bims-rednas 2025-03-30 papers

bims-rednas

Biomed News

on Repetitive DNA sequences

Issue of 2025–03–30
nineteen papers selected by
Anna Zawada, International Centre for Translational Eye Research

Tissue-Specific Effects of the DNA Helicase FANCJ/BRIP1/BACH1 on Repeat Expansion in a Mouse Model of the Fragile X-Related Disorders.
Whole Genome Sequencing-Based Diagnosis of Spinocerebellar Ataxia Type 3 Repeat Expansion Neuromuscular Disorders in an Undiagnosed Patient: Breaking Past Diagnostic Boundaries.
Characterization of extrachromosomal circular DNA associated with genomic repeat sequences in breast cancer.
Characterizing Rare DNA Copy-Number Variants in Pediatric Obsessive-Compulsive Disorder.
Analysis of C9orf72 repeat length in progressive supranuclear palsy, corticobasal syndrome, corticobasal degeneration, and atypical parkinsonism.
Controlling the Local Conformation of RNA G-Quadruplex Results in Reduced RNA/Peptide Cytotoxic Accumulation Associated with C9orf72 ALS/FTD.
Association of Monoamine Oxidase A Gene Promoter Region (30 bp μVNTR) Polymorphism with Serum Levels in Multiple Psychiatric Disorders.
Modulating CCTG repeat expansion toxicity in DM2 Drosophila model through TDP1 inhibition.
Sustained Epigenetic Reactivation in Fragile X Neurons with an RNA-Binding Small Molecule.
Formation of the i-motif Structures by Human Telomeric c-Rich Sequences d(CCCTAA)n and Its Recognition by Bisbenzylisoquinoline Alkaloids.
Possible role of human ribonuclease dicer in the regulation of R loops.
STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci.
ONT in Clinical Diagnostics of Repeat Expansion Disorders: Detection and Reporting Challenges.
Subtelomeric repeat expansion in Hydractinia symbiolongicarpus chromosomes.
Considerations for the Implementation of Massively Parallel Sequencing into Routine Kinship Analysis.
LocusMasterTE: integrating long-read RNA sequencing improves locus-specific quantification of transposable element expression.
Analyses of Transposable Elements in Arbuscular Mycorrhizal Fungi Support Evolutionary Parallels With Filamentous Plant Pathogens.
Direct Targeted Degradation of Transposon RNAs by the Non-Canonical RNAi Pathway of the Fungus Mucor lusitanicus.
Genomic alterations of marine yeast Scheffersomyces spartinae under spontaneous and mutagenic conditions.

Int J Mol Sci. 2025 Mar 15. pii: 2655. [Epub ahead of print]26(6):

Tissue-Specific Effects of the DNA Helicase FANCJ/BRIP1/BACH1 on Repeat Expansion in a Mouse Model of the Fragile X-Related Disorders.

Diego Antonio Jimenez, Alexandra Walker, Karen Usdin, Xiaonan Zhao.

  Fragile X-related disorders (FXDs) are caused by the expansion of a CGG repeat tract in the 5'-UTR of the FMR1 gene. The expansion mechanism is likely shared with the 45+ other human diseases resulting from repeat expansion, a process that has been shown to require key mismatch repair (MMR) factors. FANCJ, a DNA helicase involved in unwinding unusual DNA secondary structures, has been implicated in a number of DNA repair processes including MMR. To test the role of FANCJ in repeat expansion, we crossed FancJ-null mice to an FXD mouse model. We found that loss of FANCJ resulted in a trend towards more extensive expansion that was significant for the small intestine and male germline. This finding has interesting implications for the expansion mechanism and raises the possibility that other DNA helicases may be important modifiers of expansion risk in certain cell types.

Keywords:  DNA helicase; FANCJ; FMR1 gene; genetic modifier; repeat expansion diseases; somatic instability

DOI:  https://doi.org/10.3390/ijms26062655
Neurol India. 2025 Mar 28.

Whole Genome Sequencing-Based Diagnosis of Spinocerebellar Ataxia Type 3 Repeat Expansion Neuromuscular Disorders in an Undiagnosed Patient: Breaking Past Diagnostic Boundaries.

Hari Shankar Kumar, Nidhi Shah, Parth Shah, Udhaya Kotecha, Mehul Mistri, Bushra Jarullah.

