Trinucleotide Repeat Research Articles

Upregulated Chaperone-Mediated Autophagy May Perform a Key Role in Reduced Cancer Incidence in Huntington's Disease.

Incidence of cancer is markedly reduced in patients with the hereditary neurodegenerative polyglutamine (polyQ) diseases. We have very poor knowledge of the underlying molecular mechanisms, but the expanded polyQ sequence is assumed to play a central role, because it is common to the respective disease related proteins. The inhibition seems to take place in all kinds of cells, because the lower cancer frequency applies to nearly all types of tumors and is not related with the characteristic pathological changes in specific brain tissues. Further, the cancer repressing mechanisms appear to be active early in life including in pre-symptomatic and early phase polyQ patients. Autophagy plays a central role in clearing proteins with expanded polyQ tracts, and autophagy modulation has been demonstrated and particularly investigated in Huntington's disease (HD). Macroautophagy may be dysfunctional due to defects in several steps of the process, whereas increased chaperone-mediated autophagy (CMA) has been shown in HD patients, cell and animal models. Recently, CMA is assumed to play a key role in prevention of cellular transformation of normal cells into cancer cells. Investigations of normal cells from HD and other polyQ carriers could therefore add further insight into the protective mechanisms of CMA in tumorigenesis, and be important for development of autophagy based strategies to prevent malignant processes leading to cancer and neurodegeneration.

Dysregulation of Human Juvenile Huntington's Disease Brain Proteomes in Cortex and Putamen Involves Mitochondrial and Neuropeptide Systems.

Huntington's disease (HD) is a genetic neurodegenerative disease caused by trinucleotide repeat CAG expansions in the human HTT gene. Early onset juvenile HD (JHD) in children is the most severe form of the disease caused by high CAG repeat numbers of the HTT gene. To gain understanding of human HD mechanisms hypothesized to involve dysregulated proteomes of brain regions that regulate motor and cognitive functions, this study analyzed the proteomes of human JHD cortex and putamen brain regions compared to age-matched controls. JHD and age-matched control brain tissues were assessed for CAG repeat numbers of HTT by PCR. Human brain JHD brain cortex regions of BA4 and BA6 with the putamen region (n = 5) were analyzed by global proteomics, compared to age-matched controls (n = 7). Protein interaction pathways were assessed by gene ontology (GO), STRING-db, and KEGG bioinformatics. JHD brain tissues were heterozygous for one mutant HTT allele containing 60 to 120 CAG repeats, and one normal HTT allele with 10 to 19 CAG repeats. Proteomics data for JHD brain regions showed dysregulated mitochondrial energy pathways and changes in synaptic systems including peptide neurotransmitters. JHD compared to control proteomes of cortex and putamen displayed (a) proteins present only in JHD, (b) proteins absent in JHD, and (c) proteins that were downregulated or upregulated. Human JHD brain cortex and putamen regions display significant dysregulation of proteomes representing deficits in mitochondrial and synaptic neurotransmission functions. These findings advance understanding of JHD brain molecular mechanisms associated with HD disabilities.

“Difficult” deoxyribonucleotide sequences in the solid-phase synthesis by the phosphoramidite chemistry

This work catalogued oligonucleotide sequences and sequence compositions based on the overall yield of full-length product obtained by the phosphoramidite chemistry-based solid phase synthesis. In total, 76 sequences with different dinucleotide and trinucleotide repeats were synthesized, and the fully-deprotected products were analyzed by denaturing anion exchange HPLC. Overall, sequences containing more 2’-deoxyadenosine residues were obtained in relatively lower yields, likely due to the relative ease of 2’-deoxyadenosine to undergo depurination during the detritylation reaction. Furthermore, dinucleotide steps, such as d(CG)/d(GC) and d(AG)/d(GA), likely contribute the overall lower yields of full-length products as well.

Transcriptomic meta-analysis reveals ERRα-mediated oxidative phosphorylation is downregulated in Fuchs' endothelial corneal dystrophy.

