Biology subjects

Galande, S.

Publications and source records attributed to Galande, S..

16 recordsLinked to original sources

bioRxiv2026

Conserved Roles of Sp1 in Zebrafish Development and Early Organogenesis

Transcription factors (TFs) function in combinatorial networks to orchestrate gene expression during development and disease. Yet, the mechanisms underlying their context-specific regulatory roles remain poorly understood. Here, we investigate Specificity Protein 1 (Sp1), the first sequence-specific transcription factor identified and a key regulator of TATA-less gene promoters as a model to elucidate conserved and lineage-specific functions in vertebrate development. While Sp1 is extensively studied in mammalian systems, particularly in cancer progression, its evolutionary acquisition and developmental roles in early vertebrates remain unexplored. Using zebrafish as a model, we characterized the spatiotemporal expression dynamics and functional significance of sp1 during embryogenesis. Loss-of-function analyses revealed profound morphological defects across multiple organ systems, including skeletal, neural, and gastrointestinal tissues. Complementary stage-specific transcriptomic profiling uncovered widespread dysregulation of lineage-defining genes and perturbations in core cellular pathways related to the cell cycle, DNA metabolism, and apoptosis. Together, our findings establish Sp1 as a pivotal transcriptional regulator in early vertebrate development and reveal mechanistic insights into how conserved TF networks coordinate developmental programs and context-dependent disease states. Summary statementThis study characterizes the expression profile and establishes the conserved role of SP1 in specific processes during zebrafish development, which were previously unreported.

developmental biology↗

bioRxiv2025

Satb1 integrates cohesin mediated genome organization and transcriptional regulation during T cell development

Three-dimensional (3D) genome folding, which is highly cell type-specific, plays a crucial role in orchestrating spatiotemporal gene expression. Although factors such as CTCF have been extensively studied in the hierarchical regulation of 3D chromatin organization, the mechanisms driving dynamic genome folding during T cell fate transitions remain incompletely defined. In this study, we reveal that Satb1, a chromatin organizer enriched in the T cell lineage, co-occupies genomic regions with the cohesin complex and Ctcf in double-positive (DP) thymocytes, where chromatin interactions are notably increased. We show that Satb1 physically interacts with the cohesin subunit Smc1a, and its deletion results in aberrant Smc1a binding and reduced chromatin contacts at sites co-occupied by Satb1 and cohesin. In both DP and immature CD4 single-positive (SP) T cells, Satb1 is essential for proper T cell activation and cytokine signaling. At the Cd3 locus, Satb1 and cohesin collaboratively regulate gene expression, with Satb1 loss leading to disrupted Smc1a occupancy and compromised chromatin interactions. Furthermore, Satb1 shows in vitro properties consistent with liquid-liquid phase separation, and disease-associated mutations impair these properties. Together, our findings uncover a molecular mechanism in which Satb1 facilitates chromatin looping through direct interaction with the cohesin complex and its ability to form nuclear condensates, thereby governing transcriptional regulation during T cell development.

immunology↗

bioRxiv2025

SP1 amplifies the effects of cellular proliferation via the Wnt/β-catenin pathway in colon development and cancer

Wnt/{beta}-catenin signaling is a highly conserved pathway across multicellular organisms, playing a pivotal role in various cellular processes essential for development and tissue homeostasis. Aberrant activation of this pathway is a major driver of colorectal cancer (CRC). The transcription factor SP1 has been identified as a key component of the Wnt/{beta}-catenin signaling pathway through its physical interaction with {beta}-catenin in colorectal cancer. However, the distinct roles played by this complex during development versus in disease contexts remain poorly understood. In this study, we conducted molecular and functional analyses by individually depleting SP1 and {beta}-catenin. Interestingly, genes co-regulated by the SP1:{beta}-catenin complex were significantly enriched for functions related to the cell cycle and DNA replication--key processes required for sustaining proliferation, whose disruption can promote tumorigenesis. These findings were further supported by data from mouse tumor models and clinical datasets. Additionally, cross-species analysis using zebrafish larvae revealed a synergistic interaction between SP1 and {beta}-catenin, leading to excessive cell proliferation and developmental defects. Collectively, our results suggest a conserved role for the SP1:{beta}-catenin complex in regulating cell proliferation during development and maintaining cellular homeostasis, processes critical for preventing cancer progression.