BACKGROUND: Spinocerebellar ataxia type 3 (SCA3) is a neuromuscular disorder (NMD) that is a complicated and progressive genetic disorder. SCA3 is predominantly caused by repeat expansions (REs) of short tandem repeats (STRs). SCA3 is caused by a CAG repeat expansion of the ATXN3 gene and is transmitted in an autosomal dominant manner and located on chromosomal position 14q32.
OBJECTIVE: The objective of this study was to identify the ATNX3 gene and assess the clinical accuracy of whole genome sequencing (WGS) in finding REs in previously undiagnosed patients with SCA3 for better management.
METHODS AND MATERIALS: Thirty-three referral cases for SCA3 were analyzed using WGS and triplet-repeat PCR (TP-PCR) techniques to detect REs for the ATXN3 gene.
RESULTS: A case of SCA3 was discovered to be positive for the ATXN3 gene for 59 CAG REs revealed by WGS and validated by TP-PCR. This mutation was found in a 26-year-old male patient who had previously been undiagnosed by other genetic tests.
CONCLUSION: To identify REs in the ATXN3 gene by validating WGS with previously inconclusive genetic tests, the study propose that WGS could potentially be implemented as the frontline, cost-effective, less turnaround time molecular testing for more accurate diagnoses and better-informed treatment strategies.

DOI: https://doi.org/10.4103/neurol-india.Neurol-India-D-24-00552
Int J Cancer. 2025 Mar 26.

Characterization of extrachromosomal circular DNA associated with genomic repeat sequences in breast cancer.

Wenxiang Lu, Lingsong Yao, Ying Wang, Fuyu Li, Bingbo Zhou, Wenlong Ming, Yali Jiang, Xiaoan Liu, Yun Liu, Xiao Sun, Yan Wang, Yunfei Bai.

  Extrachromosomal circular DNA (eccDNA) has emerged as a potential biomarker for disease due to its stable closed circular structure. However, the diagnostic utility of eccDNA remains underexplored. In this study, we demonstrate that the characteristics of eccDNA associated with genomic repetitive elements change in breast cancer patient tissues and plasma. These changes can serve as signatures for accurate cancer classification. We profiled eccDNA annotated to repeat elements across the genome in tissues and plasma, aggregating each repeat element to the superfamily and subfamily level. Our findings indicate that eccDNA associated with repetitive elements in cancer exhibits regular patterns of enrichment or depletion in specific elements, particularly at the family level. Additionally, these repeat element changes are present in different subtypes of breast cancer, correlated with varying hormone receptor expression. Although there are differences in the landscapes of eccDNA on repetitive elements between cancer tissues and paired plasma, the unique characteristics of eccDNA associated with repetitive sequences in the plasma of cancer patients facilitate better differentiation from normal individuals. These analyses reveal that changes in eccDNA associated with repeat sequences in human cancers can be used as diagnostic biomarkers for cancer patients.

Keywords:  biomarkers; breast cancer; extrachromosomal circular DNA; genomic repetitive elements

DOI:  https://doi.org/10.1002/ijc.35423
J Am Acad Child Adolesc Psychiatry. 2025 Mar 19. pii: S0890-8567(25)00160-1. [Epub ahead of print]

Characterizing Rare DNA Copy-Number Variants in Pediatric Obsessive-Compulsive Disorder.

Sarah B Abdallah, Emily Olfson, Carolina Cappi, Samantha Greenspun, Gwyneth Zai, Maria C Rosário, A Jeremy Willsey, Roseli G Shavitt, Euripedes C Miguel, James L Kennedy, Margaret A Richter, Thomas V Fernandez.

   OBJECTIVE: Pediatric obsessive-compulsive disorder (OCD) is a common neuropsychiatric disorder for which genetic factors play an important role. Recent studies have demonstrated an enrichment of rare de novo DNA single nucleotide variants in OCD cases compared to controls, and larger studies have examined copy-number variants (CNVs) using microarray data. Our study examines rare de novo CNVs using whole-exome sequencing (WES) data to provide additional insight into genetic factors and biological processes underlying OCD.
METHOD: We detected CNVs using whole-exome DNA sequencing (WES) data from 183 OCD trio families (unaffected parents and children with OCD) and 771 control families to test the hypothesis that rare de novo CNVs are enriched in OCD cases compared to controls. Our primary analysis used the eXome-Hidden Markov Model (XHMM) to identify CNVs in silico. We performed burden analyses comparing individuals with OCD vs. controls and downstream biological systems analyses of CNVs in probands with OCD. We then used a second algorithm (GATK-gCNV) to confirm our primary analysis.
RESULTS: Our findings demonstrate a higher rate of rare de novo CNVs detected by WES in individuals with OCD (0.07 CNVs per proband) compared to controls (0.005) (corrected rate ratio = 11.7 95% CI, 3.6-50.0, p = 4.00x10-6). We confirmed this enrichment using GATK-gCNV. The majority of these rare de novo CNVs in OCD cases are predicted to be pathogenic or likely pathogenic, and an examination of genes disrupted by rare de novo CNVs in OCD cases finds enrichment of several gene-ontology sets.
CONCLUSION: This study shows for the first time an enrichment of rare de novo CNVs detected by WES in OCD, complementing previous larger CNV studies and providing additional insight into genetic factors underlying OCD risk.

