Review
Biochemistry & Molecular Biology
Susanna Tornroth-Horsefield, Clara Chivasso, Helin Strandberg, Claudia D'Agostino, Carla V. T. O'Neale, Kevin L. Schey, Christine Delporte
Summary: This review provides a comprehensive overview of the current knowledge of AQP interactomes and discusses the molecular basis and functional significance of these protein-protein interactions in health and diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Joana Damas, Marco Corbo, Jaebum Kim, Jason Turner-Maier, Marta Farre, Denis M. Larkin, Oliver A. Ryder, Cynthia Steiner, Marlys L. Houck, Shaune Hall, Lily Shiue, Stephen Thomas, Thomas Swale, Mark Daly, Jonas Korlach, Marcela Uliano-Silva, Camila J. Mazzoni, Bruce W. Birren, Diane P. Genereux, Jeremy Johnson, Kerstin Lindblad-Toh, Elinor K. Karlsson, Martin T. Nweeia, Rebecca N. Johnson, Harris A. Tewin
Summary: Decrypting the rearrangements that drive mammalian chromosome evolution is crucial for understanding speciation, adaptation, and disease susceptibility. By computationally reconstructing ancestral karyotypes and syntenic relationships, the study reveals the chromosome structure and evolutionary history of the mammalian ancestors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Cell Biology
Alissa D. Guarnaccia, Kristie L. Rose, Jing Wang, Bin Zhao, Tessa M. Popay, Christina E. Wang, Kiana Guerrazzi, Salisha Hill, Chase M. Woodley, Tyler J. Hansen, Shelly L. Lorey, J. Grace Shaw, William G. Payne, April M. Weissmiller, Edward T. Olejniczak, Stephen W. Fesik, Qi Liu, William P. Tansey
Summary: This study demonstrates how WIN site inhibitors alter the WDR5 interactome by using quantitative proteomics, showing that the inhibitors change the interaction of WDR5 with numerous proteins, including those related to the PI3K signaling pathway. The research also proves that the master kinase PDPK1 is a high-affinity binding protein for the WIN site, modulating gene transcription in the G2 phase of the cell cycle.
Article
Multidisciplinary Sciences
Yang Zhou, Linda Shearwin-Whyatt, Jing Li, Zhenzhen Song, Takashi Hayakawa, David Stevens, Jane C. Fenelon, Emma Peel, Yuanyuan Cheng, Filip Pajpach, Natasha Bradley, Hikoyu Suzuki, Masato Nikaido, Joana Damas, Tasman Daish, Tahlia Perry, Zexian Zhu, Yuncong Geng, Arang Rhie, Ying Sims, Jonathan Wood, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, Qiye Li, Huanming Yang, Jian Wang, Stephen D. Johnston, Adam M. Phillippy, Kerstin Howe, Erich D. Jarvis, Oliver A. Ryder, Henrik Kaessmann, Peter Donnelly, Jonas Korlach, Harris A. Lewin, Jennifer Graves, Katherine Belov, Marilyn B. Renfree, Frank Grutzner, Qi Zhou, Guojie Zhang
Summary: The study of egg-laying mammals' genomes offers insights into mammalian evolution, highlighting ancestral and lineage-specific genomic changes in monotremes and mammals. Unique chromosome complex in monotremes may have originated from ancestral chromosome configuration, and differences in specific genes underlie ecological adaptations of monotremes compared to therians.
Article
Biology
Dawn M. Wenzel, Douglas R. Mackay, Jack J. Skalicky, Elliott L. Paine, Matthew S. Miller, Katharine S. Ullman, Wesley Sundquist, Aurelien Roux
Summary: In this study, the interactions between human MIT domains and ESCRT-III tails were comprehensively mapped and quantified. Several new interactions were discovered, and the structure of the SPASTIN MIT domain in complex with the IST1 C-terminal tail was reported. The study also revealed the localization and functions of three MIT enzymes in cytokinetic abscission.
Article
Cell Biology
Teerna Bhattacharyya, Ramanathan Sowdhamini
Summary: The age of genomics has provided us with valuable information and tools to study whole genomes, leading to genome-wide studies that uncover interesting evolutionary patterns and the crucial role of phosphorylation in various organisms.
CELLULAR SIGNALLING
(2021)
Article
Biochemistry & Molecular Biology
Jing Zhang, Jimin Pei, Jesse Durham, Tasia Bos, Qian Cong
Summary: Protein-protein interactions (PPIs) are crucial in cellular processes and their perturbation is important in cancer. Using deep learning methods like AlphaFold, we predicted cancer-related PPIs and gained structural insights into cancer-related processes. Additionally, we explored the cancer mutation landscape on PPI interfaces, revealing functional preferences and potential drug targets.
Article
Plant Sciences
Merve Yilmaz, Merle Paulic, Thorsten Seidel
Summary: This study reports a protein-protein interaction network of Arabidopsis thaliana, combining various types of information such as subcellular localization, gene ontologies, biochemical properties, and co-expression. The resulting network shows enrichment in nuclear, cytosolic, and plasma membrane proteins, while being depleted in extracellular and mitochondrial proteins. Additionally, proteins involved in transcription are highly abundant in the network.
