Journal of Genetics最新文献

After the arrival of the CRISPR/Cas9 genome editing technology, genetic engineering of model organisms has become much faster and more efficient. The development of genetically modified mouse models is also facilitated by the application of various CRISPR methodologies. Although the very first studies utilized pronuclear injection (PNI) of Cas9 mRNA and sgRNAs into the zygote stage embryos to create knockout and knockin mutations, the repertoire of techniques and collection of reagents for CRISPR editing has rapidly expanded. This presents researchers in the field with a versatility of choices for genetic engineering. However, there are not many comparative studies that analysed the efficacy of gene editing when Cas9 and sgRNA/ssDNA oligos were transferred to the embryos by different methodologies. Here, we aimed to compare two different methods, electroporation and PNI. One of the recent developments gaining wide use in mouse model research is the application of electroporation for the introduction of Cas9/sgRNA ribonucleoprotein complexes into zygote stage embryos. Here, we have used this technique to generate albino coat-coloured C57BL/6J mice by targeted inactivation of the mouse tyrosinase gene through indel or knockin mutations. We have also applied the PNI protocol with the same set of reagents, to compare the efficiency of the two techniques in generation of indel and knockin mutations. Although PNI results in signifi- cantly higher efficiency for knockin mutations, it requires specialized equipment setup and advanced training in embryo micromanipulation and microinjection. Therefore, for the generation of simple gene knockouts by indel mutations, electroporation can be used.

Red tilapia has gained increasing popularity worldwide in the commercial aquaculture production due to its rapid growth and delightful taste. However, the occurrence of skin colour variation poses a significant challenge to the advancement of commercial culture. Furthermore, the molecular regulatory mechanism and genetic basis for the distinct skin colouration in red tilapia remain undisclosed. In this study, a comprehensive transcriptome analysis was conducted on red tilapia with different skin colour by integrating PacBio Iso-seq technology with Illumina short-read sequencing methods. A total of 41.38 Gb of clean data was generated, resulting in the acquisition of 30,970 transcripts. Among them, 10,829 transcripts were successfully annotated in at least one public database. In addition, 10,827 coding sequences, 452 transcription factors, and 781 lncRNAs were identified in new transcripts. Furthermore, we performed RNA-seq analysis to identify skin colour-associated genes in red tilapia with three colour spots (white spots, W; black spots, B; red spots, R). The results revealed the identification of 278 differentially expressed genes (DEGs) between the comparison groups, which included B vs R, B vs W, and W vs R. Among them, some known genes were found to be involved in regulating the skin pigment synthesis, including PMEL, Wnt-4, melanoregulin and ALK in red tilapia with different skin colour. In addition, some pathways, including melanogenesis (ko04916), ECMreceptor interaction (ko04512), Hedgehog signaling pathway (ko04340) and steroid hormone biosynthesis (ko00140), were associated with the skin pigment synthesis in red tilapia. Furthermore, the quantitative real-time PCR analysis confirmed a moderate correlation (coefficient of 0.68) between the results obtained from the qPCR and RNA-seq methodologies. In summary, our findings will significantly contribute to the enhanced comprehension of the molecular regulatory mechanisms underlying the variation in skin colour observed in red tilapia.

Congenital amegakaryocytic thrombocytopenia (CAMT) is a rare inherited bone marrow failure syndrome, which is characterized by a severe thrombocytopenia at birth without predictive stigmata and by a risk for progression into aplastic anaemia and myeloid malignancy. While CAMT primarily arises from mutations in the MPL gene, recent discoveries have linked biallelic THPO mutations to some CAMT cases. In addition, loss of function monoallelic mutations in this gene have been identified as causing benign autosomal dominant thrombocytopenia. In this study, we report a case of CAMT linked to a homozygous mutation in the promoter region of THPO (c.-324C>T, NM_000460.4). computational analysis indicates that this mutation suppresses the binding of some essential transcription factors to the THPO promoter. Family segregation analysis shows a significant reduction in platelet counts among carriers of the mutation. Our patient received allogeneic haematopoietic stem cell transplantation (HSCT) from her HLA-matched sister (MSD), who carries the mutation. After allogeneic HSCT, the patient showed 100% full donor chimerism, but 1 year after HSCT, despite full donor chimerism, the patient did not complete recover from platelet count, and she has received romiplostim several times. Understanding the MPL-THPO pathway is vital for managing CAMT, emphasizing the importance of identifying and assessing patients' mutations for tailored treatment.

