Biology subjects

Barugahare, A.

Publications and source records attributed to Barugahare, A..

5 recordsLinked to original sources

bioRxiv2026

Ancient origin of the dorso-ventral patterning system of vertebrate paired fins

The origin of paired fins was a major event in early vertebrate history that fuelled the adaptive radiation of the gnathostome clade. Evidence for the conservation of ancient regulatory systems between paired and median fins supports a model in which appendage-patterning mechanisms first evolved in the midline and were later redeployed to a new embryonic context, the flank. However, while paired fins and limbs are asymmetric along the dorso-ventral (DV) axis, the equivalent axis does not exist in median fins, which are symmetric across the midline, raising questions of how DV patterning evolved. Here, we combine genetic tools in zebrafish with comparative expression analyses in representative ray-finned and cartilaginous fishes to show that a subset of limb dorsoventral (DV) patterning genes are expressed during median fin development. Using genetic lineage tracing of the canonical limb dorsalizing factor lmx1bb, we further demonstrate that, although lmx1bb-derived cells occupy distinct spatial domains across fin types, a subset of this lineage is fated to differentiate into fin-ray osteoblasts in both paired and median fins. To test the potential conservation of regulatory modules across fin types, we generated a series of deletion mutants for two known lmx1b mouse limb enhancers, LARM1 and LARM2, that we show are partially conserved upstream of zebrafish lmx1bb. These experiments revealed that LARM function is essential for dorsoventral patterning in the paired pectoral and pelvic fins of zebrafish but is dispensable for formation of the unpaired dorsal and anal fins. To determine if the paired fin specificity of LARM-mediated lmx1b regulation is a feature of more basal gnathostomes, we used a single cell multiomics (RNAseq + ATACseq) approach in the epaulette shark Hemiscyllium ocellatum, a representative chondrichthyan and outgroup to osteichthyans. Strikingly, these analyses demonstrated linkages between the LARM1 enhancer and lmx1b in the unpaired dorsal fins of epaulette sharks, as well as the deployment of a Lmx1b-mediated regulatory network whose core downstream components are conserved between dorsal fins, paired fins, and limbs. Collectively, these data support the ancient origin of a "DV" regulatory module in median fins that was redeployed during the early evolution paired fins, facilitating the assembly of the DV patterning axis. Intriguingly, multiome-based inference of global fin network architecture in epaulette shark also revealed reduced regulatory complexity in pectoral relative to median fins, suggesting that co-option as a mechanism for anatomical innovation can proceed through selective streamlining of ancestral network components.

developmental biology↗

bioRxiv2025

SATB1 maintains naive-like identity in antiviral CD8⁺ T cells by limiting chromatin remodelling at effector gene loci.

Optimal CD8+ T cell differentiation requires the engagement of transcriptional programs that drive effector phenotypes and function, whilst also shutting down transcriptional programs that maintain the naive state. While the distinct factors that underpin each state are well studied, the molecular mechanisms that control the switch from the naive to effector state are not fully understood. Utilising integrated analysis of single-cell genomic data, we identified CD8+ T cell effector transcriptional networks that are restrained in the naive state by the chromatin binding protein Special AT-rich sequence binding protein-1 (SATB1). Utilising a SATB1-Tg model, whereby activated CD8+ T cells are unable to down regulate SATB1 upon activation, we observed limited effector differentiation and an inability to engage effector programs in response to both primary and secondary influenza A virus infection. Mechanistically, SATB1 limited chromatin remodelling at key gene loci required for the full engagement of the CD8+ T cell effector program. Hence, SATB1 is a master gatekeeper that maintains the naive T cell state and whose downregulation is necessary to allow transition from a naive to effector state upon T cell activation. SATB1 modulation may provide new strategies for improving CD8+ T cell longevity and self-renewal capacity in different immunotherapeutic treatments.

immunology↗

bioRxiv2023

Active maintenance of CD8+ T cell naivety through regulation of global genome architecture