Keywords:  Genomic structural variation; Obsessive-compulsive disorder; behavioral; child psychiatry; exome Sequencing; genetics

DOI:  https://doi.org/10.1016/j.jaac.2025.03.014
J Neurol. 2025 Mar 26. 272(4): 293

Analysis of C9orf72 repeat length in progressive supranuclear palsy, corticobasal syndrome, corticobasal degeneration, and atypical parkinsonism.

PROSPECT consortium

   BACKGROUND: Pathogenic hexanucleotide repeat expansions in C9orf72 are the commonest genetic cause of frontotemporal dementia and/or amyotrophic lateral sclerosis. There is growing interest in intermediate repeat expansions in C9orf72 and their relationship to a wide range of neurological presentations, including Alzheimer's disease, Parkinson's disease, progressive supranuclear palsy, corticobasal degeneration, and corticobasal syndromes.
AIMS: To assess the prevalence of intermediate C9orf72 repeat expansions in a large cohort of prospectively-recruited patients clinically diagnosed with progressive supranuclear palsy (PSP), corticobasal syndrome (CBS), and atypical parkinsonism (APS), compared with healthy controls. We also sought to replicate the association between C9orf72 repeat length and CBD in neuropathologically confirmed cases.
METHODS: 626 cases, including PSP (n = 366), CBS (n = 130), and APS (n = 53) from the PROSPECT study, and 77 cases with pathologically confirmed CBD were screened for intermediate repeat expansions in C9orf72 using repeat-primed PCR. These were compared to controls from the PROSPECT-M-UK study and from the 1958 Birth Cohort.
RESULTS: There was no difference in the mean or largest allele size in any affected patient group compared with controls. A higher proportion of our affected cohort had large C9orf72 repeat expansions compared to controls, but there was no difference when comparing the frequency of intermediate expansions between affected patients and controls. There was no relationship between repeat length and age at onset, level of disability, or survival.
CONCLUSIONS: Intermediate expansions in C9orf72 do not appear to be a genetic risk factor for PSP, CBS, CBD, or atypical parkinsonism. They are not associated with age at onset, disability, or survival in our study.

Keywords:   C9orf72 ; Corticobasal degeneration; Genetics; Parkinsonism; Progressive supranuclear palsy

DOI:  https://doi.org/10.1007/s00415-025-12990-9
Small Methods. 2025 Mar 27. e2401630

Controlling the Local Conformation of RNA G-Quadruplex Results in Reduced RNA/Peptide Cytotoxic Accumulation Associated with C9orf72 ALS/FTD.

Saki Matsumoto, Hisae Tateishi-Karimata, Tatsuya Ohyama, Naoki Sugimoto.

  Repeat expansion of d(G4C2) in the noncoding region of the C9orf72 gene contributes to neurodegenerative diseases. The repeat expansion transcript r(G4C2) induces RNA/peptide accumulation, which, in turn, induces cytotoxicity and accelerates the development of neurodegenerative diseases. Such cytotoxic accumulation is triggered by peptide aggregation. Here, a technique is developed to prevent accumulation by regulating RNA interactions, assuming that RNA structure is important for peptide interactions. A screening method is used to identify compounds that suppress RNA accumulation of r(G4C2) repeats. The four compounds are identified with wide π-planes containing hydroxyl, methoxy, and cyclic ether groups that suppressed RNA accumulation. Interestingly, these compounds also suppressed RNA/peptide accumulation in neuroblastoma cells, indicating that RNA accumulation is a key regulator of RNA/peptide cytotoxic aggregate formation. In vitro and in silico physicochemical analyses reveal that these compounds bind to the loop region of the G-quadruplex via hydrogen bonds or CH-π interactions, resulting in an altered loop conformation. Importantly, these conformational changes inhibited RNA G-quadruplex associations. These results show that conformational changes are promising for controlling the interactions between G-quadruplexes and further RNA accumulation. These findings may be useful in the development of therapeutic strategies for the treatment of neurodegenerative diseases.

Keywords:  G‐quadruplex; RNA gelation; compound screening; liquid–liquid phase separation; neurodegenerative diseases

DOI:  https://doi.org/10.1002/smtd.202401630
Biomedicines. 2025 Mar 12. pii: 698. [Epub ahead of print]13(3):

Association of Monoamine Oxidase A Gene Promoter Region (30 bp μVNTR) Polymorphism with Serum Levels in Multiple Psychiatric Disorders.