cancer biology↗

bioRxiv2024

Statins attenuate Wnt/β-catenin signaling by targeting SATB family proteins in colorectal cancer

Colorectal cancer is the second leading cause of cancer-related deaths worldwide, highlighting the need for improved treatments and advanced molecular research. A recent therapeutic approach focuses on repurposing drugs to target dysregulated pathways involved in tumorigenesis. Among these, statins, commonly known for lowering cholesterol, have attracted attention for their potential anti-cancer properties. Here, we provide direct evidence for the same by assessing the impact of statin treatment on lipid, transcript, and protein levels. Our findings reveal that statins specifically target key components of the Wnt/{beta}-catenin pathway, a major factor in adenoma formation, including the SATB (Special AT-rich Binding protein) family proteins. While SATB1 is recognized as a regulator of tumorigenesis, particularly under Wnt signaling, SATB2 appears to exert an opposing role. We demonstrate that statin treatment reciprocally alters the expression pattern of these proteins. Furthermore, a human clinical trial evaluating statins as an anti-cancer therapy supports the hypothesis that differential expression of SATB proteins is crucial in tumorigenic outcomes. In conclusion, this modulation by statin treatment suggests promising new therapeutic avenues through drug repurposing.

cancer biology↗

bioRxiv2023

PRDM16 co-operates with LHX2 to shape the human brain

PRDM16 is a dynamic transcriptional regulator of various stem cell niches, including adipocytic, hematopoietic, cardiac progenitors, and neural stem cells. PRDM16 has been suggested to contribute to 1p36 deletion syndrome, one of the most prevalent subtelomeric microdeletion syndromes. We report a patient with a de novo nonsense mutation in the PRDM16 coding sequence, accompanied by lissencephaly and microcephaly features. Human stem cells were genetically modified to mimic this mutation, generating cortical organoids that exhibited altered cell cycle dynamics. RNA sequencing of cortical organoids at day 32 unveiled changes in cell adhesion and WNT-signaling pathways. ChIP-seq of PRDM16 identified binding sites in postmortem human fetal cortex, indicating the conservation of PRDM16 binding to developmental genes in mice and humans, potentially at enhancer sites. A shared motif between PRDM16 and LHX2 was identified and further examined through comparison with LHX2 ChIP-seq data from mice. These results suggested a collaborative partnership between PRDM16 and LHX2 in regulating a common set of genes and pathways in cortical radial glia cells, possibly via their synergistic involvement in cortical development.

developmental biology↗

bioRxiv2023

A prebiotic genetic alphabet as an early Darwinian ancestor for pre-RNA evolution

RNA-based genetic code is thought to be central to lifes emergence due to its dual ability for information transfer and catalysis. Nonetheless, the genetic code of early life was potentially not restricted to canonical genetic alphabets alone. The presence of an extensive repertoire of modified nucleobases in extant biology as signatures of the past, highlights the relevance of non-canonical alphabets, ably strengthened by experiments demonstrating their ready conversion into nucleosides and nucleotides. All these strongly support a pre-RNA World, wherein informational molecules are posited to have contained alternate genetic alphabets. Nevertheless, understanding pre-RNA molecules capacity to acquire emergent function has remained less prevalent. Further, the steps involved in their transition to a canonical RNA World has not been systematically studied in the origins of life framework. In this study, we report the synthesis of a prebiotically relevant genetic alphabet containing the non-canonical nucleobase, barbituric acid. We demonstrate for the first instance the enzymatic incorporation of this prebiotically plausible alphabet (BaTP) into an RNA, using proteinaceous T7 RNA polymerase. Pertinently, the incorporation of this genetic alphabet into a baby spinach aptamer did not affect its overall secondary structure, while also allowing it to retain its aptameric function. Furthermore, we demonstrate the faithful transfer of genetic information from pre-RNA-containing barbitudine nucleotides to DNA, using a high-fidelity RNA-dependent DNA polymerase. These findings allude to a putative pathway for the early molecular evolution of the genetic code of extant life.

