Biology subjects

Ashraf, H.

Publications and source records attributed to Ashraf, H..

9 recordsLinked to original sources

bioRxiv2026

Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures

The human Y chromosome is among the most structurally dynamic chromosomes in the human genome, yet much of its diversity remains unresolved because of extensive palindromes, ampliconic gene families, satellite-rich heterochromatin and large segmental duplications. What remained unclear was how these diverse forms of variation fit together across the full chromosome, how often similar structures recur in different lineages, and which aspects of organization remain constrained despite rapid sequence turnover. Here, we generated and analyzed 142 nearly complete human Y chromosome assemblies from 17 major haplogroups spanning approximately 180,000 years of evolution, creating a population-scale resource for studying Y chromosome biology and diversity. These assemblies show that structural change on the Y chromosome is recurrent but constrained, even in its most repetitive regions. In the fertility-associated azoospermia factor c (AZFc) region, recurrent inversions, deletions, and complex rearrangements generate a limited repertoire of structural haplotypes. Multicopy ampliconic gene families follow distinct evolutionary paths: DAZ paralogues differ in structural constraint, RBMY evolves within a modular array, and TSPY copy number varies mainly through local expansion and contraction. The centromere and Yq12 heterochromatin vary greatly in size but retain a stable higher-order organization, including a single hypomethylated centromeric core and conserved Yq12 repeat composition and orientation. Methylation across palindromic and ampliconic regions is likewise structured by repeat class, copy order and local architecture. Together, these results provide a population-scale resource for the human Y chromosome and show that its rapid structural evolution is repeatedly funneled into a limited set of architectural outcomes.

genomics↗

bioRxiv2025

Activin/TGF-beta signaling levels coordinate whole-body regeneration with genotoxic stress in Schmidtea mediterranea

Highly regenerative animals often have a seemingly limitless capacity for tissue growth and stem cell proliferation, which often requires molecular and organismal capacities associated with pre-malignancy. Yet, these same organisms do not develop stem cell driven cancers. Here, we explored if the regenerative flatworm Schmidtea mediterranea has evolved mechanisms to modulate regeneration depending on underlying DNA damage or neoplastic risk. We first challenged worms to regenerate after increasing doses of ionizing radiation and found that even sublethal doses (500-1250Rads) transiently inhibit regeneration. After amputation, stem cells could divide and accumulate near injuries but did not increase proliferation rates in response to amputation or restore missing tissues. By leveraging published single cell sequencing datasets, we found that ionizing radiation increased activin ligand expression, particularly in the intestine. RNAi knockdown of 18 different activin signaling homologs identified activin ligands, activin receptors, and downstream Smad transcription factors whose depletion partially or fully rescued regenerative capacity after radiation. Notably, depletion of activin-2 did not alter radiation-induced stem cell loss. Instead, it increased stem cell expansion and amputation-induced proliferation, fully restoring regeneration despite prior DNA damage and depleted stem cell numbers. Together, our results indicate that Activin signaling levels are a central regulator of planarian stem cell behaviors, coordinating shifts between repair of pre-existing tissues following systemic damage, homeostatic tissue turnover, and whole-body regeneration. Moreover, Activin signaling may function as a conserved tumor suppressor in Schmidtea mediterranea by inhibiting stem-cell driven regeneration when damage levels are too high. In BriefBrownlee et al. uncover an activin/TGF-beta dependent inhibition of regenerative capacity following ionizing radiation in the highly regenerative flatworm Schmidtea mediterranea. While activin depletion had little effect on irradiation-induced stem cell loss, it significantly increased stem cell expansion and proliferation when irradiated worms were amputated, restoring regeneration despite reduced stem cell numbers. HighlightsO_LISub-lethal exposures of ionizing radiation transiently inhibit regenerative ability in the planarian Schmidtea mediterranea C_LIO_LIIonizing radiation does not prevent surviving stem cells from dividing but reduces their ability to increase proliferation rates and regenerate missing tissues after amputation. C_LIO_LIDepletion of different Activin/TGF-beta signaling components rescues regenerative capacity after irradiation C_LIO_LIHeightened stem cell expansion and amputation-induced proliferation underlie increased regenerative capacity upon activin depletion C_LI

developmental biology↗

bioRxiv2025

MAPK and mTORC1 signaling converge on Cyclin D to enable cell-cycle re-entry in melanoma persister cells

