Review
Biochemistry & Molecular Biology
Hyun-Sun Park, Jongbok Lee, Hyun-Shik Lee, Seong Hoon Ahn, Hong-Yeoul Ryu
Summary: The relationship between transcription and aging has been extensively studied. The nuclear mRNA export plays a crucial role in cellular aging and age-related neurodegenerative disorders.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Congyao Xu, Xiaofeng Fang, Tiancong Lu, Caroline Dean
Summary: The study reveals that the Arabidopsis floral repressor gene FLC is co-transcriptionally repressed by COOLAIR, with the involvement of AGO1 in promoting COOLAIR splicing dynamics and chromatin silencing. AGO1 is shown to associate with COOLAIR and influence its processing, leading to the resolution of R-loops and local chromatin environment conducive to low transcription initiation. These findings suggest a conserved cotranscriptional regulation mechanism involving AGO1 that influences transcriptional output.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Belen Pacheco-Fiallos, Matthias K. Vorlaender, Daria Riabov-Bassat, Laura Fin, Francis J. O'Reilly, Farja I. Ayala, Ulla Schellhaas, Juri Rappsilber, Clemens Plaschka
Summary: Newly made mRNAs are recognized and organized by the essential TREX complex for nuclear export. Cryo-electron microscopy and tomography structures reveal that mRNAs are recognized through multivalent interactions between TREX subunit ALYREF and mRNP-bound exon junction complexes. Endogenous mRNPs form compact globules that are coated by multiple TREX complexes, providing a framework to understand mRNA biogenesis and export.
Article
Biochemistry & Molecular Biology
Zhiling Kuang, Jiyuan Ke, Jiong Hong, Zhongliang Zhu, Liwen Niu
Summary: PCI domain proteins play important roles in post-transcriptional gene regulation. In this study, the structure of yeast Thp3-Csn12-Sem1 ternary complex was determined, revealing significant structural differences compared to the Sac3-Thp1-Sem1 complex. This structure provides a foundation for further exploring its specific recruitment to the spliceosome.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Suji Lim, Yan Liu, Byung-Ho Rhie, Chun Kim, Hong-Yeoul Ryu, Seong Hoon Ahn
Summary: The study finds that Sus1 is a key factor in linking transcription and mRNA nuclear export. SAGA DUB module and TREX-2 have distinct roles in yeast replicative lifespan. Loss of Sus1 affects growth and lifespan, which depends on TREX-2. Increasing mRNA export factors can rescue the effects.
Article
Biochemistry & Molecular Biology
Rita Valador Fernandes, Joachim Lingner
Summary: The study reveals the role of THOC in telomeric homeostasis through the co- and post-transcriptional regulation of TERRA R-loops. THOC counteracts the association of TERRA with telomeres by interfering with the formation of R-loops. THOC also promotes telomere stability by suppressing telomeric sister-chromatid exchange and C-circle accumulation in ALT cancer cells.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Paola De Magistris
Summary: Nuclear export of mRNA through the NPC is crucial for protein translation in eukaryotic cells, with mRNAs forming ribonuclear particles with proteins for translocation. mRNPs undergo compositional and conformational changes during NPC transport, with multiple quality control steps to ensure proper export of mature transcripts to the cytoplasm. Opportunities for mechanistic understanding of nuclear export are mentioned in the review.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Parasitology
Susanne Kramer
Summary: The passage of mRNAs through nuclear pores into the cytoplasm is essential for all eukaryotes, with mRNA export tightly connected to nuclear mRNA processing. Trypanosoma brucei exhibits unusual features in nuclear mRNA processing, lacking key complexes and proteins found in opisthokonts. Further investigation is needed to determine the extent of mRNA export regulation in trypanosomes and the evolutionary implications of mRNA export across eukaryotes.
Article
Biochemistry & Molecular Biology
Nengxu Sun, Xiangjiu Kong, Yueyan Liu, Tingting Gong, Xiaoyong Gu, Lijing Liu
Summary: This study demonstrates that the THO/TREX complex plays a critical role in plant defenses induced by both salicylic acid (SA) and jasmonic acid (JA). Mutants of THO complex subunits EDS8 and THO3 showed compromised responses to SA and JA, highlighting the importance of alternative splicing events regulated by EDS8 in plant immunity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Yi-Fang Zhu, Jinliang Guo, Yang Zhang, Chao-Feng Huang
Summary: RAE2 and RAE3 play overlapping but distinct roles in modulation of Al resistance and low Pi response, with RAE2 affecting not only the expression of AtALMT1 downstream genes but also regulating an independent pathway of AtALMT1.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Medicine, Research & Experimental
Chia-En Wong, Lee-Way Jin, Yuan-Ping Chug, Wei-Yen Wei, Pei-Chuan Ho, Kuen-Jer Tsai
Summary: This study provides evidence for the postsynaptic localization of TDP-43 in mammalian synapses and its role as a component of neuronal mRNP granules. Through activity stimulation and molecular approaches, the research further demonstrates activity-dependent mRNP granule dynamics, highlighting the impairment of granule disassembly in models of TDP-43 proteinopathy.