biochemistry↗

bioRxiv2022

Combined promoter-capture Hi-C and Hi-C analysis reveals a fine-tuned regulation of 3D chromatin architecture in colorectal cancer

Hi-C is a widely used method for profiling chromosomal interactions in the 3-dimensional context. Due to limitations on the depth of sequencing, the resolution of most Hi-C datasets is often insufficient for scoring fine-scale interactions. We therefore used promoter-capture Hi-C (PCHi-C) data for mapping these subtle interactions. From multiple colorectal cancer (CRC) studies, we combined PCHi-C with Hi-C datasets to understand the dynamics of chromosomal interactions from cis regulatory elements to topologically associated domain (TAD)-level, enabling detection of fine-scale interactions of disease-associated loci within TADs. Our integrated analyses of PCHi-C and Hi-C datasets from CRC cell lines along with histone modification landscape and transcriptome signatures highlight significant genomic structural instability and their association with tumor-suppressive transcriptional programs. Such analyses also yielded nine dysregulated genes. Transcript profiling revealed a dramatic increase in their expression in CRC cell lines as compared to NT2D1 human embryonic carcinoma cells, supporting the predictions of our bioinformatics analysis. We further report increased occupancy of activation associated histone modifications H3K27ac and H3K4me3 at the promoter regions of the targets analyzed. Our study provides deeper insights into the dynamic 3D genome organization in CRC and identification of affected genes which may serve as potential biomarkers for CRC. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/515643v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@11a9fc8org.highwire.dtl.DTLVardef@f01eb4org.highwire.dtl.DTLVardef@6ff038org.highwire.dtl.DTLVardef@103fc24_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2022

H4K20me1 plays a dual role in transcriptional regulation during regeneration and axispatterning of Hydra

The evolution of the first body axis in the animal kingdom and an extensive ability to regenerate makes Hydra, a Cnidarian, an excellent model system for understanding the underlying epigenetic mechanisms. We identify that SETD8 is critical for regeneration due to its interaction with {beta}-catenin to fine-tune the underlying gene regulatory network. Its target histone mark, H4K20me1, colocalizes with transcriptional activation machinery locally at the {beta}-catenin bound TCF/LEF binding sites on the promoters of head-associated genes, marking an epigenetic activation node. Contrastingly, genome-wide analysis of the H4K20me1 occupancy revealed a negative correlation with transcriptional activation. We propose H4K20me1 as a general repressive histone mark in Cnidaria and describe its dichotomous role in transcriptional regulation in Hydra.

molecular biology↗

bioRxiv2021

Mapping Interactome Networks of FOSL1 and FOSL2 in Human Th17 Cells

Dysregulated function of Th17 cells has implications in immunodeficiencies and autoimmune disorders. Th17 cell-differentiation is orchestrated by a complex network of transcription factors, including several members of the activator protein (AP-1) family. Among these, FOSL1 and FOSL2 influence the effector responses of Th17 cells. However, the molecular mechanisms underlying these functions are unclear, owing to the poorly characterized protein interaction networks of these factors. Here, we establish the first interactomes of FOSL1 and FOSL2 in human Th17 cells, using affinity purification-mass spectrometry analysis. In addition to the known JUN proteins, we identified several novel binding partners of FOSL1 and FOSL2. Gene ontology analysis found a major fraction of these interactors to be associated with RNA binding activity, which suggests new mechanistic links. Intriguingly, 29 proteins were found to share interactions with FOSL1 and FOSL2, and these included key regulators of Th17-fate. We further validated the binding partners identified in this study by using parallel reaction monitoring targeted mass-spectrometry and other methods. Our study provides key insights into the interaction-based signaling mechanisms of FOSL factors that potentially govern Th17 cell-differentiation and associated pathologies.

