Review
Cell Biology
Monika Vilimova, Sebastien Pfeffer
Summary: A significant portion of miRNA genes in animal genomes tend to cluster together. These miRNA clusters are transcribed as polycistronic transcripts, benefiting from common transcriptional regulation. However, there are discrepancies in the accumulation of mature miRNAs produced from the same cluster, suggesting unforeseen post-transcriptional regulatory mechanisms.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2023)
Article
Cell Biology
Sai Aung Phyo, Keita Uchida, Christina Yingxian Chen, Matthew A. Caporizzo, Kenneth Bedi, Joanna Griffin, Kenneth Margulies, Benjamin L. Prosser
Summary: This study investigates the transcriptional, autoregulatory, and post-translational mechanisms that contribute to microtubule network remodeling in different stages of heart disease using heart failure patient samples and murine models. The study reveals the operability of autoregulation across tubulin isoforms in the heart and the rapid induction of microtubule detyrosination after hypertrophic stimulus. It provides insights into the rapid rewriting of the tubulin code and the tunable autoregulation of tubulin during pathological progression.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Biochemical Research Methods
Mattia Furlan, Stefano de Pretis, Mattia Pelizzola
Summary: Despite RNA abundance being commonly assumed as a proxy for transcriptional activity, it is now possible to calculate how synthesis, processing, and degradation rates collectively determine the abundance of each gene's RNA. Different transcriptional outputs can correspond to different combinations of kinetic rates, indicating the existence of markedly different modes of gene expression regulation and their profound effects on gene self-expression regulation.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Cell Biology
Qiuqin Ma, Shihui Long, Zhending Gan, Gianluca Tettamanti, Kang Li, Ling Tian
Summary: Autophagy, a widely conserved process in eukaryotes, is regulated by nutrient deprivation, energy stress, and other unfavorable conditions through multiple pathways. It is primarily governed at the RNA and protein levels in a synergistic manner.
Review
Pharmacology & Pharmacy
Guang-Qiong Zhang, Sheng-Quan Wang, Yan Chen, Ling-Yun Fu, Yi-Ni Xu, Ling Li, Ling Tao, Xiang-Chun Shen
Summary: Mitochondria are crucial organelles for cellular energy supply, and miRNAs play a key role in mediating cardiac diseases by regulating mitochondrial function-related genes. Understanding the crosstalk between miRNAs and mitochondria is important for the prevention and treatment of cardiac diseases.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Biology
Vivek Kumar Raxwal, Somya Singh, Manu Agarwal, Karel Riha
Summary: The study revealed that new genes in rice have relatively low expression levels, possibly controlled by distal enhancers and chromatin conformation at their TSS; the chromatin in TSS regions may be remodeled in response to abiotic stress, indicating conditional expression of young genes. Furthermore, transcripts of young genes in Arabidopsis are prone to nonsense-mediated RNA decay, restricting their expression.
Review
Biochemistry & Molecular Biology
Stephanie L. Padula, Nivedhitha Velayutham, Katherine E. Yutzey
Summary: During the postnatal period, mammalian cardiomyocytes undergo significant maturational changes related to increased cardiac function, such as hypertrophic growth, cell cycle exit, sarcomeric protein isoform switching, and mitochondrial maturation. These changes lead to a loss of regenerative capacity in the heart, contributing to heart failure after cardiac injury in adults. Understanding the transcriptional regulators responsible for these maturation processes could have potential therapeutic implications in cardiovascular disease.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Editorial Material
Plant Sciences
Rodrigo S. Reis
Summary: There is a significant gap in our understanding of thermomorphogenesis regulation, specifically in processes involving RNA. This gap presents opportunities for exciting new discoveries in post-transcriptional regulation, while also posing manageable challenges.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Review
Plant Sciences
William Agbemafle, Min May Wong, Diane C. Bassham
Summary: This review summarizes key regulatory mechanisms for modulating autophagy through post-translational modification or transcriptional regulation. Plants activate cellular responses to adapt to changing environmental conditions, one of which is autophagy, where cellular components are delivered to the vacuole for degradation. Autophagy is activated by various conditions, and the pathways controlling its activation are being elucidated. However, there is still much to discover regarding how these factors work together to properly modulate autophagy in response to specific signals.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biochemistry & Molecular Biology
Yan Fang, Yu Tao, Haiwen Zhou, Hengli Lai
Summary: Research has shown that the relationship between cardiac hypertrophy and Celf1, miR-129-5p, and circ-Jarid2 is significant. MiR-129-5p plays an inhibitory role in cardiac hypertrophy, while Circ-Jarid2 promotes it.
