Biology subjects

GAYEN, S.

Publications and source records attributed to GAYEN, S..

8 recordsLinked to original sources

bioRxiv2026

Evolutionary origins and chromatin state shape X-chromosome upregulation pattern during eutherian and metatherian embryogenesis

In mammals, silent state of one of the X-chromosomes in female balance the X-dosage between sexes. In parallel, X to autosome imbalance due to monoallelic expression of X-linked genes relative to biallelic autosomal genes, is primarily compensated through the X-chromosome upregulation (XCU). It has been demonstrated that X-chromosome inactivation (XCI) and XCU coincides during embryogenesis, however, XCU is not global and it occurs in a gene-specific manner. The underlying mechanistic aspects of such specificity of XCU remain unknown. Here, we provide systematic and comparative analysis across eutherians (mouse, human and pig) and metatherian (opossum) embryogenesis to determine if evolutionary origins shape the XCU. Intriguingly, we show that while evolutionary older X-linked genes (predating mammalian divergence) undergo robust XCU consistently across developmental stages, younger mammalianLJorigin genes do not. Similarly, the eutherian X-linked genes conserved in metatherian X (X-ortholog) undergo robust XCU, whereas genes orthologus to metatherian autosome (Auto-ortholog) exhibit weaker pattern of XCU. Further, strata-wise comparison revealed that genes in older XLJchromosome strata (1-2) consistently undergo upregulation, whereas strata 3-4 genes do not. Importantly, we show that different evolutionary classes of X-linked genes, which undergo robust XCU, are often enriched with active chromatin marks (H3K36me3, H3K27ac and H3K4me1) relative to the autosome, suggesting that chromatin state mediate the XCU. Moreover, we show that often active-marks enrichment correlates with differential XCU dynamics of different class of genes. Taken together, our study provides significant insight into the evolutionary dynamics of XCU and underlying mechanistic framework.

genetics↗

bioRxiv2024

Single-cell allelic transcriptomic analysis unravels intratumoral gene expression heterogeneity linked to TNBC pathogenesis

Triple-negative breast cancer (TNBC) is the most aggressive subclass of breast cancer, which exhibits high intratumoral heterogeneity. Intratumoral heterogeneity often drives the evolution of drug resistance towards tumour therapy in TNBC. However, the contributing factors and mechanisms behind the intratumoral heterogeneity in TNBC remain poorly understood. It has been implicated that copy number variations (CNVs) often create allelic imbalance and thereby contribute to intratumoral gene expression heterogeneity. However, other processes, such as epigenetic and transcriptional processes, can also contribute to allelic expression heterogeneity in tumour cells. Here, we have investigated how allelic expression heterogeneity contributes to intratumoral heterogeneity in TNBC by performing genome-wide allelic gene expression analysis, excluding most of the CNVs, using single-cell RNA-sequencing datasets. We found widespread monoallelic expression of many genes across different cell types of TNBC. Notably, we found a profound heterogeneity of allelic expression patterns of many genes within TNBC epithelial cells, creating distinct subpopulations of epithelial cells. Importantly, we show that these genes with allelic expression pattern heterogeneity between subpopulations are linked to TNBC immune-surveillance and drug-resistance related pathways, thereby overall shaping the pathogenesis outcomes. Finally, we show that the promoter regions of these genes with profound monoallelic expression are often hypermethylated in TNBC patients. Altogether, our findings reveal that heterogeneous allelic expression patterns contribute to intratumoral heterogeneity and are linked to TNBC pathogenesis.

cancer biology↗

bioRxiv2024

Gestational exposure to high heat-humidity conditions impairs mouse embryonic development