Late-onset Fuchs' endothelial corneal dystrophy (FECD) is a degenerative disease of cornea and the leading indication for corneal transplantation. Genetically, FECD patients can be categorized as with (RE+) or without (RE-) the CTG trinucleotide repeat expansion in the transcription factor 4 gene. The molecular mechanisms underlying FECD remain unclear, though there are plausible pathogenic models proposed for RE+ FECD. In this study, we performed a meta-analysis on RNA sequencing datasets of FECD corneal endothelium including 3 RE+ datasets and 2 RE- datasets, aiming to compare the transcriptomic profiles of RE+ and RE- FECD. Gene differential expression analysis, co-expression networks analysis, and pathway analysis were conducted. There was a striking similarity between RE+ and RE- transcriptomes. There were 1,184 genes significantly upregulated and 1,018 genes significantly downregulated in both RE+ and RE- cases. Pathway analysis identified multiple biological processes significantly enriched in both-mitochondrial functions, energy-related processes, ER-nucleus signaling pathway, demethylation, and RNA splicing were negatively enriched, whereas small GTPase mediated signaling, actin-filament processes, extracellular matrix organization, stem cell differentiation, and neutrophil mediated immunity were positively enriched. The translational initiation process was downregulated in the RE+ transcriptomes. Gene co-expression analysis identified modules with relatively distinct biological processes enriched including downregulation of mitochondrial respiratory chain complex assembly. The majority of oxidative phosphorylation (OXPHOS) subunit genes, as well as their upstream regulator gene estrogen-related receptor alpha (ESRRA), encoding ERRα, were downregulated in both RE+ and RE- cases, and the expression level of ESRRA was correlated with that of OXPHOS subunit genes. Meta-analysis increased the power of detecting differentially expressed genes. Integrating differential expression analysis with co-expression analysis helped understand the underlying molecular mechanisms. FECD RE+ and RE- transcriptomic profiles are much alike with the hallmark of downregulation of genes in pathways related to ERRα-mediated OXPHOS.

Intranuclear inclusions of polyQ-expanded ATXN1 sequester RNA molecules.

Spinocerebellar ataxia type 1 (SCA1) is an autosomal dominant neurodegenerative disease caused by a trinucleotide (CAG) repeat expansion in the ATXN1 gene. It is characterized by the presence of polyglutamine (polyQ) intranuclear inclusion bodies (IIBs) within affected neurons. In order to investigate the impact of polyQ IIBs in SCA1 pathogenesis, we generated a novel protein aggregation model by inducible overexpression of the mutant ATXN1(Q82) isoform in human neuroblastoma SH-SY5Y cells. Moreover, we developed a simple and reproducible protocol for the efficient isolation of insoluble IIBs. Biophysical characterization showed that polyQ IIBs are enriched in RNA molecules which were further identified by next-generation sequencing. Finally, a protein interaction network analysis indicated that sequestration of essential RNA transcripts within ATXN1(Q82) IIBs may affect the ribosome resulting in error-prone protein synthesis and global proteome instability. These findings provide novel insights into the molecular pathogenesis of SCA1, highlighting the role of polyQ IIBs and their impact on critical cellular processes.

Length-independent and selective sensing of CCG trinucleotide repeat foldings by a monovalency-binding fluorogenic probe

Tandem CNG (N = C, T, A, G) DNA trinucleotide repeats (TNRs) are the main expansion to cause severe neurodegenerative diseases. Small molecule ligands with a capacity to sense the CNG TNRs foldings have received considerable attention because of therapeutic and diagnostic perspectives. This requires development of effectual ligands that have a preference to a particular CNG TNRs foldings. However, the previously developed ligands using hydrogen-bonding interaction as the dominantly driving force usually exhibit a multimolecular binding behavior with TNRs. This multivalency interaction usually compromises the sensing selectivity towards CNG TNRs. Herein, we reported a monovalency probe of pseudohypericin (PHP) to selectively sense only the CCG TNRs foldings by a signal-on fluorescence, while total signal-off responses were otherwise observed for CTG, CAG, and CGG TNRs. In addition, the monovalency association of PHP to CCG TNRs is independent of the repeat length. This selective sensing occurs in the loop region, in which a triad is formed between the terminal Watson-Crick CG base pair and the mismatched cytosine adopting an extrahelical conformation. We believe that the specific interaction of PHP with the triad is in charge of the selective association of CCG TNRs over other counterparts. Furthermore, the sensitivity to CCG TNRs can be strengthened by the repeat-activated photocatalysis activity of the TNRs-based DNAzymes via a singlet oxygen (1O2) pathway. Our work offers an alternative way to sense CNG TNRs with a high selectivity and promising applications in developing TNRs-based sensors.