RNA modifications play a crucial role in regulating gene expression, splicing, decoding, translation, and degradation. Among the most studied modifications are adenosine-to-inosine (A-to-I) RNA editing and N⁶-methyladenosine (m⁶A). While m⁶A is reversible, enabling dynamic regulation of gene expression; A-to-I editing is irreversible, leading to permanent changes in RNA sequences. This raises a thought-provoking question: why do different RNA modifications have such distinct reversibility? Is this feature random or governed by evolutionary constraints? We interrogate the mechanistic (proximate cause) and evolutionary (ultimate cause) reasons for how and why inosine cannot be reversed by adding an amino group but m⁶A remains reversible, despite both modifications have the option to be degraded along with host RNAs. We also discuss whether inosine can have reader proteins like m⁶A to exert dynamic and regulatory control. Finally, we explore the evolutionary significance of these differences and their implications for future research in RNA modifications.

The family Syngnathidae includes seahorses, sea dragons, and pipefishes. We sequenced the complete mitochondrial DNA (mtDNA) genome of the belly pipefish, Hippichthys heptagonus Bleeker, 1849. The genome is 16,646-bp long, and includes the standard complement for bony fishes of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region, in the same order and strand distribution as other syngnathids. Maximum likelihood and Bayesian analysis of 58 complete mtDNA protein-coding sequences from 18 genera of Syngnathidae supports the inclusion of H. heptagonus with Phoxocampus in the tribe Leptonotini of the Syngnathinae, monophyly of the Nerophinae and Syngnathinae, and within the latter monophyly of the tribes Haliichthytini, Hippocampini, Leptonotini, Solegnathini, and Syngnathini. This is the first comprehensive mtDNA genome-based phylogenetic analysis of the evolutionary and systematic relationships within Syngnathidae.

Nonalcoholic fatty liver disease (NAFLD) occurs in a significant number of nonobese individuals, especially in Asian populations. Many genetic loci are associated with NAFLD. However, no exome-wide analysis of polymorphism data to identify asso- ciations with NAFLD is available for nonobese individuals from Asia. We have sought to fill this gap. With informed consent, we selected individuals from a defined population in India and assessed their liver fat-graded per international recommendations, and their demo- graphic and anthropometric data were collected. A set of 153 individuals were identified with high-grade liver fat. For each of these fatty- liver individuals (cases), two controls of the same sex with no or little liver fat were selected, the age and BMI of each control not exceeding 5 years and 5 kg/m², respectively, of the case. Whole-genome sequencing was done for each individual. For association analysis, we selected only nonsynonymous germline single-nucleotide polymorphisms (SNPs) in coding regions located on genes expressed in the liver. We removed SNPs and individuals with compromised quality and informativeness. We carried out association analysis in this high-quality data set and validated the results using a novel bootstrap procedure. On the basis of this high-stringency association analysis using exome- wideSNP data on 438 cases and controls, we identified 30 significant SNPs on 24 genes. Of these, 21 SNPs from 17 genes are hitherto unreported. We have determined that most of the significant SNPs are functionally relevant. Pathway analysis revealed that the genes on which these SNPs are located are involved in liver dysfunction.