The differentiation of naive CD8+ cytotoxic T lymphocytes (CTLs) into effector and memory states results in large scale changes in transcriptional and phenotypic profiles. Little is known about how large-scale changes in genome organisation reflect or underpin these transcriptional programs. We utilised Hi-C to map changes in the spatial organisation of long-range genome contacts within naive, effector and memory virus-specific CD8+ T cells. We observed that the architecture of the naive CD8+ T cell genome was distinct from effector and memory genome configurations with extensive changes within discrete functional chromatin domains. However, deletion of the BACH2 or SATB1 transcription factors was sufficient to remodel the naive chromatin architecture and engage transcriptional programs characteristic of differentiated cells. This suggests that the chromatin architecture within naive CD8+ T cells is preconfigured to undergo autonomous remodelling upon activation, with key transcription factors restraining differentiation by actively enforcing the unique naive chromatin state. One Sentence SummaryCD8+ T cell naivety is actively maintained by transcription factors that enforce a distinct, naive chromatin architecture. HighlightsO_LICD8+ T cell differentiation states are underscored by distinct chromatin looping architectures. C_LIO_LIChromatin loops juxtapose CTL state appropriate enhancers, transcription factors and genes. C_LIO_LIEffector and memory CTLs have similar genome architectures, explaining rapid memory recall. C_LIO_LICTL differentiation is restrained by BACH2 and SATB1, which enforce a naive loop architecture. C_LI

immunology↗

bioRxiv2020

KDM6B-dependent chromatin remodelling underpins effective virus-specific CD8+ T cell differentiation.

Naive CD8+ T cell activation results in an autonomous program of cellular proliferation and differentiation. However, the mechanisms that underpin this process are unclear. Here we profiled genome-wide changes in chromatin accessibility, gene transcription and the deposition of a key chromatin modification (H3K27me3) early after naive CD8+ T cell activation. Rapid upregulation of the histone demethylase, KDM6B, prior to first cell division was required for initiating H3K27me3 removal at genes essential for subsequent T cell differentiation and proliferation. Inhibition of KDM6B-dependent H3K27me3 demethylation limited the magnitude of an effective primary virus-specific CD8+ T cell response and the formation of memory CD8+ T cell populations. Accordingly, we define the early spatio-temporal events underpinning early lineage-specific epigenetic reprogramming that is necessary for autonomous CD8+ T cell proliferation and differentiation.

immunology↗

bioRxiv2018

Widespread cytoplasmic polyadenylation programs asymmetry in the germline and early embryo

BACKGROUNDThe program of embryonic development is launched by selective activation of a silent maternal transcriptome. In Caenorhabditis elegans, nuclei of the adult germline are responsible for the synthesis of at least two distinct mRNA populations; those required for housekeeping functions, and those that program the oocyte-to-embryo transition. We mapped this separation by changes to the length-distribution of poly(A)-tails that depend on GLD-2 mediated cytoplasmic polyadenylation and its regulators genome-wide.\n\nRESULTSMore than 1000 targets of cytoplasmic polyadenylation were identified by differential polyadenylation. Amongst mRNA with the greatest dependence on GLD-2 were those encoding RNA binding proteins with known roles in spatiotemporal patterning such as mex-5 and pos-1. In General, the 3 UTR of GLD-2 targets were longer, contained cytosine-patches, and were enriched for non-standard polyadenylation-motifs. To identify the deadenylase that initiated transcript silencing, we depleted the known deadenylases in the gld-2(0) mutant background. Only the loss of CCF-1 suppressed the short-tailed phenotype of GLD-2 targets suggesting that in addition to its general role in RNA turnover, this is the major deadenylase for regulatory silencing of maternal mRNA. Analysis of poly(A)-tail length-change in the embryo lacking specific RNA-binding proteins revealed new candidates for asymmetric expression in the first embryonic divisions.\n\nCONCLUSIONThe concerted action of RNA binding proteins exquisitely regulates GLD-2 activity in space and time. We present our data as interactive web resources for a model where GLD-2 mediated cytoplasmic polyadenylation regulates target mRNA at each stage of worm germline and early embryonic development.

developmental biology↗