Dissecting the role of GGGGCC repeat RNA secondary structure in cellular toxicity associated with C9 FTD/ALS

AbstractBackgroundAberrant expansions of simple nucleotide repeat sequences can cause more than fifty human diseases. For example, the most common genetic cause of Frontotemporal dementia (FTD) and Amyotrophic Lateral Sclerosis (ALS) is the expansion of an intronic GGGGCC hexanucleotide repeat sequence in C9orf72 gene (C9 FTD/ALS). Transcribed GGGGCC repeat RNAs can form complex secondary structures, which facilitate unusual interactions with cellular RNA‐binding proteins (RBPs). Sequestration of crucial RBPs into nuclear foci can inhibit the normal functions of those proteins. In addition, expanded GGGGCC repeat RNAs can support the translation of highly toxic repetitive peptides through a non‐canonical process known as repeat associated non‐AUG translation (RAN translation), which may require some specialized factors. Here we sought to understand how RNA secondary structure influence GGGGCC RAN translation and repeat elicited toxicity in C9 FTD/ALS.MethodWe used chemical modification coupled with traditional high‐throughput sequencing and nano‐pore sequencing approaches to probe GGGGCC repeat RNA secondary structures inside cells. We further use in vitro and in vivo RAN translation assays to determine whether repeat RNA secondary structures influence RAN translation efficiency.ResultOur RNA structural studies revealed that GGGGCC repeat RNAs form primarily form hairpin structures in cells. With nanopore sequencing, we were also able to detect the possible presence of unfolded and/or g‐quadruplex folded GGGGCC repeat RNAs in cells. Folding GGGGCC RNAs into hairpins supports RAN translation whereas folding repeat RNAs into g‐quadruplex structures strongly inhibits RAN translation in both in vitro and in vivo assays. Our results suggest that RNA secondary structure can affect the RAN translation elongation efficiency and g‐quadruplex structures may lead to the termination of elongating ribosomes.ConclusionWe present a deep sequencing‐based chemical probing technique to evaluate the roles of repeat RNA secondary structures in RNA toxicity underlying dementia‐associated repeat expansion disorders. Repeat RNA structural information can be used to identify chemical compounds that can bind to the RNA and prevent cytotoxicity in cells.

Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome

Short tandem repeat (STR) instability causes transcriptional silencing in several repeat expansion disorders. In fragile X syndrome (FXS), mutation-length expansion of a CGG STR represses FMR1 via local DNA methylation. Here, we find megabase-scale H3K9me3 domains on autosomes and encompassing FMR1 on the X chromosome in FXS patient-derived iPSCs, iPSC-derived neural progenitors, EBV-transformed lymphoblasts, and brain tissue with mutation-length CGG expansion. H3K9me3 domains connect via inter-chromosomal interactions and demarcate severe misfolding of TADs and loops. They harbor long synaptic genes replicating at the end of S phase, replication-stress-induced double-strand breaks, and STRs prone to stepwise somatic instability. CRISPR engineering of the mutation-length CGG to premutation length reverses H3K9me3 on the X chromosome and multiple autosomes, refolds TADs, and restores gene expression. H3K9me3 domains can also arise in normal-length iPSCs created with perturbations linked to genome instability, suggesting their relevance beyond FXS. Our results reveal Mb-scale heterochromatinization and trans interactions among loci susceptible to instability.

Spinal bulbar muscular atrophy-Kennedy's disease.

A middle age man complained of progressive bilateral hand tremor and occasional muscle cramps. Examination showed tongue muscle atrophy and limb muscle fasciculation with resting and postural tremor in the upper extremities. Deep tendon reflexes were decreased. He had bilateral breast enlargement. Nerve conduction study and Electromyography revealed chronic sensory-motor neuropathy. DNA analysis identified an expanded number of CAG trinucleotide repeats in the androgen receptor gene consistent with a diagnosis of Kennedy's disease (KD). KD, also known as Spinal Bulbar Muscular Atrophy (SBMA), is a rare X-linked recessive lower motor neuron disorder characterized by proximal and bulbar muscle wasting due to degeneration of motor neurons in the brain stem and spinal cord. KD can present with non-specific symptoms initially and may be misdiagnosed as Amyotrophic Lateral Sclerosis or other neurological conditions. Molecular genetic testing enables the diagnosis by identifying the CAG trinucleotide repeat expansion.

