Article
Cell Biology
Sean O'Connor, Elisabeth A. Murphy, Sarah K. Szwed, Matt Kanke, Francois Marchildon, Praveen Sethupathy, Robert B. Darnell, Paul Cohen
Summary: The study comprehensively analyzed the network of miRNA:mRNA interactions in white and brown fat using HITS-CLIP, revealing numerous unique AGO binding sites and an inverse correlation between depot-enriched miRNAs and their targets. Furthermore, experimental validation showed that miR-29 is a novel regulator of leptin expression, providing important insights into the unique identities of white and brown fat cells.
GENES & DEVELOPMENT
(2021)
Article
Biochemistry & Molecular Biology
Prachi Deshmukh, Shubha Markande, Vikas Fandade, Yogendra Ramtirtha, Mallur Srivatsan Madhusudhan, Jomon Joseph
Summary: Micro-RNA mediated suppression of mRNA translation is a key regulatory mode of gene expression. Nup358-SIM has multiple interacting regions on AGO2, facilitating the coupling of miRISC with target mRNA. Specific residues are involved in the interaction of AGO2 with miRNA-loading components.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Kijun Kim, S. Chan Baek, Young-Yoon Lee, Carolien Bastiaanssen, Jeesoo Kim, Haedong Kim, V. Narry Kim
Summary: Only 758 pri-miRNAs are confidently processed by DROSHA, while the majority may be non-canonical or false entries. Analyses of the DROSHA-dependent pri-miRNAs show key cis-elements for processing, and widespread alternative processing and unproductive cleavage events were observed.
Article
Chemistry, Multidisciplinary
Okke Melse, Iris Antes, Ville R. I. Kaila, Martin Zacharias
Summary: We systematically investigate the behavior of non-polarizable Zn2+ models in reproducing experimentally determined metal coordination and ligand binding in metalloproteins. Key differences in the performance of these models are identified, including the preferred ligating atoms, attraction of water molecules, and coordination geometry preferences. Suitable simulation conditions for different Zn2+ site geometries are suggested based on the results.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Computer Science, Artificial Intelligence
Nan Wu, Leonie Stromich, Sophia N. Yaliraki
Summary: Allostery is a mechanism that regulates protein activity through ligand binding at a different site. Predicting allosteric sites is challenging, but bond-to-bond propensity analysis has shown promise. This study extended the analysis to a larger dataset and introduced statistical measures to characterize potential allosteric sites and mechanisms involved.
Article
Biochemical Research Methods
Yuning Yang, Zilong Hou, Yansong Wang, Hongli Ma, Pingping Sun, Zhiqiang Ma, Ka-Chun Wong, Xiangtao Li
Summary: This study presents a novel end-to-end framework called HCRNet for identifying circRNA-RBP binding events. By fusing multiple sources of biological information to represent circRNAs and using a deep temporal convolutional network, HCRNet performs well across various circRNA datasets and exhibits good interpretability.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Medicine, General & Internal
Olga Bryzgunova, Maria Konoshenko, Ivan Zaporozhchenko, Alexey Yakovlev, Pavel Laktionov
Summary: Recent research has shown the potential of utilizing microRNA in clinical and medical settings, but the challenge lies in extracting high-quality miRNA samples. Researchers need to choose appropriate extraction methods and consider the structural properties and stability of miRNA.
Article
Automation & Control Systems
Xiangtao Li, Shixiong Zhang, Ka-Chun Wong
Summary: RNA-binding proteins play a crucial role in mRNA processing and post-transcriptional gene expression control. CLIP-seq technologies have enabled sequencing of genome-wide RNA-binding event data, leading to the development of methods for identifying protein-RNA interactions on a genome-wide scale, facilitating the understanding of protein functions in cellular processes. The computational method presented in this study, MFA, utilizing multiobjective biogeography-based optimization with random forest, demonstrates superior performance in identifying protein-RNA interactions compared to current methods, with insights gained through various analyses.
IEEE TRANSACTIONS ON CYBERNETICS
(2021)
Article
Medicine, General & Internal
Anton Tyurin, Daria Shapovalova, Halida Gantseva, Valentin Pavlov, Rita Khusainova
Summary: This study identified miRNA target sites as genetic markers for the development of OA in various ethnic groups, and clarified the association between polymorphic variants in several genes and the incidence of OA.
