Biology subjects

Pradhan, S. J.

Publications and source records attributed to Pradhan, S. J..

7 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

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↗

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

Drosophila FMRP recruits the miRISC to target mRNAs to repress translation

Fragile X syndrome (FXS) is the most common inherited form of intellectual disability and is caused by mutations in the gene encoding for the Fragile X messenger ribonucleoprotein (FMRP). FMRP is an evolutionarily conserved and neuronally enriched RNA binding protein (RBP) with functions in the control of processes including RNA editing, RNA transport, and protein translation. Specific target RNAs play critical roles in neurodevelopment including the regulation of neurite morphogenesis, synaptic plasticity, and cognitive function. The different biological functions of FMRP are modulated by its cooperative interaction with distinct sets of neuronal RNA and protein binding partners. Here, we focus on interactions between FMRP and components of the microRNA (miRNA) pathway. Using the Drosophila model system, we show that dFMRP can repress the translation of a reporter mRNA via a deadenylation-independent mechanism. This repression requires the activity of both AGO1 and GW182, conserved components of the miRNA-containing RISC (miRISC). Interestingly, we find that dFMRP can bind directly to a short stem loop structure in the reporter and that dFMRP binding is a prerequisite for repression by miR-958. Finally, we show that dFmr1 interacts genetically with GW182 to control neurite morphogenesis. Collectively, these data suggest the dFMRP can directly recruit the miRISC to nearby miRNA binding sites and then repress translation via the activity of the miRISC effector, GW182.

molecular biology↗

bioRxiv2021

A micro-evolutionary change in target binding sites as key determinant of Ultrabithorax function in Drosophila.

Hox genes encode Homeodomain-containing transcription factors, which specify segmental identities along the anterior-posterior axis. Functional changes in Hox genes have been directly implicated in the evolution of body plans across the metazoan lineage. The Hox protein Ultrabithorax (Ubx) is expressed and required in developing third thoracic (T3) segments in holometabolous insects studied so far, particularly, of the order Coleoptera, Lepidoptera and Diptera. Ubx function is key to specify differential development of the second (T2) and T3 thoracic segments in these insects. While Ubx is expressed in the third thoracic segment in developing larvae of Hymenopteran Apis mellifera, the morphological differences between T2 and T3 are subtle. To identify evolutionary changes that are behind the differential function of Ubx in these two insects, which are diverged for more than 350 million years, we performed comparative analyses of genome wide Ubx-binding sites between Drosophila and Apis. Our studies reveal that a motif with a TAAAT core is a preferred binding site for Ubx in Drosophila, but not in Apis. Biochemical and transgenic assays suggest that in Drosophila, TAAAT core sequence in the Ubx binding sites is required for Ubx-mediated regulation of two of its target genes studied here. CG13222, a gene that is normally upregulated by Ubx and vestigial (vg), whose expression is repressed by Ubx in T3. Interestingly, changing the TAAT site to a TAAAT site was sufficient to bring an otherwise unresponsive enhancer of the vg gene from Apis under the control of Ubx in a Drosophila transgenic assay. Taken together, our results suggest an evolutionary mechanism by which critical wing patterning genes might have come under the regulation of Ubx in the Dipteran lineage.

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↗

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↗