant role. Also, telomere length can vary in different cells in the same individual based on variable local gene expression. Idiopathic pulmonary fibrosis (IPF) is the most common telomere defect and approximately 30% of patients with sporadic or familial IPF have genetic defects in telomere-related genes. This talk will cover fundamental concepts of telomeres and discuss short and long telomere defects and measurement of telomere length in the clinical laboratory.

Quantitative magnetic resonance imaging assessment of muscle composition in myotonic dystrophy mice

Myotonic dystrophy type 1 (DM1) is a severe autosomal dominant neuromuscular disease in which the musculoskeletal system contributes substantially to overall mortality and morbidity. DM1 stems from a noncoding CTG trinucleotide repeat expansion in the DMPK gene. The human skeletal actin long repeat (HSALR) mouse model reproduces several aspects of the disease, but the muscle-wasting phenotype of this model has never been characterized in vivo. Herein, we used quantitative MRI to measure the fat and muscle volumes in the leg compartment (LC) of mice. These acquired data were processed to extract relevant parameters such as fat fraction and fat infiltration (fat LC/LC) in HSALR and control (FBV) muscles. These results showed increased fat volume (fat LC) and fat infiltration within the muscle tissue of the leg compartment (muscle LC), in agreement with necropsies, in which fatty clumps were observed, and consistent with previous findings in DM1 patients. Model mice did not reproduce the characteristic impaired fat fraction, widespread fat replacement through the muscles, or reduced muscle volume reported in patients. Taken together, the observed abnormal replacement of skeletal muscle by fat in the HSALR mice indicates that these mice partially reproduced the muscle phenotype observed in humans.

Systematic identification and characterization of repeat sequences in African swine fever virus genomes

African swine fever virus (ASFV) is a large DNA virus that infects domestic pigs with high morbidity and mortality rates. Repeat sequences, which are DNA sequence elements that are repeated more than twice in the genome, play an important role in the ASFV genome. The majority of repeat sequences, however, have not been identified and characterized in a systematic manner. In this study, three types of repeat sequences, including microsatellites, minisatellites and short interspersed nuclear elements (SINEs), were identified in the ASFV genome, and their distribution, structure, function, and evolutionary history were investigated. Most repeat sequences were observed in noncoding regions and at the 5’ end of the genome. Noncoding repeat sequences tended to form enhancers, whereas coding repeat sequences had a lower ratio of alpha-helix and beta-sheet and a higher ratio of loop structure and surface amino acids than nonrepeat sequences. In addition, the repeat sequences tended to encode penetrating and antimicrobial peptides. Further analysis of the evolution of repeat sequences revealed that the pan-repeat sequences presented an open state, showing the diversity of repeat sequences. Finally, CpG islands were observed to be negatively correlated with repeat sequence occurrences, suggesting that they may affect the generation of repeat sequences. Overall, this study emphasizes the importance of repeat sequences in ASFVs, and these results can aid in understanding the virus's function and evolution.

Short Telomere Syndromes and Inherited Predisposition to Bone Marrow Diseases: The MDACC Experience