Aisha Nasir Hashmi, Rizwan Taj, Zehra Agha, Raheel Qamar, Jamal B Williams, Maleeha Azam.

  Background: Monoamine oxidase A (MAOA) has a role in metabolising different biogenic amines, including dopamine. Functional studies have revealed the effect of promoter region variants on the transcriptional activity of the MAOA that consequently affects the homeostasis of the biogenic amines which might implicate in the aetiology of multiple psychiatric conditions. Objectives: The current study aimed to determine the influence of the promoter region 30 base pair (bp), a variable number of tandem repeats (VNTR) of the MAOA, on its serum levels and association with schizophrenia (SHZ), bipolar disorder (BD), and major depressive disorder (MDD) in the Pakistani population. Methods: A total of 1062 subjects [MDD n = 416, BD n = 200, SHZ n = 97 and controls n = 349], were genotyped for MAOA-30bp µVNTR through standard polymerase chain reaction technique and logistic regression was applied to determine the genetic association. Serum MAOA levels were determined through enzyme-linked immunosorbent assay (ELISA) and the Mann-Whitney U test was applied. Results: In genotype analysis, eight different repeat (R) alleles of MAOA-30 bp µVNTR were observed, where 4.5R, 5.5R, and 6R were the rare repeats found in the current Pakistani cohort. In serum-based analysis the total MAOA serum levels were found to be significantly elevated in SHZ; however, in sub-group analysis, significantly higher serum levels of MAOA were observed only in the rare allele groups of MDD, BD, and SHZ. Conclusions: The current study gives us further insights into the complex nature of MAOA regulation and its genetic and serum-levels association with different psychiatric conditions.

Keywords:  functional polymorphisms; monoamine oxidase; population genetics; psychiatric disorders

DOI:  https://doi.org/10.3390/biomedicines13030698
EMBO Mol Med. 2025 Mar 25.

Modulating CCTG repeat expansion toxicity in DM2 Drosophila model through TDP1 inhibition.

Yingbao Zhu, Shengwei Xiao, Xinxin Guan, Haitao Deng, Liqiang Ai, Kaijing Fan, Jin Xue, Guangxu Li, Xiaoxue Bi, Qiao Xiao, Yuanjiang Huang, Lin Jiang, Wen Huang, Peng Jin, Ranhui Duan.

  Myotonic dystrophy type 2 (DM2), caused by CCTG repeat expansion, is a common adult-onset disorder characterized by myotonia and progressive muscle degeneration with no effective treatment. Here, we identified Tyrosyl-DNA phosphodiesterase 1 (TDP1) as a novel modifier for DM2 therapeutic intervention through a high-throughput chemical screening of 2160 compounds. Moreover, we detailed how both genetic and pharmacological inhibition of TDP1 translates to a cascade of beneficial effects, including improved motor functions, amelioration of progressive muscle degeneration, repair of muscle fiber damage, and normalization of aberrant molecular pathology. Remarkably, the TDP1 inhibition led to substantial CCTG repeat contractions, a mechanism that underlies the observed muscle toxicity and neurodegeneration. Our results highlighted the potential of TDP1 as a molecular target for addressing the complex interplay between repeat expansions and neuromuscular degeneration in DM2, hinting at broader applicability in a spectrum of repeat expansion disorders.

Keywords:   TDP1 ; CCTG Repeat Expansion; Chemical Screen; DM2; Repeat Instability

DOI:  https://doi.org/10.1038/s44321-025-00217-3
Genes (Basel). 2025 Feb 25. pii: 278. [Epub ahead of print]16(3):

Sustained Epigenetic Reactivation in Fragile X Neurons with an RNA-Binding Small Molecule.

Christina W Kam, Jason G Dumelie, Gabriele Ciceri, Wang-Yong Yang, Matthew D Disney, Lorenz Studer, Samie R Jaffrey.