Article
Biochemistry & Molecular Biology
Sharof Khudayberdiev, Michael Soutschek, Irina Ammann, Anika Heinze, Marco B. Rust, Stefan Baumeister, Gerhard Schratt
Summary: SYNCRIP, a member of the hnRNP family, regulates neuronal development and plasticity. Through its interaction with various mRNAs involved in neurogenesis and neurite outgrowth, SYNCRIP has been found to promote early neuronal differentiation. Additionally, SYNCRIP synergizes with pro-neural miRNAs to enhance its effects on neuronal morphogenesis.
Article
Multidisciplinary Sciences
Hua-Jun Wu, Alexandro Landshammer, Elena K. Stamenova, Adriano Bolondi, Helene Kretzmer, Alexander Meissner, Franziska Michor
Summary: The disruption of a SOX17 boundary in human pluripotent stem cells interferes with proper differentiation, and germline variations affecting such boundaries are selectively retained, leading to underrepresentation in the human population.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Medicinal
Li-Yan Zhai, Jing-Fan Liu, Jian-Jin Zhao, Ai-Min Su, Xu-Guang Xi, Xi-Miao Hou
Summary: In recent years, G-quadruplexes (G4s) have been found in many harmful viruses, and G4 ligands have been designed to target these structures, showing promising antiviral effects. This perspective summarizes the diverse roles of RNA G4s in different viruses, introduces small-molecule ligands developed as G4 modulators, and reviews the medical intervention of G4-interacting proteins from both the virus and the host. The challenges and opportunities in G4-based antiviral therapy are also discussed.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Review
Cell Biology
Xuwen Li, Zijian Zhang, Xinlong Luo, Jacob Schrier, Andrew D. Yang, Tao P. Wu
Summary: N-6-methyladenine (N-6-mA, m(6)dA, or 6mA) is a prevalent DNA modification in prokaryotes and has been recently identified in higher eukaryotes, such as mammals. It can serve as an epigenetic mark and play critical roles in various biological processes, but the function and regulatory mechanism of 6mA in eukaryotes, especially mammals, are still poorly understood and require further research.
Article
Multidisciplinary Sciences
Mayank N. K. Choudhary, Kara Quaid, Xiaoyun Xing, Heather Schmidt, Ting Wang
Summary: Transposable elements (TEs), previously considered as junk DNA, contribute to species-specific 3D-genome structure by providing binding sites for CTCF protein. These elements play a role in gene regulation during mammalian evolution.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Igor Ivanov, Alejandro Cruz, Alexander Zhuravlev, Almerinda Di Venere, Eleonora Nicolai, Sabine Stehling, Jose M. Lluch, Angels Gonzalez-Lafont, Hartmut Kuhn
Summary: Recent data suggests that ALOXs may function in a dynamic monomer-dimer equilibrium with subtle structural differences. Experimental observations reveal that different conformers with distinct electrophoretic mobilities may impact the enzymatic properties.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Cell Biology
Jose Antonio Sanchez Milan, Maria Fernandez-Rhodes, Xue Guo, Maria Mulet, SoFong Cam Ngan, Ranjith Iyappan, Maryam Katoueezadeh, Siu Kwan Sze, Aida Serra, Xavier Gallart-Palau
Summary: This study provides a comprehensive analysis of the impact of oxidative stress and phosphorylation on the aging process. The results show that trioxidized cysteine residues accumulate in the aging proteome and interact with enzymes involved in phosphorylation signaling, altering their structures in a similar way to phosphorylated serine residues. These findings are significant for understanding the interplay between oxidative stress and phosphorylation in aging, and open new avenues for research on protein modifications in chronic diseases and aging.
Article
Biochemistry & Molecular Biology
Kirstine Belling, Francesco Russo, Anders B. Jensen, Marlene D. Dalgaard, David Westergaard, Ewa Rajpert-De Meyts, Niels E. Skakkebaek, Anders Juul, Soren Brunak
HUMAN MOLECULAR GENETICS
(2017)
Article
Cell Biology
Milena Doroszko, Marcin Chrusciel, Kirstine Belling, Susanna Vuorenoja, Marlene Dalgaard, Henrik Leffers, H. Bjorn Nielsen, Ilpo Huhtaniemi, Jorma Toppari, Nafis A. Rahman
MOLECULAR AND CELLULAR ENDOCRINOLOGY
(2017)
Article
Developmental Biology
Grete Lottrup, Kirstine Belling, Henrik Leffers, John E. Nielsen, Marlene D. Dalgaard, Anders Juul, Niels E. Skakkebaek, Soren Brunak, Ewa Rajpert-De Meyts
MOLECULAR HUMAN REPRODUCTION
(2017)
Article
Biochemistry & Molecular Biology
Francesco Russo, Sebastiano Di Bella, Federica Vannini, Gabriele Berti, Flavia Scoyni, Helen V. Cook, Alberto Santos, Giovanni Nigita, Vincenzo Bonnici, Alessandro Lagana, Filippo Geraci, Alfredo Pulvirenti, Rosalba Giugno, