Biology subjects

Reeck, S.

Publications and source records attributed to Reeck, S..

3 recordsLinked to original sources

bioRxiv2023

Proximal termination generates a transcriptional state that determines the rate of establishment of Polycomb silencing

Chromatin-mediated transcriptional silencing by Polycomb Repressive Complex 2 (PRC2) is critical for gene regulation in development and environmental responses. However, the mechanism and timescales controlling de novo establishment of PRC2 silencing are unclear. Here, we investigate PRC2 silencing at Arabidopsis FLOWERING LOCUS C (FLC), known to involve co-transcriptional RNA processing, histone demethylation activity, and PRC2 function; but so far not mechanistically connected. We develop and then test a computational model that describes how proximal polyadenylation/termination mediated by the RNA binding protein FCA induces H3K4me1 removal by the histone demethylase FLD. H3K4me1 removal feeds back to reduce RNA Pol II processivity and thus enhance early termination, thereby repressing productive transcription. The model predicts that this transcription-coupled repression controls the level of transcriptional antagonism to Polycomb action, Thus, the effectiveness of this repression dictates the timescale for establishment of Polycomb H3K27me3 silencing. Experimental validation of these model predictions allowed us to mechanistically connect co-transcriptional processing to setting the level of productive transcription at the locus, which then determines the rate of the ON to OFF switch to PRC2 silencing.

molecular biology↗

bioRxiv2022

Integrating analog and digital modes of gene expression at Arabidopsis FLC

Quantitative gene regulation at the cell population-level can be achieved by two fundamentally different modes of regulation at individual gene copies. A "digital" mode involves binary ON/OFF expression states, with population-level variation arising from the proportion of gene copies in each state, while an "analog" mode involves graded expression levels at each gene copy. At the Arabidopsis floral repressor FLOWERING LOCUS C (FLC), "digital" Polycomb silencing is known to facilitate quantitative epigenetic memory in response to cold. However, whether FLC regulation before cold involves analog or digital modes is unknown. Using quantitative fluorescent imaging of FLC mRNA and protein, together with mathematical modelling, we find that FLC expression before cold is regulated by both analog and digital modes. We observe a temporal separation between the two modes, with analog preceding digital. The analog mode can maintain intermediate expression levels at individual FLC gene copies, before subsequent digital silencing, consistent with the copies switching OFF stochastically and heritably without cold. This switch leads to a slow reduction in FLC expression at the cell population-level. These data present a new paradigm for gradual repression, elucidating how analog transcriptional and digital epigenetic memory pathways can be integrated.

molecular biology↗

bioRxiv2021

Live-cell chromosome dynamics in Arabidopsis thaliana reveals increased chromatin mobility in response to DNA damage

Homologous recombination (HR) is a conservative DNA repair pathway in which intact homologous sequences are used as a template for repair. How the homology search happens in the crowded space of the cell nucleus is, however, still poorly understood. Here, we measured global chromosome and double-strand break (DSB) site mobility in Arabidopsis thaliana, using lacO/LacI lines and two GFP-tagged HR reporters. We observed an increase in global chromatin mobility upon the induction of DNA damage, specifically at the S/G2 phases of the cell cycle. DSB sites showed remarkably high mobility levels at the early HR stage, with a subsequent drastic decrease in mobility associated with the relocation of DSBs to the nucleus periphery. Importantly, the increase in mobility was lost in sog1-1 mutant, a central transcription factor of the DNA damage response in plants. Our results indicate that repair mechanisms actively regulate chromatin mobility upon DNA damage, implying an important role for this process during the early steps of the DNA damage response.

cell biology↗