Biology subjects

Fukaya, T.

Publications and source records attributed to Fukaya, T..

8 recordsLinked to original sources

bioRxiv2026

Polymeric mechanism of enhancer-promoter cooperativity in transcriptional bursting

Emerging evidence suggest that gene expression is controlled though the modulation of transcriptional bursting across species. However, the underlying regulatory mechanisms remain largely uncertain. Recent live-imaging studies have reported that transcription factors (TFs) form a cluster at enhancers just prior to gene activation, thereby locally concentrating the active transcription machinery. This process is thought to be mediated by multivalent interaction between Mediator recruited by TFs. Conversely, transcription itself is also suggested that to influence the assembly of the TF clustering, implicating the presence of a feedback mechanism. To understand the theoretical framework underlying the interplay between TF clustering and transcription, we here develop a polymer micelle model of transcriptional bursting. With this model, multiple RNA polymerase II (Pol II) molecules loaded to the promoter, together with enhancer-bound Mediator, assemble a micelle-like structure due to their connectivity via DNA when the chromatin fiber connecting enhancer and promoter adopts closed conformation, analogous to polysoap micelle. This assembly further recruits freely diffusing Pol II and Mediator in the nucleoplasm even at low concentration up to the optimal size. Our theoretical framework enables quantitative prediction of how dynamic transitions of enhancer-promoter conformation and the stability of the micelle impact the kinetics of transcriptional bursting.

biophysics↗

bioRxiv2026

The Drosophila ZAD zinc finger protein Mulberry shapes the organization of the regulatory genome in the early embryo

Long-range regulatory interactions play a fundamentally important role in the control of gene activity during animal development, yet the underlying mechanisms remain largely unclear. Here, we identified a zinc finger-associated domain (ZAD)-C2H2 zinc finger protein, CG31365/Mulberry, as a looping factor that mediates long-range tethering activity in the early Drosophila embryo. Evidence is provided that Mulberry is specifically recruited to a subset of loop anchors and topological boundaries at key developmental loci to shape genome organization and gene activity. Super-resolution imaging analysis revealed that Mulberry forms nuclear condensates that associate with its target loci through the structured N-terminal ZAD domain. Micro-C analysis further demonstrated that the formation of loops and boundaries is lost in the condensation-deficient Mulberry mutant in a locus-specific manner. We propose that Mulberry acts as a condensation-dependent structural regulator of genome topology, organizing "multi-way regulatory hubs" that mediate long-range gene activation during early embryogenesis.

molecular biology↗

bioRxiv2025

Decoding the molecular logic of rapidly evolving ZAD zinc-finger proteins in Drosophila

The zinc-finger associated domain (ZAD)-containing C2H2 zinc-finger proteins (ZAD-ZnFs) represent the most abundant class of transcription factors that emerged during insect evolution, yet their molecular diversity and biological functions remain largely unclear. Here, we established a systematic CRISPR-based protein-tagging approach that enables direct, unambiguous comparison of nuclear localization and genome-wide binding profiles of endogenous ZAD-ZnFs in developing Drosophila embryos. Evidence is provided that a subset of ZAD-ZnFs forms nuclear condensates through the stacking of the N-terminal ZAD dimerization surface. Disruption of condensation activity leads to misregulation of genome-wide binding profiles and lethality, underscoring its functional and physiological significance in development. Importantly, integrative ChIP-seq and Micro-C data analyses reveal that many ZAD-ZnFs colocalize with core insulator proteins such as CTCF and CP190 to strengthen the formation of topological boundaries. We suggest that the diverse molecular functions of ZAD-ZnFs have evolutionally arisen from their ancestral role as insulator-binding proteins.

molecular biology↗

bioRxiv2022

Dynamic interplay between non-coding enhancer transcription and gene activity in development

Non-coding transcription at the intergenic regulatory regions is a prevalent feature of metazoan genomes, but its biological function remains uncertain. Here, we devised a live-imaging system that permits simultaneous visualization of gene activity along with intergenic non-coding transcription at the single-cell resolution in Drosophila. Quantitative image analysis revealed that elongation of RNA polymerase II across the internal core region of enhancers leads to suppression of transcriptional bursting from linked genes. Super-resolution imaging and genome-editing analysis further demonstrated that enhancer transcription antagonizes molecular crowding of transcription factors, thereby interrupting the formation of transcription hub at the gene locus. We also show that a certain class of developmental enhancers are structurally optimized to co-activate gene transcription together with non-coding transcription effectively. We suggest that enhancer function is flexibly tunable through the modulation of hub formation via surrounding non-coding transcription during development.

