Biology subjects

Syed, S. A.

Publications and source records attributed to Syed, S. A..

8 recordsLinked to original sources

bioRxiv2026

A Denisovan-derived Alu insertion in OCA2 contributes to pigmentation diversity in present-day Melanesians

Modern humans inherited DNA from Neanderthals and Denisovans, but the contribution of introgressed structural variants (SVs) to present-day human phenotypes and adaptation remains poorly understood. Here, we used a graph-genome approach to genotype 96,277 SVs in 3,332 present-day humans and three high-coverage archaic hominin genomes, identifying 153 candidate introgressed SVs. These SVs are enriched for signatures of local adaptation compared to non-introgressed SVs (p-value = 3.04 x 10-7). Among these, we focused on a Denisovan-derived Alu insertion located in intron 18 of OCA2, a gene central to pigmentation. This introgressed Alu insertion is most frequently observed (> 60%) in Indigenous people from Bougainville Island of Melanesia, and is significantly associated with increased skin pigmentation in this region. To assess its functional impact, the Alu insertion was introduced into human induced pluripotent stem cells (iPSCs), which were subsequently differentiated into melanocytes. Melanocytes harboring the Alu insertion demonstrated elevated OCA2 expression, increased pigmentation, and higher levels of enhancer activity compared to controls. Collectively, these findings highlight introgressed SVs as a significant source of adaptive and phenotypic diversity in modern humans and implicate the Denisovan-derived Alu insertion in OCA2 in pigmentation variation among present-day Melanesian populations.

genomics↗

bioRxiv2025

Satellite DNA fragility accompanies complex genome rearrangements and ecDNA oncogene amplification in canine osteosarcomas

Canine osteosarcoma (OS) is an aggressive bone cancer with remarkable similarity to human OS. Despite its value as a comparative oncology model, the drivers of genomic instability remain poorly defined, hindering cross-species insights into disease progression. We applied long-read PacBio HiFi whole genome sequencing to matched tumor and blood samples from four purebred dogs to generate high-resolution maps of somatic structural variants (SVs). Tumor genomes showed extensive rearrangement complexity, with satellite repeat regions, particularly SAT1_CF, enriched near somatic SV breakpoints and occurring within genomic contexts marked by focal hypomethylation. We also identified multiple extrachromosomal DNA (ecDNA) elements carrying oncogenes indicating ecDNA-mediated oncogene amplification. Together, these data provide an integrated genomic and epigenomic view of canine OS, implicating satellite repeats as recurrent substrates for rearrangement and ecDNA as a prominent mode of genome remodeling. This work advances our understanding of OS genome dynamics and establishes a comparative framework for investigating repeat-driven instability and oncogene amplification across species.

genomics↗

bioRxiv2025

Structural Variants at Intronic CTCF Loop Anchors Drive Differential Exon Usage

CTCF-mediated chromatin loops are known to influence gene regulation, yet their role in pre-mRNA splicing remains incompletely understood. Here, we demonstrate that structural variants (SVs) at the anchors of intronic CTCF loops can modulate exon usage. By integrating high-resolution three-dimensional (3D) genome organization and gene expression datasets from C57BL/6J (B6) and 129S1/SvImJ (129S) mouse embryonic stem cells (ESCs), with structural variant (SV) maps from the 129S mouse, we identified thousands of intron-anchored CTCF loops. Our data indicate that SVs intersecting loop anchors are more frequently associated with differential exon inclusion events than with changes in overall gene expression. CRISPR/Cas9 deletion of two SV-harboring intronic CTCF sites in Numbl and Ireb2 validated the predicted splicing shifts observed between B6 and 129S ESC that correspond with diminished long-range chromatin looping. Our findings reveal a direct mechanistic link between 3D genome architecture and alternative splicing and highlight non-coding SVs as modulators of transcript diversity. Our study has thus identified a novel class of CTCF-bound regulatory elements regulating alternative splicing. Cataloging and validating these functional elements will elucidate molecular mechanisms underlying phenotypic variation within populations.

molecular biology↗

bioRxiv2023

Protein arginine methyltransferase 5 (Prmt5) localizes to chromatin loop anchors and modulates expression of genes at TAD boundaries during early adipogenesis

Protein arginine methyltransferase 5 (Prmt5) is an essential regulator of embryonic development and adult progenitor cell functions. Prmt5 expression is mis-regulated in many cancers, and the development of Prmt5 inhibitors as cancer therapeutics is an active area of research. Prmt5 functions via effects on gene expression, splicing, DNA repair, and other critical cellular processes. We examined whether Prmt5 functions broadly as a genome-wide regulator of gene transcription and higher-order chromatin interactions during the initial stages of adipogenesis using ChIP-Seq, RNA-seq, and Hi-C using 3T3-L1 cells, a frequently utilized model for adipogenesis. We observed robust genome-wide Prmt5 chromatin-binding at the onset of differentiation. Prmt5 localized to transcriptionally active genomic regions, acting as both a positive and a negative regulator. A subset of Prmt5 binding sites co-localized with mediators of chromatin organization at chromatin loop anchors. Prmt5 knockdown decreased insulation strength at the boundaries of topologically associating domains (TADs) adjacent to sites with Prmt5 and CTCF co-localization. Genes overlapping such weakened TAD boundaries showed transcriptional dysregulation. This study identifies Prmt5 as a broad regulator of gene expression, including regulation of early adipogenic factors, and reveals an unappreciated requirement for Prmt5 in maintaining strong insulation at TAD boundaries and overall chromatin organization.

genomics↗

bioRxiv2023

Differential requirements for different subfamilies of the mammalian SWI/SNF chromatin remodeling enzymes in myoblast differentiation

Mammalian SWI/SNF (mSWI/SNF) complexes are ATP-dependent chromatin remodeling enzymes that are critical for normal cellular functions and that are mis-regulated in [~]20% of human cancers. These enzymes exhibit significant diversity in the composition of individual enzyme complexes. mSWI/SNF enzymes are classified into three general sub-families based on the presence or absence of specific subunit proteins. The three sub-families are called BAF (BRM or BRG1-associated factors), ncBAF (non-canonical BAF), and PBAF (Polybromo-associated BAF). The biological roles for the different subfamilies of mSWI/SNF enzymes are poorly described. We knocked down (KD) the expression of genes encoding subunit proteins unique to each of the three subfamilies, Baf250A, Brd9, and Baf180, which mark the BAF, ncBAF, and PBAF sub-families, respectively, and examined the requirement for each in myoblast differentiation. We found that BAF250A and the BAF complex was required to drive lineage-specific gene expression during myoblast differentiation. KD of Baf250A reduced the expression of the lineage determinant Myogenin and other differentiation markers, due to decreased binding of BAF250A to myogenic gene promoters. KD of Brd9 delayed myoblast differentiation. However, RNA-seq analysis revealed that while the Baf250A-dependent gene expression profile included genes involved in myogenesis, the Brd9-dependent gene expression profile did not. Moreover, no-colocalization of Baf250A and Brd9 was observed in differentiating cells, suggesting independent mechanisms of action for BAF and ncBAF complexes in myogenesis. The PBAF complex was dispensable for myoblast differentiation. The results distinguish between the roles of the mSWI/SNF enzyme subfamilies during myoblast differentiation.

molecular biology↗

bioRxiv2022

PRMT5 links lipid metabolism to contractile function of skeletal muscles

The skeletal muscle plays a key role in systemic energy homeostasis besides its canonical contractile function, but what couples these functions is poorly defined. Protein Arginine MethylTransferase 5 (PRMT5) is a well-known oncoprotein but also expressed in healthy tissues with unclear physiological functions. As adult muscles express high levels of Prmt5, we generated myocyte-specific Prmt5 knockout (Prmt5MKO) mice. We observed reduced muscle mass, oxidative capacity, force production and exercise performance in Prmt5MKO mice. The motor deficiency is associated with scarce lipid droplets in myofibers due to defects in lipid biosynthesis and degradation. First, Prmt5MKO reduced demethylation and stability of Sterol Regulatory Element-Binding Transcription Factor 1a (SREBP1a), a master regulator of de novo lipogenesis. Second, Prmt5MKO impaired the repressive H4R3Me2s (histone H4 arginine-3 symmetric demethylation) at the Pnpla2 gene, elevating the level of its encoded protein ATGL, the rate-limiting enzyme catalyzing lipolysis. Accordingly, myocyte-specific double knockout of Pnpla2 and Prmt5 normalized muscle mass and function. Together, our findings delineate a physiological function of PRMT5 in linking lipid metabolism to contractile function of myofibers.

molecular biology↗

bioRxiv2022

High-fructose feeding suppresses cold-stimulated brown adipose tissue glucose uptake in young men independently of changes in thermogenesis and the gut microbiome

Diets rich in added sugars, especially high in fructose, are associated with metabolic diseases such as insulin resistance, and non-alcoholic fatty liver disease. Studies have shown a link between these pathologies and changes in the microbiome and its metabolites. Given the reported associations in animal models between the microbiome and brown or beige adipose tissue (BAT) function, and the alterations in the microbiome induced by high glucose or high fructose diets, we investigated the potential causal link between high glucose or fructose diets and BAT dysfunction in humans. We show that BAT glucose uptake, but not thermogenesis, is impaired by a high fructose but not high glucose diet, in the absence of changes in body mass, the gastrointestinal microbiome, and faecal short-chain fatty acids. We conclude that BAT metabolic dysfunction occurs independently from changes in gut microbiome composition, and earlier than other pathophysiological abnormalities associated with insulin resistance and dyslipidemia during fructose overconsumption in humans.

physiology↗

bioRxiv2019

Calcineurin broadly regulates the initiation of skeletal muscle-specific gene expression by binding target promoters and facilitating the interaction of the SWI/SNF chromatin remodeling enzyme

Calcineurin (Cn) is a calcium-activated serine/threonine protein phosphatase that is broadly implicated in diverse cellular processes, including the regulation of gene expression. During skeletal muscle differentiation, Cn activates the NFAT transcription factor but also promotes differentiation by counteracting the negative influences of protein kinase C beta (PKC{beta}) via dephosphorylation and activation of BRG1, an enzymatic subunit of the mammalian SWI/SNF ATP-dependent chromatin remodeling enzyme. Here we identified four major temporal patterns of Cn-dependent gene expression in differentiating myoblasts and determined that Cn is broadly required for the activation of the myogenic gene expression program. Mechanistically, Cn promotes gene expression through direct binding to myogenic promoter sequences and facilitating the binding of BRG1, other SWI/SNF subunit proteins, and MyoD, a critical lineage determinant for skeletal muscle differentiation. We conclude that the Cn phosphatase directly impacts the expression of myogenic genes by promoting ATP-dependent chromatin remodeling and formation of transcription-competent promoters.

molecular biology↗