bims-rednas 2025-05-11 papers

bims-rednas

Biomed News

on Repetitive DNA sequences

Issue of 2025–05–11
nineteen papers selected by
Anna Zawada, International Centre for Translational Eye Research

Simple sequence repeats and their expansions: role in plant development, environmental response and adaptation.
Large tandem repeats of grass frog (Rana temporaria) in silico and in situ.
A study of repetitive sequences in the genome of Sinopodisma qinlingensis.
Comparative Analysis of the Chloroplast Genomes of Cypripedium: Assessing the Roles of SSRs and TRs in the Non-Coding Regions of LSC in Shaping Chloroplast Genome Size.
Regulatory roles of transposable elements on autism molecular neuropathology.
Binding of NF-Y to transposable elements in mouse and human cells.
Transposable elements as genome regulators in normal and malignant haematopoiesis.
How repeats rearrange chromosomes: The molecular basis of chromosomal inversions in deer mice.
Posttranscriptional RNA stabilization of telomeric RNAs FRG2, DBE-T, D4Z4 at human 4q35 in response to genotoxic stress and D4Z4 macrosatellite repeat length.
Huntingtin inclusion bodies have distinct immunophenotypes and ubiquitination profiles in the Huntington's disease human cerebral cortex.
Cerulenin Partially Corrects the Disrupted Developmental Transcriptomic Signature in Huntington's Disease Striatal Medium Spiny Neurons.
Interventionally targeting somatic CAG expansions can be a rapid disease-modifying therapeutic avenue: Preclinical evidence.
PI3P: Rising to the (DPR) challenge in C9-ALS/FTD.
Approach to Progressive Myoclonic Epilepsies: Clinical Clues for Genetic Testing.
Structural and biochemical studies of mobile retrotransposon proteins in action.
Tandemly Repeated G-Quadruplex Structures in the Pseudorabies Virus Genome: Implications for Epiberberine-Based Antiviral Therapy.
Role of the multiple telomeric repeat arrays in integration, persistence, and efficacy of the commercial CVI988 vaccine.
Highly sensitive and specific markers for detection of mismatch repair deficiency by next-generation sequencing.
Adaptive dynamics of extrachromosomal circular DNA in rice under nutrient stress.

New Phytol. 2025 May 05.

Simple sequence repeats and their expansions: role in plant development, environmental response and adaptation.

Sridevi Sureshkumar, Aaryan Chhabra, Ya-Long Guo, Sureshkumar Balasubramanian.

  Repetitive DNA is a feature of all organisms, ranging from archaea and plants to humans. DNA repeats can be seen both in coding and in noncoding regions of the genome. Due to the recurring nature of the sequences, simple DNA repeats tend to be more prone to errors during replication and repair, resulting in variability in their unit length. This feature of simple sequence repeats led to their use as molecular markers for mapping traits in diverse organisms. Advances in genomics, and the ever-reducing costs of genome sequencing have empowered us to assess the functional impacts of DNA repeats. The variability in repeat lengths can cause phenotypic differences depending on where they are present in the genome. Variability in the repeat length in coding regions of genes results in poly amino acid stretches that appear to interfere with protein function, including the perturbation of protein-protein interactions with diverse phenotypic impacts. These are often common allelic variations that can significantly impact evolutionary dynamics. In extreme situations, repeats can undergo massive expansions and appear as outliers. Repeat expansions underlie several genetic defects in plants to diseases in humans. This review systematically analyses tandem DNA repeats in plants, their role in development and environmental response and adaptation in plants. We identify and synthesise emerging themes, differentiate repeat length variability and repeat expansions, and argue that many repeat-associated phenotypes in plants are yet to be discovered. We emphasise the underexplored nature and immense potential of this area of research, particularly in plants, and suggest ways in which this can be achieved and how it might contribute to evolution and agricultural productivity.

Keywords:  epigenetic gene silencing; microsatellites; polyQ/polyglutamine; protein–protein interactions; repeat variability

DOI:  https://doi.org/10.1111/nph.70173
BMC Genomics. 2025 May 06. 26(1): 445

Large tandem repeats of grass frog (Rana temporaria) in silico and in situ.

Marina A Popova, Aleksey S Komissarov, Dmitrii I Ostromyshenskii, Olga I Podgornaya, Aleksandra O Travina.

