Biology subjects

Menon, G.

Publications and source records attributed to Menon, G..

3 recordsLinked to original sources

bioRxiv2023

Antisense transcription and PRC2 repression function in parallel during vernalization

Non-coding transcription induces chromatin changes that can mediate environmental responsiveness, but the causes and consequences of these mechanisms are still unclear. Here, we investigate how antisense transcription interfaces with Polycomb Repressive Complex 2 silencing during winter-induced epigenetic regulation of Arabidopsis FLOWERING LOCUS C (FLC). Through genetic, chromatin, and computational analyses, we show that FLC is silenced through pathways that function with different dynamics: an antisense transcription-mediated pathway capable of fast response; and in parallel a slow Polycomb Repressive Complex 2 (PRC2) switching mechanism that maintains each allele in an epigenetically silenced state. Components of both the antisense and PRC2 pathways are regulated by a common transcriptional regulator (NTL8), which accumulates slowly due to reduced growth at low temperatures. The parallel activities of the regulatory steps, which we encapsulate in a mathematical model, creates a flexible system for registering widely fluctuating natural temperature conditions that change year on year, and yet ensure robust epigenetic silencing of FLC. SignificanceThe role of non-coding transcription in establishing and maintaining chromatin states is controversial, mainly because of extensive feedbacks complicating analysis of the relationship between co-transcriptional processing, chromatin state and transcription. This controversy has extended to the role of antisense transcription in the Polycomb-mediated epigenetic silencing of Arabidopsis FLC, a key step in the process of vernalization. Here, we show that antisense transcription and PRC2 silence FLC in parallel pathways that are affected by growth dynamics and temperature fluctuations. These features explain the varied importance of antisense transcription in cold-induced FLC epigenetic silencing seen in various studies using different environmental and growth conditions. The parallel repressive inputs and extensive feedbacks make the mechanism counter-intuitive but provide great flexibility to the plant.

molecular biology↗

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↗