Introduction: Telomeres are noncoding nucleotide repeats at chromosomal ends, which provide genomic stability and are maintained and regulated by specific protein complexes. Their length physiologically decreases with age, although it is known that germline mutations in telomeric regulators can accelerate this process, which is related to a wide variety of clinical situations. Herein we report on the experience of patients diagnosed with Short Telomere Syndromes (STS) evaluated in the Hereditary Hematologic Malignancy Clinic (HHMC) of the MD Anderson Cancer Center. Methods: We retrospectively analyzed clinical characteristics and outcomes of patients with a diagnosis of STS referred or diagnosed in the HHMC. Germline mutation origin was confirmed by genetic analysis of cultured skin fibroblasts or blood/saliva in patients without hematologic disease. Telomere length was assessed by Flow-FISH techniques in a clinically validated external laboratory (John Hopkins Medical Laboratories, Baltimore, MD). Individuals with confirmed STS were recommended to follow a specialized cancer surveillance program to achieve early-diagnosis or prevention of potential complications related to STS. A baseline bone marrow evaluation was recommended to evaluate underlying morphology and assess for somatic comutations. Results: A total of 24 patients with STS were identified (13 males, 54%), with a median age of presentation to the clinic of 53 years old (5-78). Although the reasons of referral for STS testing for each individual patient were diverse, they can be summarized in these categories: unexplained cytopenia (n=9), myeloid malignancy with relevant PMH or FH (n=8), affected sibling (n=5), skin lesions (n=1) and multiple cancer diagnosis (n=1). Pathogenic or likely pathogenic germline variants were confirmed in the TERT gene (n=13, 54%), TERC gene (n=7, 29%), RTEL1 (n=2, 8%), while 2 patients had no telomere-related detectable mutations (Figure 1). Telomere flow-FISH confirmed age-predicted telomere length <1st percentile for age in 67(%). All patients underwent a bone marrow biopsy, being described as hypocellullar in 17 patients (71%). With the bone marrow evaluation, eleven patients were diagnosed with myelodysplastic syndrome (MDS, 46%), two patients with acute leukemia (myeloid and mixed phenotype, 8%), two patients with clonal cytopenia of unknown significance (CCUS, 8%), one aplastic anemia (4%) and eight patients (33%) did not have hematologic malignancy. During the follow-up, three patients underwent an allogeneic stem cell transplantation due to their hematologic disease. Solid neoplasms are frequent in patients with STS, and 11 patients (46%) had a PMH of at least one solid tumor with a median age of 54 (33-78 yrs). Squamous cell carcinoma was the most frequent histology (6/11 patients). Sixteen patients (67%) had a positive FH of cancer in one or more first or second-degree sibling. Pulmonary fibrosis (PF) was diagnosed in 4 patients (17%), two with TERT mutations and two with TERC mutations. Moreover, 7 patients (4 diagnosed with PF,30%) had a positive FH of PF in first degree siblings. Liver diseases were also frequent: 3 patients had non-alcoholic hepatic cirrhosis, one patient had chronic hepatitis with periportal fibrosis and one with idiopathic portal hypertension. One patient had received a liver transplantation and one required a lung transplantation prior to presentation to the HHMC. Finally, twelve patients (50%) were reported to have premature grey hair and eight patients were reported to have nail dysplasia and/or skin abnormalities related to STS (such as unexplained reticular rash). A summary of the described patients is depicted in Figure 2. Conclusion: STS are genetic diseases that can go unnoticed until adulthood. Patients with myeloid malignancies (especially MDS) with hypocellular bone marrow and suspicious findings (i.e. FH or PMH of PF, premature grey hair, long standing cytopenias) should be considered for underlying STS. An early diagnosis is essential to start cancer surveillance programs and provide timely genetic counseling to the patient and relatives. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Mutation spectrum of chinese amyotrophic lateral sclerosis patients with frontotemporal dementia

BackgroundStudies have reported that a noncoding hexanucleotide repeat in C9ORF72, is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) among Caucasian population, nevertheless it is rare in Chinese population. Therefore, we aimed to investigate the mutation spectrum of Chinese ALS patients with FTD (ALS-FTD).MethodsALS patients with and without cognitive impairments were enrolled. Clinical features were collected including age, sex, disease duration, ALSFRS-r, family history and cognitive evaluation. Thirty-six ALS genes were screened by whole exome sequencing (WES) and repeat-primed polymerase chain reaction (PCR) were used for detection of and abnormal repeat expansions of C9ORF72.ResultsA total of 1208 patients, including 66 familial ALS (FALS) and 1142 sporadic ALS (SALS) patients were included. Twenty-three patients with sporadic ALS and one familial ALS index had concomitant FTD, which accounts for 1.99% (24/1208) of patients with ALS. In sporadic ALS-FTD, one case harboring C9ORF72 expansion variant, two cases harboring ANXA11 variants and one individual carrying CCNF variant were identified. A recurrent UBQLN2 variant was detected in a familial ALS-FTD patient. All of the ALS-FTD patients carrying variants in known causative genes manifested motor symptom onset (two bulbar onset and three limb onset) and developed cognitive impairment thereafter. It is not easy to draw a conclusion of the genotype-phenotype association in ALS-FTD with certain variants, limited by the small number of patients.ConclusionOur findings provide an overview of spectrum of genetic variants in Chinese ALS-FTD patients. Variants of uncertain significance in UBQLN2, ANXA11 and CCNF were identified and further studies are required for causal relations of these variants with ALS-FTD.