   BACKGROUND: Genomes of higher eukaryotes contain a large fraction of non-coding repetitive DNA, including tandem repeats (TRs) and transposable elements (TEs). The impact of TRs on genome structure and function and the importance of TR transcripts have been described for several model species. Amphibians have one of the most diverse genome sizes among vertebrates, attributed to the abundance of repetitive non-coding DNA. Consequently, amphibians are good models for the analysis of repetitive sequences, including TRs. However, few studies have focused on amphibian genomes.
RESULTS: Bioinformatic analyses were performed to characterise the content and localisation of TRs in the sequenced grass frog Rana temporaria genome. By applying different bioinformatic approaches, 76 TR families and 314 single TR arrays (not grouped into families) were identified. Each TR was characterised on the basis of chromosomal position, monomer length and variability and GC content. Bioinformatic analysis revealed a great diversity of TRs, with a clear predominance of TRs with short monomers (< 100 bp), although TRs with long monomers (> 1000 bp) also exist. The six most abundant TRs were successfully mapped by fluorescence in situ hybridization (FISH), which highlighted the presence of specific TR sequences in strategic chromosomal regions, i.e., the pericentromeric regions. A comparison of the results of in situ and in silico TR mapping revealed some inaccuracies in the assembly of heterochromatic regions. A putative new non-autonomous TE called "FEDoR" (Frog Element Dispersed organised Repeat) is also described. FEDoR is ∼ 3.5 kb in length, has no significant similarity to any known TE family, contains multiple internal TR motifs, and is flanked on both sides by pairs of inverted repeat sequences (IRSs) and target site duplications (TSDs).
CONCLUSION: Characterisation of TRs in this frog species has provided some insights regarding TR biology in Anuran amphibians.

Keywords:  Amphibian; FISH; Satellite DNA; Tandem repeats; Transposable elements

DOI:  https://doi.org/10.1186/s12864-025-11643-5
PeerJ. 2025 ;13 e19358

A study of repetitive sequences in the genome of Sinopodisma qinlingensis.

Xiongyan Yin, Nan Zhang, Xiaoyu Li, Lijia Gan, Yimeng Nie, Yuan Huang.

  The family Acrididae characterized by a remarkable genome size and a significant proportion of repetitive sequences. In this study, we find a considerable characteristics by examining the Sinopodisma qinlingensis, which has an average genome size within the range observed in Acrididae. The genome size of S. qinlingensis was determined to be 11.37 pg for females and 10.95 pg for males using flow cytometry. The analysis of low-coverage sequencing data revealed that the total repeat content of the genome was 63.58%, with long terminal repeat (LTR) elements accounting for 17.74% of the genome contents. Phylogenetic analysis of the reverse transcriptase (RT) domains, which are found within LTR and LINE sequences with consistent conserved motifs, showed that LTR elements belong to multipl within a monophyletic branch. This finging suggests that LTR elements did not originate independently, but rather shared a common evolutionary history. Additionally, the content of Ty3-Gypsy sequences within LTR elements was found to be significantly increased. Fluorescence in situ hybridisation (FISH) showed that most satellite DNA and LTR elements exhibited an aggregated distribution pattern on the chromosome.

Keywords:  Acrididae; FISH; Genome size; LTR; Repeat sequence; Satellite DNA

DOI:  https://doi.org/10.7717/peerj.19358
Int J Mol Sci. 2025 Apr 14. pii: 3691. [Epub ahead of print]26(8):

Comparative Analysis of the Chloroplast Genomes of Cypripedium: Assessing the Roles of SSRs and TRs in the Non-Coding Regions of LSC in Shaping Chloroplast Genome Size.

Huanchu Liu, Hans Jacquemyn, Yanlin Wang, Yuanman Hu, Xingyuan He, Ying Zhang, Yue Zhang, Yanqing Huang, Wei Chen.

  Cypripedium is renowned for its high morphological diversity and complex genetic and evolutionary characteristics. The chloroplast genome serves as a valuable tool for investigating phylogenetic relationships and evolutionary processes in plants. Currently, research on the evolution of the chloroplast genome within the Cypripedium genus is limited due to insufficient large-scale sampling and a lack of comprehensive understanding. Consequently, the mechanisms underlying the significant differences in chloroplast genome size among Cypripedium species remain poorly understood. In this study, we conducted a comprehensive comparative analysis of the chloroplast genomes of 29 Cypripedium species. The lengths of these genomes ranged from 162,092 to 246,177 base pairs (bp) and contained between 127 and 134 genes. Our results indicate that, while the overall structure of the chloroplast genomes in Cypripedium species is relatively conserved, significant differences were observed among the large single-copy (LSC), small single-copy (SSC), and inverted repeat (IR) regions. Several genes, including psaC, rpl32, ycf1, and psbK, exhibited higher levels of variability and may serve as molecular markers in taxonomic studies. The results of our correlation analysis suggest that the expansion of the LSC region, the increase in simple sequence repeats (SSRs), and tandem repeats (TRs) have significantly enlarged the size of the chloroplast genome in Cypripedium species. Phylogenetic signal testing supports the notion that genetic variation has driven species divergence within the genus. Overall, our findings provide insights into the substantial differences in chloroplast genome length observed among Cypripedium species. However, the relationship between diversification and the evolutionary mechanisms affecting Cypripedium, including ecological adaptive evolution, incomplete lineage sorting (ILS), hybridization, and reticulate events, requires further investigation.

Keywords:  Cypripedium; Orchidaceae; SSRs; TRs; chloroplast genome; phylogenomics

DOI:  https://doi.org/10.3390/ijms26083691
Epigenomics. 2025 May 06. 1-9

Regulatory roles of transposable elements on autism molecular neuropathology.

Peerapa Techaniyom, Chawin Korsirikoon, Pitaksin Chitta, Chanachai Sae-Lee.

  Autism Spectrum Disorder (ASD) is a complex neurodevelopmental condition characterized by challenges in social communication and the presence of repetitive behaviors, typically diagnosed in early childhood. In this review, we searched PubMed and Google Scholar databases for relevant articles. ASD displays considerable heterogeneity in symptomatology and is more common in males, though shifting demographics indicate rising rates among minority populations. Transposable elements (TEs), which constitute approximately 50% of the mammalian genome, are increasingly recognized for their contribution to neurodevelopmental disorders, including ASD. These mobile genetic elements can induce genomic instability and modulate gene expression, thereby influencing ASD pathology. Evidence suggests that specific TEs, such as L1 and Alu elements, can disrupt genes critical for neurodevelopment and contribute to the disorder's genetic complexity. Furthermore, prenatal environmental exposures may activate TEs, potentially contributing to neuroinflammation observed in ASD. While the precise regulatory roles of non-coding TEs in ASD are still under investigation and require careful interpretation, integrating epigenetic aging markers like epigenetic clocks holds promise for advancing the field. Future research focused on the intricate relationship between TEs, environmental factors, epigenetic mechanisms, and neurodevelopmental processes is essential for identifying novel biomarkers and therapeutic targets, ultimately improving early diagnosis and interventions for ASD.

Keywords:  Alu; DNA methylation; Epigenetics; LINE-1; autism; epigenetic clock; repetitive elements; transposable elements

DOI:  https://doi.org/10.1080/17501911.2025.2501520
Mob DNA. 2025 May 09. 16(1): 22

Binding of NF-Y to transposable elements in mouse and human cells.

Mirko Ronzio, Andrea Bernardini, Alberto Gallo, Roberto Mantovani, Diletta Dolfini.

   BACKGROUND: Transposable Elements (TEs) represent a sizeable amount of mammalian genomes, providing regulatory sequences involved in shaping gene expression patterns. NF-Y is a Transcription factor -TF- trimer that binds to the CCAAT box, belonging to a selected group implicated in determining initiation of coding and noncoding RNAs.
RESULTS: We focus on NF-Y TE locations in 8 human and 8 mouse cells. Binding is exclusive for retroviral LTR12, MLT1 and MER in human and RLTR10 and IAPLTR in mouse cells. Cobinding and analysis of the DNA matrices signal enrichment of distinct TFs neighboring CCAAT in the three TE classes: MAFK/F/G in LTR12 and USF1/2 in MLT1 with precise alignment of sites, PKNOX1, MEIS2, PBX2/3 TALE TFs in MER57. The presence of "epigenetic" marks in human cells indicate prevalent co-association with open chromatin in MER, closed in LTR12 and mixed in MLT1. Based on chromatin features, these locations are mostly marked as enhancers, as confirmed by analysis of loci predicted to generate eRNAs.
CONCLUSIONS: These results are discussed in the context of functional data, suggesting a complex -positive and potentially-negative role of NF-Y on distinct classes of repetitive sequences.

Keywords:  LTR12; MER; MLT1; NF-Y; Repetitive sequences; Transcription factor

DOI:  https://doi.org/10.1186/s13100-025-00358-9
Blood Cancer J. 2025 May 06. 15(1): 87

Transposable elements as genome regulators in normal and malignant haematopoiesis.