Article
Biotechnology & Applied Microbiology
Maria Katsantoni, Erik van Nimwegen, Mihaela Zavolan
Summary: We present RCRUNCH, an end-to-end solution for CLIP data analysis that identifies binding sites and sequence specificity of RNA-binding proteins. RCRUNCH can analyze reads that map uniquely to the genome as well as reads that map to multiple genome locations or across splice boundaries, considering various background types for read enrichment estimation. Applying RCRUNCH to eCLIP data from the ENCODE project, we have created a comprehensive and homogeneous resource of in-vivo-bound RBP sequence motifs. RCRUNCH automates reproducible analysis of CLIP data, facilitating studies on post-transcriptional control of gene expression.
Article
Biochemistry & Molecular Biology
Sam Bryce-Smith, Dominik Burri, Matthew R. Gazzara, Christina J. Herrmann, Weronika Danecka, Christina M. Fitzsimmons, Yuk Kei Wan, Farica Zhuang, Mervin M. Fansler, Jose M. Fernandez, Meritxell Ferret, Asier Gonzalez-Uriarte, Samuel Haynes, Chelsea Herdman, Alexander Kanitz, Maria Katsantoni, Federico Marini, Euan McDonnel, Ben Nicolet, Chi-Lam Poon, Gregor Rot, Leonard Scharfen, Pin-Jou Wu, Yoseop Yoon, Yoseph Barash, Mihaela Zavolan
Summary: The APAeval project provides benchmarks and quantification for tools used in identifying and quantifying alternative polyadenylation (APA) sites. The results are integrated into an online platform to support continuous method evaluation.
Article
Multidisciplinary Sciences
Sayed Mehedi Azim, Alok Sharma, Iman Noshadi, Swakkhar Shatabda, Iman Dehzangi
Summary: AMPylation is an emerging post-translational modification that plays a role in neurodevelopment and neurodegeneration. However, there is a lack of computational approaches for predicting AMPylation due to a lack of peptide sequence datasets. In this study, a new dataset and machine learning tool called DeepAmp were introduced, achieving promising results in predicting AMPylation sites in proteins.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Brittany Cain, Jordan Webb, Zhenyu Yuan, David Cheung, Hee-Woong Lim, Rhett A. Kovall, Matthew T. Weirauch, Brian Gebelein
Summary: Homeodomain proteins can form cooperative homodimer complexes on DNA sites with precise spacing requirements, with approximately one third of the paired-like homeodomain proteins binding to palindromic sequences spaced 3 bp apart. Other homeodomain proteins bind to sites with distinct orientation and spacing requirements. Computational analysis using structural models and computational mining of HT-SELEX data allowed the identification of key amino acid differences that differentiate between cooperative and non-cooperative factors. In vivo validation using available genomic data confirmed the predicted cooperative dimer sites for a subset of factors.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Sophie Stebel, Janina Breuer, Oliver Rossbach
Summary: Transcriptome-wide analysis of RNA-binding partners is commonly achieved using UV crosslinking and immunoprecipitation (CLIP). This study optimized an Ago2-specific CLIP protocol for small quantities of cell material, avoiding methodological biases and employing the latest advances in CLIP library preparation.
METHODS AND PROTOCOLS
(2022)
Article
Biochemistry & Molecular Biology
Himani Tandon, Alexandre G. de Brevern, Narayanaswamy Srinivasan
Summary: Analysis of 58 protein-protein complexes revealed that approximately 55% of cases showed significant dynamics change upon binding, even without accompanying structural change. Binding of a protein partner was found to alter inter-residue communication within the tertiary structure in about 90% of cases, and accessible residue motions in unbound proteins were not always maintained in the bound form. Overall, the results strongly suggest that alteration of protein dynamics due to binding is a common occurrence.
Article
Biochemistry & Molecular Biology
Carly G. K. Ziegler, Samuel J. Allon, Sarah K. Nyquist, Ian M. Mbano, Vincent N. Miao, Constantine N. Tzouanas, Yuming Cao, Ashraf S. Yousif, Julia Bals, Blake M. Hauser, Jared Feldman, Christoph Muus, Marc H. Wadsworth, Samuel W. Kazer, Travis K. Hughes, Benjamin Doran, G. James Gatter, Marko Vukovic, Faith Taliaferro, Benjamin E. Mead, Zhiru Guo, Jennifer P. Wang, Delphine Gras, Magali Plaisant, Meshal Ansari, Ilias Angelidis, Heiko Adler, Jennifer M. S. Sucre, Chase J. Taylor, Brian Lin, Avinash Waghray, Vanessa Mitsialis, Daniel F. Dwyer, Kathleen M. Buchheit, Joshua A. Boyce, Nora A. Barrett, Tanya M. Laidlaw, Shaina L. Carroll, Lucrezia Colonna, Victor Tkachev, Christopher W. Peterson, Alison Yu, Hengqi Betty Zheng, Hannah P. Gideon, Caylin G. Winchell, Philana Ling Lin, Colin D. Bingle, Scott B. Snapper, Jonathan A. Kropski, Fabian J. Theis, Herbert B. Schiller, Laure-Emmanuelle Zaragosi, Pascal Barbry, Alasdair Leslie, Hans-Peter Kiem, JoAnne L. Flynn, Sarah M. Fortune, Bonnie Berger, Robert W. Finberg, Leslie S. Kean, Manuel Garber, Aaron G. Schmidt, Daniel Lingwood, Alex K. Shalek, Jose Ordovas-Montanes
Review
Cell Biology
Marie Legendre, Laure-Emmanuelle Zaragosi, Hannah M. Mitchison
Summary: The article discusses the role of regulated airway epithelial development in the differentiation of motile ciliated cells in the human respiratory tract, as well as ciliary dysfunction caused by genetic mutations. Advances in understanding respiratory epithelial development and ciliary biology have the potential to improve disease diagnosis, management, and family counseling.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Vera L. Costa, Jean-Bernard Ruidavets, Vanina Bongard, Bertrand Perret, Emanuela Repetto, Maria G. Stathopoulou, Fabrizio Serra, Mohamed Benahmed, Claire Mauduit, Valerie Grandjean, Jean Ferrieres, Laurent O. Martinez, Michele Trabucchi
Summary: The study shows that the elevated expression of serum s-RNY1-5p is associated with an increased risk of coronary heart disease (CHD) events in the male population, suggesting its potential as a predictive biomarker for detection of cardiovascular diseases.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Christoph Muus, Malte D. Luecken, Gokcen Eraslan, Lisa Sikkema, Avinash Waghray, Graham Heimberg, Yoshihiko Kobayashi, Eeshit Dhaval Vaishnav, Ayshwarya Subramanian, Christopher Smillie, Karthik A. Jagadeesh, Elizabeth Thu Duong, Evgenij Fiskin, Elena Torlai Triglia, Meshal Ansari, Peiwen Cai, Brian Lin, Justin Buchanan, Sijia Chen, Jian Shu, Adam L. Haber, Hattie Chung, Daniel T. Montoro, Taylor Adams, Hananeh Aliee, Samuel J. Allon, Zaneta Andrusivova, Ilias Angelidis, Orr Ashenberg, Kevin Bassler, Christophe Becavin, Inbal Benhar, Joseph Bergenstrahle, Ludvig Bergenstrahle, Liam Bolt, Emelie Braun, Linh T. Bui, Steven Callori, Mark Chaffin, Evgeny Chichelnitskiy, Joshua Chiou, Thomas M. Conlon, Michael S. Cuoco, Anna S. E. Cuomo, Marie Deprez, Grant Duclos, Denise Fine, David S. Fischer, Shila Ghazanfar, Astrid Gillich, Bruno Giotti, Joshua Gould, Minzhe Guo, Austin J. Gutierrez, Arun C. Habermann, Tyler Harvey, Peng He, Xiaomeng Hou, Lijuan Hu, Yan Hu, Alok Jaiswal, Lu Ji, Peiyong Jiang, Theodoros S. Kapellos, Christin S. Kuo, Ludvig Larsson, Michael A. Leney-Greene, Kyungtae Lim, Monika Litvinukova, Leif S. Ludwig, Soeren Lukassen, Wendy Luo, Henrike Maatz, Elo Madissoon, Lira Mamanova, Kasidet Manakongtreecheep, Sylvie Leroy, Christoph H. Mayr, Ian M. Mbano, Alexi M. McAdams, Ahmad N. Nabhan, Sarah K. Nyquist, Lolita Penland, Olivier B. Poirion, Sergio Poli, CanCan Qi, Rachel Queen, Daniel Reichart, Ivan Rosas, Jonas C. Schupp, Conor Shea, Xingyi Shi, Rahul Sinha, Rene Sit, Kamil Slowikowski, Michal Slyper, Neal P. Smith, Alex Sountoulidis, Maximilian Strunz, Travis B. Sullivan, Dawei Sun, Carlos Talavera-Lopez, Peng Tan, Jessica Tantivit, Kyle J. Travaglini, Nathan R. Tucker, Katherine A. Vernon, Marc H. Wadsworth, Julia Waldman, Xiuting Wang, Ke Xu, Wenjun Yan, William Zhao, Carly G. K. Ziegler
Summary: Our study reveals that cell-type-specific expression patterns of ACE2, TMPRSS2, and CTSL are associated with the pathogenesis of COVID-19. Factors such as age, sex, and smoking status are linked to the expression of viral entry genes in respiratory cell populations, suggesting potential therapeutic targets for intervention. The integrated analysis of single-cell and single-nucleus transcriptomics studies highlights coexpression patterns of SARS-CoV-2 viral entry genes across different human tissues.
