Biology subjects

Cisse, I.

Publications and source records attributed to Cisse, I..

3 recordsLinked to original sources

bioRxiv2025

Acetylation-dependent clustering of BRD2 instructs transcription dynamics

BET protein inhibitors represent one of the most prominent classes of epigenetic drugs. However, the specific contributions of individual BET family members to transcription regulation remain largely unknown. Here, by acutely co-depleting BET proteins, we uncover an essential role of BRD2 in maintaining RNA Polymerase II recruitment at promoters, which becomes especially critical in the absence of BRD4 or when pause release is inhibited. Combining rapid protein degradation, chemogenomics, and super-resolution microscopy, we show that H4 acetylation, particularly H4K16ac, serves as a template for BRD2 function, driving sub-diffraction BRD2 cluster formation at chromatin. Accordingly, depletion of BRD2 or the writer of H4K16ac, MOF decreases sub-diffraction RNA Polymerase II clusters, which are associated with transcription initiation. Thus, this study highlights the importance of acetylated chromatin in transcriptional coactivator organization and the distinct role of BRD2 in transcription initiation dynamics.

genomics↗

bioRxiv2020

Comparison of potential plant-pollinator network structure for 3 seed mixes (lawn, roadside, and pollinator-planting) in western NY, USA

There is growing concern, locally and globally, about the health of pollinating insects and their decreasing abundance and diversity. While roads may also be contributing to insect pollinator declines (roads can contribute to habitat fragmentation and habitat destruction), roadsides may provide opportunities for pollinating insect conservation. Yet to use these areas to support local pollinating insects, we need to understand which plants will support wild pollinators, especially of conservation concern. To that end, we researched the potential plant-pollinator networks of three existing seed mixes in western New York (USA) - a roadside seed mix, a pollinator-friendly planting mix, and a lawn seed mix. We used publicly available information and built bipartite graphs to show the resulting networks. The pollinator-friendly seed mix supported the most pollinating insects overall and taxa of conservation concern. Yet the roadside mix, with the same species richness as the lawn seed mix, supported a different network based on the plants in the mix. Our results inform which particular plant species in existing seed mixes in western New York can support wild pollinating insect species of concern in the region. Additionally, our results show potentially how roadside and lawn plantings may be altered to support a broader network of pollinating insects.

ecology↗

bioRxiv2020

A dual role for H2A.Z.1 in modulating the dynamics of RNA Polymerase II initiation and elongation

RNAPII pausing immediately downstream of the transcription start site (TSS) is a critical rate limiting step at most metazoan genes that allows fine-tuning of gene expression in response to diverse signals1-5. During pause-release, RNA Polymerase II (RNAPII) encounters an H2A.Z.1 nucleosome6-8, yet how this variant contributes to transcription is poorly understood. Here, we use high resolution genomic approaches2,9 (NET-seq and ChIP-nexus) along with live cell super-resolution microscopy (tcPALM)10 to investigate the role of H2A.Z.1 on RNAPII dynamics in embryonic stem cells (ESCs). Using a rapid, inducible protein degron system11 combined with transcriptional initiation and elongation inhibitors, our quantitative analysis shows that H2A.Z.1 slows the release of RNAPII, impacting both RNAPII and NELF dynamics at a single molecule level. We also find that H2A.Z.1 loss has a dramatic impact on nascent transcription at stably paused, signal-dependent genes. Furthermore, we demonstrate that H2A.Z.1 inhibits re-assembly and re-initiation of the PIC to reinforce the paused state and acts as a strong additional pause signal at stably paused genes. Together, our study suggests that H2A.Z.1 fine-tunes gene expression by regulating RNAPII kinetics in mammalian cells.

genomics↗