Novel intragenic deletion within the FXN gene in a patient with typical phenotype of Friedreich ataxia: may be more prevalent than we think?

BackgroundFriedreich ataxia is the most common inherited ataxia in Europe and is mainly caused by biallelic pathogenic expansions of the GAA trinucleotide repeat in intron 1 of the FXN gene that lead to a decrease in frataxin protein levels. Rarely, affected individuals carry either a large intragenic deletion or whole-gene deletion of FXN on one allele and a full-penetrance expanded GAA repeat on the other allele.Case presentationWe report here a patient that presented the typical clinical features of FRDA and genetic analysis of FXN intron 1 led to the assumption that the patient carried the common biallelic expansion. Subsequently, parental sample testing led to the identification of a novel intragenic deletion involving the 5’UTR upstream region and exons 1 and 2 of the FXN gene by MLPA.ConclusionsWith this case, we want to raise awareness about the potentially higher prevalence of intragenic deletions and underline the essential role of parental sample testing in providing accurate genetic counselling.

Leishmania infection upregulates and engages host macrophage Argonaute 1, and system-wide proteomics reveals Argonaute 1-dependent host response.

Leishmania donovani, an intracellular protozoan parasite, is the causative agent of visceral leishmaniasis, the most severe form of leishmaniasis in humans. It is becoming increasingly clear that several intracellular pathogens target host cell RNA interference (RNAi) pathways to promote their survival. Complexes of Argonaute proteins with small RNAs are core components of the RNAi. In this study, we investigated the potential role of host macrophage Argonautes in Leishmania pathogenesis. Using Western blot analysis of Leishmania donovani-infected macrophages, we show here that Leishmania infection selectively increased the abundance of host Argonaute 1 (Ago1). This increased abundance of Ago1 in infected cells also resulted in higher levels of Ago1 in active Ago-complexes, suggesting the preferred use of Ago1 in RNAi in Leishmania-infected cells. This analysis used a short trinucleotide repeat containing 6 (TNRC6)/glycine-tryptophan repeat protein (GW182) protein-derived peptide fused to Glutathione S-transferase as an affinity matrix to capture mature Ago-small RNAs complexes from the cytosol of non-infected and Leishmania-infected cells. Furthermore, Ago1 silencing significantly reduced intracellular survival of Leishmania, demonstrating that Ago1 is essential for Leishmania pathogenesis. To investigate the role of host Ago1 in Leishmania pathogenesis, a quantitative whole proteome approach was employed, which showed that expression of several previously reported Leishmania pathogenesis-related proteins was dependent on the level of macrophage Ago1. Together, these findings identify Ago1 as the preferred Argonaute of RNAi machinery in infected cells and a novel and essential virulence factor by proxy that promotes Leishmania survival.

Correction of symptoms of Huntington disease by genistein through FOXO3-mediated autophagy stimulation

ABSTRACT Huntington disease (HD) is a neurodegenerative disorder caused by a mutation in the HTT gene. The expansion of CAG triplets leads to the appearance of misfolded HTT (huntingtin) forming aggregates and leading to impairment of neuronal functions. Here we demonstrate that stimulation of macroautophagy/autophagy by genistein (4′,5,7-trihydroxyisoflavone or 5,7-dihydroxy-3-(4-hydroxyphenyl)-4 H-1-benzopyran-4-one) caused a reduction of levels of mutated HTT in brains of HD mice and correction of their behavior as assessed in a battery of cognitive, anxiety and motor tests, even if the compound was administered after symptoms had developed in the animals. Biochemical and immunological parameters were also improved in HD mice. Studies on molecular mechanisms of genistein-mediated stimulation of autophagy in HD cells indicated the involvement of the FOXO3-related pathway. In conclusion, treatment with genistein stimulates the autophagy process in the brains of HD mice, leading to correction of symptoms of HD, suggesting that it might be considered as a potential drug for this disease. Combined with a very recently published report indicating that impaired autophagy may be a major cause of neurodegenerative changes, these results may indicate the way to the development of effective therapeutic approaches for different neurodegenerative diseases by testing compounds (or possibly combinations of compounds) capable of stimulating autophagy and/or unblocking this process. Abbreviations: CNS: central nervous system; EPM: elevated plus-maze; GOT1/ASPAT: glutamic-oxaloacetic transaminase 1, soluble; GPT/ALAT/ALT: glutamic pyruvic transaminase, soluble; HD: Huntington disease; HTT: huntingtin; IL: interleukin; mHTT: mutant huntingtin; NOR: novel object recognition; MWM: Morris water maze; OF: open field; ROS: reactive oxygen species; TNF: tumor necrosis factor

