Article
Oncology
Morgane Le Bras, Noah Gorelick, Sylvain Pautet, Betty Tyler, Stephane Manenti, Nicolas Skuli, Stefania Millevoi, Anne Cammas
Summary: This study investigates the molecular mechanisms underlying protein synthesis deregulation in glioblastoma (GBM) and its impact on tumor progression and resistance to therapy. The results reveal the crucial role of RNA-binding proteins hnRNP H/F in controlling protein synthesis in GBM through overlapping mechanisms. Furthermore, hnRNP H/F are shown to potentiate cellular processes that contribute to the aggressive and resistant phenotype of GBMs, indicating their potential as therapeutic targets.
Article
Biochemistry & Molecular Biology
Poulomi Das, Khac Huy Ngo, Fernaldo Richtia Winnerdy, Arijit Maity, Blaz Bakalar, Yves Mechulam, Emmanuelle Schmitt, Anh Tuan Phan
Summary: This study investigates the adaptability of left-handed G4 structures towards the presence of bulges, presenting the structural characteristics of left-handed G4s accommodating varying numbers of bulges. Bulges in left-handed G4s exhibit distinct features compared to those in right-handed G4s, and elucidation of the intricate structural details may enhance understanding of the potential roles and limitations of these unique structures.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Marco Caterino, Katrin Paeschke
Summary: The nucleic acid structure known as G-quadruplex (G4) plays a significant role in nucleic acid-based mechanisms that impact cellular processes. DNA G4 is well-studied, while RNA G4 is gaining attention for its role in cellular homeostasis. Proper regulation of G4 structures within cells is crucial, and helicases are important in resolving them. However, only a few rG4 unwinding helicases have been identified and characterized so far.
Article
Biochemistry & Molecular Biology
Min Zou, Jing-Yan Li, Meng-Jia Zhang, Jun-Hui Li, Jun-Tao Huang, Pei-Dan You, Shu-Wen Liu, Chun-Qiong Zhou
Summary: The study indicates that the G-quadruplex binder PDS can serve as a multi-target ZIKV inhibitor with high antiviral activity, effectively suppressing ZIKV replication and protein expression, and reducing ZIKV catalytic activity.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Chemistry, Medicinal
Domen Oblak, Hadzi, Crtomir Podlipnik, Jurij Lah
Summary: The authors investigated the (un)folding and binding process of a human telomeric fragment with ligands through calorimetry and spectroscopy. The results showed that the presence of specific ligands can alter the topology of G-quadruplex nucleic acids. By analyzing thermodynamic parameters and conducting molecular modeling, the driving forces behind the topological transformations were clarified.
Article
Biochemistry & Molecular Biology
Xiaobin Ling, Yuqi Yao, Lei Ding, Jinbiao Ma
Summary: The study reveals that the nucleic acid binding protein UP1 can bind and unfold the G-quadruplexes in human telomere DNA. The RNA recognition motifs RRM1 and RRM2 in UP1 are responsible for initial binding, unfolding, and completion of G-quadruplexes unfolding, respectively. The TAG binding motif in the telomeric G-quadruplex Loop2 is critical for UP1 recognition and initiation of G-quadruplexes unfolding.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2023)
Article
Neurosciences
Muhammad I. Khan, Juan Zhang, Qiang Liu
Summary: The study revealed a significant association between hnRNP F and hnRNP H1 with APP, demonstrating their importance in neuronal function.
Article
Biochemistry & Molecular Biology
Marijana Ugrina, Ines Burkhart, Diana Mueller, Harald Schwalbe, Nadine Schwierz
Summary: In this study, the folding pathways of a G-quadruplex from the telomeric repeat-containing RNA were characterized using a combination of molecular dynamics simulations and circular dichroism experiments. The presence of ions stabilized the quadruplex fold, and the folding process was guided by the formation of an ion double layer surrounding the charged quadruplex. Coarse-grained simulations accurately captured the ionic double layer using a matching procedure based on all-atom simulations. The results showed that the folding progressed through a series of intermediate states, stabilized by transient Hoogsteen interactions, before reaching the final folded structure. The study also proposed that conformational entropy is a hallmark of rG4 folding, which was supported by the analysis of free energy landscapes and folding pathways of four rG4 systems with varying loop length.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Nuria Escaja, Bartomeu Mir, Miguel Garavis, Carlos Gonzalez
Summary: Tetrads are arrangements of four nucleobases commonly used to stabilize nucleic acid structures. In addition to the well-known G-quadruplex, non-G tetrads formed by different nucleobases have been observed in experimental structures. They are mostly found in the context of G-quadruplex structures but also occur in other unusual four-stranded structures.
