Genes

Environmental and dietary factors can exert multigenerational effects on health and development. In this study, we investigated whether early-life metabolic challenge affects the germline genome and epigenome across three generations. Using a murine model of early life obesity via litter size reduction (overnutrition group, ON) and a control group (CT), we followed the paternal lineage focusing on germline genomic and methylation changes employing Genotyping-by-Sequencing (GBS) coupled with methyl-immunoprecipitation (GBS-MeDIP). We found that unrelated ON families clustered together based on identified Single-Nucleotide Polymorphism (SNP), suggesting that the treatment may have genomic impact. Copy number variations (CNVs) events were identified in ON individuals, being enriched in Long Interspersed Nuclear Elements (LINEs) and Long Terminal Repeats (LTRs). While Principal Component Analysis (PCA) of the methylome showed no clear treatment effect, pathway enrichment and regional analyses revealed methylation changes associated with transposable elements and developmental genes. Notably, the ON group exhibited a disruption in the methylation of Repetitive Elements (RE), which was significant in the same type of RE that were also enriched in the observed CNVs. The ON also showed reduced emergence of novel SNPs in offspring compared to the CT group. These findings suggest that multigenerational metabolic challenge can constrain genetic variability and induce genome instability, potentially mediated by transposable element activity rather than widespread changes in DNA methylation. This work highlights the importance of studying both genome and epigenome dynamics under realistic, multigenerational exposure scenarios and suggests that early metabolic challenges can have long-lasting impacts on genomic architecture and evolutionary potential.

A population-specific missense variant, rs373863828 (G > A, p.Arg457Gln), has been identified in Pacific Islanders and is associated with increased body mass index and lower odds of type 2 diabetes. However, the mechanism underlying these associations is unknown. The variant is located in exon 5 of CREBRF, a gene which is rapidly upregulated in response to nutrient deprivation. This study aimed to assess the effect of rs373863828 on gene expression in adipose tissue from Samoan adults from the Soifua Manuia (''Good Health'') study. Needle subcutaneous adipose (upper buttock) biopsies were obtained in Apia, Samoa, from fasting Samoans without diabetes. RNA isolated from adipose tissue (n=91, 65.9% female) was subjected to bulk paired-end mRNA-sequencing (2x150 base pair). Differential gene expression among the three rs373863828 genotypes (GG, AG, AA) was assessed using a likelihood-ratio test implemented in DESeq2, and overrepresentation analysis for significant differentially expressed genes (DEGs) (padj < 0.1) was performed with clusterProfiler and oRG.DB. Bulk expression was deconvoluted to determine the cell type composition of the adipose tissue. Twenty-two DEGs were associated with rs373863828 genotype including CBX7 (padj=0.026 ) and SELENOM (padj= 0.004), both of which have roles in adipogenesis and metabolism. A single expression profile comprising 13 of the 22 DEGs corresponding to CREBRF genotype was identified, and overrepresentation analysis supported this finding, with terms such as ''keratinocyte differentiation'' and ''skin development'' enriched among significant DEGs. However, PERMANOVA of adipose cell type proportions showed no difference (p > 0.05) among the three genotypes. rs373863828 genotype was associated with expression of 22 genes in whole subcutaneous adipose tissue of this sample of fasting Samoan adults without diabetes. Future work should assess cell- and tissue-specific rs373863828 genotype effects using a combination of single-cell approaches and human cell models with perturbations associated with nutritional stress.