Article
Biochemistry & Molecular Biology
Estefania Lozano-Velasco, Carlos Garcia-Padilla, Maria del Mar Munoz-Gallardo, Francisco Jose Martinez-Amaro, Sheila Cano-Carrillo, Juan Manuel Castillo-Casas, Cristina Sanchez-Fernandez, Amelia E. Aranega, Diego Franco
Summary: This article reviews the contribution of non-coding RNAs, including miRNAs and lncRNAs, to cardiac development. These non-coding RNAs modulate major growth factor signaling pathways and transcriptional regulators involved in cardiac morphogenesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Plant Sciences
Shirong Zhou, Shanshan Zhu, Song Cui, Haigang Hou, Haoqin Wu, Benyuan Hao, Liang Cai, Zhuang Xu, Linglong Liu, Ling Jiang, Haiyang Wang, Jianmin Wan
Summary: Rice, as a facultative short day plant, plays a vital role as both a model plant for genetic studies and a staple crop for much of the world's population. Recent research has focused on the transcriptional and post-transcriptional regulation of heading date genes in rice, with an emphasis on post-translational modifications. Efforts are being made to collect genetic resources in a common background to improve breeding strategies for rice cultivars that can adapt to diverse environments.
Article
Cell Biology
Matthew A. Reyer, Shriram Chennakesavalu, Emily M. Heideman, Xiangqian Ma, Magda Bujnowska, Lu Hong, Aaron R. Dinner, Carin K. Vanderpool, Jingyi Fei
Summary: Small RNAs (sRNAs) are important gene regulators in bacteria, acting post-transcriptionally by affecting translation and degradation of target mRNAs. Some sRNAs can regulate targets co-transcriptionally early in an mRNA's lifetime, potentially mediated by Rho-dependent termination. Data also reveals that certain kinetic steps and sRNA binding to target mRNA may dictate the regulation hierarchy within sRNA regulons.
Review
Biochemistry & Molecular Biology
Weijin Xu, Jeetayu Biswas, Robert H. Singer, Michael Rosbash
Summary: RNA binding proteins (RBPs) regulate post-transcriptional processes in cells, and it is crucial to identify their in vivo targets for understanding their function. Standard techniques for profiling RBP targets have limitations in certain situations, but new genetic approaches have been developed for such circumstances. These approaches, including TRIBE, RNA tagging, and STAMP, provide useful tools for studying post-transcriptional regulation and RBP identification, with potential therapeutic implications.
Article
Plant Sciences
Madhushree Dutta, Surbhi Mali, Vidhi Raturi, Gaurav Zinta
Summary: The transition from juvenile to adult stage is an important switch in the plant's life cycle. Potato tuberization is influenced by various environmental factors and regulated by a complex signaling network involving hormones, sugars, phloem mobile signals, and transcriptional/post-transcriptional regulators. This review provides mechanistic insights into the signaling networks that coordinate potato tuberization under different conditions and highlights the importance of genetic and epigenetic regulation.
JOURNAL OF PLANT GROWTH REGULATION
(2023)
Article
Peripheral Vascular Disease
Robin Verjans, Tim Peters, Francisco Javier Beaumont, Rick van Leeuwen, Tessa van Herwaarden, Wouter Verhesen, Chantal Munts, Mitchell Bijnen, Michiel Henkens, Javier Diez, Leon J. de Windt, Frans A. van Nieuwenhoven, Marc van Bilsen, Marie Jose Goumans, Stephane Heymans, Arantxa Gonzalez, Blanche Schroen
Article
Pharmacology & Pharmacy
Burcu Duygu, Rio Juni, Lara Ottaviani, Nicole Bitsch, Jan B. M. Wit, Leon J. de Windt, Paula A. da Costa Martins
BIOCHEMICAL PHARMACOLOGY
(2019)
Article
Cardiac & Cardiovascular Systems
Martina Calore, Alessandra Lorenzon, Libero Vitiello, Giulia Poloni, Mohsin A. F. Khan, Giorgia Beffagna, Emanuela Dazzo, Claudia Sacchetto, Roman Polishchuk, Patrizia Sabatelli, Roberto Doliana, Daniela Carnevale, Giuseppe Lembo, Paolo Bonaldo, Leon De Windt, Paola Braghetta, Alessandra Rampazzo
CARDIOVASCULAR RESEARCH
(2019)
Article
Biotechnology & Applied Microbiology