Exonic trinucleotide repeat expansions in ZFHX3 cause spinocerebellar ataxia type 4: A poly-glycine disease

Autosomal-dominant ataxia with sensory and autonomic neuropathy is a highly specific combined phenotype that we described in two Swedish kindreds in 2014; its genetic cause had remained unknown. Here, we report the discovery of exonic GGC trinucleotide repeat expansions, encoding poly-glycine, in zinc finger homeobox 3 (ZFHX3) in these families. The expansions were identified in whole-genome datasets within genomic segments that all affected family members shared. Non-expanded alleles carried one or more interruptions within the repeat. We also found ZFHX3 repeat expansions in three additional families, all from the region of Skåne in southern Sweden. Individuals with expanded repeats developed balance and gait disturbances at 15 to 60 years of age and had sensory neuropathy and slow saccades. Anticipation was observed in all families and correlated with different repeat lengths determined through long-read sequencing in two family members. The most severely affected individuals had marked autonomic dysfunction, with severe orthostatism as the most disabling clinical feature. Neuropathology revealed p62-positive intracytoplasmic and intranuclear inclusions in neurons of the central and enteric nervous system, as well as alpha-synuclein positivity. ZFHX3 is located within the 16q22 locus, to which spinocerebellar ataxia type 4 (SCA4) repeatedly had been mapped; the clinical phenotype in our families corresponded well with the unique phenotype described in SCA4, and the original SCA4 kindred originated from Sweden. ZFHX3 has known functions in neuronal development and differentiation n both the central and peripheral nervous system. Our findings demonstrate that SCA4 is caused by repeat expansions in ZFHX3.

Families with non-Hodgkin lymphoma and plasma cell dyscrasias in their pedigrees.

Although reports of familial clustering of hematologic malignancies have appeared for decades, the cause(s) of this uncommon occurrence is still not completely understood. Most modern investigations, however, support a genetic rather than an environmental exposure as a cause of this observation. Most pedigrees of families with familial hematologic malignancies demonstrate age of onset anticipation, with the disease diagnosed at an earlier age in successive generations. The cause of this phenomenon is clear in some familial neurologic disorders (trinucleotide repeat expansion) but not at all clear in familial hematologic malignancies. In preparation for molecular studies of familial clustering of hematologic malignancies, we have collected pedigrees on 738 families and have previously demonstrated anticipation in those with familial plasma cell myeloma, chronic lymphocytic leukemia, Hodgkin lymphoma or non-Hodgkin lymphoma (NHL). Here we present data on 36 families with both plasma cell myeloma and NHL in their pedigrees and demonstrate strong evidence for anticipation in these families. We encourage all health care personnel to ask patients multiple times about family medical history and carefully take note of family histories from individuals with uncommon illnesses and to refer families with clustering of such illnesses for further investigation.

Ювенильная форма болезни Гентингтона: клинический случай из практики педиатра

Background. Huntington's disease (Hd) is a hereditary neurodegenerative disease with an autosomal dominant type of inheritance and manifested by motor, behavioral and mental disorders. The essence of the mutation is an increase in the trinucleotide repeats of "cytosine – adenine – guanine" (cAG) in the first exon of the HTT gene encoding the huntingtin protein, more than 35. Aim. The purpose of the presentation of this clinical case is to consider the features of the clinical picture and the course of the disease of the juvenile form of Hd. In addition to the rarity of the disease, the dependence of the onset and course of the disease on the number of cAG repeats in the HTT gene, rapid progression and lack of etiopathogenetic treatment, which inevitably leads patients to disability, and later to death, is of interest. Results. The article presents a clinical case of a juvenile form of the disease in an 11-year-old boy with the first symptoms of Hd at the age of 4. Conclusion. The presented clinical case provides an opportunity to verify the difficulty of the juvenile form of Hd and its diagnosis, for which sometimes the only method is genetic analysis.