Complex rearrangements are one of the rarest types of structural variants (SVs) and can be divided into two categories: complex chromosomal rearrangements (CCRs) and complex genomic rearrangements (CGRs). CCRs include structural rearrangements that present at least three breakpoints and show exchange of genetic material between more than two chromosomes and CGRs are rearrangements that present more than one junction and/or more than one SV in cis. They are usually formed by one of the chromoanagenesis mechanisms, where a massive disruptive cellular event leads to multiple structural rearrangements. Classical cytogenomic techniques have been commonly applied for their characterization, but methodologies that involve longer DNA molecules, namely optical genome mapping (OGM) and long-read genome sequencing (lrGS), present a considerably higher SV detection resolution, revealing more details about the rearrangements, including precise breakpoint location. Here, we describe six patients with complex rearrangements investigated through a combination of different techniques: karyotyping, chromosomal microarray, and OGM were performed to characterize the rearrangements. Subsequently, lrGS was used to further resolve the alterations, refine their breakpoints' location, and sequence their junction points. Three patients presented CCRs involving three, four, and six chromosomes, while three exhibited CGRs involving one different chromosome each, providing a variety of complex SVs to show the importance of each technique and their combination in rearrangement resolution. In total, the complex rearrangements presented 127 breakpoints, 66 junction points and involved 14 of the 24 chromosomes. Higher-resolution techniques revealed additional complexity in all cases. Despite the advances provided by OGM and lrGS, conventional karyotyping remained indispensable for complete rearrangement resolution. In two patients, the findings supported a novel mechanism combining features of the different chromoanagenesis processes. Furthermore, evidence of inherited alterations was identified, and the comprehensive characterization of the rearrangements enabled more accurate genotype-phenotype correlations. Our findings indicate that an integrated approach combining karyotyping, OGM, and lrGS can completely resolve SVs, including complex rearrangements.

Trisomy 21 (T21) is the most common genetic cause of intellectual disability, yet the molecular mechanisms underlying maternal meiosis I errors--responsible for ~70% of free T21 cases--remain poorly understood. In this preliminary study, we used long-read sequencing and genome assembly to investigate the DNA sequence and epigenetic features of chromosome 21 (chr21) centromeres in a family with recurrent free T21 due to maternal meiosis I errors. The mother, who had two affected and three unaffected children, showed no mosaicism or structural rearrangements. One of her two chr21 centromeres lacked a pronounced centromere dip region (CDR), displaying instead a diffuse hypomethylation pattern (dCDR) with much higher methylated CpG levels (55%) compared to its homologue (36%). This dCDR was transmitted to an unaffected child and the affected proband analyzed, suggesting it was present in one of the maternal chr21 since she was at least 32 years of age. Chr21 dCDRs were not observed in seven young mothers with children with T21 or previously described in the literature in 108 population haplotypes. We hypothesize that dCDRs may weaken kinetochore function, increasing nondisjunction risk, and propose two models linking such epigenetic variation to maternal age-related T21 risk. These findings highlight the value of complete centromere characterization in families with children with T21 and suggest centromere methylation status of chr21 as a potential T21 risk factor for future investigation.

Background: Short-read whole-genome sequencing (sWGS) has limitations in characterizing tandem-repeat expansions and variants in highly homologous or pseudogene-associated regions. Long-read sequencing can address some of these challenges but often benefits from high-molecular-weight DNA. TruPath Genome incorporates spatial proximity information into a short-read sequencing framework. This study evaluated its performance in characterizing selected complex genomic variants using archived clinical DNA specimens. Methods: Ten archived peripheral blood DNA specimens were analyzed, comprising seven cases with disease-associated short tandem repeat (STR) expansions and three cases involving homologous or pseudogene-associated loci (STRC, SMN1/SMN2, and CYP21A2). TruPath results were compared with previously available orthogonal assay results, including triplet repeat-primed PCR (TP-PCR), multiplex ligation-dependent probe amplification (MLPA), quantitative PCR (qPCR), and sWGS-based ExpansionHunter analysis. Results: TruPath generated repeat-length estimates across the evaluated STR loci. For two FMR1 full-mutation alleles, TruPath estimated 284 and 295 CGG repeats, respectively, while TP-PCR reported expansions exceeding 200 repeats. In a DMPK case, TruPath estimated an expanded allele of 1,203 CTG repeats, compared with a TP-PCR result exceeding 100 repeats. At the STRC and SMN1/SMN2 loci, TruPath findings were consistent with available orthogonal results for deletion and copy-number status. At the CYP21A2 locus, TruPath reconstructed the RCCX gene arrangement and assigned the I2G variant and a chimeric allele to different haplotypes. Conclusions: In this small series of archived clinical DNA specimens, TruPath Genome enabled characterization of selected repeat expansions and homologous or pseudogene-associated variants. The findings support further evaluation of proximity-mapped sequencing as a complementary approach for complex genomic regions, particularly when conventional short-read sequencing is limited.