molecular biology↗

bioRxiv2022

Mod(mdg4) variants repress telomeric retrotransposonHeT-A by blocking subtelomeric enhancers

Telomeres in Drosophila are composed of sequential non-LTR retrotransposons: HeT-A, TART, and TAHRE. Although they are repressed by the piRNA pathway in the germline, how these retrotransposons are regulated in somatic cells is poorly understood. Here, we show that specific splice variants of Mod(mdg4) repress HeT-A by blocking subtelomeric enhancers in ovarian somatic cells. We found that the Mod(mdg4)-N variant represses HeT-A expression most efficiently among the variants. Mod(mdg4)-N mutant flies show elevated HeT-A expression and female sterility. Mod(mdg4)-N-binding subtelomeric sequences exhibit enhancer-blocking activity, and recruitment of RNA polymerase II (Pol II) on subtelomeres by Mod(mdg4)-N is essential for this enhancer-blocking. Moreover, Mod(mdg4)-N functions to form chromatin boundaries of higher-order chromatin conformation but this mechanism is independent of its Pol II recruitment activity at telomeres/subtelomeres. This study provides a link between enhancer-blocking and telomere regulation, and two different molecular mechanisms exhibited by an insulator protein to orchestrate precise gene expression.

molecular biology↗

bioRxiv2021

Regulation of transcriptional bursting by core promoter elements in the Drosophila embryo

Regulatory interactions between enhancers and core promoters are fundamental for the temporal and spatial specificity of gene expression in development. The central role of core promoters is to initiate productive transcription in response to enhancers activation cues. However, it has not been systematically assessed how individual core promoter elements affect the induction of transcriptional bursting by enhancers. Here, we provide evidence that each core promoter element dynamically alters "enhancer responsiveness" by changing functional parameters of transcriptional bursting in developing Drosophila embryos. Quantitative live imaging analysis revealed that the timing and the continuity of burst induction are common regulatory steps on which core promoter elements impact. We also show that core promoters use the upstream TATA box as an amplifier of transcriptional bursting upon interaction with enhancers. Genome editing analysis of the pair-rule gene fushi tarazu further revealed that the endogenous TATA box and the downstream core promoter element are both essential for the correct expression and the function of key developmental genes in early embryos. We suggest that core promoter elements serve as a key regulatory module in converting enhancer activity into transcription dynamics during animal development.

molecular biology↗

bioRxiv2020

Dynamic regulation of anterior-posterior patterning genes in living Drosophila embryos

Expression of the gap and pair-rule genes plays an essential role in body segmentation during Drosophila embryogenesis [1-5]. However, it remains unclear how precise expression patterns of these key developmental genes arise from stochastic transcriptional activation at the single cell level. Here, I employed genome editing and live imaging approaches to comprehensively visualize regulation of the gap and pair-rule genes at the endogenous loci. Quantitative image analysis revealed that the total duration of active transcription (transcription period) is a major determinant of spatial patterning of gene expression in early embryos. The length of transcription period is regulated by the continuity of bursting activities in individual nuclei, with core expression domain producing more bursts than boundary region. Each gene exhibits distinct rate of nascent RNA production during transcriptional bursting, which contributes to gene-to-gene variability in the total output. I also provide evidence for "enhancer competition", wherein a distal weak enhancer interferes with transcriptional activation by a strong proximal enhancer to downregulate the length of transcription period without changing the transcription rate. Analysis of endogenous hunchback (hb) locus revealed that the removal of distal shadow enhancer induces strong ectopic transcriptional activation, which suppresses refinement of broad expression domain into narrower stripe pattern at the anterior part of embryos. This study provides key insights into the link between transcriptional bursting, enhancer-promoter interaction and spatiotemporal patterning of gene expression during animal development.

developmental biology↗

bioRxiv2018

High prevalence of the antibody against Syncytin-1 in schizophrenia

Both genetic and environmental factors have been considered causative agents for schizophrenia (SZ). However, no single gene has been shown responsible for the development of SZ. Furthermore, the pathophysiological roles of environmental factors including psychological stress, autoimmunity, and microbial infection have not been fully understood. Previous studies have suggested the involvement of one of the human endogenous retroviruses (HERVs), HERV-W, in SZ. In this study, prevalence of antibodies against the HERV-W Syncytin-1 protein was examined using a newly developed ELISA test. Fifty percent of patients with SZ (24 out of 48 cases) were antibody-positive, with a specificity of greater than 95% (less than 5% of control cases, 3 out of 79). No significant effect of medication was evident, nor did any SZ cases become seropositive after diagnosis. These findings indicate a possible involvement of HERV-W expression in the development of SZ and support its applicability to laboratory diagnoses.

neuroscience↗