Article
Biochemistry & Molecular Biology
Juliette A. Kamp, Bennie B. L. G. Lemmens, Ron J. Romeijn, Roman Gonzalez-Prieto, Jesper Olsen, Alfred C. O. Vertegaal, Robin van Schendel, Marcel Tijsterman
Summary: This study uncovers the crosstalk between RNA surveillance and DNA repair in living animals, revealing the role of SMG-1 in this process through genetic screens and genome-wide analyses. The findings shed light on how defects in RNA processing can affect DNA repair, and highlight the importance of SMG-1 in regulating this interaction.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Yihu Xie, Shengyan Gao, Ke Zhang, Prasanna Bhat, Bradley P. Clarke, Kimberly Batten, Menghan Mei, Matthew Gazzara, Jerry W. Shay, Kristen W. Lynch, Alexia E. Angelos, Pate S. Hill, Austin L. Ivey, Beatriz M. A. Fontoura, Yi Ren
Summary: This study reveals the importance of the high-order SARNP/Tho1 complex interacting with DDX39B/RNA in mRNP assembly and export.
Article
Biochemistry & Molecular Biology
Carina Kern, Christin Radon, Wolfgang Wende, Alexander Leitner, Katja Straesser
Summary: The conserved TREX complex is involved in multiple functions in gene expression and is composed of various proteins. In Saccharomyces cerevisiae, the endogenous TREX complex forms a dimeric structure.
Review
Oncology
Katherine L. B. Borden
Summary: This review highlights the importance of RNA export in cellular trafficking and the aberrant phenomena observed in cancer. Studies on RNA export machinery and relevant NPC components offer potential therapeutic strategies for targeting cancer.
Review
Biophysics
Amnon Horovitz, Tali Haviv Reingewertz, Jorge Cuellar, Jose Maria Valpuesta
Summary: Chaperonins are essential nanomachines that assist in protein folding in an ATP-driven manner. Despite being intensively studied for more than three decades, the key aspects of their reaction mechanisms remain under debate. It is unclear whether there is a universal reaction mechanism for all substrates and whether it is passive or active.
ANNUAL REVIEW OF BIOPHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Zuzanna Kaczmarska, Mariusz Czarnocki-Cieciura, Karolina M. Gorecka-Minakowska, Robert J. Wingo, Justyna Jackiewicz, Weronika Zajko, Jaroslaw T. Poznanski, Michal Rawski, Timothy Grant, Joseph E. Peters, Marcin Nowotny
Summary: The study presents the cryoelectron microscopy structure of Tn7 transposase TnsB, revealing its beads-on-a-string architecture when interacting with the transposon end DNA. The spacing or overlap of TnsB binding sites explains the functional differences in the left and right ends of the element.
Review
Cell Biology
Aleksandra Bilska, Pawel Szczepan Krawczyk, Andrzej Dziembowski, Seweryn Mroczek
Summary: The 3'-end poly(A) tail is an important feature of mRNA molecules that affects gene expression at the mRNA level. Recent research has discovered different regulatory mechanisms of polyadenylation occurring in the nucleus and cytoplasm. Advances in RNA sequencing technology and software development have provided a better understanding of polyadenylation research methods and uncovered new enzymes and the correlation between tail length and RNA translatability.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2023)
Article
Multidisciplinary Sciences
Seong-Su Han, Kuo-Kuang Wen, Maria L. Garcia-Rubio, Marc S. Wold, Andres Aguilera, Wojciech Niedzwiedz, Yatin M. Vyas
Summary: This study identifies a crucial role for WASp in the DNA stress-resolution pathway, specifically in promoting the function of Replication Protein A at replication forks after DNA damage. Deficiency of WASp leads to RPA dysfunction, resulting in genomic instability.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Juan Carlos Canas, Maria Luisa Garcia-Rubio, Alicia Garcia, Francisco Antequera, Belen Gomez-Gonzalez, Andres Aguilera
Summary: The chromatin modifier Rtt109 plays a crucial role in the metabolism and repair of DNA-RNA hybrids and R-loops, with histone acetylation helping to prevent DNA damage and promote repair.