   BACKGROUND/OBJECTIVES: Fragile X syndrome (FXS) is a disease of pathologic epigenetic silencing induced by RNA. In FXS, an expanded CGG repeat tract in the FMR1 gene induces epigenetic silencing during embryogenesis. FMR1 silencing can be reversed with 5-aza-deoxyctidine (5-aza-dC), a nonspecific epigenetic reactivator; however, continuous administration of 5-aza-dC is problematic due to its toxicity. We describe an approach to restore FMR1 expression in FXS neurons by transient treatment with 5-aza-dC, followed by treatment with 2HE-5NMe, which binds the CGG repeat expansion in the FMR1 mRNA and could block the resilencing of the FMR1 gene after withdrawal of 5-aza-dC.
METHODS: This study uses immunofluorescence and fluorescent in situ hybridization (FISH) to measure whether FMR1 expression is maintained in FXS post-mitotic neurons treated with 2HE-5NMe. Genome-wide profiling of histone marks was used to monitor epigenetic changes and drug selectivity in response to 5-aza-dC followed by 2HE-5NMe treatment. Changes to dendritic morphology were visualized using confocal microscopy.
RESULTS: In this study, we find that 2HE-5Nme maintains FMR1 in a reactivated state after reactivation using 5-aza-dC in post-mitotic neurons. FMR1 reactivation in neurons results in the re-expression of FMRP and reversal of FXS-associated dendritic spine defects.
CONCLUSIONS: These results demonstrate that an RNA-binding small molecule can achieve gene-specific epigenetic control and provide an approach for the restoration of FMRP in FXS neurons.

Keywords:  RNA-binding small molecule; epigenetics; fragile X syndrome

DOI:  https://doi.org/10.3390/genes16030278
ACS Chem Biol. 2025 Mar 27.

Formation of the i-motif Structures by Human Telomeric c-Rich Sequences d(CCCTAA)n and Its Recognition by Bisbenzylisoquinoline Alkaloids.

Junliu Huang, Zexuan Lin, Jishun Yang, Huining Tang, Yang Yang, Yi Tang, Feixian Luo, Wenshu Wang, Xiaojie Cui.

The human telomeric repeat CCCTAA has been reported to form a higher-order structure called an intercalated motif (i-motif) that plays important roles in telomere function and telomerase activity regulation, and small molecule ligands targeting human telomeric i-motif (hTelo-iM) is a promising therapeutic strategy for cancer treatment, yet the i-motif folding pattern of long CCCTAA repeats and the hTelo-iM ligand screening have not been studied extensively. In this study, we systematically investigated the i-motif structures formed by four and eight telomeric C-rich repeats d(CCCTAA)4 (hTeloC-24mer) and d(CCCTAA)8 (hTeloC-48mer) under varied conditions and found that the long hTeloC-48mer probably forms unstacked tandem i-motif consisting of two hTeloC-24mer i-motif monomers under near physiological conditions. Moreover, natural bisbenzylisoquinoline (BBI) alkaloids, isofangchinoline, fangchinoline, cepharanthine, and tetrandrine, were screened from 33 natural small molecules to effectively disrupt and destabilize the hTelo-iM structures mainly through major groove hydrogen bonding and van der Waals interactions. Further, telomerase repeated amplification protocol (TRAP) assay suggested that the selected BBI alkaloids can inhibit the telomere extension by telomerase. These findings provide a theoretical basis for further telomere structure research as well as a novel class of natural small molecule compounds regulating the hTelo-iM structure and telomerase activity, which may contribute to the anticancer drug design and strategy development taking the hTelo-iM as a target.

DOI: https://doi.org/10.1021/acschembio.4c00844
FEBS Open Bio. 2025 Mar 24.

Possible role of human ribonuclease dicer in the regulation of R loops.

Klaudia Wojcik, Paulina Krzeminska, Anna Kurzynska-Kokorniak.

  R loops are three-stranded nucleic acid structures that form naturally in cells under various conditions, mainly as intermediates during replication or as by-products during transcription. R loops are involved in the regulation of many important cellular processes, including replication, transcription, centromere stabilization, protection of chromosome ends, or control of telomere length. Unscheduled R loops are linked to many diseases, including cancer, neurodegenerative, or inflammatory disorders. The list of cancer diseases linked to excessive R loop accumulation is growing rapidly. There is currently much debate about the understanding of abnormal R loop formation and its impact on genome instability and cancer development. In this review, we briefly describe the nature of R loops, their formation under physiological and pathological conditions, and the proteins involved in the regulation of R loops. In addition, we emphasize the possible role of the human ribonuclease Dicer, a multi-tasking protein mostly known for its important role in microRNA biogenesis, in the regulation of R loops. We also discuss the involvement of R loops in cancer development and their potential use as diagnostic biomarkers. Knowledge of the molecular mechanisms underlying R loop dysregulation may significantly improve our understanding of cancer biology and provide new directions for research.

Keywords:  G‐quadruplexes; R loops; TERRA; cancer; long non‐coding RNAs; ribonuclease Dicer

DOI:  https://doi.org/10.1002/2211-5463.70026
Genome Med. 2025 Mar 26. 17(1): 29

STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci.

Laurel Hiatt, Ben Weisburd, Egor Dolzhenko, Vincent Rubinetti, Akshay K Avvaru, Grace E VanNoy, Nehir Edibe Kurtas, Heidi L Rehm, Aaron R Quinlan, Harriet Dashnow.

