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1. Local Rather than Global H3K27me3 Dynamics Are Associated with Differential Gene Expression in Verticillium dahliae

   https://doi.org/10.1128/mbio.03566-21  

   Kramer, H. Martin; Seidl, Michael F.; Thomma, Bart P.; Cook, David E. (February 2022, mBio)

   Fudal, Isabelle; Di Pietro, Antonio (Ed.)

   ABSTRACT Differential growth conditions typically trigger global transcriptional responses in filamentous fungi. Such fungal responses to environmental cues involve epigenetic regulation, including chemical histone modifications. It has been proposed that conditionally expressed genes, such as those that encode secondary metabolites but also effectors in pathogenic species, are often associated with a specific histone modification, lysine27 methylation of H3 (H3K27me3). However, thus far, no analyses on the global H3K27me3 profiles have been reported under differential growth conditions in order to assess if H3K27me3 dynamics govern differential transcription. Using chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing data from the plant-pathogenic fungus Verticillium dahliae grown in three in vitro cultivation media, we now show that a substantial number of the identified H3K27me3 domains globally display stable profiles among these growth conditions. However, we observe local quantitative differences in H3K27me3 ChIP-seq signals that are associated with a subset of differentially transcribed genes between media. Comparing the in vitro results to expression during plant infection suggests that in planta -induced genes may require chromatin remodeling to achieve expression. Overall, our results demonstrate that some loci display H3K27me3 dynamics associated with concomitant transcriptional variation, but many differentially expressed genes are associated with stable H3K27me3 domains. Thus, we conclude that while H3K27me3 is required for transcriptional repression, it does not appear that transcriptional activation requires the global erasure of H3K27me3. We propose that the H3K27me3 domains that do not undergo dynamic methylation may contribute to transcription through other mechanisms or may serve additional genomic regulatory functions. IMPORTANCE In many organisms, including filamentous fungi, epigenetic mechanisms that involve chemical and physical modifications of DNA without changing the genetic sequence have been implicated in transcriptional responses upon developmental or environmental cues. In fungi, facultative heterochromatin that can decondense to allow transcription in response to developmental changes or environmental stimuli is characterized by the trimethylation of lysine 27 on histone H3 (H3K27me3), and H3K27me3 has been implicated in transcriptional regulation, although the precise mechanisms and functions remain enigmatic. Based on ChIP and RNA sequencing data, we show for the soilborne broad-host-range vascular wilt plant-pathogenic fungus Verticillium dahliae that although some loci display H3K27me3 dynamics that can contribute to transcriptional variation, other loci do not show such a dependence. Thus, although we recognize that H3K27me3 is required for transcriptional repression, we also conclude that this mark is not a conditionally responsive global regulator of differential transcription upon responses to environmental cues. 

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2. Understanding the molecular mechanisms of transcriptional bursting

   https://doi.org/10.1039/d1cp03665c  

   Klindziuk, Alena; Kolomeisky, Anatoly B. (October 2021, Physical Chemistry Chemical Physics)

   null (Ed.)

   In recent years, it has been experimentally established that transcription, a fundamental biological process that involves the synthesis of messenger RNA molecules from DNA templates, does not proceed continuously as was expected. Rather, it exhibits a distinct dynamic behavior of alternating between productive phases when RNA molecules are actively synthesized and inactive phases when there is no RNA production at all. The bimodal transcriptional dynamics is now confirmed to be present in most living systems. This phenomenon is known as transcriptional bursting and it attracts significant amounts of attention from researchers in different fields. However, despite multiple experimental and theoretical investigations, the microscopic origin and biological functions of the transcriptional bursting remain unclear. Here we discuss the recent developments in uncovering the underlying molecular mechanisms of transcriptional bursting and our current understanding of them. Our analysis presents a physicochemical view of the processes that govern transcriptional bursting in living cells. 

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3. RNA polymerase II dynamics and mRNA stability feedback determine mRNA scaling with cell size

   https://doi.org/10.1101/2021.09.20.461005  

   Swaffer, M.P.; Marinov, G.K.; Zheng, H.; Jones, A.W.; Greenwood, J.; Kundaje, A.; Snijders, A.P.; Greenleaf, W.J.; Reyes-Lamothe, R.; Skotheim, J.M. (September 2021, bioRxiv)

   null (Ed.)