Article
Biochemistry & Molecular Biology
Fabrizio Serra, Silvia Bottini, David Pratella, Maria G. Stathopoulou, Wanda Sebille, Loubna El-Hami, Emanuela Repetto, Claire Mauduit, Mohamed Benahmed, Valerie Grandjean, Michele Trabucchi
Summary: The study established a new computational framework, optiCLIP, to characterize the modes of miRNA-binding and their role in gene silencing. Clustering the binding preferences revealed heterogeneity in the modes of miRNA binding. A quantitative model, miRgame, was developed to demonstrate the relationships between miRNA binding sites and miRNAs.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Julien Fassy, Caroline Lacoux, Sylvie Leroy, Latifa Noussair, Sylvain Hubac, Aurelien Degoutte, Georges Vassaux, Vianney Leclercq, David Rouquie, Charles-Hugo Marquette, Martin Rottman, Patrick Touron, Antoinette Lemoine, Jean-Louis Herrmann, Pascal Barbry, Jean-Louis Nahon, Laure-Emmanuelle Zaragosi, Bernard Mari
Summary: The emergence and fast spread of SARS-CoV-2 has highlighted the insufficient testing capacity in many countries due to limitations in resources, technology, and personnel. While traditional RT-qPCR diagnostic tests remain the standard method, a quantitative nanofluidic assay based on the Biomark™ instrument from Fluidigm offers a more efficient and cost-effective approach to testing, overcoming some of the limitations of traditional methods. This advanced system allows for high-throughput testing, monitoring of specific SARS-CoV-2 variants, and detection of other pathogens and host cellular responses.
Article
Biology
Georges Raad, Fabrizio Serra, Luc Martin, Marie-Alix Derieppe, Jerome Gilleron, Vera L. Costa, Didier F. Pisani, Ez-Zoubir Amri, Michele Trabucchi, Valerie Grandjean
Summary: Research shows that maintaining a paternal Western diet feeding for five consecutive generations in mice leads to an increase in fat mass and related metabolic diseases over generations, but progenies from these multigenerational Western-diet-fed males develop a healthy overweight phenotype characterized by normal glucose metabolism and without fatty liver, which persists for four subsequent generations. Sperm RNA is suggested to be sufficient for the establishment but not for long-term maintenance of epigenetic inheritance of metabolic pathologies.
Article
Biochemistry & Molecular Biology
Pengfei Gong, Danielle Bailbe, Lola Bianchi, Gaelle Pommier, Junjun Liu, Stefania Tolu, Maria G. Stathopoulou, Bernard Portha, Valerie Grandjean, Jamileh Movassat
Summary: The study found that paternal high-protein diet has a sex-specific impact on the metabolic health of offspring, particularly affecting male descendants.
Article
Multidisciplinary Sciences
Linh T. Bui, Nichelle I. Winters, Mei-I Chung, Chitra Joseph, Austin J. Gutierrez, Arun C. Habermann, Taylor S. Adams, Jonas C. Schupp, Sergio Poli, Lance M. Peter, Chase J. Taylor, Jessica B. Blackburn, Bradley W. Richmond, Andrew G. Nicholson, Doris Rassl, William A. Wallace, Ivan O. Rosas, R. Gisli Jenkins, Naftali Kaminski, Jonathan A. Kropski, Nicholas E. Banovich
Summary: Patients with chronic lung disease (CLD) have an increased risk for severe coronavirus disease-19 and poor outcomes. A study comparing the transcriptomes of single cells isolated from healthy and CLD lungs found differences in gene expression that may contribute to worse COVID-19 outcomes in these patients.