Histone modifications and FMR role in Fragile X syndrome: A review

Fragile X syndrome is the most common cause of genetically acquired mental disability and one of the most frequent single-gene disorders. FXS serves as an excellent model disorder for studies investigating disturbed molecular mechanisms and synapse function. FXS is an X-linked disorder that affects approximately 1 in 4000 males and females, with females experiencing milder cognitive deficits. It is caused due to expansion of trinucleotide CGG repeat above the normal range (>54 repeats) in the 5’ noncoding region of the fragile x mental retardation 1 (FMR1) gene located in the q27.3 loci of the X chromosome, which results in hypermethylation of CpG islands and eventually to transcriptional silencing of the gene hence suppressing the production of the Fragile X mental retardation protein (FMRP). The lack of FMRP, involved in multiple aspects of mRNA metabolism in the brain causing intellectual disability, autism spectrum disorder, and deregulation of multiple pathways, is thought to be the direct cause of the FXS phenotypes. The purpose of this review is to summarize the basic models used to study the aspects of fragile x syndrome, the relation of FMR1 gene and FMRP with the disease, histone modifications, and various targeted molecular therapy used for cure.

Cost-Effective Cas9-Mediated Targeted Sequencing of Spinocerebellar Ataxia Repeat Expansions

Hereditary repeat diseases are caused by an abnormal expansion of short tandem repeats in the genome. Among them, spinocerebellar ataxia (SCA) is a heterogeneous disease, and currently, 16 responsible repeats are known. Genetic diagnosis is obtained by analyzing the number of repeats through separate testing of each repeat. Although simultaneous detection of candidate repeats using current massively parallel sequencing technologies has been developed to avoid complicated multiple experiments, these methods are generally expensive. This study developed a cost-effective SCA repeat panel [Flongle SCA repeat panel sequencing (FLO-SCAp)] using Cas9-mediated targeted long-read sequencing and the smallest long-read sequencing apparatus, Flongle. This panel enabled the detection of repeat copy number changes, internal repeat sequences, and DNA methylation in seven patients with different repeat expansion diseases. The median (interquartile range) values of coverage and on-target rate were 39.5 (12 to 72) and 11.6% (7.5% to 16.5%), respectively. This approach was validated by comparing repeat copy number changes measured by FLO-SCAp and short-read whole-genome sequencing. A high correlation was observed between FLO-SCAp and short-read whole-genome sequencing when the repeat length was ≤250 bp (r=0.98; P<0.001). Thus, FLO-SCAp represents the most cost-effective method for conducting multiplex testing of repeats and can serve as the first-line diagnostic tool for SCA.

Microsatellite diversity and complexity in the viral genomes of the family Caliciviridae

BackgroundMicrosatellites or simple sequence repeats (SSR) consist of 1–6 nucleotide motifs of DNA or RNA which are ubiquitously present in tandem repeated sequences across genome in viruses: prokaryotes and eukaryotes. They may be localized to both the coding and non-coding regions. SSRs play an important role in replication, gene regulation, transcription, and protein function. The Caliciviridae (CLV) family of viruses have ss-RNA, non-enveloped, icosahedral symmetry 27–35 nm in diameter in size. The size of the genome lies between 6.4 and 8.6 kb. ResultsThe incidence, composition, diversity, complexity, and host range of different microsatellites in 62 representatives of the family of Caliciviridae were systematically analyzed. The full-length genome sequences were assessed from NCBI (https://www.ncbi.nlm.nih.gov), and microsatellites were extracted through MISA software. The average genome size is about 7538 bp ranging from 6273 (CLV61) to 8798 (CLV47) bp. The average GC content of the genomes was ~ 51%. There are a total of 1317 SSRs and 53 cSSRs in the studied genomes. CLV 41 and CLV 49 contain the highest and lowest value of SSRs with 32 and 10 respectively, while CLV16 had maximum cSSR incidence of 4. There were 29 species which do not contain any cSSR. The incidence of mono-, di-, and tri-nucleotide SSRs was 219, 884, and 206, respectively. The most prevalent mono-, di-, and tri-nucleotide repeat motifs were “C” (126 SSRs), AC/CA (240 SSRs), and TGA/ACT (23 SSRs), respectively. Most of the SSRs and cSSRs are biased toward the coding region with a minimum of ~ 90% incident SSRs in the genomes’ coding region. Viruses with similar host are found close to each other on the phylogenetic tree suggesting virus host being one of the driving forces for their evolution. ConclusionsThe Caliciviridae genomes does not conform to any pattern of SSR signature in terms of incidence, composition, and localization. This unique property of SSR plays an important role in viral evolution. Clustering of similar host in the phylogenetic tree is the evidence of the uniqueness of SSR signature.

