Biology subjects

Cho, C.-Y.

Publications and source records attributed to Cho, C.-Y..

10 recordsLinked to original sources

bioRxiv2025

A mitotic bookmark coordinates transcription and replication

Collisions between advancing replication forks and elongating transcripts pose a universal threat. During the rapid nuclear division cycles in early Drosophila embryos, coordinating transcription and replication is critical to reduce the risk of collisions. In each cycle, replication begins immediately after mitosis, while transcription starts 3 minutes later, overlapping with replication for the remainder of interphase. We previously showed that transcription depends on the coactivator Brd4, which forms hubs at active genes. Here, we show that Brd4 persists on mitotic chromosomes as bookmarks of transcriptional activity and, upon anaphase entry, recruits the replication activator Cdc7 to specify early-replicating genomic regions in the following interphase. Additionally, Cdc7 activity removes Brd4 bookmarks such that post-mitotic transcription occurs only after a new round of Brd4 hub assembly. Early initiation of replication while deferring initiation of transcription is proposed to allow unimpeded transcriptional elongation behind advancing replication forks. Supporting this, inhibiting Cdc7 delayed replication, stabilized Brd4 bookmarks, and resulted in premature transcription with elongation defects. We propose that Cdc7 triggers a functional switch in Brd4 that enforces temporal ordering of the initiation of transcription and replication, thereby minimizing collisions. This switching process might underlie the widespread correlation between transcriptional activity and early replication.

cell biology↗

bioRxiv2024

Cell cycle-regulated transcriptional pausing of Drosophila replication-dependent histone genes

Coordinated expression of replication-dependent (RD) histones genes occurs within the Histone Locus Body (HLB) during S phase, but the molecular steps in transcription that are cell cycle regulated are unknown. We report that Drosophila RNA Pol II promotes HLB formation and is enriched in the HLB outside of S phase, including G1-arrested cells that do not transcribe RD histone genes. In contrast, the transcription elongation factor Spt6 is enriched in HLBs only during S phase. Proliferating cells in the wing and eye primordium express full-length histone mRNAs during S phase but express only short nascent transcripts in cells in G1 or G2 consistent with these transcripts being paused and then terminated. Full-length transcripts are produced when Cyclin E/Cdk2 is activated as cells enter S phase. Thus, activation of transcription elongation by Cyclin E/Cdk2 and not recruitment of RNA pol II to the HLB is the critical step that links histone gene expression to cell cycle progression in Drosophila.

cell biology↗

bioRxiv2022

Stepwise modifications of transcriptional hubs link pioneer factor activity to a burst of transcription

Eukaryotic transcription begins with the binding of transcription factors (TFs), which promotes the subsequent recruitment of coactivators and pre-initiation complexes. It is commonly assumed that these factors eventually co-reside in a higher-order structure, allowing distantly bound TFs to activate transcription at core promoters. Here we performed live imaging of endogenously tagged proteins, including the pioneer TF Zelda, the coactivator dBrd4, and RNA polymerase II (RNAPII), in early Drosophila embryos. We show that these factors are sequentially and transiently recruited to discrete clusters during activation of non-histone genes. We present evidence that Zelda acts with the acetyltransferase dCBP to nucleate dBrd4 hubs, which then trigger pre-transcriptional clustering of RNAPII; continuous transcriptional elongation then disperses clusters of dBrd4 and RNAPII. Our results suggest that activation of transcription by eukaryotic TFs involves a succession of distinct biochemical complexes that culminate in a self-limiting burst of transcription.

cell biology↗

bioRxiv2022

The Parasite Intraerythrocytic Cycle and Human Circadian Cycle are Coupled During Malaria Infection

During infections with malaria parasites P. vivax, patients exhibit rhythmic fevers every 48 hours. These fever cycles correspond with the time parasites take to traverse the Intraerythrocytic Cycle (IEC) and may be guided by a parasite-intrinsic clock. Different species of Plasmodia have cycle times that are multiples of 24 hours, suggesting they may be coordinated with the host circadian clock. We utilized an ex vivo culture of whole blood from patients infected with P. vivax to examine the dynamics of the host circadian transcriptome and the parasite IEC transcriptome. Transcriptome dynamics revealed that the phases of the host circadian cycle and the parasite IEC were correlated across multiple patients, suggesting that the cycles are coupled. In mouse model systems, host-parasite cycle coupling appears to provide a selective advantage for the parasite. Thus, understanding how host and parasite cycles are coupled in humans could enable anti-malarial therapies that disrupt this coupling.