Individuals carrying a G4C2 repeat expansion in C9orf72 can develop amyotrophic lateral sclerosis (ALS) and/or frontotemporal dementia (FTD), at various and unpredictable ages. The contribution of the expansion to this extreme clinical variability remained a matter of debate. In this work, we validated the use of optical genome mapping to efficiently size this expansion from blood and applied this method to a cohort of 54 repeat expansion carriers including patients with FTD (n = 23), ALS (n = 22) and presymptomatic individuals (n = 9). Despite the high variability in expansion profiles, distinct groups can be inferred. Although consensus repeat profiles were similar between FTD and ALS patients, relationships between repeat number, indexes of repeat instability, and the age at sampling differed between clinical conditions. An age at sampling-dependent increase of repeat instability in blood was observed in presymptomatic carriers and FTD patients (p = 0.01 and p = 0.04 respectively), in contrast to patients with ALS (p = 0.9). The proportion of shorter repeats ([500-1500 repeats]) increased with the age at sampling in ALS patients but decreased in presymptomatic and FTD cohorts, while the proportion of larger repeats (>2000 G4C2), in particular those exceeding 4000 repeats, increased along with the age at sampling in presymptomatic carriers and FTD cases (p <1.10-e4 and p = 0.006 respectively) conversely to patients with ALS (p = 0.98). In conclusion, this work strongly supports different dynamics of repeat instability of the C9orf72 pathogenic expansion in blood linked to the clinical evolution. These findings provide new insights into the relationship between expansion profiles and clinical variability.

CBX1-related syndrome is characterized by developmental delay, hypotonia, autistic features, and mild dysmorphic features. This syndrome is caused by heterozygous missense variants in CBX1, which encodes heterochromatin protein 1 beta (HP1{beta}). These variants are situated within the chromodomain of HP1{beta}, a critical region that mediates the interaction between HP1{beta} and trimethylated H3K9. While a prior study identified three individuals with pathogenic CBX1 variants, the variant and clinical spectrum of CBX1-related syndrome remains largely unknown. Here we report three patients with novel de novo heterozygous variants in CBX1. Patients with CBX1 p.(Leu40Pro) and p.(Cys60Arg) manifested with global developmental delay, while the patient with CBX1 p.(Cys60Gly) primarily exhibited speech delay without concurrent motor developmental delay. All variants reside within chromodomain of the HP1{beta} protein. Interestingly, in vitro cellular assays revealed that CBX1 p.(Cys60Gly) variant showed an intermediate cellular phenotype between the wild type and the CBX1 p.(Leu40Pro) and p.(Cys60Arg) variants, suggesting a possible genotype-phenotype correlation. This report provides further evidence that missense variants within the chromodomain of HP1{beta} cause a syndromic neurodevelopmental disorder, CBX1-related syndrome.

ABSTRACT Objective: Skeletal muscle growth rate differs substantially among diverse pig breeds. In the present study, RNA-seq was performed to identify differentially expressed genes (DEGs) across pig breeds with distinct growth rates. CCND2 showed obvious differential expression among pig breeds. Although CCND2 is essential for cell cycle control, its biological function in skeletal muscle differentiation has rarely been reported. This work aims to identify DEGs in pig breeds with different growth rates and explore CCND2 role in porcine skeletal muscle development. Methods: RNA-seq was performed to identify differentially expressed genes (DEGs) across pig breeds with distinct growth rates. Weighted gene co-expression network analysis (WGCNA) was used to identify gene modules potentially associated with skeletal muscle growth and development. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis was performed to validate the role of CCND2 in skeletal muscle differentiation. Results We identified 5,416, 4,846, and 2,777 DEGs in the Duroc pig (DU) vs. Jiangquan black pig (JQ), DU vs. Laiwu pigs (LW), and JQ vs. LW comparison groups, respectively. WGCNA identified two gene modules (lightgreen and darkmagenta) potentially associated with skeletal muscle growth and development. CCND2 exhibited differential expression in comparisons between DU vs JQ and DU vs LW, with higher expression observed in Duroc pigs. qRT-PCR analysis revealed that overexpression of CCND2 at day 6 (D6) of cell differentiation significantly increased the expression levels of CCND2 gene and markers of myogenic differentiation (p < 0.05). Conversely, knockdown of CCND2 significantly decreased the expression levels of CCND2 gene and myogenic differentiation markers (p < 0.05). Conclusions This study identified breed-specific DEGs and key gene modules in porcine skeletal muscle and verified that CCND2 promotes myogenic differentiation. These findings provide a genetic theoretical basis for further investigations into skeletal muscle growth and development. Keywords pig, skeletal muscle, transcriptome, WGCNA, CCND2