Dmitry Prokopov, Hale Tunbak, Eve Leddy, Bryce Drylie, Francesco Camera, Özgen Deniz.

Transposable elements (TEs) constitute over half of the human genome and have played a profound role in genome evolution. While most TEs have lost the ability to transpose, many retain functional elements that serve as drivers of genome innovation, including the emergence of novel genes and regulatory elements. Recent advances in experimental and bioinformatic methods have provided new insights into their roles in human biology, both in health and disease. In this review, we discuss the multifaceted roles of TEs in haematopoiesis, highlighting their contributions to both normal and pathological contexts. TEs influence gene regulation by reshaping gene-regulatory networks, modulating transcriptional activity, and creating novel regulatory elements. These activities play key roles in maintaining normal haematopoietic processes and supporting cellular regeneration. However, in haematological malignancies, TE reactivation can disrupt genomic integrity, induce structural variations, and dysregulate transcriptional programmes, thereby driving oncogenesis. By examining the impact of TE activity on genome regulation and variation, we highlight their pivotal roles in both normal haematopoietic processes and haematological cancers.

DOI: https://doi.org/10.1038/s41408-025-01295-9
Cell Rep. 2025 May 05. pii: S2211-1247(25)00415-2. [Epub ahead of print]44(5): 115644

How repeats rearrange chromosomes: The molecular basis of chromosomal inversions in deer mice.

Landen Gozashti, Olivia S Harringmeyer, Hopi E Hoekstra.

  Large genomic rearrangements, such as chromosomal inversions, can play a key role in evolution, but the mechanisms by which these rearrangements arise remain poorly understood. To study the origins of inversions, we generated chromosome-level de novo genome assemblies for four subspecies of the deer mouse (Peromyscus maniculatus) with known inversion polymorphisms. We identified ∼8,000 inversions, including 47 megabase-scale inversions, that together affect ∼30% of the genome. Analysis of inversion breakpoints suggests that while most small (<1 Mb) inversions arose via ectopic recombination between retrotransposons, large (>1 Mb) inversions are primarily associated with segmental duplications (SDs). Large inversion breakpoints frequently occur near centromeres, which may be explained by an accumulation of retrotransposons in pericentromeric regions driving SDs. Additionally, multiple large inversions likely arose from ectopic recombination between near-identical centromeric satellite arrays located megabases apart, suggesting that centromeric repeats may also facilitate inversions. Together, our results illuminate how repeats give rise to massive shifts in chromosome architecture.

Keywords:  CP: Genomics; CP: Molecular biology; centromeres; chromosomal inversions; deer mouse; genome evolution; segmental duplications; structural variation; transposable elements

DOI:  https://doi.org/10.1016/j.celrep.2025.115644
Clin Epigenetics. 2025 May 04. 17(1): 73

Posttranscriptional RNA stabilization of telomeric RNAs FRG2, DBE-T, D4Z4 at human 4q35 in response to genotoxic stress and D4Z4 macrosatellite repeat length.

Valentina Salsi, Francesca Losi, Monica Salani, Paul D Kaufman, Rossella Tupler.

   BACKGROUND: Reduced copy number of the D4Z4 macrosatellite at human chromosome 4q35 is associated with facioscapulohumeral muscular dystrophy (FSHD). A pervasive idea is that chromatin alterations at the 4q35 locus following D4Z4 repeat unit deletion lead to disease via inappropriate expression of nearby genes. Here, we sought to analyze transcription and chromatin characteristics at specific regions of 4q35 and how these are affected by D4Z4 deletions and exogenous stresses.
RESULTS: We found that the 4q subtelomere is subdivided into discrete domains, each with characteristic chromatin features associated with distinct gene expression profiles. Centromeric genes within 4q35 (SLC25A4, FAT1 and FRG1) display active histone marks at their promoters. In contrast, poised or repressed markings are present at telomeric loci including FRG2, DBE-T and D4Z4. We discovered that these discrete domains undergo region-specific chromatin changes upon treatment with chromatin enzyme inhibitors or genotoxic drugs. We demonstrated that the 4q35 telomeric FRG2, DBE-T and D4Z4-derived transcripts are induced upon DNA damage to levels inversely correlated with the D4Z4 repeat number, are stabilized through posttranscriptional mechanisms upon DNA damage and are bound to chromatin.
CONCLUSION: Our study reveals unforeseen biochemical features of RNAs from clustered transcription units within the 4q35 subtelomere. Specifically, the FRG2, DBE-T and D4Z4-derived transcripts are chromatin-associated and are stabilized posttranscriptionally after induction by genotoxic stress. Remarkably, the extent of this response is modulated by the copy number of the D4Z4 repeats, raising new hypotheses about their regulation and function in human biology and disease.