systems biology↗

bioRxiv2022

Temporal control of late replication and coordination of origin firing by self-stabilizing Rif1-PP1 hubs in Drosophila

In the metazoan S phase, coordinated firing of clusters of origins replicates different parts of the genome in a temporal program. Despite advances, neither the mechanism controlling timing nor that coordinating firing of multiple origins is fully understood. Rif1, an evolutionarily conserved inhibitor of DNA replication, recruits protein phosphatase 1 (PP1) and counteracts firing of origins by S-phase kinases. During the mid-blastula transition (MBT) in Drosophila embryos, Rif1 forms subnuclear hubs at each of the large blocks of satellite sequences and delays their replication. Each Rif1 hub disperses abruptly just prior to the replication of the associated satellite sequences. Here, we show that the level of activity of the S-phase kinase, DDK, accelerated this dispersal program, and that the level of Rif1-recruited PP1 retarded it. Further, Rif1-recruited PP1 supported chromatin association of nearby Rif1. This influence of nearby Rif1 can create a "community effect" counteracting kinase-induced dissociation such that an entire hub of Rif1 undergoes switch-like dispersal at characteristic times that shift in response to the balance of Rif1-PP1 and DDK activities. We propose a model in which the spatiotemporal program of late replication in the MBT embryo is controlled by self-stabilizing Rif1-PP1 hubs, whose abrupt dispersal synchronizes firing of associated late origins. SIGNIFICANCESeventy years ago, it was discovered that large domains of the eukaryotic genome replicate at different times. Detailed descriptions left significant questions unresolved. How are the many origins in the large domains coordinated to fire in unison? What distinguishes different domains and gives rise to a temporal program? When Drosophila embryos first establish late replication, an inhibitor of DNA replication, Rif1, forms hubs over domains of late replicating DNA. Rif1 recruits protein phosphatase 1 (PP1), which prevents kinases from dispersing Rif1 hubs or activating associated origins. When kinase activity eventually exceeds a hub-specific threshold, the self-stabilization of Rif1-PP1 breaks down, hubs disperse abruptly, and all associated origins are free to initiate.

cell biology↗

bioRxiv2022

Mandatory coupling of zygotic transcription to DNA replication in early Drosophila embryos

Collisions between transcribing RNA polymerases and DNA replication forks are disruptive. The threat of collisions is particularly acute during the rapid early embryonic cell cycles of Drosophila when S phase occupies the entirety of interphase. We hypothesized that collision-avoidance mechanisms safeguard the onset of zygotic transcription in these cycles. To explore this hypothesis, we used real-time imaging of transcriptional events at the onset of each interphase. Endogenously tagged RNA polymerase II (RNAPII) abruptly formed clusters before nascent transcripts accumulated, indicating recruitment prior to transcriptional engagement. Injection of inhibitors of DNA replication prevented RNAPII clustering, blocked formation of foci of the pioneer factor Zelda, and largely prevented expression of transcription reporters. Knockdown of Zelda or the histone acetyltransferase CBP prevented RNAPII cluster formation except at the replication-dependent (RD) histone gene locus. We suggest a model in which the passage of replication forks allows Zelda and a distinct pathway at the RD histone locus to reconfigure chromatin to nucleate RNAPII clustering and promote transcriptional initiation. The replication dependency of these events defers initiation of transcription and ensures that RNA polymerases transcribe behind advancing replication forks. The resulting coordination of transcription and replication explains how early embryos circumvent collisions and promote genome stability.

cell biology↗

bioRxiv2018

Rapid embryonic cell cycles defer the establishment of heterochromatin by Eggless/SetDB1 in Drosophila