Article
Multidisciplinary Sciences
Fabien Guegan, K. Shanmugha Rajan, Fabio Bento, Daniel Pinto-Neves, Mariana Sequeira, Natalia Guminska, Seweryn Mroczek, Andrzej Dziembowski, Smadar Cohen-Chalamish, Tirza Doniger, Beathrice Galili, Antonio M. Estevez, Cedric Notredame, Shulamit Michaeli, Luisa M. Figueiredo
Summary: This study identified 1428 previously uncharacterized lncRNA genes in the T. brucei genome. The key regulator, grumpy lncRNA, was found to promote parasite differentiation into the quiescent stumpy form, with this function being promoted by the encoded small nucleolar RNA. Overexpression of grumpy reduced parasitemia in infected mice.
Article
Biochemistry & Molecular Biology
Malgorzata Figiel, Marta Gapinska, Mariusz Czarnocki-Cieciura, Weronika Zajko, Malgorzata Sroka, Krzysztof Skowronek, Marcin Nowotny
Summary: Abortive infection (Abi) is a bacterial defense strategy that involves suicide of the infected cell. Abi pathways often involve polymerases related to reverse transcriptases. The crystal and cryo-electron microscopy structures of two Abi polymerases, AbiK and Abi-P2, were determined. These polymerases adopt unique structures and oligomeric configurations, which are crucial for their DNA synthesis activity. The structures provide insights into the unusual protein-priming mechanism of these polymerases.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Vladyslava Liudkovska, Pawel S. Krawczyk, Aleksandra Brouze, Natalia Guminska, Tomasz Wegierski, Dominik Cysewski, Zuzanna Mackiewicz, Jonathan J. Ewbank, Krzysztof Drabikowski, Seweryn Mroczek, Andrzej Dziembowski
Summary: This study reveals that cytoplasmic polyadenylation is a previously unknown component of the posttranscriptional regulation of innate immunity in animals, enhancing the expression of secreted innate immunity effector proteins.
Article
Biochemistry & Molecular Biology
Cristina Tous, Carmen Munoz-Redondo, Nereida Bravo-Gil, Angela Gavilan, Raquel Maria Fernandez, Juan Antinolo, Elena Navarro-Gonzalez, Guillermo Antinolo, Salud Borrego
Summary: Thyroid carcinoma (TC) can be classified into medullary (MTC) and non-medullary (NMTC). This study aimed to identify susceptibility genes for familial NMTC and non-RET MTC using whole exome sequencing. Rare candidate segregating variants were found in 12 families, with enriched biological processes related to cell proliferation, differentiation, survival, and adhesion. These findings provide insights into molecular mechanisms underlying familial forms of MTC and NMTC, which may contribute to early detection, tailored therapies, and patient management.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Shivlee Nirwal, Mariusz Czarnocki-Cieciura, Anuradha Chaudhary, Weronika Zajko, Krzysztof Skowronek, Sebastian Chamera, Malgorzata Figiel, Marcin Nowotny
Summary: In this study, the authors investigate the cooperation mechanism of RecFOR proteins in bacteria using Thermus thermophilus proteins. Cryo-electron microscopy structures of the RecF-dsDNA complex and the interaction between RecF and the tetrameric RecR ring are presented. Lower-resolution reconstructions of the RecR-RecO subcomplex and the RecFOR-DNA assembly are also provided. These results shed light on the biochemical data available for the RecFOR system.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Belen Gomez-Gonzalez, Andres Aguilera
Summary: Double-strand breaks (DSBs) are highly harmful DNA damages that have significant effects on cell proliferation and genome integrity. Recent studies have shown that DSBs can enhance the formation of DNA-RNA hybrids, called break-induced RNA-DNA hybrids (BIRDHs). The source and impact of BIRDHs are still unresolved questions.
Article
Multidisciplinary Sciences
Aleix Bayona-Feliu, Emilia Herrera-Moyano, Nibal Badra-Fajardo, Ivan Galvan-Femenia, Maria Eugenia Soler-Oliva, Andres Aguilera
Summary: The chromatin network prevents genomic instability and mutagenic signatures associated with cancer by inhibiting R-loops and transcription-replication conflicts.
NATURE COMMUNICATIONS
(2023)
Meeting Abstract
Environmental Sciences
Sergio Munoz, Sonia Barroso, Javier Marqueta-Gracia, Maria Eugenia Soler, Andres Aguilera
ENVIRONMENTAL AND MOLECULAR MUTAGENESIS
(2022)
Meeting Abstract
Environmental Sciences
Andres Aguilera, Yesenia Rodriguez, Philip Hanawalt, Karlene A. Cimprich
ENVIRONMENTAL AND MOLECULAR MUTAGENESIS
(2022)