Approximately 8% of the human genome consists of repetitive elements called tandem repeats (TRs): short tandem repeats (STRs) of 1-6 bp motifs and variable number tandem repeats (VNTRs) of 7 + bp motifs. TR variants contribute to several dozen monogenic diseases but remain understudied and enigmatic. It remains comparatively challenging to interpret the clinical significance of TR variants, particularly relative to single nucleotide variants. We present STRchive ( http://strchive.org/ ), a dynamic resource consolidating information on TR disease loci from the research literature, up-to-date clinical resources, and large-scale genomic databases, streamlining TR variant interpretation at disease-associated loci.

DOI: https://doi.org/10.1186/s13073-025-01454-4
Int J Mol Sci. 2025 Mar 18. pii: 2725. [Epub ahead of print]26(6):

ONT in Clinical Diagnostics of Repeat Expansion Disorders: Detection and Reporting Challenges.

Ludmila Kaplun, Greice Krautz-Peterson, Nir Neerman, Yocheved Schindler, Elinor Dehan, Claudia S Huettner, Brett K Baumgartner, Christine Stanley, Alexander Kaplun.

  While whole-genome sequencing (WGS) using short-read technology has become a standard diagnostic test, this technology has limitations in analyzing certain genomic regions, particularly short tandem repeats (STRs). These repetitive sequences are associated with over 50 diseases, primarily affecting neurological function, including Huntington disease, frontotemporal dementia, and Friedreich's ataxia. We analyzed 2689 cases with movement disorders and dementia-related phenotypes processed at Variantyx in 2023-2024 using a two-tiered approach, with an initial short-read WGS followed by ONT long-read sequencing (when necessary) for variant characterization. Of the 2038 cases (75.8%) with clinically relevant genetic variants, 327 (16.0%) required additional long-read analysis. STR variants were reported in 338 cases (16.6% of positive cases), with approximately half requiring long-read sequencing for definitive classification. The combined approach enabled the precise determination of repeat length, composition, somatic mosaicism, and methylation status. Notable advantages included the detection of complex repeat structures in several genes such as RFC1, FGF14, and FXN, where long-read sequencing allowed to determine somatic repeat unit variations and accurate allele phasing. Further studies are needed to establish technology-specific guidelines for the standardized interpretation of long-read sequencing data for the clinical diagnostics of repeat expansion disorders.

Keywords:  Nanopore; ONT; WGS; ataxia; dementia; genetic testing; long reads; repeat expansion

DOI:  https://doi.org/10.3390/ijms26062725
Mob DNA. 2025 Mar 25. 16(1): 14

Subtelomeric repeat expansion in Hydractinia symbiolongicarpus chromosomes.

Tetsuo Kon, Koto Kon-Nanjo, Oleg Simakov.

  Despite the striking conservation of animal chromosomes, their repetitive element complements are vastly diverse. Only recently, high quality chromosome-level genome assemblies enabled identification of repeat compositions along a broad range of animal chromosomes. Here, utilizing the chromosome-level genome assembly of Hydractinia symbiolongicarpus, a colonial hydrozoan cnidarian, we describe an accumulation of a single 372 bp repeat unit in the subtelomeric regions. Based on the sequence divergence, its partial affinity with the Helitron group can be detected. This sequence is associated with a repeated minisatellite unit of about 150 bp. Together, they account for 26.1% of the genome (126 Mb of the 483 Mb). This could explain the genome size increase observed in H. symbiolongicarpus compared with other cnidarians, yet distinguishes this expansion from other large cnidarian genomes, such as Hydra vulgaris, where such localized propagation is absent. Additionally, we identify a derivative of an IS3EU-like DNA element accumulated at the putative centromeric regions. Our analysis further reveals that Helitrons generally comprise a large proportion of H. symbiolongicarpus (11.8%). We investigated Helitron presence and distributions across several cnidarian genomes. We find that in Nematostella vectensis, an anthozoan cnidarian, Helitron-like sequences were similarly accumulated at the subtelomeric regions. All these findings suggest that Helitron derivatives are prone to forming chromosomal extensions in cnidarians through local amplification in subtelomeric regions, driving variable genome expansions within the clade.

Keywords:   Helitron ; Hydractinia symbiolongicarpus ; Cnidarian; Genome expansion; IS3EU; Rolling-circle transposon; Subtelomere; Tandem repeats; Transposable elements

DOI:  https://doi.org/10.1186/s13100-025-00355-y
Genes (Basel). 2025 Feb 20. pii: 238. [Epub ahead of print]16(3):

Considerations for the Implementation of Massively Parallel Sequencing into Routine Kinship Analysis.