Unprecedented rates of global warming have created an existential challenge for the sustainable survival of species on this planet. Tropical conditions of high ambient temperature and relative humidity are extremely vulnerable to maternal-child health. Emerging epidemiological studies depict that exposure to extremely hot weather conditions during pregnancy leads to an array of adverse pregnancy outcomes, such as low birth weight, stillbirth, preterm delivery, congenital abnormalities and adult-onset disorders. A lack of understanding of the underlying molecular pathophysiology limits us from developing an effective combat strategy in terms of targeted therapeutics to improvise the combined teratogenic effects of high heat-humidity in pregnancy. To address this, it is important to delineate the effect of hot-humid weather conditions on the process of embryogenesis. However, working with human embryos is technically and ethically challenging. In this study, we have established a mouse model of heat-humidity stress during pregnancy, which essentially recapitulates the adverse pregnancy outcomes observed in humans. Importantly, we have profiled the impact of high heat-humidity exposure during gestation at different stages of embryogenesis using this mouse model. Our results indicate that the teratogenicity of heat-humidity stress gets manifested in a cumulative manner, starting from the pre-implantation stage and becomes severe at the mid-gestation, culminating in significantly higher embryonic deaths and malformations at the late gestational stage of mouse embryogenesis. Overall, our study paves the path for exploring the underlying molecular players that get dysregulated under gestational exposure to hot and humid conditions, resulting in severe embryonic defects.

developmental biology↗

bioRxiv2024

Role of m6A RNA methylation in dosage compensation

In therian mammals, inactivation of one of the X-chromosomes in females balances the dosage of X-linked gene expression between the sexes. On the other hand, upregulation of active-X balances the dosage of monoallelically expressed X-linked genes with biallelic autosomal genes (AA). Factors and mechanisms involved in the maintenance of X-chromosome inactivation (XCI) and X to autosome dosage compensation remain underexplored. Recently, it has been implicated that N6-methyladenosine (m6A) RNA modification contributes to XCI and X to autosome dosage compensation. Here, we have investigated the role of m6A RNA methylation in the maintenance of XCI and X to autosome dosage compensation in early embryonic lineages. Surprisingly, we find that the depletion of m6A RNA methylation does not affect the maintenance of inactive-X gene silencing in mouse epiblast stem cells (EpiSC), trophoblast stem cells (TSC) and extraembryonic endoderm stem cells (XEN). On the other hand, we show that m6A marks are less enriched on X-linked transcripts than the autosomal transcripts in early embryonic lineages. It is believed that less enrichment of m6A in X-linked transcript increases the stability of the X-linked transcript and thereby contributes to the X to autosome dosage compensation. Interestingly, we find that while X-linked transcripts without m6A are fully dosage compensated, transcripts with m6A undergo partial X to autosome dosage compensation in EpiSC, TSC and XEN. However, we find that the depletion of m6A has a minor effect on the X to autosome dosage compensation. Taken together, our study provides significant insight into the role of m6A RNA methylation in dosage compensation of early embryonic lineages.

genetics↗

bioRxiv2023

Gene-specific reactivation of X-linked genes upon Xist loss is linked to the chromatin states in extraembryonic endoderm and epiblast stem cells

In eutherian mammals, X-chromosome dosage between sexes is balanced through the inactivation of one of the two X-chromosomes in female cells. In mouse, X-inactivation initiates at [~]4-8 cell stages of embryogenesis, where paternal-X undergoes imprinted X-inactivation. Subsequently, it switches to random X-inactivation in post-iplantation epiblast. The initiation of XCI is orchestrated by Xist. However, the role of Xist in the maintenance of X-chromosome inactivation remains underexplored. Here, we have explored the role of Xist in the maintenance of X-inactivation in extraembryonic endoderm stem cells (XEN) and epiblast stem cells (EpiSC), which undergo imprinted and random form of X-inactivation respectively. We show that removal of Xist leads to the partial reactivation of inactive-X chromosome. Intriguingly, many reactivated genes were found to be common between XEN and EpiSC, indicating these genes require Xist to maintain their silent state irrespective of the lineages or forms of X-inactivation. Notably, despite Xist ablation and the subsequent removal of DNA methylation, several X-linked genes remained resistant to reactivation, indicating the involvement of other factors in maintaining the silencing of these genes. On the other hand, we show that genes on the inactive-X with low levels of H3K9me3 and high levels of H3K27me3 are more susceptible to reactivation upon the loss of Xist. Interestingly, active-X homolog of the reactivated genes was found to be enriched with H3K4me3 and H3K27ac. Taken together, our study sheds light on the role of chromatin states in the reactivation of X-linked genes following the loss of Xist in XEN and EpiSC.

genetics↗

bioRxiv2023

Deletion of Xist upstream sequences alters TAD interactions and leads to defects in Xist coating and expression