Non-coding repeat expansions associated with familial adult myoclonic epilepsy: a new paradigm of gene-independent monogenic disorders

Abstract Familial adult myoclonic epilepsy (FAME) is a rare autosomal dominant disorder characterized by cortical myoclonic tremor and seizures. FAME has been mapped to chromosomes (chr) 2, 3, 5 and 8, but the cause has remained elusive for more than a decade. An expansion of intronic TTTTA and TTTCA repeats in SAMD12 was identified as the cause of FAME1 in Japanese families linked to chr 8 in 2018. This discovery triggered the identification of identical repeat expansions at five additional loci (FAME2: STARD7; FAME3: MARCHF6; FAME4: YEATS2; FAME6: TNRC6A and FAME7: RAPGEF2). These genes encode proteins with different functions and subcellular localizations and their expression is unaltered in available peripheral tissues, suggesting that the expansion is pathogenic independently of the gene itself. The pathophysiological mechanisms are not yet known but possibly include toxicity at the RNA level or translation of toxic polypeptides from the repeats, a mechanism known as repeat-associated non-AUG (RAN) translation. FAME is a paradigm of human genetic disorder caused by a non-coding expansion unrelated to the gene where it occurs.

Development and characterization of non-coding RNA-derived simple sequence repeat markers in coconut (Cocos nucifera L.).

Non-coding RNA (ncRNA)-based SSR markers are highly useful in molecular breeding as ncRNAs play a significant role in gene regulation. In the present study, for the first time in coconut, we have identified 597 ncRNA-derived SSR markers, including 509 long non-coding RNASSRs (lncRNASSRs) and 88 micro RNASSRs (miRNASSRs). Of these, 20 primers (10 each from lncRNA-SSR and miRNA-SSR) were selected, screened on 6 coconut accessions, and 50% produced polymorphic fragments. These 10 polymorphic primers were used for genotyping 96 palms of 16 coconut accessions, comprising eight tall and dwarf accessions each. The number of alleles ranged from 2 to 9 per SSR marker, with an average of 4.6 alleles per locus. The average heterozygosity and Shannon index were 0.5 and 1.1, respectively, suggesting that ncRNA-SSRs show high polymorphism level. Distance-based cluster analyses revealed that all the tall and dwarf accessions were differentiated and grouped in different clusters. The study demonstrates the usefulness of ncRNA-based SSR markers for assessing genetic diversity and genetic improvement in coconut.

Familial Cerebellar Ataxia and Amyotrophic Lateral Sclerosis/Frontotemporal Dementia with DAB1 and C9ORF72 Repeat Expansions: An 18-Year Study.

Coding and noncoding repeat expansions are an important cause of neurodegenerative diseases. This study determined the clinical and genetic features of a large German family that has been followed for almost 2 decades with an autosomal dominantly inherited spinocerebellar ataxia (SCA) and independent co-occurrence of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). We carried out clinical examinations and telephone interviews, reviewed medical records, and performed magnetic resonance imaging and positron emission tomography scans of all available family members. Comprehensive genetic investigations included linkage analysis, short-read genome sequencing, long-read sequencing, repeat-primed polymerase chain reaction, and Southern blotting. The family comprises 118 members across seven generations, 30 of whom were definitely and five possibly affected. In this family, two different pathogenic mutations were found, a heterozygous repeat expansion in C9ORF72 in four patients with ALS/FTD and a heterozygous repeat expansion in DAB1 in at least nine patients with SCA, leading to a diagnosis of DAB1-related ataxia (ATX-DAB1; SCA37). One patient was affected by ALS and SCA and carried both repeat expansions. The repeat in DAB1 had the same configuration but was larger than those previously described ([ATTTT]≈75 [ATTTC]≈40-100 [ATTTT]≈415 ). Clinical features in patients with SCA included spinocerebellar symptoms, sometimes accompanied by additional ophthalmoplegia, vertical nystagmus, tremor, sensory deficits, and dystonia. After several decades, some of these patients suffered from cognitive decline and one from additional nonprogressive lower motor neuron affection. We demonstrate genetic and clinical findings during an 18-year period in a unique family carrying two different pathogenic repeat expansions, providing novel insights into their genotypic and phenotypic spectrums. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

Multi-type RFC1 repeat expansions as the most common cause of hereditary sensory and autonomic neuropathy.