   A defining feature of cellular growth is that protein and mRNA amounts scale with cell size so that concentrations remain approximately constant, thereby ensuring similar reaction rates and efficient biosynthesis. A key component of this biosynthetic scaling is the scaling of mRNA amounts with cell size, which occurs even among cells with the same DNA template copy number. Here, we identify RNA polymerase II as a major limiting factor increasing transcription with cell size. Other components of the transcriptional machinery are only minimally limiting and the chromatin environment is largely invariant with size. However, RNA polymerase II activity does not increase in direct proportion to cell size, inconsistent with previously proposed DNA-titration models. Instead, our data support a dynamic equilibrium model where the rate of polymerase loading is proportional to the unengaged nucleoplasmic polymerase concentration. This sublinear transcriptional increase is then balanced by a compensatory increase in mRNA stability as cells get larger. Taken together, our results show how limiting RNA polymerase II and feedback on mRNA stability work in concert to ensure the precise scaling of mRNA amounts across the physiological cell size range. 

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4. Theoretical Investigation of Transcriptional Bursting: A Multistate Approach

   https://doi.org/DOI: 10.1021/acs.jpcb.8b09676  

   Klindziuk, Alena; Kolomeisky, Anatoly B (November 2018, Journal of physical chemistry)

   Variability in gene expression causes genetically identical cells to exhibit different phenotypes. One probable cause of this variability is transcriptional bursting, where the synthesis of RNA molecules randomly alternates with periods of silence in the transfer of genetic information. Yet, the molecular mechanisms behind this variability remain unclear. Experiments indicate that multiple biochemical states might be involved in the production of RNA molecules. Stimulated by these observations, we developed a theoretical framework to investigate the mechanisms of transcriptional bursting. It is based on a multi-state stochastic approach that provides a full quantitative description of the dynamic properties in the system. We found that the degree of stochastic fluctuations during transcription directly correlates with the number of biochemical states. This explains experimentally observed variability and fluctuations in the quantities of the produced RNA molecules. The procedure to estimate the number of relevant biochemical states participating in the transcription is outlined and applied for analysis of experimental results. We also developed a general dynamic phase diagram for the transcription process. The presented theoretical method clarifies physical−chemical aspects of the transcriptional bursting and presents a minimal chemical-kinetic description of the process. 

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5. Histone modification dynamics at H3K27 are associated with altered transcription of in planta induced genes in Magnaporthe oryzae

   https://doi.org/10.1371/journal.pgen.1009376  

   Zhang, Wei; Huang, Jun; Cook, David E. (February 2021, PLOS Genetics)

   Mittelsten Scheid, Ortrun (Ed.)

   Transcriptional dynamic in response to environmental and developmental cues are fundamental to biology, yet many mechanistic aspects are poorly understood. One such example is fungal plant pathogens, which use secreted proteins and small molecules, termed effectors, to suppress host immunity and promote colonization. Effectors are highly expressed in planta but remain transcriptionally repressed ex planta , but our mechanistic understanding of these transcriptional dynamics remains limited. We tested the hypothesis that repressive histone modification at H3-Lys27 underlies transcriptional silencing ex planta , and that exchange for an active chemical modification contributes to transcription of in planta induced genes. Using genetics, chromatin immunoprecipitation and sequencing and RNA-sequencing, we determined that H3K27me3 provides significant local transcriptional repression. We detail how regions that lose H3K27me3 gain H3K27ac, and these changes are associated with increased transcription. Importantly, we observed that many in planta induced genes were marked by H3K27me3 during axenic growth, and detail how altered H3K27 modification influences transcription. ChIP-qPCR during in planta growth suggests that H3K27 modifications are generally stable, but can undergo dynamics at specific genomic locations. Our results support the hypothesis that dynamic histone modifications at H3K27 contributes to fungal genome regulation and specifically contributes to regulation of genes important during host infection. 

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