Biology subjects

Koromila, T.

Publications and source records attributed to Koromila, T..

4 recordsLinked to original sources

bioRxiv2025

Differential Roles of Broadly Expressed Transcription Factors in Early Cardiac Cell Specification

Early embryogenesis is governed by intricate gene regulatory networks that orchestrate cell fate specification across all three germ layers. While the role of transcription factors (TFs) and pioneer factors (PFs) in shaping chromatin accessibility is well established, the mechanisms coordinating spatiotemporal gene expression before gastrulation remain poorly understood. Here, we investigate how a coordinated network of early-acting regulators, including the pioneer factors Zelda (Zld), GAGA factor (GAF), and the pioneer-like timing factor Odd-paired (Opa/ZIC3), along with Dorsal (Dl), Twist (Twi), the Polycomb subunit Enhancer of Zeste (E(z)), and the co-activator CBP, govern early transcriptional events in the Drosophila embryo. Using integrated chromatin accessibility, histone modification, TF binding, and transcriptomic data (bulk and single-cell), we identify two distinct classes of regulatory elements that govern early gene expression. The first class includes distal, PF-dependent enhancers that are inaccessible early and require PFs such as Opa and Zld to overcome Su(H) activities and H3K27me3-mediated repression and initiate transcription. The second class, enriched for PcG domains, comprises proximal enhancers that are accessible from the earliest nuclear cycles, despite being marked by H3K27me3 and bound by E(z). These regions are preloaded with RNA Polymerase II and positioned near promoters, suggesting a regulatory state primed for activation. While bound by multiple early TFs, these enhancers maintain accessibility independently of PF activity, functioning instead as autoregulatory elements that rely on PFs for maintenance rather than initiation. This study expands our understanding of how early TFs and PFs coordinate to balance transcriptional precision and developmental plasticity across germ layers, and redefines the role of PFs as both activators and stabilizers of gene regulatory architecture. Within this framework, Opa regulates key mesodermal and neuroectodermal genes such as slp1 and odd, and its activity is modulated by Suppressor of Hairless (Su(H)). At earlier stages, Su(H) represses Opa target genes, but rising Opa levels at later timepoints override this repression, enabling activation. Together, these findings support a dual-mode enhancer logic: one mode driven by PF-mediated chromatin opening at distal, repressed enhancers, and another where proximal, pre-accessible enhancers within PcG-marked regions are reinforced by PF binding. This study redefines the role of PFs in early development, emphasizing their maintenance and stabilizing roles at poised enhancers, and provides a framework for how embryos balance transcriptional plasticity with spatial precision across all germ layers.

developmental biology↗

bioRxiv2024

Notch/Hairless Pathway Modulation of sog Transcriptional Bursting in Prelude to Gastrulation

Transcriptional regulation, orchestrated by the interplay between transcription factors (TFs) and enhancers, governs gene expression dynamics crucial for cellular processes. While gross, qualitative fluctuations in transcription factor-dependent gene expression patterning have a long history of characterization, the roles of these factors in the nuclei retaining expression in the presence or absence of these factors are now observable using modern techniques. Our study investigates the impact of Suppressor of Hairless (Su(H)), a broadly expressed transcription factor, on enhancer-driven transcriptional modulation using Drosophila early embryos as a model system. Building upon previous findings, we employ super-resolution microscopy to dissect Su(H)s influence on sog Distal (sogD) enhancer activity specifically in nuclei with preserved sogD-driven expression in the absence of Su(H) binding. We demonstrate that Su(H) occupancy perturbations alter expression levels and bursting dynamics. Notably, Su(H) absence during embryonic development exhibits region-specific effects, inhibiting expression dorsally and enhancing expression ventrally, implying a nuanced role in enhancer regulation. Our findings shed light on the intricate mechanisms that govern transcriptional dynamics and suggest a patterning role for Notch/Hairless signaling in sog expression during the transition to gastrulation.

developmental biology↗

bioRxiv2022

Cell-specific occupancy dynamics between the pioneer-like factor Opa/ZIC and Ocelliles/OTX regulate early head development in embryos

During development, embryonic patterning systems direct a set of initially uncommitted pluripotent cells to differentiate into a variety of cell types and tissues. A core network of transcription factors, such as Zelda/POU5F1, Odd-paired (Opa)/ZIC and Ocelliless (Oc)/OTX, are conserved across animals. While Opa is essential for a second wave of zygotic activation after Zelda, it is unclear whether Opa drives head cell specification past gastrulation onset, in the Drosophila embryo. Our hypothesis is that Opa and Oc are interacting with distinct cis-regulatory regions for shaping cell fates in the embryonic head. Using super-resolution microscopy and epigenomic meta-analysis of single cell RNAseq datasets we find that opas and ocs overlapping expression domains are dynamic in the head region, with both factors being simultaneously transcribed at the blastula stage. However, analysis of single-embryo RNAseq data reveals a subgroup of Opa-bound genes to be Opa-independent in the cellularized embryo. Interrogation of these genes against Oc ChIPseq combined with in situ data, suggests that Opa is competing with Oc for the regulation of a subgroup of genes later in gastrulation. Specifically, we find that Oc binds to late, head-specific enhancers independently and activates them in a head-specific wave of zygotic transcription, suggesting distinct roles for Oc in the blastula and gastrula stages.

developmental biology↗

bioRxiv2019

Odd-paired is a late-acting pioneer factor coordinating with Zelda to broadly regulate gene expression in early embryos

Pioneer factors such as Zelda help initiate zygotic transcription in Drosophila early embryos, but whether other factors support this dynamic process is unclear. Odd-paired (Opa), a zinc-finger transcription factor expressed at cellularization, controls transition of genes from pair-rule to segmental patterns along the anterior-posterior axis. Finding that Opa also regulates late expression through enhancer sog_Distal, along the dorso-ventral axis, we hypothesized that Opa acts as a general timing factor. Chromatin-immunoprecipitation (ChIP-seq) confirmed Opa in vivo binding to sog_Distal but also identified widespread binding throughout the genome, comparable to Zelda. Furthermore, chromatin assays (ATAC-seq) demonstrate that Opa, like Zelda, influences chromatin accessibility genome-wide, suggesting both are pioneer factors with common as well as distinct targets. Lastly, embryos lacking opa exhibit widespread, late patterning defects spanning both axes. Collectively, these data suggest Opa, a general timing factor and likely a late-acting pioneer factor, heralds in a secondary wave of zygotic gene expression.

developmental biology↗