The topological organization of the genome plays an important role in regulating gene expression. However, the connection between the two remains poorly understood. X-chromosome inactivation is a unique model system to explore the interlink between topologically associated domains (TADs) and gene expression. TADs are largely lost upon X-inactivation, and the inactive-X gets bipartitely reorganized into two large mega domains. However, the X-inactivation center (XIC) harbors two TADs - at the locus of long non-coding RNA Xist (Xist-TAD) and Tsix (Tsix-TAD). Xist is the master regulator of X-inactivation, which coat the inactive-X and facilitates heterochromatinization. Here, we deleted Xist upstream sequences ([~]6 kb) near the Xist TADs boundary in extraembryonic endoderm stem cells (XEN), which undergo imprinted X-inactivation. This deletion led to the major rearrangement of TADs and affected the expression of genes located within Xist and Tsix TAD, specially the expression of Xist was upregulated, suggesting TADs are essential for proper transcriptional regulation. On the other hand, Xist-upstream deletion on the inactive-X resulted in dispersal of Xist coating and loss of enrichment of repressive chromatin marks on the inactive-X but no effect on X-linked gene silencing. However, we found that autosomal genes were dysregulated in Xist-upstream deleted cells, probably because of misregulation of genes located in Xist and Tsix-TAD, specially Xist. We conclude that Xist upstream sequences are necessary for proper organization of the TADs at the XIC, maintenance of Xist coating/expression and autosomal gene expression.

genetics↗

bioRxiv2023

Chromatin states contribute to coordinated allelic transcriptional bursting to drive iPSC reprogramming

Molecular mechanisms behind the reprogramming of somatic cells to induced pluripotent stem cells (iPSC) remain poorly understood. While dynamic changes in gene expression are considered to drive reprogramming, the contribution of individual alleles of genes to reprogramming remains unexplored. It is thought that two alleles of a gene can transcribe independently or coordinatedly, which in turn can lead to temporal expression heterogeneity with potentially distinct impacts on cell fate. Here, we profiled genome-wide transcriptional burst kinetics with an allelic resolution during the reprogramming of mouse embryonic fibroblast (MEF) to iPSC. We show that many genes involved in iPSC reprogramming pathways exhibit bursty expression and contribute to dynamic autosomal random monoallelic expression (aRME). Moreover, we find that the degree of coordination of allelic bursting differs among genes and changes dynamically during iPSC reprogramming. Importantly, we show that alleles of many reprogramming-related genes burst in a highly coordinated fashion. ATAC-seq analysis revealed that coordination of allelic bursting is linked to allelic chromatin accessibility. Consistently, we show that highly coordinated genes are enriched with chromatin accessibility regulators such as H3K36me3, H3K27ac, histone variant H3.3 and BRD4. Collectively, our study demonstrates that chromatin states contribute to coordinated allelic bursting to fine-tune the expression of genes involved in iPSC reprogramming and provides insights into the implications of allelic bursting coordination in cell fate specification. O_FIG O_LINKSMALLFIG WIDTH=195 HEIGHT=200 SRC="FIGDIR/small/548864v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@162ec20org.highwire.dtl.DTLVardef@17c2db0org.highwire.dtl.DTLVardef@19b9d59org.highwire.dtl.DTLVardef@1775052_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2020

Transcriptional bursting shape autosomal dynamic random monoallelic expression inpre-gastrulation embryos

In recent years, allele-specific single-cell RNA-seq (scRNA-seq) analysis has demonstrated wide-spread dynamic random monoallelic expression of autosomal genes (aRME) in different cell types. However, the prevalence of dynamic aRME during pre-gastrulation development remains unknown. Here, we show that dynamic aRME is wide-spread in different lineages of pre-gastrulation embryos. Additionally, the origin of dynamic aRME remains poorly understood. Theoretically, it is believed that independent transcriptional bursting from each allele leads to the dynamic aRME. However, based on analysis of allele-specific burst kinetics of autosomal genes, we found that allelic burst is not perfectly independent, rather it happens in semi-coordinated fashion. Importantly, we show that semi-coordinated allelic bursting of the genes; particularly with low burst frequency, leads to frequent asynchronous allelic bursting, thereby shaping the landscape of dynamic aRME in pre-gastrulation embryos. Altogether, our study provides significant insight into the prevalence and origin of dynamic aRME and cell to cell expression heterogeneity during early mammalian development. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

genetics↗