Background: Short-rib polydactyly syndrome type IV (Beemer-Langer syndrome) is a lethal skeletal ciliopathy that can result from biallelic pathogenic variants in KIAA0586 (TALPID3). Earlier clinical observations suggested an unusually high occurrence of this phenotype in Romani families from the Carpathian Basin. Methods: Whole-exome sequencing was performed in affected individuals from five independent families, and the frequency of KIAA0586 c.1815G>A was assessed in a Hungarian Romani genetic database of 500 individuals. Results: The affected individuals were homozygous for c.1815G>A, a splice-disrupting variant previously shown to cause exon 14 skipping. Four families self-identified as Roma from Hungary and one affected individual was from Turkey. Six heterozygous carriers were identified among 500 individuals in the Hungarian Romani cohort, corresponding to an allele frequency of 0.6%. This was markedly higher than the frequencies cited from ALFA (0.01%) and gnomAD (0.0014%). The Hungarian-Romani and Turkish affected individuals also shared genotypes at informative markers flanking the variant, supporting a shared ancestral haplotype. Conclusions: These observations strengthen evidence that KIAA0586 c.1815G>A is a founder allele enriched in at least some Romani populations. The data support consideration of ancestry-informed carrier testing in appropriately counseled families. Historical admixture may explain the occurrence of the same haplotype in a Turkish case, but this remains a hypothesis requiring broader population-genomic confirmation.

Background: More than five years after the COVID-19 outbreak, the infection by the SARS-CoV-2 virus should still be considered as a global threat with highly heterogeneous clinical outcomes from asymptomatic to fatal depending on existing genetic and phenotypic inter-individual and inter-population variability. Our objective is to identify risk loci associated with COVID-19 in an admixed Latin American population. Methods: We performed a genome-wide association study in the framework of the Chilean C19-GenoNet team, analyzing a cohort of 3,417 individuals recruited from the northernmost to the southernmost regions of the country, who presented variations in the severity of their COVID-19 clinical manifestations. Results: Our investigation replicated the extensively reported association of several variants at the 3p21.31 locus with COVID-19 severity and found a suggestive association for a variant within the FOXP4 gene at 6p21.1 with COVID-19 hospitalization. Both associations appear to be shared with other populations. Importantly, our study identified three previously unreported loci associated with COVID-19 severity or hospitalization at 7q21.11, 16p13.12 and 6p25.3, and one additional locus at 4p13 associated with SARS-CoV-2 positivity, a proxy for infection susceptibility. Conclusions: these new risk loci may represent population-specific effects in Chilean and, potentially, other Latin American admixed groups. Our study highlights the importance of expanding efforts to study underrepresented and genetically different populations, which may provide new clues on the genetic basis of human diseases and may help to anticipate global responses to emerging viral infections and future pandemics.

