Review
Biochemistry & Molecular Biology
Marcos Morgan, Lokesh Kumar, Yin Li, Marine Baptissart
Summary: Multiple RNA pathways are essential in producing functional sperm, with a particular focus on 3' end modifications. Studies have shown a correlation between RNA 3' end metabolism and male germ cell differentiation, as well as the importance of RNA pathways in maintaining genomic integrity.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Review
Endocrinology & Metabolism
Nathalia de Lima e Martins Lara, Sadman Sakib, Ina Dobrinski
Summary: Organoids are 3-dimensional structures grown in vitro that mimic true organs, and testicular organoids are important for research on male reproductive biology. Factors such as the developmental stage of Sertoli cells and spermatogonial stem cells influence the generation, structure, and outcomes of testicular organoids. While the testicular organoid approach is promising for male reproductive biology research, more studies and improvements are needed to fully realize its potential.
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)
Article
Multidisciplinary Sciences
Lorena Di Pietro, Marta Barba, Daniela Palacios, Federica Tiberio, Chiara Prampolini, Mirko Baranzini, Ornella Parolini, Alessandro Arcovito, Wanda Lattanzi
Summary: The research suggests that sequence changes in the RUNX2 locus may have contributed to human skull globularization through altering binding of Znf263, miRNA affinity, and regulation of RUNX2 expression and related RNAs. These changes could have led to adaptive phenotypic evolution of RUNX2, explaining the delayed suture fusion and globular skull shape in modern humans.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Randi Yeager, G. Guy Bushkin, Emily Singer, Rui Fu, Benjamin Cooperman, Michael McMurray
Summary: Researchers found that dormant yeast spores of each mating type contain transcripts representing mating pheromones and receptors, with translation of these components being repressed until germination. Additionally, a rare yeast gene Mata1 was found to be enriched in a spores of mating type a, with its transcripts remaining mostly unspliced.
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.
Article
Biochemistry & Molecular Biology
Yanqiang Li, Yang Yi, Jie Lv, Xinlei Gao, Yang Yu, Sahana Suresh Babu, Ivone Bruno, Dongyu Zhao, Bo Xia, Weiqun Peng, Jun Zhu, Hong Chen, Lili Zhang, Qi Cao, Kaifu Chen
Summary: Cell identity genes possess unique transcription regulation mechanisms involving super-enhancers and broad H3K4me3 domains, but their mRNA stability has not been well understood. Through transcriptome-wide analysis in nine cell types, we found that unstable transcripts were enriched in pathways related to cell identity, while stable transcripts were enriched in housekeeping pathways. Joint analysis of RNA stability and chromatin state revealed significant enrichment of super-enhancers and broad H3K4me3 domains at the gene loci of unstable transcripts. Interestingly, the RNA m(6)A methyltransferase METTL3 preferentially binds to chromatin at super-enhancers, broad H3K4me3 domains, and their associated genes.
NUCLEIC ACIDS RESEARCH
(2023)
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
Developmental Biology
Nikolai Slavov
Summary: Robust single-cell mass spectrometry methods allow accurate quantification of proteins and their modification, providing insights into post-transcriptional regulatory mechanisms and their role in developmental cell fate specification. These methods also enable the analysis of protein conformations and activities, linking protein functions to developmental processes in single cells.
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
Valeria Canu, Sara Donzelli, Andrea Sacconi, Federica Lo Sardo, Claudio Pulito, Noa Bossel, Anna Di Benedetto, Paola Muti, Claudio Botti, Eytan Domany, Silvio Bicciato, Sabrina Strano, Yosef Yarden, Giovanni Blandino
Summary: SPAG5 is a crucial driver of cell mitotic spindle, and its overexpression in breast cancer is associated with poor prognosis. It is a direct target of miR-10b-3p and is involved in an oncogenic feedback loop with YAP and TAZ.
CELL DEATH AND DIFFERENTIATION
(2021)
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
Microbiology
Murat C. Kalem, Harini Subbiah, Jay Leipheimer, Virginia E. Glazier, John C. Panepinto
Summary: Research has shown that the lack of Puf4 in Cryptococcus neoformans results in increased resistance to caspofungin, while overexpression of Puf4 leads to increased sensitivity to the drug. Additionally, Puf4 regulates multiple cell wall biosynthesis genes and affects cell wall composition. These findings reveal a potential mechanism by which caspofungin resistance and cell wall biogenesis are post-transcriptionally regulated by Puf4.