immunology↗

bioRxiv2021

The AP-1 factors FOSL1 and FOSL2 co-regulate human Th17 responses

Th17 cells protect mucosal barriers, but their aberrant activity can cause autoimmunity. Molecular networks dictating human Th17 function are largely unexplored, and this hinders disease-studies. Here, we investigated the roles of the AP-1 factors, FOSL1 and FOSL2, in inducing human Th17 responses. Transient knockdown and over-expression strategies found the two proteins to inhibit Th17-cell identity, while revealing a distinct cooperativity between their functions. Strikingly, FOSL1 plays different roles in human and mouse and FOSL-mediated Th17 regulation is opposed by the AP-1 factor, BATF. Genome-wide occupancy analysis demonstrated the co-localization of FOSL1, FOSL2 and BATF in the vicinity of key Th17 genes. The functional interplay among these factors is possibly governed by sharing interactions with a common set of lineage-associated proteins. We further discovered that the genomic binding sites of these factors harbour a large number of disease-linked SNPs, many of which alter the ability of a given factor to bind DNA. Our findings thus provide crucial insights into the transcriptional regulation of human Th17 function and associated pathologies. ONE SENTENCE SUMMARYFOSL1- and FOSL2-mediated transcription during early human Th17 differentiation

immunology↗

bioRxiv2021

The Hippo pathway transcriptional co-activator YAP is involved in head regeneration and bud development in Hydra

The Hippo signaling pathway has been shown to be involved in the regulation of cellular identity, cell/tissue size maintenance and mechanotransduction. The Hippo pathway consists of a kinase cascade which determines the nucleo-cytoplasmic localization of YAP in the cell. YAP is the effector protein in the Hippo pathway which acts as a transcriptional cofactor for TEAD. Phosphorylation of YAP upon activation of the Hippo pathway prevents it from entering the nucleus and hence abrogates its function in transcription of target genes. In Cnidaria, the information on the regulatory roles of the Hippo pathway is virtually lacking. Here, we report for the first time the existence of a complete set of Hippo pathway core components in Hydra. By studying their phylogeny and domain organization, we report evolutionary conservation of the components of the Hippo pathway. Protein modelling suggested conservation of YAP-TEAD interaction in Hydra. We also characterized the expression pattern of the homologs of yap, hippo, mob and sav in Hydra using whole mount RNA in situ hybridization and report their possible role in stem cell maintenance. Immunofluorescence assay revealed that Hvul_YAP expressing cells occur in clusters in the body column and are excluded in the terminally differentiated regions. The YAP expressing cells are recruited early during head regeneration and budding implicating the Hippo pathway in early response to injury or establishment of oral fate. These cells exhibit a non-clustered existence at the site of regeneration and budding, indicating the involvement of a new population of YAP expressing cells during oral fate specification. Collectively, we posit that the Hippo pathway is an important signaling system in Hydra, its components are ubiquitously expressed in the Hydra body column, and may play crucial role in Hydra oral fate specification.

developmental biology↗

bioRxiv2020

Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis

Zygotic genome activation (ZGA) initiates regionalized transcription responsible for the acquisition of distinct cellular identities. ZGA is dependent upon dynamic chromatin architecture sculpted by conserved DNA-binding proteins. However, whether the tissue-specific transcription is mechanistically linked with the onset of ZGA is unknown. Here, we have addressed the involvement of chromatin organizer SATB2 in orchestrating these processes during vertebrate embryogenesis. Integrative analysis of transcriptome, genome-wide occupancy and chromatin accessibility revealed contrasting molecular functions of maternal and zygotic pools of Satb2. Maternal Satb2 represses zygotic genes by influencing the interplay between the pluripotency factors. By contrast, zygotic Satb2 activates transcription of the same group of genes during neural crest development and organogenesis. Comparative analysis of maternal versus zygotic function of Satb2 underscores how these antithetical activities are temporally coordinated and functionally implemented. We discuss the evolutionary implications of the biphasic and bimodal regulation of landmark developmental transitions by a single determinant.

developmental biology↗

bioRxiv2020

Differential tissue stiffness of body column facilitates locomotion of Hydra on solid substrates

The bell-shaped members of Cnidaria typically move around by swimming, whereas the Hydra polyp can perform locomotion on solid substrates in aquatic environment. To address the biomechanics of locomotion on rigid substrates, we studied the somersaulting locomotion in Hydra. We applied atomic force microscopy to measure the local mechanical properties of Hydras body column and identified the existence of differential Youngs modulus between the shoulder region versus rest of the body column at 3:1 ratio. We show that somersault primarily depends on differential tissue stiffness of the body column and is explained by computational models that accurately recapitulate the mechanics involved in this process. We demonstrate that perturbation of the observed stiffness variation in the body column by modulating the extracellular matrix (ECM) polymerization impairs the somersault movement. These results provide mechanistic basis for the evolutionary significance of differential extracellular matrix properties and tissue stiffness.