Andrea Raso, Ellen Dirkx, Leonne E. Philippen, Amaya Fernandez-Celis, Federica De Majo, Vasco Sampaio-Pinto, Marida Sansonetti, Rio Juni, Hamid el Azzouzi, Martina Calore, Nicole Bitsch, Serve Olieslagers, Martinus I. F. J. Oerlemans, Manon M. Huibers, Roel A. de Weger, Yolan J. Reckman, Yigal M. Pinto, Lorena Zentilin, Serena Zacchigna, Mauro Giacca, Paula A. da Costa Martins, Natalia Lopez-Andres, Leon J. De Windt
Review
Cardiac & Cardiovascular Systems
Filippos Triposkiadis, Javed Butler, Francois M. Abboud, Paul W. Armstrong, Stamatis Adamopoulos, John J. Atherton, Johannes Backs, Johann Bauersachs, Daniel Burkhoff, Robert O. Bonow, Vijay K. Chopra, Rudolf A. de Boer, Leon de Windt, Nazha Hamdani, Gerd Hasenfuss, Stephane Heymans, Jean-Sebastien Hulot, Marvin Konstam, Richard T. Lee, Wolfgang A. Linke, Ida G. Lunde, Alexander R. Lyon, Christoph Maack, Douglas L. Mann, Alexandre Mebazaa, Robert J. Mentz, Petros Nihoyannopoulos, Zoltan Papp, John Parissis, Thierry Pedrazzini, Giuseppe Rosano, Jean Rouleau, Petar M. Seferovic, Ajay M. Shah, Randall C. Starling, Carlo G. Tocchetti, Jean-Noel Trochu, Thomas Thum, Faiez Zannad, Dirk L. Brutsaert, Vincent F. Segers, GillesW. De Keulenaer
EUROPEAN HEART JOURNAL
(2019)
Review
Biochemistry & Molecular Biology
Claudia Sacchetto, Libero Vitiello, Leon J. de Windt, Alessandra Rampazzo, Martina Calore
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Multidisciplinary Sciences
Federica De Majo, Jana-Charlotte Hegenbarth, Frank Ruehle, Christian Baer, Thomas Thum, Martine de Boer, Dirk J. Duncker, Blanche Schroen, Anne-Sophie Armand, Monika Stoll, Leon J. De Windt
SCIENTIFIC REPORTS
(2020)
Article
Cell Biology
Indira G. C. Vonhoegen, Hamid el Azzouzi, Serve Olieslagers, Aliaksei Vasilevich, Jan de Boer, Francisco J. Tinahones, Paula A. da Costa Martins, Leon J. de Windt, Mora Murri
Article
Cardiac & Cardiovascular Systems
Christian Bar, Shambhabi Chatterjee, Ines Falcao Pires, Patricia Rodrigues, Joost P. G. Sluijter, Reinier A. Boon, Rosa M. Nevado, Vicente Andres, Marida Sansonetti, Leon de Windt, Michele Ciccarelli, Nazha Hamdani, Stephane Heymans, Raquel Figuinha Videira, Carlo G. Tocchetti, Mauro Giacca, Serena Zacchigna, Stefan Engelhardt, Stefanie Dimmeler, Rosalinda Madonna, Thomas Thum
CARDIOVASCULAR RESEARCH
(2020)
Review
Physiology
Despoina Kesidou, Paula A. da Costa Martins, Leon J. de Windt, Mairi Brittan, Abdelaziz Beqqali, Andrew Howard Baker
FRONTIERS IN PHYSIOLOGY
(2020)
Article
Biotechnology & Applied Microbiology
Shrey Gandhi, Anika Witten, Federica De Majo, Martijn Gilbers, Jos Maessen, Ulrich Schotten, Leon J. de Windt, Monika Stoll
Summary: The study revealed evolutionarily conserved transcription patterns within different heart chambers, with most lncRNAs conserved by synteny. Regional co-expression patterns of transcripts are modulated by factors such as genomic overlap, strandedness, and transcript biotype. The research provides a community resource called EvoACTG, informing researchers about the conserved yet intertwined nature of the coding and non-coding cardiac transcriptome across popular model organisms in CVD research.
Article
Biochemistry & Molecular Biology
Indira G. C. Vonhogen, Zenab Mohseni, Bjorn Winkens, Ke Xiao, Thomas Thum, Martina Calore, Paula A. da Costa Martins, Leon J. de Windt, Marc E. A. Spaanderman, Chahinda Ghossein-Doha
NON-CODING RNA RESEARCH
(2020)
Meeting Abstract
Cardiac & Cardiovascular Systems
Lara M. Ottaviani, Rio P. Juni, Marida Sansonetti, Vasco Sampaio-Pinto, Julie Halkein, Hamid El Azzouzi, Serve Olieslagers, Diana S. Nascimento, Leon J. de Windt, Martins Paula A. da Costa
CIRCULATION RESEARCH
(2019)
Meeting Abstract
Cardiac & Cardiovascular Systems
A. M. C. Koop, R. F. Videira, L. Ottaviani, E. M. Poels, K. W. Van De Kolk, A. Lourenco, D. S. Nascimento, L. J. De Windt, I. Falcao-Pires, R. M. F. Berger, P. A. Da Costa Martins
EUROPEAN HEART JOURNAL
(2019)
Meeting Abstract
Biochemistry & Molecular Biology
M. Calore, A. Lorenzon, L. Vitiello, G. Poloni, G. Beffagna, E. Dazzo, R. Polishchuk, P. Sabatelli, R. Doliana, D. Carnevale, G. Lembo, P. Bonaldo, L. J. de Windt, P. Braghetta, A. Rampazzo
EUROPEAN JOURNAL OF HUMAN GENETICS
(2019)