Duchenne muscular dystrophy (DMD) is a severe genetic disorder characterized by progressive muscle degeneration and loss of function due to the absence of dystrophin. In this study, we utilized a zebrafish model with a dmd gene knockout to explore the therapeutic potential of JAG1 overexpression in mitigating DMD-associated muscle dysfunction. Dystrophic zebrafish larvae displayed significant impairments in muscle function, evidenced by reduced swimming abilities, decreased birefringence, and disrupted β-dystroglycan localization, indicative of structural degeneration. Overexpression of JAG1, achieved via plasmid injection, partially restored muscle function, as reflected by improvements in stride length and total swimming distance. However, the structural integrity of slow oxidative muscle fibers remained largely unaffected, with a functional decline from 4 to 8 days post-fertilization (dpf) being more indicative of disease progression than structural changes. These findings suggest that the rescue effect of JAG1 overexpression may not be due to the preservation of slow oxidative fibers but rather through a mechanism that reduces susceptibility to contraction-induced injury. Notably, our study faced limitations related to the control of JAG1 expression levels and tissue specificity. Our results highlight the complexity of DMD pathology, where muscle structure and function do not always correlate, emphasizing the need for refined functional assays to better assess therapeutic outcomes. By incorporating functional recovery assessments at 8-10 dpf, zebrafish models can serve as more predictive preclinical tools, potentially enhancing the translational relevance of findings and reducing risks for patients in clinical trials. This study investigates how increasing the levels of a protein called JAG1 can help improve muscle function in a zebrafish model of DMD. By showing partial recovery of muscle activity, the findings suggest new therapeutic strategies that could potentially slow disease progression and improve patient outcomes.

The neurite extension and migration factor (NEXMIF) encephalopathy is an X-linked disorder that is characterized by intellectual disability, behavioural abnormalities and seizures. The majority of pathogenic variants are de novo. Here, we report two siblings with NEXMIF encephalopathy exhibiting variable clinical presentations. The younger female sibling (proband) presented predominantly with refractory myoclonic and atonic epilepsy and milder intellectual disability, and the male sibling exhibited severe intellectual disability, and significant behavioural abnormalities without seizures. Exome sequencing in the proband revealed a novel heterozygous stop gain variant c.3206C>A p.(Ser1069Ter) in the NEXMIF gene, which was validated by Sanger sequencing. Targeted sequencing in the male sibling revealed the hemizygous nature of the variant. The asymptomatic mother was found to carry the wild-type allele, suggesting the possibility of gonadal mosaicism. This report represents the second documented case of NEXMIF encephalopathy associated with gonadal mosaicism.

The father of sociobiology, Edward Wilson, described him as 'the most unpleasant human being I had ever met'. He was the first living laureate to auction his Nobel Prize. He said that because of some of his views and beliefs, he had become an 'unperson'. 'No one really wants to admit I exist.' 'Because I was an ''unperson'', I was fired from the boards of companies, so I have no income, apart from my academic income.' The 'unperson' is James Dewey Watson. He won the Nobel Prize at the age of 34, for the work he published in 1953, when he was only 25. The 1953 article in Nature, co-authored with Francis Crick, concluded with the famous understatement: 'It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.' Watson died on 6 November 2025 at the age of 97.

Genomic biomarkers are essential aspects of personalized medicine. They offer an opportunity for early detection and appropriate intervention, thereby leading to improved patient outcomes and cost-effective treatment. However, different populations have varied genetic landscapes, and thus, may have unique biomarkers. Here we study the prevalence of mutation-specific oncogenic biomarkers in the Indian population and analyse their presence across disease cohorts. We annotate the IndiGen data obtained from whole genome sequencing of 1029 self-declared healthy Indian individuals with biomarker information obtained from the OncoKB knowledgebase, a repository of evidence-based information about somatic biomarkers and structural alterations in patient tumours. We further establish the utility of this study by analysing these biomarkers across GUaRDIAN, a nationwide multi-cohort database, and MUSTARD, a repository of mutation-specific therapies in cancer. In this study, we discovered 34 biomarker variants of therapeutic actionability across 16 genes linked to 23 unique drugs or drug combinations in 23 unique types of cancer. In all, we have found 52 biomarker variants with 172 different biomarker types including therapeutic, resistance, diagnostic, and prognostic. We establish that nearly 7% of the population were found to be carriers of at least one of the four evidence-based biomarkers. Finally, we also establish the prevalence of 42 biomarker variants across 23 genes in both AD and AR modes of inheritance. We have calculated the prevalence of cancer biomarkers of therapeutic, diagnostic and prognostic value in the globally underrepresented Indian population. The known biomarker landscape so established can be used for clinical advantage to improve patient care. Cancers without corresponding biomarker matches can also be further studied to discover biomarkers unique to Indian populations.