Resistance to targeted therapy in BRAF-mutant melanomas can arise from drug-tolerant persister cells, which can non-genetically escape drug-induced quiescence to resume proliferation. To investigate how melanoma cells escape drug to re-enter the cell cycle within 3-4 days of BRAF and MEK inhibition, we computationally reconstructed single-cell lineages from time-lapse imaging data, linking key signaling pathways to cell-cycle fate outcomes. We found that ERK reactivation, while necessary, is insufficient for cell-cycle re-entry under MAPK inhibition. Instead, mTORC1 emerged as an additional critical mediator, enhancing translation and cell growth in cells destined for drug escape. We further found that ERK and mTORC1 signaling converge to produce Cyclin D1 protein levels, a key bottleneck for cell-cycle re-entry. Using CRISPR to tag endogenous Cyclin D1, we found that future escapees markedly upregulate Cyclin D1 at least 15 hours prior to drug escape, compared to non-escapees. Importantly, this early upregulation enables accurate prediction of future escapees from non-escapees, underscoring how differences in Cyclin D1 accumulation precede and govern the timing and likelihood of cell-cycle re-entry in persister cells. Our findings suggest that variability in ERK and mTORC1 activity underlies the heterogeneous Cyclin D1 levels observed, influencing the proliferative potential of persister cells and ultimately shaping the diverse cell-cycle behaviors observed under drug treatment. Cyclin D1 protein therefore emerges as both a critical biomarker and a therapeutic target for preventing cell-cycle re-entry in BRAF/MEK-treated melanoma. One Sentence SummaryCyclin D1 accumulation, driven by the integration of heterogeneous MAPK and mTORC1 signaling, is a critical bottleneck for cell-cycle re-entry in drug-treated melanoma cells.

systems biology↗

bioRxiv2024

Complex genetic variation in nearly complete human genomes

Diverse sets of complete human genomes are required to construct a pangenome reference and to understand the extent of complex structural variation. Here, we sequence 65 diverse human genomes and build 130 haplotype-resolved assemblies (130 Mbp median continuity), closing 92% of all previous assembly gaps1,2 and reaching telomere-to-telomere (T2T) status for 39% of the chromosomes. We highlight complete sequence continuity of complex loci, including the major histocompatibility complex (MHC), SMN1/SMN2, NBPF8, and AMY1/AMY2, and fully resolve 1,852 complex structural variants (SVs). In addition, we completely assemble and validate 1,246 human centromeres. We find up to 30-fold variation in -satellite high-order repeat (HOR) array length and characterize the pattern of mobile element insertions into -satellite HOR arrays. While most centromeres predict a single site of kinetochore attachment, epigenetic analysis suggests the presence of two hypomethylated regions for 7% of centromeres. Combining our data with the draft pangenome reference1 significantly enhances genotyping accuracy from short-read data, enabling whole-genome inference3 to a median quality value (QV) of 45. Using this approach, 26,115 SVs per sample are detected, substantially increasing the number of SVs now amenable to downstream disease association studies.

genomics↗

bioRxiv2024

Long-read sequencing and structural variant characterization in 1,019 samples from the 1000 Genomes Project

Structural variants (SVs) contribute significantly to human genetic diversity and disease1-4. Previously, SVs have remained incompletely resolved by population genomics, with short-read sequencing facing limitations in capturing the whole spectrum of SVs at nucleotide resolution5-7. Here we leveraged nanopore sequencing8 to construct an intermediate coverage resource of 1,019 long-read genomes sampled within 26 human populations from the 1000 Genomes Project. By integrating linear and graph-based approaches for SV analysis via pangenome graph-augmentation, we uncover 167,291 sequence-resolved SVs in these samples, considerably advancing SV characterization compared to population-wide short-read sequencing studies3,4. Our analysis details diverse SV classes--deletions, duplications, insertions, and inversions--at population-scale. LINE-1 and SVA retrotransposition activities frequently mediate transductions9,10 of unique sequences, with both mobile element classes transducing sequences at either the 3'- or 5'-end, depending on the source element locus. Furthermore, analyses of SV breakpoint junctions suggest a continuum of homology-mediated rearrangement processes are integral to SV formation, and highlight evidence for SV recurrence involving repeat sequences. Our open-access dataset underscores the transformative impact of long-read sequencing in advancing the characterisation of polymorphic genomic architectures, and provides a resource for guiding variant prioritisation in future long-read sequencing-based disease studies.

genomics↗

bioRxiv2022

Association Analysis of LCORL Genetic Variant (rs657074013A>AT) with Body-Height and Skeletal Frame in Pakistani Goats

Goat is one of the most valued and cost-effective household animals serving humanity by providing its meat, milk, fiber, skin and manure. Particularly, meat and milk production depends on the physical traits of the animals e.g., large body-size/skeletal frame. Previous studies has shown that the LCORL gene is associated with the subject traits in humans and many other animal species. So, the current study is aimed to investigate the genetic variability/association of rs657074013A>AT variant within diverse goats from Pakistan. By using ARMS-PCR, a total of 51 samples were genotyped with allele-specific primer-set, results of the current study depicted that, 27% population is homozygous wild-type (A/A), 24% homozygous-mutant (AT/AT) and 49% is heterozygous (A/AT). Hardy Weinberg Equilibrium (HWE) analysis revealed that our overall sampled population obeys this principle with{chi} 2(2, N = 51) = 0.046, p = 0.9730. Similarly, a significant genetic association was also envisioned by Chi-square statistics p = 9.60 x 10-5 using the PLINK data analysis toolset. Furthermore, alternative allele frequencies of 0.68 and 0.28 were also calculated within cases (n=25) and control (n=26) cohorts respectively along with an odds ratio of 5.242. As a nutshell, this pilot study improved our genomic insight by observing the variability and association of the subject LCORL genetic variant (c.828_829insA) in the Pakistani goat population, which may be used to improve this economically important trait by adopting marker-assisted breeding strategies and further investigated within other livestock species as well.

genetics↗

bioRxiv2022

Inversion polymorphism in a complete human genome assembly

The completion of the human genome significantly improved our ability to discover and interpret genome copy number variation. In order to understand its impact on the characterization of inversion polymorphisms, we remapped data from 41 human genomes and 10 new samples against the telomere-to-telomere (T2T) reference genome as compared to the standard GRCh38 reference. Our analysis shows a ~21% increase in sensitivity identifying and improving mapping of 63 inversions. We further identify 26 misorientations within GRCh38, and show that the T2T reference is three times more likely to represent the correct orientation of the major human allele. As a result, we report a significant bias for inversions accumulating within the pericentromeric regions of specific chromosomes and show that functional annotations around inverted regions, such as topological-associated domains, can be better interpreted.

genomics↗

bioRxiv2021

Haplotype-resolved inversion landscape reveals hotspots of mutational recurrence associated with genomic disorders

Unlike copy number variants (CNVs), inversions remain an underexplored genetic variation class. By integrating multiple genomic technologies, we discover 729 inversions in 41 human genomes. Approximately 85% of inversions <2 kbp form by twin-priming during L1-retrotransposition; 80% of the larger inversions are balanced and affect twice as many base pairs as CNVs. Balanced inversions show an excess of common variants, and 72% are flanked by segmental duplications (SDs) or mobile elements. Since this suggests recurrence due to non-allelic homologous recombination, we developed complementary approaches to identify recurrent inversion formation. We describe 40 recurrent inversions encompassing 0.6% of the genome, showing inversion rates up to 2.7x10-4 per locus and generation. Recurrent inversions exhibit a sex- chromosomal bias, and significantly co-localize to the critical regions of genomic disorders. We propose that inversion recurrence results in an elevated number of heterozygous carriers and structural SD diversity, which increases mutability in the population and predisposes to disease- causing CNVs.

genomics↗

bioRxiv2020

De novo assembly of 64 haplotype-resolved human genomes of diverse ancestry and integrated analysis of structural variation

Long-read and strand-specific sequencing technologies together facilitate the de novo assembly of high-quality haplotype-resolved human genomes without parent-child trio data. We present 64 assembled haplotypes from 32 diverse human genomes. These highly contiguous haplotype assemblies (average contig N50: 26 Mbp) integrate all forms of genetic variation across even complex loci such as the major histocompatibility complex. We focus on 107,590 structural variants (SVs), of which 68% are inaccessible by short-read sequencing. We identify new SV hotspots (spanning megabases of gene-rich sequence), characterize 130 of the most active mobile element source elements, and find that 63% of all SVs arise by homology-mediated mechanisms--a twofold increase from previous studies. Our resource now enables reliable graph-based genotyping from short reads of up to 50,340 SVs, resulting in the identification of 1,525 expression quantitative trait loci (SV-eQTLs) as well as SV candidates for adaptive selection within the human population.

genetics↗