Keywords:  D4Z4 chromatin signature; DNA damage; Epigenetic regulation; FSHD

DOI:  https://doi.org/10.1186/s13148-025-01881-5
Sci Rep. 2025 May 03. 15(1): 15546

Huntingtin inclusion bodies have distinct immunophenotypes and ubiquitination profiles in the Huntington's disease human cerebral cortex.

Molly E V Swanson, Adelie Y S Tan, Lynette J Tippett, Clinton P Turner, Maurice A Curtis, Emma L Scotter, Hilal A Lashuel, Mike Dragunow, Richard L M Faull, Helen C Murray, Malvindar K Singh-Bains.

Huntington's disease (HD) is a hereditary neurodegenerative condition caused by a CAG repeat expansion mutation in the gene encoding the huntingtin (HTT) protein. The accumulation of HTT inclusion bodies is a pathological hallmark of HD and a common target for therapeutic strategies. However, the limited efficacy of treatments targeting the HTT protein highlights the need for a better understanding of the role of HTT inclusion bodies in HD pathogenesis. This study examined the heterogeneity of HTT inclusion body composition by co-labelling with three HTT epitope-specific antibodies to characterize HTT inclusion body 'immunophenotype'. We then characterized the size and sub-cellular location of HTT inclusions with distinct immunophenotypes. Using multiplex immunohistochemistry, we also examined the ubiquitination profile of each immunophenotype. Our findings demonstrate that HTT inclusions have a range of immunophenotypes, with some labelled by only one of the three antibodies and others exhibiting co-labelling by several antibodies, thus demonstrating the heterogeneity in inclusion composition and structure. We outline evidence that inclusion bodies exclusively labelled with the EM48 antibody are small, non-nuclear, and more abundant in HD cases with increased CAG repeat length, higher Vonsattel grade, and earlier age of onset. We also find that HTT inclusion bodies labelled by multiple antibodies are more likely to be ubiquitinated, predominantly by K63- rather than K48-linked ubiquitin, suggesting preferential degradation by autophagy. Lastly, we show that ubiquitinated HTT inclusion bodies are more highly immunoreactive for ubiquilin 2 than p62. Our findings highlight the need for multiple antibodies to capture the full spectrum of HTT pathology in HD and imply that future studies should consider the diversity of inclusion body composition and structure when correlating pathology formation to neurodegeneration, clinical symptoms, or disease severity.

DOI: https://doi.org/10.1038/s41598-025-00465-w
Stem Cells. 2025 May 08. pii: sxaf029. [Epub ahead of print]

Cerulenin Partially Corrects the Disrupted Developmental Transcriptomic Signature in Huntington's Disease Striatal Medium Spiny Neurons.

Carlos Galicia Aguirre, Kizito-Tshitoko Tshilenge, Elena Battistoni, Alejandro Lopez-Ramirez, Swati Naphade, Kevin Perez, Akos A Gerencser, Sicheng Song, Sean D Mooney, Simon Melov, Michelle E Ehrlich, Lisa M Ellerby.

  Huntington's disease (HD) is a neurodegenerative disorder caused by an expansion of CAG repeats in exon 1 of the huntingtin (HTT) gene, resulting in a mutant HTT (mHTT) protein. Although mHTT is expressed in all tissues, it significantly affects medium spiny neurons (MSNs) in the striatum, resulting in their loss and the subsequent motor function impairment in HD. While HD symptoms typically emerge in midlife, disrupted MSN neurodevelopment is important. To explore the effects of mHTT on MSN development, we differentiated HD-induced pluripotent stem cells (iPSC) and isogenic controls into neuronal stem cells, and then generated a developing MSN population encompassing early, intermediate progenitors, and nascent MSNs. Single-cell RNA sequencing revealed that the developmental trajectory of MSNs in our model closely emulated the trajectory of human fetal striatal neurons. However, in the HD MSN cultures, several crucial genes required for proper MSN maturation were downregulated, including members of the DLX family of transcription factors. Our analysis also uncovered a progressive dysregulation of multiple HD-related pathways as MSNs developed, including the NRF2-mediated oxidative stress response and mitogen-activated protein kinase signaling. Using the transcriptional profile of developing HD MSNs, we searched the L1000 dataset for small molecules that induce the opposite gene expression pattern. We pinpointed numerous small molecules with known benefits in HD models and previously untested novel molecules. A top candidate, Cerulenin, partially restored the DARPP-32 levels and electrical activity in HD MSNs, and also modulated genes involved in multiple HD-related pathways.