Evaluation for Parental Polymorphism and Identification of Microsatellites Linked to Drought Tolerance in Rice (Oryza sativa L.)

Aims: To identify the ready-to-use polymorphic microsatellite markers associated with drought tolerance for marker-assisted backcross breeding through a polymorphism survey between Jyothi and Chuvannamodan rice varieties.&#x0D; Place and Duration of Study: Centre for plant biotechnology and molecular biology, Thrissur, Kerala, India, during January to May 2023.&#x0D; Methodology: The genomic DNA of Jyothi and Chuvannamodan was isolated by following CTAB (Cetyltrimethyl Ammonium Bromide) method with modification. Isolated DNA from both varieties was subjected to PCR amplification using 208 Simple Sequence Repeats (SSRs) primer pairs distributed in 12 chromosomes. The amplified PCR products were electrophoresed in 3% agarose gel and separated fragments were visualized and documented in the Gel Documentation System. Different allele sizes produced by the same SSRs primers between two varieties are identified as polymorphic markers. Polymorphism per-cent was calculated, and frequency distribution and chromosome distribution of polymorphic markers were analyzed.&#x0D; Results: A total of 208 SSR primers were surveyed for the parental polymorphism. Out of which, 85 SSR primers exhibited clear polymorphism between Jyothi and Chuvannamodan and the remaining 123 were monomorphic primers. The amplicon size ranged from 83bp (RM430) to 495bp (RM18919) among the different primers. The survey revealed maximum parental polymorphism on chromosome 4 (69.23%), followed by chromosome 5 (64.28%), and minimum polymorphism on chromosome 8 (21.73%). The average per cent of polymorphism between the parents was 40.86%. Among the 85 polymorphic markers, 66 had dinucleotide repeats, 17 had trinucleotide repeats, and 1 had tetranucleotide repeats.&#x0D; Markers with dinucleotide repeats showed higher level of polymorphism. A group of 28 polymorphic markers were identified to be linked with traits including root-related traits, grain yield, leaf rolling and leaf drying under drought conditions.&#x0D; Conclusion: The polymorphic markers identified in the present study form the basis for tagging drought-tolerant QTLs/genes, fine mapping of those genes, and subsequently in marker-assisted breeding programs. The polymorphic markers linked with the QTLs for grain yield under drought can be pyramided in Jyothi through marker-assisted backcross breeding.

Altered anterograde axonal transport of mitochondria in cultured striatal neurons of a knock-in mouse model of Huntington's disease

Huntington's disease (HD) is a progressive genetic neurodegenerative disease caused by an abnormal expansion of a cytosine-adenine-guanine trinucleotide repeat in the huntingtin gene. One pathological feature of HD is neuronal loss in the striatum. Despite many efforts, mechanisms underlying neuronal loss in HD striatum remain elusive. It was suggested that the mutant huntingtin protein interacts mitochondrial proteins and causes mitochondrial dysfunction in striatal neurons. However, whether axonal transport of mitochondria is altered in HD striatal neurons remains controversial. Here, we examined axonal transport of single mitochondria labelled with Mito-DsRed2 in cultured striatal neurons of zQ175 knock-in mice (a knock-in mouse model of HD). We observed decreased anterograde axonal transport of proximal mitochondria in HD striatal neurons compared with wild-type (WT) striatal neurons. Decreased anterograde transport in HD striatal neurons was prevented by overexpressing mitochondrial Rho GTPase 1 (Miro1). Our results offer a new insight into mechanisms underlying neuronal loss in the striatum in HD.