Hurthle cell carcinoma (HCC) is an aggressive form of thyroid cancer. While mitochondrial DNA mutations and chromosomal losses have been identified in HCC, isoform switching, and its functional consequences remain uncharacterized. This study reanalyzed NCBI GEO dataset GSE228870 (n = 32), using Salmon and IsoformSwitchAnalyzeR() to identify isoform switching. The analysis resulted in 371 switches across 335 genes showing functional consequences including loss of protein domains, shorter open reading frames (ORFs), loss of signal peptides and novel sub-cellular localizations. Most significant isoform switches (q-value < 0.05, |dIF| > 0.1) were observed in LAMA2, LSP1, MAD2L2, FBLN2 and CXCL12, implicating extracellular matrix dysregulation, DNA damage response, immune signaling and cytoskeleton regulation. These genes are expressed in normal thyroid (median TPM 20.69, 11.66, 14.79, 134.1 & 80.76). However, specific isoforms of LAMA2 and MAD2L2 are not expressed in normal thyroid, explaining tumor-specific expression in HCC. Alternative transcription termination site (ATTS) gain was significant, suggesting altered 3 end in HCC transcripts. TCGA SpliceSeq showed LSP1, FBLN2 and CXCL12 undergo alternative promoter (LSP1 exon1 PSI=94.5%, FBLN2 exon2 PSI=99.0%) and alternative termination (CXCL12 exon3.3 PSI=53.9%) in thyroid cancer, suggesting ATTS and alternative transcription start site (ATSS) as shared splicing dysregulation mechanisms. This is the first systematic characterization of isoform-level dysregulation in HCC.

Non-coding variants altering mRNA splicing are increasingly recognized as important cause of Mendelian disorders. Deep intronic variants (DIV) that activate cryptic exons (CEs) cause ~20% inherited retinal diseases (IRD) cases, yet it remains challenging to predict intronic variant pathogenicity accurately, thus we used a high throughput splicing assay (HTSA) to measure the effects of rare deep intronic variants in recessive IRDs with one confirmed pathogenic variant. 640 very rare deep intronic variants were chosen in trans-position with known mutation from 76 patients. We tested them with HTSA, which consists of a split-GFP minigene, separated by an SMN1 gene intron into which the 270bp sequences flanking the DIVs were cloned. The plasmid library was transfected into 293HEK cells, and 48 hours later total RNA was extracted from the transfected cells. RNA transcripts produced by HTSA minigene were amplified by RT-PCR and sequenced. The intron sequences spliced between the two GFP exons were identified and quantified. 98 variants activated CE >100 times more in altered oligo compared to reference oligo and were classified as pathogenic in this experimental setting, validated in longer context, 26 variants were classified as VUS. Interestingly, only 6 from 90 variants (6,6%) were predicted to be pathogenic by in silico algorithms (Splice AI) which leaves room for significant improvement of prediction algorithms. The results of this experiment confirmed diagnosis for 50 of 78 patients (64%). So, 19,4% of deep intronic variants were shown to cause CE activation. This can lead to conclusion that significant portion of undiagnosed patients with recessive IRDs carry pathogenic intronic mutation which causes the disease.

Grecia Salentina (GS) is the label assigned to a geographic area in Southern Italy where a Greek dialect has historically been spoken. The origins of this Greek-speaking community, whether dating from ancient or Medieval settlement, are a controversial and essentially unsolved issue. To evaluate which historical-linguistic scenario is best supported on genomic grounds, we used whole genome sequencing of 27 GS natives and 21 controls, embedding them in a 799 modern samples dataset in which Greece and Anatolia were evenly represented, an uncommon feature in the genomic literature on the area. We considered different aspects of the genetic structuring, at different spatial and temporal scales. Analyses also included 4021 ancient samples from the literature. All analyses pointed to the same conclusion: the GS genomic profile displays the same characteristic features of the rest of Southern Italy, with no definite evidence for a single source population from outside Italy. Correspondingly, we detected strong genetic connectivity among GS municipalities and between GS and the rest of Italy. Only a subset of our analyses suggested a slightly increased affinity of GS with Greece, or with the Anatolian peninsula. These results indicate that GS has been all but a genetically closed community, and that the Greek language did not act as a barrier to gene flow. By endorsing a ''transient mobility model'' we support the most recent linguistic hypothesis: the prolonged resilience of the Greek language in GS, maintained in situ and periodically rejuvenated through recurrent external inputs from the Greek and Byzantine worlds.