Keywords:  Huntington’s disease; development; induced pluripotent stem cells; medium spiny neurons; neurodegeneration; single-cell RNAseq

DOI:  https://doi.org/10.1093/stmcls/sxaf029
bioRxiv. 2025 Apr 28. pii: 2025.04.25.650652. [Epub ahead of print]

Interventionally targeting somatic CAG expansions can be a rapid disease-modifying therapeutic avenue: Preclinical evidence.

Terence Gall-Duncan, Sangyoon Y Ko, Isabelle K Quick, Mahreen Khan, Kristie Feng, Chase P Kelley, Annabelle Coleman, Alexiane Touze, Shuqian Tang, Mustafa Mehkary, Katsuyuki Yokoi, Casey R Herrington, Justin You, Scott C Lambie, Tanya K Prasolava, Gagan B Panigrahi, Jeehye Park, Kazuhiko Nakatani, Lauren M Byrne, Peixiang Wang, John S Schneekloth, Masayuki Nakamori, Paul W Frankland, Eric T Wang, Christopher E Pearson.

Huntington disease (HD) is caused by inherited CAG expansions, which continue expanding somatically in affected brain regions to hasten disease onset and progression. Therapeutically diminishing somatic expansions is expected to be clinically beneficial. However, it is not known if interventionally modifying somatic CAG expansions will actually modify in vivo clinically-relevant phenotypes, what the therapeutic window is, or which phenotypes will be altered. Here we show that acute (6-week) delivery of the contraction-inducing slipped-CAG DNA ligand naphthyridine-azaquinolone to young (4-week-old) (CAG)120 HD mice, induces contractions throughout brain regions, improves motor function (locomotion, balance, coordination, muscle strength), molecular disease landmarks (mHTT aggregates, nuclear envelope morphology, nucleocytoplasmic mRNA transport, transcriptomic dysregulation, neuroinflammation), and neurodegeneration. Beneficial effects of modifying somatic expansions were also evident in muscle and blood, where blood CAG instability correlated with brain instability and blood serum had diminished levels of neurofilament light (a biomarker for neurodegeneration) - offering blood as having elements of target engagement and efficacy. These data support that targeting somatic repeat expansions can be a rapid disease-modifying therapeutic avenue for HD and possibly other repeat expansion diseases. Our findings support an etiologic pathway interconnected to somatic CAG expansions that will inform the design of clinical trials expecting clinical benefit by modulating somatic expansions.

DOI: https://doi.org/10.1101/2025.04.25.650652
Neuron. 2025 May 07. pii: S0896-6273(25)00286-7. [Epub ahead of print]113(9): 1301-1303

PI3P: Rising to the (DPR) challenge in C9-ALS/FTD.

Janani Parameswaran, Zachary T McEachin.

A hexanucleotide G4C2 repeat expansion in C9orf72 causes accumulation of dipeptide repeat (DPR) proteins and is the leading genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). In a recent issue of Neuron, Zhang et al.1 report that elevating PI3P levels mitigates endolysosomal deficits and DPR-associated neurotoxicity.

DOI: https://doi.org/10.1016/j.neuron.2025.04.007
J Child Neurol. 2025 May 08. 8830738251337972

Approach to Progressive Myoclonic Epilepsies: Clinical Clues for Genetic Testing.

Prasanthi Aripirala, Sujit Abajirao Jagtap.

  Progressive myoclonic epilepsy is a heterogeneous group of disorders characterized by drug-resistant epilepsy, cognitive decline, and ataxia. Genetic testing is crucial for diagnosis, but the choice of test depends on the variant type. We present a case of an adult with a PME phenotype since age 17 years, remaining undiagnosed for 4 years because of improper genetic testing. His father had progressive ataxia with a spinocerebellar ataxia phenotype. The unique presentation, combined with autosomal dominant inheritance and anticipation, suggested dentatorubral-pallidoluysian atrophy. ATN1 gene polymerase chain reaction testing confirmed trinucleotide repeat expansion. This case highlights the importance of selecting the appropriate genetic test for accurate diagnosis. We propose a flowchart based on clinical history and findings to narrow down differential diagnoses and guide the choice of testing.

