Biology subjects

Saka, S.

Publications and source records attributed to Saka, S..

6 recordsLinked to original sources

bioRxiv2026

Conserved cerebellar rhombic lip compartmentalization and Eomes regulatory networks govern unipolar brush cell development

The rhombic lip (RL) gives rise to all cerebellar glutamatergic cell types, including unipolar brush cells (UBCs). Disruptions to UBC development can lead to the neurodevelopmental disorder Dandy-Walker Syndrome and the pediatric brain tumor medulloblastoma, but these diseases have not been adequately modeled in mice. To evaluate conservation of UBC development in mouse and human, we examined UBC localization, lineage decisions, and the underlying molecular mechanisms of UBC differentiation using multiplex immunofluorescence and single-cell RNA-seq of wild-type and conditional knockout animals of the primary UBC transcription factor Eomes. Similar to the human RL, the murine RL is molecularly compartmentalized, cycling EOMES+ UBC progenitors are highly abundant, and persist after birth. Eomes regulates the transcriptional networks important for UBC differentiation and migration, but not UBC fate. Overall, our findings suggest that murine UBC development recapitulates many features of human UBC development, with EOMES playing a central role in UBC maturation.

developmental biology↗

bioRxiv2026

Yin Yang 1-Dependent PcG Function is Essential for TET2 Expression and Early T cell Development

Yin Yang 1 (YY1) is a multifunctional transcription factor and mammalian Polycomb Group (PcG) protein critical for lymphocyte development. While YY1 is required for early T-cell development and survival, the underlying mechanisms remain incompletely defined. Herein, we utilize the YY1 REPO domain conditional knockout mouse model (Yy1-/{Delta}REPO) to further dissect the YY1-PcG domain dependent epigenetic regulation in early T cell development. Yy1-/{Delta}REPO mice show a developmental block at the double-negative (DN) 3 to DN4 T cell transition, with expansion of the DN3 population and reduced TCR{beta}+ DN4 T cells. The genetic network governing T cell differentiation is dysregulated in Yy1-/{Delta}REPO DN3 T cells. YY1 binds directly to the Tet2 promoter, and deletion of the YY1 REPO domain leads to downregulation of the DNA demethylase TET2 in DN3 T cells. Although deletion of the YY1 REPO domain does not impair YY1 binding at the Tet2 promoter, H3K4me3 enrichment at the promoter is reduced. Pharmacologic inhibition of TET catalytic activity in wild-type DN thymocytes partially recapitulates the developmental defects in Yy1-/{Delta}REPO DN thymocytes, whereas re-expression of TET2 catalytic domain in Yy1-/{Delta}REPO DN thymocytes partially rescues T cell development. Collectively, these findings reveal a previously unappreciated link between YY1 REPO domain-dependent regulation and TET2-mediated epigenetic control during early T-cell development.

molecular biology↗

bioRxiv2026

YY1-Mediated Polycomb Group Function Safeguards Hematopoietic Stem Cells from Premature Aging

Hematopoietic stem cells (HSCs) undergo functional decline with age, characterized by myeloid-biased differentiation, loss of quiescence, and altered metabolic homeostasis. The molecular mechanisms driving these changes remain incompletely understood. Yin Yang 1 (YY1) is a multifunctional transcription factor and mammalian Polycomb group (PcG) protein that recruits PcG complexes to specific genomic loci via its 26-amino acid REPO (Recruitment of Polycomb) domain. To define the role of YY1 PcG function in adult HSCs, we generated a conditional YY1 REPO domain knockout mouse model (Yy1-/{Delta}REPO). Deletion of the REPO domain led to premature HSC aging, with expansion of immunophenotypic HSCs but loss of long-term self-renewal capacity. Yy1-/{Delta}REPO HSCs exhibited myeloid-biased output, expansion of myeloid-primed multipotent progenitors, increased myeloid colony formation, and an elevated myeloid-to-lymphoid ratio in peripheral blood. These cells displayed reduced quiescence, elevated reactive oxygen species, increased mitochondrial oxidative capacity, and enhanced {beta}-galactosidase activity--hallmarks of cellular aging. RNA-seq demonstrated dysregulation of gene networks governing HSC metabolism. Together, these findings establish YY1 PcG activity as a key epigenetic mechanism that preserves metabolic quiescence, sustains long-term self-renewal, and delays HSC aging. Our studies reveal a fundamental PcG-dependent epigenetic mechanism that dictate cell fate decisions and function decline during HSC aging.

molecular biology↗

bioRxiv2025

Artemis Regulates Homology-Independent Prime Editing (PRINS) for Enhanced Genomic Insertions