Purpose A significant proportion of cases with rare inherited retinal disease (IRD) remain genetically unresolved following short-read whole genome sequencing (WGS). This study aimed to increase the diagnostic yield of two cohorts in a research setting. One cohort was previously screened by short-read WGS (n=120 cases), while the second cohort (n=28 cases) was not included in any previous short-read WGS studies. In contrast to the larger cohort, these cases only underwent either exome sequencing (ES) or single-molecule molecular inversion probe (smMIPs) sequencing as pre-screening in earlier studies. For all cases, we performed a stepwise, case by case reanalysis in which short-read WGS was generated (n=28 cases) and (re)analyzed short-read WGS data using an optimized approach. For a subset of cases (n=20) that remained unresolved, this was followed by long read WGS. Together, these steps aimed to improve the diagnostic yield in these cohorts. Methods Short-read WGS data of 148 IRD-cases were (re)analyzed using updated allele frequency databases, new variant caller and variant predictor tools, as well as updated and extended gene-panels to identify causal single nucleotide variants (SNVs) and structural variants (SVs). For 20 genetically unresolved cases with sufficient high-quality DNA available, long-read WGS was performed. Results The (re)analysis of short-read WGS data in the 120 previously WGS-screened unresolved cases resulted in a diagnostic yield of 15% (18/120). For the 28 individuals without prior WGS, performing WGS analysis within this study provided an additional yield of 32% (9/28). Furthermore, long-read WGS contributed two genetic diagnoses among the 20 long-read WGS-sequenced probands. Amongst other reasons, new genetic diagnoses were attributed to pathogenic variants in genes newly associated with IRDs and in genes that were not included in the gene panels applied in previous WGS studies. The Mobile Element Locator Tool facilitated the identification of two pathogenic Alu insertions in short-read WGS. Long-read WGS identified two additional pathogenic variants. Conclusion These results support periodic reanalysis of existing short-read WGS data as a key component of IRD genetic diagnostics, with selective long-read WGS representing a valuable additional approach for unresolved cases. Together, these complementary strategies offer a practical framework for improving molecular diagnosis and narrowing the remaining diagnostic gap in IRDs.

Background: Uveal melanoma (UM) and cutaneous melanoma (CM) both originate from the same cell line. This proposes the possibility of a shared mechanism between entities, requiring explicit investigation. Methods: Data from GWAS Catalog and DisGeNET were used to identify shared variation-disease associations (VDAs) between UM and CM. The results were validated using the Ensembl database. In the next step, the STRING database was used to identify the protein-protein interaction. Results: Subsequently, 109 unique VDAs were identified for UM and 880 for CM. However, only 2 VDAs were found to be shared among UM and CM in different ethnic groups. These shared VDAs were rs12203592 of the IRF4 gene, rs12913832 of the HECT and RLD domain-containing E3 ubiquitin protein ligase 2 (HERC2) gene. Notably, PPI network assessment through STRING showcased that OCA2 and IRF4 directly interacted with HERC2. Conclusion: While HERC2 acts as a poor prognostic factor in uveal melanoma, IRF4 status is a key prognostic indicator in both UM and CM. Identifying IRF4 allele contributions enables a better understanding of melanoma pathogenesis and fosters the development of disease-specific approaches.

Gene model for the ortholog of Insulin-like peptide 3 (Ilp3) in the D. pseudoobscura Apr. 2013 (BCM-HGSC Dpse_3.0/DpseGB3) Genome Assembly (GenBank Accession: GCA_000001765.2) of Drosophila pseudoobscura. This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