NATURE COMMUNICATIONS
(2021)
Review
Respiratory System
Malte D. Luecken, Laure-Emmanuelle Zaragosi, Elo Madissoon, Lisa Sikkema, Alexandra B. Firsova, Elena De Domenico, Louis Kuemmerle, Adem Saglam, Marijn Berg, Aurore C. A. Gay, Janine Schniering, Christoph H. Mayr, Xesus M. Abalo, Ludvig Larsson, Alexandros Sountoulidis, Sarah A. Teichmann, Karen Van Eunen, Gerard H. Koppelman, Kourosh Saeb-Parsy, Sylvie Leroy, Pippa Powell, Ugis Sarkans, Wim Timens, Joakim Lundeberg, Maarten van den Berge, Mats Nilsson, Peter Horvath, Jessica Denning, Irene Papatheodorou, Joachim L. Schultze, Herbert B. Schiller, Pascal Barbry, Ilya Petoukhov, Alexander V. Misharin, Ian M. Adcock, Michael von Papen, Fabian J. Theis, Christos Samakovlis, Kerstin B. Meyer, Martijn C. Nawijn
Summary: The Human Cell Atlas consortium aims to establish an atlas of all organs in the healthy human body at single-cell resolution to increase our understanding of biological processes and accelerate disease diagnosis and treatment. The Lung Biological Network of the HCA aims to generate the Human Lung Cell Atlas as a reference for normal lung homeostasis. The discovAIR project aims to create the first draft of an integrated Human Lung Cell Atlas, which will be a valuable resource for researchers, clinicians, and patients.
EUROPEAN RESPIRATORY JOURNAL
(2022)
Article
Andrology
Sarah Saget, Laurent Kappeler, Valerie Grandjean, Patricia Leneuve, Isabelle Berthaut, Celine Faure, Sebastien Czernichow, Chrystele Racine, Rachel Levy, Charlotte Dupont
Summary: Specific miRNAs in seminal plasma are correlated with metabolic and anthropometric disorders, with the correlations appearing to be specific to seminal plasma and not present in blood plasma. Further studies are needed to explore potential implications of other small non-coding RNAs in male reproductive function alterations related to obesity or metabolic disorders.
BASIC AND CLINICAL ANDROLOGY
(2022)
Article
Biochemistry & Molecular Biology
Amelie Cavard, Elisa Redman, Olivier Mercey, Sophie Abelanet, Magali Plaisant, Marie-Jeanne Arguel, Virginie Magnone, Sandra Ruiz Garcia, Geraldine Rios, Marie Deprez, Kevin Lebrigand, Gilles Ponzio, Ignacio Caballero, Pascal Barbry, Laure-Emmanuelle Zaragosi, Brice Marcet
Summary: The MIR449 genomic locus contains regulators of multiciliated cell formation, and miR-34b/c from the MIR34B/C locus are additional regulators. Through single-cell RNA-seq and super-resolution microscopy, the expression of BTG4, LAYN, and HOATZ in the MIR34B/C locus was characterized. These transcripts were expressed in both precursors and mature multiciliated cells. Layilin/LAYN protein was absent from primary cilia but expressed in apical membrane regions or throughout motile cilia. Silencing LAYN affected actin cap formation and multiciliogenesis. HOATZ protein was detected in primary cilia or throughout motile cilia. These findings suggest that the MIR34B/C locus may gather potential regulators of multiciliogenesis.
Article
Biochemistry & Molecular Biology
Charlotte Dupont, Maria G. Stathopoulou, Pierre-Julien Illy, Nathalie Sermondade, Rachel Levy, Michele Trabucchi, Marie Prades, Rahaf Haj Hamid, Isabelle Berthaut, Valerie Grandjean
Summary: Testicular germ cell tumours (TGCTs) are common in young European adults. This study suggests that the abundance of sperm small non-coding RNAs may be useful in diagnosing men with TGCT.