Review
Biochemistry & Molecular Biology
Huiling Shu, Rongxin Zhang, Ke Xiao, Jing Yang, Xiao Sun
Summary: G-quadruplexes are non-canonical secondary nucleic acid structures that play important roles in genome regulation. Interactions between G-quadruplexes and proteins have diverse biological functions and potential therapeutic applications.
Review
Cell Biology
Aaron Antcliff, Louise D. McCullough, Andrey S. Tsvetkov
Summary: G-Quadruplex (G4) DNA and RNA are secondary nucleic acid structures that play multiple roles in cellular processes. DHX36, a helicase, unwinds both G4 DNA and G4 RNA, regulating transcription, genomic stability, telomere maintenance, translation, and RNA metabolism in the process. This review explores the potential role of DHX36 in neuronal development and neurodegeneration, as well as discussing the possible functions of G4s and DHX36 in the aging brain.
Article
Biochemistry & Molecular Biology
Petra Skolakova, Martin Gajarsky, Jan Palacky, Denis Subert, Daniel Renciuk, Lukas Trantirek, Jean-Louis Mergny, Michaela Vorlickova
Summary: Based on various techniques, this study demonstrates that Cytosine-rich DNA regions can form four-stranded structures called i-motifs (iMs) under neutral or slightly alkaline conditions. These iMs exhibit long-lasting kinetics and melt with significant hysteresis. Furthermore, the presence of different iM species, the proportion of which is dependent on temperature and incubation time, is observed in sequences with a length greater than 6.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Analytical
Jia-Hong Lin, Xiao Chen, Ming-Hao Hu
Summary: G-quadruplexes (G4s) are non-canonical DNA or RNA secondary structures implicated in the regulation of key biological processes. This study designed and synthesized a fluorescent ligand KN-1, which can detect and stabilize RNA G4 structures in live cells. It provides a promising tool for investigating the functions of specific RNA G4s in living cells.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Article
Biochemistry & Molecular Biology
Marc-Antoine Turcotte, Jean-Michel Garant, Helene Cossette-Roberge, Jean-Pierre Perreault
Summary: This study identified the presence of G-quadruplex regulation in neurodegenerative diseases and demonstrated the folding of G4 sequences in the 5' untranslated regions of mRNAs associated with Parkinson's disease. The G4s significantly repressed the translation of Parkin RBR E3 Ubiquitin Protein Ligase (PRKN) and Vacuolar Protein Sorting-Associated Protein 35 (VPS35) in neuronal cells, and a novel G4-binding protein, GNL1, was identified through RNA affinity purification assays.
Review
Biochemistry & Molecular Biology
Ye Teng, Ming Zhu, Zhidong Qiu
Summary: Repeat expansions are the main genetic cause of various neurodegeneration diseases. G-rich repeat sequences, such as CGG and GGGGCC, form functional G-quadruplexes and play important roles in bioprocesses. This review provides an overview of the contribution of G-quadruplex in repeat expansion disorders and summarizes the related mechanisms, including genetic instabilities, toxic RNA foci, and protein/peptide dysfunction.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Carika Weldon, Isabelle Behm-Ansmant, Laurence H. Hurley, Glenn A. Burleys, Christiane Branlant, Ian C. Eperon, Cyril Dominguez
NATURE CHEMICAL BIOLOGY
(2017)
Article
Biochemistry & Molecular Biology
Marina Danilenko, Caroline Dalgliesh, Vittoria Pagliarini, Chiara Naro, Ingrid Ehrmann, Mikael Feracci, Mahsa Kheirollahi-Chadegani, Alison Tyson-Capper, Gavin J. Clowry, Philippe Fort, Cyril Dominguez, Claudio Sette, David J. Elliott
NUCLEIC ACIDS RESEARCH
(2017)
Article
Multidisciplinary Sciences
Mikael Feracci, Jaelle N. Foot, Sushma N. Grellscheid, Marina Danilenko, Ralf Stehle, Oksana Gonchar, Hyun-Seo Kang, Caroline Dalgliesh, N. Helge Meyer, Yilei Liu, Albert Lahat, Michael Sattler, Ian C. Eperon, David J. Elliott, Cyril Dominguez
NATURE COMMUNICATIONS
(2016)
Article
Biochemistry & Molecular Biology
Brighton Samatanga, Antoine Clery, Pierre Barraud, Frederic H-T Allain, Ilian Jelesarov
NUCLEIC ACIDS RESEARCH
(2017)
Article
Biochemistry & Molecular Biology
Brighton Samatanga, Alexandra Z. Andreou, Dagmar Klostermeier
NUCLEIC ACIDS RESEARCH
(2017)