Acquisition of chromatin modifications during embryogenesis distinguishes different regions of an initially naive genome. In many organisms, repetitive DNA is packaged into constitutive heterochromatin that is marked by di/tri methylation of histone H3K9 and the associated protein HP1a. These modifications enforce the unique epigenetic properties of heterochromatin. However, in the early Drosophila melanogaster embryo the heterochromatin lacks these modifications which only appear later when rapid embryonic cell cycles slow down at the Mid-Blastula Transition or MBT. Here we focus on the initial steps restoring heterochromatic modifications in the embryo. We describe the JabbaTrap, a technique for inactivating maternally provided proteins in embryos. Using the JabbaTrap we reveal a major requirement for the methyltransferase Eggless/SetDB1 in the establishment of heterochromatin. In contrast, other methyltransferases contribute minimally. Live-imaging reveals that endogenous Eggless gradually accumulates on chromatin in interphase, but then dissociates in mitosis and its accumulation must restart in the next cell cycle. Cell cycle slowing as the embryo approaches the MBT permits increasing accumulation and action of Eggless at its targets. Experimental manipulation of interphase duration shows that cell cycle speed regulates Eggless. We propose that developmental slowing of the cell cycle times embryonic heterochromatin formation.

developmental biology↗

bioRxiv2017

Non-coding Transcriptome Maps Across Twenty Tissues of the Korean Black Chicken, Yeonsan Ogye

The Yeonsan Ogye (Ogye) is a rare Korean domestic chicken breed, the entire body of which, including its feathers and skin, has a unique black coloring. Although some protein-coding genes related to this unique feature have been examined, non-coding elements have not been globally investigated. In this study, high-throughput RNA sequencing and DNA methylation sequencing were performed to dissect the expression landscape of 14,264 Ogye protein-coding and 6900 long non-coding RNA (lncRNA) genes along with DNA methylation landscape in twenty different Ogye tissues. About 75% of Ogye lncRNAs showed tissue-specific expression whereas about 45% of protein-coding genes did. For some genes, the tissue-specific expression levels were inversely correlated with DNA methylation levels in their promoters. About 39% of the tissue-specific lncRNAs displayed functional association with proximal or distal protein-coding genes. In particular, heat shock transcription factor 2 (HSF2)-associated lncRNAs were discovered to be functionally linked to protein-coding genes that are specifically expressed in black skin tissues, tended to be more syntenically conserved in mammals, and were differentially expressed in black tissues relative to white tissues. Our results not only facilitate understanding how the non-coding genome regulates unique phenotypes but also should be of use for future genomic breeding of chickens.

bioinformatics↗

bioRxiv2017

The Cell-Cycle Transcriptional Network Generates and Transmits a Pulse of Transcription Once Each Cell Cycle

Multiple studies have suggested the critical roles of cyclin-dependent kinases (CDKs) as well as a transcription factor (TF) network in generating the robust cell-cycle transcriptional program. However, the precise mechanisms by which these components function together in the gene regulatory network remain unclear. Here we show that the TF network can generate and transmit a \"pulse\" of transcription independently of CDK oscillations. The premature firing of the transcriptional pulse is prevented by early G1 inhibitors, including transcriptional corepressors and the E3 ubiquitin ligase complex APCCdh1. We demonstrate that G1 cyclin-CDKs facilitate the activation and accumulation of TF proteins in S/G2/M phases through inhibiting G1 transcriptional corepressors (Whi5 and Stb1) and APCCdh1, thereby promoting the initiation and propagation of the pulse by the TF network. These findings suggest a unique oscillatory mechanism in which global phase-specific transcription emerges from a pulse-generating network that fires once-and-only-once at the start of the cycle.

systems biology↗

bioRxiv2017

Reconciling Conflicting Models for Global Control of Cell-Cycle Transcription

How the program of periodic cell-cycle transcription is controlled has been debated for several years. Models have ranged from control by a CDK-APC/C oscillator, by a transcription factor (TF) network, or by coupled CDK-APC/C and TF networks. In contrast to current models, a recent study concluded that the cell-cycle transcriptional program is primarily controlled by a CDK-APC/C oscillator with little input from the TF network. This conclusion was largely based on an assumption that substantial drops in transcript levels of network TFs would render them unable to regulate their targets. By combining quantitative modeling and an unbiased analysis of the RNA-seq data, we demonstrate that the data from this recent study are completely consistent with previous reports indicating a critical role of a TF network. Moreover, we report substantial transcript dynamics in cells arrested with intermediate levels of B-cyclins, further supporting the model in which oscillating CDK activity is not required to produce phase-specific transcription.

cell biology↗