Keywords:  dentatorubral-pallidoluysian atrophy; progressive myoclonic epilepsy; whole exome sequencing

DOI:  https://doi.org/10.1177/08830738251337972
Curr Opin Struct Biol. 2025 May 06. pii: S0959-440X(25)00071-5. [Epub ahead of print]92 103053

Structural and biochemical studies of mobile retrotransposon proteins in action.

Akanksha Thawani, Kathleen Collins, Eva Nogales.

Autonomous non-long-terminal repeat (non-LTR) retrotransposons, including long interspersed elements (LINEs), are mobile genetic elements abundant in eukaryotic species that shape the genomic landscape and host physiology in both health and disease. Non-LTR retrotransposons create new genomic copies through a mechanism termed target-primed reverse transcription, where the retrotransposon-encoded protein nicks target DNA to prime reverse transcription templated by bound RNA, typically its own encoding mRNA. Until recently, structural information on non-LTR retrotransposons was lacking due to challenges in purification and reconstitution of active complexes. Recent biochemical studies and cryo-electron microscopy structures of complexes from insect, bird, and turtle site-specific R2 retrotransposons and the human LINE-1 retrotransposon have provided important insights. Here we discuss these studies and their implications for retrotransposon evolution and eukaryotic genome biology.

DOI: https://doi.org/10.1016/j.sbi.2025.103053
Int J Mol Sci. 2025 Apr 16. pii: 3764. [Epub ahead of print]26(8):

Tandemly Repeated G-Quadruplex Structures in the Pseudorabies Virus Genome: Implications for Epiberberine-Based Antiviral Therapy.

Songjie Fan, Xiaotian Chang, Yan Qiao, Xiaoxiao Zhao, Jiafu Zhao, Heshui Zhu, Yingqian Han, Chao Zhang.

  G-quadruplex (G4) structures have emerged as critical regulatory elements in viral genomes and represent potential targets for antiviral intervention. In this study, we identified and characterized G4 structures in the unique long (UL) region of the Pseudorabies virus (PRV) genome, highlighting their role as novel antiviral targets. Bioinformatic analysis revealed two guanine-rich regions (R1 and R2) that form stable G4 structures, as confirmed by fluorescence assays, circular dichroism (CD) spectroscopy, and immunofluorescence staining. Notably, these G4 structures exhibit a tandem repeat arrangement, a previously unreported feature in the PRV genome. Epiberberine (EPI), a natural G4-stabilizing ligand, bound to and stabilized these structures, leading to the inhibition of Taq polymerase progression. Functional assays demonstrated that EPI effectively suppressed PRV replication in vitro while having no significant impact on viral entry or release. In vivo, EPI treatment significantly improved survival rates and reduced viral loads in multiple organs, including the brain, heart, lungs, and kidneys of infected mice. These findings provide new insights into the role of G4 structures in PRV replication and demonstrate that EPI exhibits potential antiviral activity by targeting G4 structures.

Keywords:  DNAG-quadruplex; antiviral activity; epiberberine; pseudorabies virus

DOI:  https://doi.org/10.3390/ijms26083764
mSphere. 2025 May 08. e0014225

Role of the multiple telomeric repeat arrays in integration, persistence, and efficacy of the commercial CVI988 vaccine.

Luca D Bertzbach, Yu You, Tereza Vychodil, Ahmed Kheimar, Lisa Kossak, Mohammad A Sabsabi, Andelé M Conradie, Benedikt B Kaufer.

  Marek's disease virus (MDV) is a highly oncogenic alphaherpesvirus that causes fatal T cell lymphomas in chickens. Oncogenic MDV strains can integrate their genome into the host telomeres of latently infected and tumor cells. This integration process is facilitated by telomeric repeat arrays (TMR) present at the ends of the MDV genome, which consist of the hexanucleotide (TTAGGG)n that is identical to host telomere sequences. In addition, integration of the virus genome is crucial for the development of lymphomas. Live-attenuated vaccines play a vital role in protecting chickens against this deadly disease, yet our understanding of their biology remains limited. Intriguingly, the commercial gold standard MDV vaccine, the live-attenuated MDV strain CVI988, also possesses TMR at the ends of its genome. In this study, we investigated the role of the multiple TMR arrays (mTMR) in vaccine virus integration, latency, reactivation, and protection against very virulent MDV. Our data revealed that the mTMR present in CVI988 are important for virus genome integration and maintenance in latently infected cells in vitro. In addition, virus latency, reactivation, and vaccine efficacy were reduced in an mTMR deleted mutant compared to the wild-type vaccine. These results provide valuable insights into the biology of this important vaccine virus and shed light on the roles of the mTMR in vaccine integration, latency, and protection against very virulent MDV.IMPORTANCEMarek's disease virus (MDV) is an oncogenic herpesvirus and causes lethal lymphomas in chickens. The gold standard vaccine is the live-attenuated MDV strain CVI988 (a.k.a. Rispens). CVI988 is extensively used in chickens worldwide due to its high efficacy in preventing disease and lymphomas. The CVI988 vaccine harbors telomere arrays (TMR) at the ends of its genome. TMR facilitate genome integration of oncogenic MDV strains into the host telomeres. This study provides critical insights into the biology of the widely used MDV vaccine strain CVI988, demonstrating the crucial role of mTMR in viral genome integration, latency, and protection against very virulent MDV. Furthermore, our findings enhance the understanding of MDV vaccine biology and may guide future strategies to improve Marek's disease control.