biophysics↗

bioRxiv2019

A novel cis regulatory element regulates human XIST in CTCF-dependent manner

The long non-coding RNA XIST is the master regulator for the process of X chromosome inactivation (XCI) in mammalian females. Here we report the existence of a hitherto uncharacterized cis regulatory element (cRE) within the first exon of human XIST, which determines the transcriptional status of XIST during the initiation and maintenance phases of XCI. In the initiation phase, pluripotency factors bind to this cRE and keep XIST repressed. In the maintenance phase of XCI, the cRE is enriched for CTCF which activates XIST transcription. By employing a CRISPR-dCas9-KRAB based interference strategy, we demonstrate that binding of CTCF to the newly identified cRE is critical for regulating XIST in a YY1-dependent manner. Collectively, our study uncovers the combinatorial effect of multiple transcriptional regulators influencing XIST expression during the initiation and maintenance phases of XCI.

molecular biology↗

bioRxiv2018

Regulation of transcription factor SP1 by β-catenin destruction complex modulates Wnt response

The ubiquitous transcription factor Specificity protein 1 (SP1) is heavily modified post-translationally. These modifications are critical for switching its functions and modulation of its transcriptional activity, DNA-binding and stability. However the mechanism governing the stability of SP1 by cellular signaling pathways is not well understood. Here, we provide biochemical and functional evidences that SP1 is an integral part of the Wnt signaling pathway. We identified a phosphodegron motif in SP1 that is specific to mammals. In absence of Wnt signaling, GSK3{beta} kinase mediated phosphorylation and {beta}-TrCP E3 ubiquitin ligase mediated ubiquitination is required to induce SP1 degradation. When Wnt signaling is on, SP1 is stabilized in {beta}-catenin-dependent manner. SP1 directly interacts with {beta}-catenin and Wnt signaling induces the stabilization of SP1 by impeding its interaction with {beta}-TrCP and AXIN1, components of the destruction complex. Wnt signaling suppresses ubiquitination and subsequent proteosomal degradation of SP1. Furthermore, SP1 regulates Wnt-dependent stability of {beta}-catenin and their mutual stabilization is critical for target gene expression, suggesting a feedback mechanism. Upon stabilization SP1 and {beta}-catenin co-occupy the promoters of TCFL2/{beta}-catenin target genes. Collectively, this study uncovers a direct link between SP1 and {beta}-catenin in Wnt signaling pathway.

molecular biology↗

bioRxiv2017

PDZ Domains in Microorganisms: Link Between Stress Response and Protein Synthesis

The PSD-95/Dlg-A/ZO-1 (PDZ) domain is highly expanded and diversified in metazoan where it is known to assemble diverse signalling components by virtue of interactions with other proteins in sequence-specific manner. In contrast, in bacteria it monitors protein quality control during stress response. The distribution, functions and origin of PDZ domain-containing proteins in prokaryotes are largely unknown. We analyzed 7,852 PDZ domain-containing proteins in 1,474 prokaryotes and fungi. PDZ domains are abundant in eubacteria; and, this study confirms their occurrence also in archaea and fungi. Of all eubacterial PDZ domain-containing proteins, 89% are predicted to be membrane and periplasmic, explaining the depletion of bacterial domain forms in metazoan. Planctomycetes, myxobacteria and other eubacteria occupying terrestrial and aquatic niches encode more domain copies, which may have contributed towards multi-cellularity and prokaryotic-eukaryotic transition. Over 93% of the 7,852 PDZ-containing proteins classified into 12 families including 6 novel families. Out of these 88% harbour eight different protease domains, suggesting their substrate-specificity is guided by PDZ domains. The genomic context provides tantalizing insight towards the functions associated with PDZ domains and reinforces their involvement in protein synthesis. We propose that the highly variable PDZ domain of the uncharacterized Fe-S oxidoreductase superfamily, exclusively found in gladobacteria and several anaerobes and acetogens, may have preceded all existing PDZ domains.

bioinformatics↗