Lucinda Davenport, Laurence Devesse, Somruetai Satmun, Denise Syndercombe Court, David Ballard.

  Background: Investigating the way in which individuals are genetically related has been a long-standing application of forensic DNA typing. Whilst capillary electrophoresis (CE)-based STR analysis is likely to provide sufficient data to resolve regularly encountered paternity cases, its power to adequately resolve more distant or complex relationships can be limited. Massively parallel sequencing (MPS) has become a popular alternative method to CE for analysing genetic markers for forensic applications, including kinship analysis. Data workflows used in kinship testing are well-characterised for CE-based methodologies but are much less established for MPS. When incorporating this technology into routine relationship casework, modifications to existing procedures will be required to ensure that the full power of MPS can be utilised whilst maintaining the authenticity of results. Methods: Empirical data generated with MPS for forensically relevant STRs and SNPs and real-world case experience have been used to determine the necessary workflow adaptations. Results: The four considerations highlighted in this work revolve around the distinctive properties of sequence-based data and the need to adapt CE-based data analysis workflows to ensure compatibility with existing kinship software. These considerations can be summarised as the need for a suitable sequence-based allele nomenclature; methods to account for mutational events; appropriate population databases; and procedures for dealing with rare allele frequencies. Additionally, a practical outline of the statistical adjustments required to account for genetic linkage between loci, within the expanded marker sets associated with MPS, has been presented. Conclusions: This article provides a framework for laboratories wishing to implement MPS into routine kinship analysis, with guidance on aspects of the data analysis and statistical interpretation processes.

Keywords:  forensic genetics; kinship analysis; kinship casework; likelihood ratio; massively parallel sequencing; microhaplotypes; next generation sequencing; population databases; sequence allele nomenclature; sequence-based STR analysis

DOI:  https://doi.org/10.3390/genes16030238
Genome Biol. 2025 Mar 26. 26(1): 72

LocusMasterTE: integrating long-read RNA sequencing improves locus-specific quantification of transposable element expression.

Sojung Lee, Jayne A Barbour, Yee Man Tam, Haocheng Yang, Yuanhua Huang, Jason W H Wong.

  Transposable elements (TEs) can influence human diseases by disrupting genome integrity, yet their quantification has been challenging due to the repetitive nature of these sequences across the genome. We develop LocusMasterTE, a method that integrates long-read with short-read RNA-seq to increase the accuracy of TE expression quantification. By incorporating fractional transcript per million values from long-read sequencing data into an expectation-maximization algorithm, LocusMasterTE reassigns multi-mapped reads, enhancing accuracy in short-read-based TE quantification. We validate the method with simulated and human datasets. LocusMasterTE may give new insights into TE functions through precise quantification.

Keywords:  Expectation–maximization model; Short-read RNA-seq quantification; Transposable elements

DOI:  https://doi.org/10.1186/s13059-025-03522-9
Genome Biol Evol. 2025 Mar 06. pii: evaf038. [Epub ahead of print]17(3):

Analyses of Transposable Elements in Arbuscular Mycorrhizal Fungi Support Evolutionary Parallels With Filamentous Plant Pathogens.

Jordana I N Oliveira, Catrina Lane, Ken Mugambi, Gokalp Yildirir, Ariane M Nicol, Vasilis Kokkoris, Claudia Banchini, Kasia Dadej, Jeremy Dettman, Franck Stefani, Nicolas Corradi.

  Transposable elements are repetitive DNA sequences that excise or create copies that are inserted elsewhere in the genome. Their expansion shapes genome variability and evolution by impacting gene expression and rearrangement rates. Arbuscular mycorrhizal fungi are beneficial plant symbionts with large, transposable element-rich genomes, and recent findings showed these elements vary significantly in abundance, evolution, and regulation among model strains. Here, we aimed to obtain a more comprehensive understanding of transposable element function and evolution in arbuscular mycorrhizal fungi by investigating assembled genomes from representatives of all known families. We uncovered multiple, family-specific bursts of insertions in different species, indicating variable past and ongoing transposable element activity contributing to the diversification of arbuscular mycorrhizal fungi lineages. We also found that transposable elements are preferentially located within and around candidate effectors/secreted proteins, as well as in proximity to promoters. Altogether, these findings support the role of transposable elements in promoting the diversity in proteins involved in molecular dialogs with hosts and, more generally, in driving gene regulation. The mechanisms of transposable element evolution we observed in these prominent plant symbionts bear striking similarities to those of many filamentous plant pathogens.