Article
Biochemistry & Molecular Biology
Carika Weldon, Justine G. Dacanay, Vijay Gokhale, Peda Venkat L. Boddupally, Isabelle Behm-Ansmant, Glenn A. Burley, Christiane Branlant, Laurence H. Hurley, Cyril Dominguez, Ian C. Eperon
NUCLEIC ACIDS RESEARCH
(2018)
Article
Biochemical Research Methods
Lle N. Foot, Mikael Feracci, Cyril Dominguez
Article
Biochemistry & Molecular Biology
Brighton Samatanga, Dagmar Klostermeier
NUCLEIC ACIDS RESEARCH
(2014)
Article
Biochemistry & Molecular Biology
Dominik Theler, Cyril Dominguez, Markus Blatter, Julien Boudet, Frederic H. -T. Allain
NUCLEIC ACIDS RESEARCH
(2014)
Article
Cell Biology
Deeksha Munnur, Joanna Somers, George Skalka, Ria Weston, Rebekah Jukes-Jones, Mohammed Bhogadia, Cyril Dominguez, Kelvin Cain, Ivan Ahel, Michal Malewicz
Article
Biochemistry & Molecular Biology
Aalam Ameerul, Hibah Almasmoum, Lorenzo Pavanello, Cyril Dominguez, Gerlof Sebastiaan Winkler
Summary: The degradation of cytoplasmic mRNA in eukaryotes involves the shortening and removal of the mRNA poly(A) tail, which is mediated by poly(A)-selective ribonuclease enzymes. In human cells, BTG2 can stimulate deadenylation of poly(A) bound by cytoplasmic poly(A)-binding protein PABPC1. This study elucidates the molecular details of the interaction between PABPC1 and BTG2 through prediction of interaction surfaces, pulldown assays, and structural modeling.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Mohammed Bhogadia, Beth Stone, Rafael Del Villar Guerra, Frederick W. Muskett, Sudipta Ghosh, Andrea Taladriz-Sender, Glenn A. Burley, Ian C. Eperon, Andrew J. Hudson, Cyril Dominguez
Summary: The BCL2L1 gene expresses two isoforms of Bcl-x protein, with different actions, through alternative splicing. Over-expression of one isoform is associated with cancer cell survival and growth. The study shows that a G-quadruplex structure forms downstream of one isoform and is stabilized by the compound GQC-05. GQC-05 selectively binds to the Bcl-x G-quadruplex and shifts the balance between G-quadruplex and duplex structures, increasing accessibility of a specific splice site.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Nanoscience & Nanotechnology
Carlos J. Bueno-Alejo, Marina Santana Vega, Amanda K. Chaplin, Chloe Farrow, Alexander Axer, Glenn A. Burley, Cyril Dominguez, Hesna Kara, Vasileios Paschalis, Sumera Tubasum, Ian C. Eperon, Alasdair W. Clark, Andrew J. Hudson
Summary: Single-molecule imaging is important for studying the behavior and interactions of biological molecules. However, the irreversible adsorption of components onto surfaces poses a challenge for precise sampling. Interferometric scattering microscopy (iSCAT) can detect the adsorption and desorption of unlabeled proteins on glass surfaces. A surface passivation method using high-density perfluoroalkane brushes allows for continuous monitoring of protein adsorption and desorption without irreversible binding.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Biochemistry & Molecular Biology
Idir Malki, Inara Liepina, Nora Kogelnik, Hollie Watmuff, Sue Robinson, Adam Lightfoot, Oksana Gonchar, Andrew Bottrill, Andrew M. Fry, Cyril Dominguez
Summary: In this study, we comprehensively investigated the post-translational modifications of Sam68 protein at different stages of the cell cycle using mass spectrometry, nuclear magnetic resonance spectroscopy, and cell biology techniques. We found that Sam68 is specifically phosphorylated at T33 and T371 by Cdk1, which reduces its RNA binding ability, controls its cellular localization, and decreases its alternative splicing activity.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Siyu Wang, Louise Fairall, Trong Khoa Pham, Timothy J. Ragan, Dipti Vashi, Mark O. Collins, Cyril Dominguez, John W. R. Schwabe
Summary: This study reveals that MIER1 protein binds to both H2A:H2B histone dimer and complete histone octamer. Additionally, a larger MIER1:HDAC1:BAHD1:C1QBP complex co-purifies with an intact nucleosome containing di- or tri-methylated H3K27. These findings suggest that the MIER1 complex acts downstream of PRC2, expanding regions of repressed chromatin and potentially depositing histone octamer onto nucleosome-depleted regions of DNA.
NUCLEIC ACIDS RESEARCH
(2023)