The C9orf72 hexanucleotide repeat expansion (HRE) is the most common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). It follows autosomal dominant inheritance in families, however, a high proportion of cases are sporadic, raising the possibility of parental premutation. We have demonstrated that intermediate-length alleles (IAs) with >18 repeats (allele frequency ~1%) belong to the same pool of haplotypes as the HRE, suggesting shared ancestry. Here, we tested whether alleles with >18 repeats expand in parental transmission. We used two repeat-primed PCR methods to analyze allele lengths in 539 genetically unselected parent-offspring pairs and in 152 pairs known to carry the SNP (rs139185008*C) that tags >18 repeat IAs and the HRE in Finland. We discovered intergenerational repeat length changes only in >20 repeat alleles. A significant (P = 0.0059) sex bias in 6-40 repeat alleles was noted using a logistic regression model. In this allele range, 12 out of 16 expansions were paternally inherited and 6 out of 7 contractions were maternally inherited. The expansion rate of 20-40 repeat alleles was 34 % in paternal and 11 % in maternal transmissions. In the 20-40 repeat range, most intergenerational expansions were 1-4 repeats in size (15/16), but one larger jump, a paternal expansion from 27 to 73 repeats, was observed. These results demonstrate that alleles with >20 repeats have an increased likelihood of instability, that a paternal expansion bias is observed in alleles with 20-40 repeats, and that expansion events are predominantly 1-4 repeats in size.

Gene model for the ortholog of Density regulated protein (DENR) in the Apr. 2013 (BCM-HGSC Dpse_3.0/DpseGB3) Genome Assembly (GenBank Accession: GCA_000001765.2) of Drosophila pseudoobscura. This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

Background: Epigenetics, the study of reversible changes in gene expression without altering the underlying DNA sequence, is increasingly applied in medical, commercial, and policy contexts. Yet, little is known about how this emerging science is communicated to the public. The purpose of this study was to examine communication strategies, sources, and modalities in epigenetic-related videos on YouTube- the most accessed platform for informal science education. Methods: We conducted a mixed-methods content analysis of 294 YouTube videos on epigenetics by conducting a keyword-based search on October 17, 2023. Video transcripts and meta-data were coded using a codebook developed both deductively and inductively. Qualitative analysis examined how communication strategies were used within videos and identified emergent themes (RQ1). Quantitative analyses examined the frequency of video and channel characteristics (RQ2), and presentation modalities (RQ3). Results: Findings reveal poor alignment with science communication best practices (RQ1): over 92% of videos failed to acknowledge scientific uncertainty, the comprehensibility level exceeded the recommended 8th-grade level (e.g., average readability grade 10.7), and professional research organizations were notably absent. Narrators were mostly male (56.7%) and white-presenting (73.7%) (RQ2). The majority of the videos used multi-modal strategies (e.g., visual texts mixed with animation and voice-over narration) to communicate epigenetic information (RQ3). Conclusion: Findings highlight the need for professional research organizations to be more proactive in public epigenetic communication efforts. Increasing narrator demographic diversity could broaden audience reach. Evidence-based communication tools are needed for health or science communicators discussing epigenetics on social media.

Fibroblasts are readily obtained and expanded and may provide an alternative cell source for cultivated seafood if their latent myogenic potential can be accessed. We examined whether transient exposure to 5-azacytidine (AZA), a cytidine analogue known to convert mouse embryonic fibroblasts into myoblasts, elicits a persistent muscle gene program in embryo-derived zebrafish (Danio rerio) Z3 fibroblasts. Cells were exposed to 0, 2.5, 5 or 10 M AZA for 48 h and maintained in drug-free medium for 3 weeks. RNA-seq identified 744 genes that increased and 670 that decreased consistently across the concentration series. Increased genes encompassed myogenic regulators, fusion factors, sarcomeric components and excitation-contraction machinery, whereas decreased genes were enriched for extracellular-matrix and adhesion functions. In a separate six-dose RT-qPCR experiment (0-20 M AZA) with three biological replicates per concentration, all 19 selected muscle genes were significantly increased at 1.25 M, the lowest concentration tested, whereas 9 of 12 extracellular-matrix/fibroblast genes were significantly decreased. Several muscle genes plateaued or declined at higher concentrations, and multinucleated myotubes were not observed. A separate 5-aza-2'-deoxycytidine (decitabine) series showed a comparable muscle-associated response at 0.25 M. These findings indicate that zebrafish fibroblasts retain access to a myogenic-like transcriptional program, and they provide a model for identifying food-compatible approaches to control fish-cell lineage plasticity for cultivated seafood.