Keywords:  CVI988; MDV vaccine; Rispens; genome integration; herpesvirus; telomeres; vaccine effectiveness

DOI:  https://doi.org/10.1128/msphere.00142-25
Am J Clin Pathol. 2025 May 03. pii: aqaf026. [Epub ahead of print]

Highly sensitive and specific markers for detection of mismatch repair deficiency by next-generation sequencing.

Ming-Tseh Lin, Eric S Christenson, Aparna Pallavajjala, James R Eshleman.

   OBJECTIVE: To identify exonic markers that could improve analytic performance characteristics of next-generation sequencing (NGS) in detecting mismatch repair deficiency (dMMR) using colorectal cancer (CRC) as a model.
METHODS: Coding sequences of a target NGS panel (~1.13 megabase) were compared between dMMR CRC and mismatch repair-proficient (pMMR) CRC in a training cohort (41 dMMR CRCs and 213 pMMR CRCs) and a validation cohort (33 dMMR CRCs and 307 pMMR CRCs) with documented mismatch repair status by immunohistochemical and/or microsatellite instability assays.
RESULTS: The dMMR CRC cases showed significantly higher insertion/deletion (indel) mutations within exonic homopolymers (homo-indels), occurring predominantly within longer repeats of 5 to 10 nucleotides (92%, P < .0001), rather than shorter repeats of 2 to 4 nucleotides seen in pMMR CRC (62%). Homo-indels in dMMR CRC were not random. Hotspot loci were consistent between the training and validation cohorts. The dMMR defined by indels within homopolymers of 5 or more nucleotides, homopolymers of 7 or more nucleotides, or a panel of hotspots all showed 100% sensitivity and specificity with a range of cutoffs.
CONCLUSIONS: We propose that this approach allows one to identify highly sensitive and specific markers for detecting dMMR CRC by NGS alone. Further studies are warranted to test whether these markers are applicable to non-CRC neoplasms.

Keywords:  CRC; homopolymer; hotspots; microsatellite instability; mismatch repair deficiency; next-generation sequencing

DOI:  https://doi.org/10.1093/ajcp/aqaf026
Nat Commun. 2025 May 04. 16(1): 4150

Adaptive dynamics of extrachromosomal circular DNA in rice under nutrient stress.

Hanfang Ni, Lenin Yong-Villalobos, Mian Gu, Damar Lizbeth López-Arredondo, Min Chen, Liyan Geng, Guohua Xu, Luis Rafael Herrera-Estrella.

Extrachromosomal circular DNAs (eccDNAs) have been identified in various eukaryotic organisms and are known to play crucial roles in genomic plasticity. However, in crop plants, the role of eccDNAs in responses to environmental cues, particularly nutritional stresses, remains unexplored. Rice (Oryza sativa ssp. japonica), a vital crop for over half the world's population and an excellent model plant for genomic studies, faces numerous environmental challenges during growth. Therefore, we conduct comprehensive studies investigating the distribution, sequence, and potential responses of rice eccDNAs to nutritional stresses. We describe the changes in the eccDNA landscape at various developmental stages of rice in optimal growth. We also identify eccDNAs overlapping with genes (ecGenes), transposable elements (ecTEs), and full-length repeat units (full-length ecRepeatUnits), whose prevalence responds to nitrogen (N) and phosphorus (P) deficiency. We analyze multiple-fragment eccDNAs and propose a potential TE-mediated homologous recombination mechanism as the origin of rice's multiple-fragment eccDNAs. We provide evidence for the role of eccDNAs in the rice genome plasticity under nutritional stresses and underscore the significance of their abundance and specificity.

DOI: https://doi.org/10.1038/s41467-025-59572-x