Non-coding repeat expansions within RFC1 and NOTCH2NLC genes have lately been linked to multisystem neurodegenerative diseases, which also shed light on yet undiagnosed patients with inherited peripheral neuropathies. The aim of this study was to identify the genetic basis of patients with hereditary sensory and autonomic neuropathy (HSAN). We collected 79 unrelated DNA samples clinically suspected with HSAN from multiple regions of Japan. Mutation screening was first performed using gene panel sequencing and whole-exome sequencing. Pathogenic/likely pathogenic variants were identified from genes of WNK1/HSN2 (6 cases), SCN9A (3 cases), NTRK1 (3 cases), and DNMT1 (2 cases). Subsequently, long-range flanking PCR and repeat-primed PCR were applied to analyze repeat expansions in RFC1 and NOTCH2NLC. Bi-allelic RFC1 repeat expansions were detected from 20 adult-onset HSAN patients, consisting of [(AAGGG)exp/(AAGGG)exp] (8 cases), [(ACAGG)exp/(ACAGG)exp] (8 cases), and [(AAGGG)exp/(ACAGG)exp] (4 cases). GGC repeat expansion in NOTCH2NLC was found in 1 case. Single-nucleotide variant-based haplotype analysis of patients harboring disease-associated repeat expansions in RFC1 revealed distinguishable haplotypes among subgroups with different repeat genotypes. These findings substantially redefine the genetic spectrum of HSAN, where multi-type RFC1 repeat expansions account for 25.3% of all patients, highlighting the necessity of genetic screening, particularly for adult-onset patients.

Satellite repeat transcripts modulate heterochromatin condensates and safeguard chromosome stability in mouse embryonic stem cells

Heterochromatin maintains genome integrity and function, and is organised into distinct nuclear domains. Some of these domains are proposed to form by phase separation through the accumulation of HP1ɑ. Mouse heterochromatin contains noncoding major satellite repeats (MSR), which are highly transcribed in mouse embryonic stem cells (ESCs). Here, we report that MSR transcripts can drive the formation of HP1ɑ droplets in vitro, and modulate heterochromatin into dynamic condensates in ESCs, contributing to the formation of large nuclear domains that are characteristic of pluripotent cells. Depleting MSR transcripts causes heterochromatin to transition into a more compact and static state. Unexpectedly, changing heterochromatin’s biophysical properties has severe consequences for ESCs, including chromosome instability and mitotic defects. These findings uncover an essential role for MSR transcripts in modulating the organisation and properties of heterochromatin to preserve genome stability. They also provide insights into the processes that could regulate phase separation and the functional consequences of disrupting the properties of heterochromatin condensates.

C9orf72 Hexanucleotide Repeat Expansion-Related Neuropathology Is Attenuated by Nasal Rifampicin in Mice.

The non-coding GGGGCC hexanucleotide repeat expansion (HRE) in C9orf72 gene is a dominant cause of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). This intronic mutation elicits the formation of nuclear and cytoplasmic inclusions containing RNA, RNA-binding proteins, and HRE-derived dipeptide repeat proteins (DPRs), leading to neurodegeneration via the gain-of-toxic function or loss-of-function of relevant proteins. Using C9-500 mice harboring ~500 repeats of the GGGGCC sequence in human C9orf72 gene, we investigated the effects of rifampicin against HRE-related pathological phenotypes. Rifampicin was administered intranasally to 4.5- to 5-month-old mice for 1 month, and their cognitive function and neuropathology were assessed by the Morris water maze test and immunohistochemical staining. Rifampicin treatment reduced the formation of RNA foci and cytoplasmic inclusions containing DPRs or phosphorylated TDP-43, and furthermore, the levels of phosphorylated double-strand RNA-dependent protein kinase (PKR) that regulates repeat-associated non-ATG (RAN) translation. Synapse loss in the hippocampus and neuronal loss and microglial activation in the prefrontal and motor cortices were also attenuated, and mouse memory was significantly improved. Our findings suggest a therapeutic potential of nasal rifampicin in the prevention of C9orf72-linked neurodegenerative disorders.

Dual role of specific promoter tandem repeats integrating epigenetic silencing with heat response.

Satellites are ubiquitous noncoding tandemly repeated sequences, yet knowledge about their biological relevance is still scarce. In plants, the few described cases point to roles in heterochromatin biology and gene regulation; however, a direct link to plant stress responses is yet to be uncovered. We present evidence that particular non-centromere tandem repeats may display a central regulatory role in the intersection between epigenetic silencing and gene expression in dynamic environments. Within the projected promoter of Arabidopsis thaliana's imprinted SDC locus, a transcriptional gene silencing targeted tandem-repeated area largely mediates epigenetic suppression and imprinting. Here, we show that this area, possibly acting as a cis-element/enhancer, appears necessary and sufficient for SDC's heat transcriptional activity in vegetative tissues. Our results indicate that these particular noncoding tandem repeats may be genic and exhibit dual roles, not only as silencers at normal temperatures but also facilitating expression upon stress. An unusual adaptive form of abiotic transcriptional control unrelated to canonical heat signaling is implied, emphasizing a potential importance of genomic satellites for plant environmental epigenetics.