Keywords:  effector proteins; mobile genome; plant symbionts; repetitive DNA

DOI:  https://doi.org/10.1093/gbe/evaf038
Int J Mol Sci. 2025 Mar 18. pii: 2738. [Epub ahead of print]26(6):

Direct Targeted Degradation of Transposon RNAs by the Non-Canonical RNAi Pathway of the Fungus Mucor lusitanicus.

Ghizlane Tahiri, Carlos Lax, Francisco E Nicolás, Victoriano Garre, Eusebio Navarro.

  Mucor lusitanicus has emerged as a model organism for studying RNAi in early-diverging fungi. This fungus exhibits intricate RNAi pathways that play crucial roles in regulating gene expression, destroying invasive exogenous genetic material, and controlling the movement of transposable elements (TEs) to ensure genome stability. One of the most fascinating RNAi pathways of this fungus is the non-canonical RNAi pathway (NCRIP), which is independent of Dicer and Argonaute proteins and uses the atypical RNase III R3B2 to degrade specific target messenger RNAs (mRNAs), playing an essential role in genome stability and virulence. Despite accumulating data suggesting that this pathway is a degradation mechanism, there has been no conclusive evidence. Here, we conducted a comparative transcriptomic analysis of mRNA and small RNAs regulated by r3b2, identifying 35 direct NCRIP targets. Most of these direct NCRIP targets correspond to TEs, highlighting the significant role of this RNAi pathway in TE control. Detailed functional analysis of the NCRIP targets confirmed the crucial role of r3b2 in regulating gene expression of protein-coding genes and controlling TEs other than centromeric GremLINE1 transposons, emphasizing the important role of r3b2 in genome stability. Interestingly, the RNAs of the NCRIP targets harbor a unique motif consisting of CAG repeats which are known to form hairpin structures which are targeted by RNA interference. Additionally, the generation of transformants expressing mRNAs containing the luciferase reporter gene along direct NCRIP targets reveals that this RNAi pathway is a true degradation mechanism for specific mRNAs. These results are expected to contribute to the understanding of the regulation of the NCRIP pathway through the analysis of its direct targets identified here.

Keywords:  GremLINE1; NCRIP; TEs; genome stability; regulation; sRNAs

DOI:  https://doi.org/10.3390/ijms26062738
BMC Genomics. 2025 Mar 25. 26(1): 297

Genomic alterations of marine yeast Scheffersomyces spartinae under spontaneous and mutagenic conditions.

Yu-Ting Bai, Awkash Sharma, Qian Xiang, Li-Yan Tian, Ke-Jing Li, Bao-Ying Guo, Lei Qi, Dao-Qiong Zheng.

   BACKGROUND: Understanding the mechanisms of genetic evolution in marine yeasts is essential for their ecological and biotechnological applications. Scheffersomyces spartinae, an ascomycetous yeast species, characterized by its remarkable robustness and carbon source utilization capability, has garnered significant attention for its biotechnological potential.
RESULTS: In this study, we investigated the spontaneous and induced genomic alterations of the marine yeast S. spartinae under various conditions. Through mutation accumulation experiments combined with whole-genome sequencing, we revealed that the rates of spontaneous single nucleotide variations and small insertions and deletions were 6.3 × 10⁻¹¹ and 1.4 × 10⁻¹¹ per base pair per cell division, respectively, in S. spartinae. The predominant type of base substitution was C-to-T or G-to-A, likely induced by cytosine deamination. Template slippage during DNA replication emerged as the primary cause of small InDels. 50 J/m2 UV treatment elevated the SNV rate by 124-fold, with C-to-T substitutions occurring at the 5'-TC-3' motif and T-to-C substitutions at the 5'-TT-3' motif being the most prominent features. Exposure to 50 µg/mL Zeocin resulted in 76-fold and 71-fold increases in the rates of SNVs and InDels, respectively, with frequent T-to-A mutations and T deletions occurring at the 5'-GT-3' motifs. Heat stress at 37 °C increased the SNVs and InDels rates to 1.4 × 10⁻¹⁰ and 7.5 × 10⁻¹¹ per base pair per cell division. Notably, this study demonstrated that large deletions and duplications (> 1 kb) and aneuploidies are less likely to occur in S. spartinae compared to other yeast species, suggesting that this organism is less tolerant to large-scale genomic alterations. In contrast, we observed a marked decrease in rDNA copy numbers when S. spartinae cells were cultivated at elevated temperature conditions. This finding indicates that variations in rDNA copy numbers might act as an adaptive strategy for yeasts in response to fluctuating temperatures.
CONCLUSIONS: Our findings provide novel insights into the patterns and genetic mechanisms underlying genomic evolution in yeasts.

Keywords:  DNA mutation; High temperature; Marine yeast; Mutagen; rDNA copy number

DOI:  https://doi.org/10.1186/s12864-025-11479-z