Nuclease-based prime editing (PEn) offers enhanced genomic insertion efficiency compared to nickase-based prime editors, but its reliance on double-strand break (DSB) repair leads to complex and often unpredictable on-target indel distributions. PRINS editing, a PEn variant utilizing springRNAs, uniquely relies on non-homologous end joining (NHEJ) for insertions, providing an insertion-only strategy ideal for functional protein tagging or serine integrase landing pad insertions, yet it suffers from inherent imprecision. Here, we identify the DNA repair factor Artemis (DCLRE1C) as a key regulator of PEn-generated indel profiles, particularly in springRNA-mediated PRINS editing. Through a targeted genetic screen, we show that the absence of Artemis significantly shifts indel distributions away from deletions and shorter truncations towards longer, functionally acceptable insertions. Our data indicates that Artemis cleaves PEn-generated 3-overhangs in a length-dependent manner, with its impact increasing for longer reverse-transcribed overhangs. This understanding reveals that regulating Artemis activity can improve insertion frequency specifically for PRINS. We develop and validate robust epigenetic (CRISPRoff) and antisense oligonucleotide (ASO) strategies to effectively silence/knockdown Artemis expression, successfully recapitulating the beneficial PRINS editing outcomes observed in Artemis-deficient cells. Leveraging these insights, we show that Artemis modulation can enhance endogenous protein tagging in cells, including challenging hiPSC-derived non-dividing cardiomyocytes. Our findings support Artemis as a key regulator of PRINS editing outcomes and present a tunable strategy to optimize insertion efficiency for diverse genomic engineering and therapeutic applications.

molecular biology↗

bioRxiv2025

NEURO-IMMUNE CRYPT-ASSOCIATED CELLS DRIVE COLORECTAL CARCINOGENESIS VIA REST-MEDIATED PHENOTYPIC REPROGRAMMING: IMPLICATIONS FOR TUMORIGENESIS AND VIRAL SUSCEPTIBILITY

Colorectal cancer (CRC) pathogenesis remains linked to poorly defined cellular origins and microenvironmental drivers. We identify Neuro-Immune Crypt-Associated (NICA) cells as a privileged pathogen portal and a plausible epithelial cell of origin. During carcinogenesis, the repressor REST drives a neuroendocrine-to-epithelial transition by silencing NICA-associated neuroendocrine markers, a lineage loss reversible via epigenetic modulation or genetic ablation in CRC models. This landscape is further shaped by EBV-infected B-lineage cells (BLEICS), which transactivate HERV-H/F elements in CRC cells through paracrine signaling, establishing a niche-restricted viral scar. While tumor crypts sense this retroviral pressure, they exhibit an abortive antiviral signature marked by RNase L downregulation, creating a functional execution gap. We propose a pathogen-first model where chronic inflammatory pressure triggers mutation-silencing -the simultaneous genotoxic and epigenetic inactivation of tumor suppressors. Together, the convergence of NICA plasticity, BLEICS-mediated HERV induction, and compromised antiviral surveillance redefines CRC as a pathogen-driven disruption of the neuro-immune niche.

cancer biology↗

bioRxiv2024

Nucleoporin Nup153 docks the splicing machinery to the nuclear pore for efficient mRNA processing

The nuclear pore complex (NPC), composed of proteins termed nucleoporins (Nups), intercalates the nuclear envelope, and is primarily involved in protein trafficking and mRNA export. At the nuclear basket, Nups have been associated with chromatin organization and postulated to function as transcriptional hubs, working in tandem with mRNA export machinery. However, little is known about the intermediate process of RNA splicing at the NPC. Here, we used BioID to screen for interactors of basket-Nups Nup153 and TPR and discovered the enrichment of splicing proteins across all spliceosome complexes (E, A, B, B*, P). The peripheral nature of the interaction between Nup153 and selected splicing components was confirmed by in-situ proximity ligation assay and STED microscopy. The presence of splicing components at the NPC, reduced upon splicing inhibition, is partly dependent on Nup153 and functionally correlated to the splicing of Nup153-bound genes. Assessed by DamID, Nup153-bound genes ([~]500) are characterized by multiple long introns with lower-than-average GC content. Positioned at the periphery but distinct from the neighbouring lamina-associated domain (LADs) in chromatin signatures and expression levels, these genes showed Nup153-dependent splicing defect, suggesting that splicing occurs at the NPC. Altogether, our data substantiates the gene gating theory bringing transcription and export, now accompanied by speckle-distant splicing events, at the level of the NPC.

cell biology↗