Genome-wide screening for genes involved in the epigenetic basis of fragile X syndrome.

SummaryFragile X syndrome (FXS), the most prevalent heritable form of intellectual disability, is caused by the transcriptional silencing of the FMR1 gene. The epigenetic factors responsible for FMR1 inactivation are largely unknown. Here, we initially demonstrated the feasibility of FMR1 reactivation by targeting a single epigenetic factor, DNMT1. Next, we established a model system for FMR1 silencing using a construct containing the FXS-related mutation upstream to a reporter gene. This construct was methylated in vitro and introduced into a genome-wide loss-of-function (LOF) library established in haploid human pluripotent stem cells (PSCs), allowing the identification of genes whose functional loss reversed the methylation-induced silencing of the FMR1 reporter. Selected candidate genes were further analyzed in haploid- and FXS-patient-derived PSCs, highlighting the epigenetic and metabolic pathways involved in FMR1 regulation. Our work sheds light on the mechanisms responsible for CGG-expansion-mediated FMR1 inactivation and offers novel targets for therapeutic FMR1 reactivation.

Reducing the Excess Activin Signaling Rescues Muscle Degeneration in Myotonic Dystrophy Type 2 Drosophila Model.

Expanded non-coding RNA repeats of CCUG are the underlying genetic causes for myotonic dystrophy type 2 (DM2). There is an urgent need for effective medications and potential drug targets that may alleviate the progression of the disease. In this study, 3140 small-molecule drugs from FDA-approved libraries were screened through lethality and locomotion phenotypes using a DM2 Drosophila model expressing 720 CCTG repeats in the muscle. We identified ten effective drugs that improved survival and locomotor activity of DM2 flies, including four that share the same predicted targets in the TGF-β pathway. The pathway comprises two major branches, the Activin and BMP pathways, which play critical and complex roles in skeletal development, maintenance of homeostasis, and regeneration. The Drosophila model recapitulates pathological features of muscle degeneration in DM2, displaying shortened lifespan, a decline in climbing ability, and progressive muscle degeneration. Increased levels of p-smad3 in response to activin signaling were observed in DM2 flies. Decreased levels of activin signaling using additional specific inhibitors or genetic method ameliorated climbing defects, crushed thoraxes, structure, and organization of muscle fibers. Our results demonstrate that a decrease in activin signaling is sufficient to rescue muscle degeneration and is, therefore, a potential therapeutic target for DM2.

Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus.

RNA interference (RNAi) is a conserved mechanism of small RNA-mediated genome regulation commonly involved in suppression of transposable elements (TEs) through both post-transcriptional silencing, and transcriptional repression via heterochromatin assembly. The fission yeast Schizosaccharomyces pombe has been extensively utilised as a model for studying RNAi pathways. However, this species is somewhat atypical in that TEs are not major targets of RNAi, and instead small RNAs correspond primarily to non-coding pericentromeric repeat sequences, reflecting a specialised role for the pathway in promoting heterochromatin assembly in these regions. In contrast, in the related fission yeast Schizosaccharomyces japonicus, sequenced small RNAs correspond primarily to TEs. This suggests there may be fundamental differences in the operation of RNAi pathways in these two related species. To investigate these differences, we probed RNAi function in S. japonicus. Unexpectedly, and in contrast to S. pombe, we found that RNAi is essential in this species. Moreover, viability of RNAi mutants can be rescued by mutations implicated in enhancing RNAi-independent heterochromatin propagation. These rescued strains retain heterochromatic marks on TE sequences, but exhibit derepression of TEs at the post-transcriptional level. Our findings indicate that S. japonicus retains the ancestral role of RNAi in facilitating suppression of TEs via both post-transcriptional silencing and heterochromatin assembly, with specifically the heterochromatin pathway being essential for viability, likely due to a function in genome maintenance. The specialised role of RNAi in heterochromatin assembly in S. pombe appears to be a derived state that emerged after the divergence of S. japonicus.