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1. CRISPR-Mediated Synergistic Epigenetic and Transcriptional Control

   https://doi.org/10.1089/crispr.2021.0099  

   Dominguez, Antonia A.; Chavez, Michael G.; Urke, Amanda; Gao, Yuchen; Wang, Lizhong; Qi, Lei S. (April 2022, The CRISPR Journal)
2. Nanomechanics and co-transcriptional folding of Spinach and Mango

   https://doi.org/10.1038/s41467-019-12299-y  

   Mitra, Jaba; Ha, Taekjip (September 2019, Nature Communications)

   Abstract Recent advances in fluorogen-binding “light-up” RNA aptamers have enabled protein-free detection of RNA in cells. Detailed biophysical characterization of folding of G-Quadruplex (GQ)-based light-up aptamers such as Spinach, Mango and Corn is still lacking despite the potential implications on their folding and function. In this work we employ single-molecule fluorescence-force spectroscopy to examine mechanical responses of Spinach2,iMangoIII and MangoIV. Spinach2 unfolds in four discrete steps as force is increased to 7 pN and refolds in reciprocal steps upon force relaxation. In contrast, GQ-core unfolding iniMangoIII and MangoIV occurs in one discrete step at forces >10 pN and refolding occurred at lower forces showing hysteresis. Co-transcriptional folding using superhelicases shows reduced misfolding propensity and allowed a folding pathway different from refolding. Under physiologically relevant pico-Newton levels of force, these aptamers may unfold in vivo and subsequently misfold. Understanding of the dynamics of RNA aptamers will aid engineering of improved fluorogenic modules for cellular applications. 

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3. RNA in formation and regulation of transcriptional condensates

   https://doi.org/10.1261/rna.078997.121  

   Sharp, Phillip A.; Chakraborty, Arup K.; Henninger, Jonathan E.; Young, Richard A. (December 2021, RNA)

   Macroscopic membraneless organelles containing RNA such as the nucleoli, germ granules, and the Cajal body have been known for decades. These biomolecular condensates are liquid-like bodies that can be formed by a phase transition. Recent evidence has revealed the presence of similar microscopic condensates associated with the transcription of genes. This brief article summarizes thoughts about the importance of condensates in the regulation of transcription and how RNA molecules, as components of such condensates, control the synthesis of RNA. Models and experimental data suggest that RNAs from enhancers facilitate the formation of a condensate that stabilizes the binding of transcription factors and accounts for a burst of transcription at the promoter. Termination of this burst is pictured as a nonequilibrium feedback loop where additional RNA destabilizes the condensate. 

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4. Prediction and functional characterization of transcriptional activation domains

   https://doi.org/10.1109/CISS56502.2023.10089768  

   Mahatma, Saloni; Van den Broeck, Lisa; Morffy, Nicholas; Staller, Max V; Strader, Lucia C; Sozzani, Rosangela (January 2023, 2023 57th Annual Conference on Information Sciences and Systems (CISS))
5. Transcriptional and post-translational regulation of plant autophagy

   https://doi.org/10.1093/jxb/erad211  

   Agbemafle, William; Wong, Min May; Bassham, Diane C.; Aroca, ed., Angeles (June 2023, Journal of Experimental Botany)

   Abstract In response to changing environmental conditions, plants activate cellular responses to enable them to adapt. One such response is autophagy, in which cellular components, for example proteins and organelles, are delivered to the vacuole for degradation. Autophagy is activated by a wide range of conditions, and the regulatory pathways controlling this activation are now being elucidated. However, key aspects of how these factors may function together to properly modulate autophagy in response to specific internal or external signals are yet to be discovered. In this review we discuss mechanisms for regulation of autophagy in response to environmental stress and disruptions in cell homeostasis. These pathways include post-translational modification of proteins required for autophagy activation and progression, control of protein stability of the autophagy machinery, and transcriptional regulation, resulting in changes in transcription of genes involved in autophagy. In particular, we highlight potential connections between the roles of key regulators and explore gaps in research, the filling of which can further our understanding of the autophagy regulatory network in plants. 

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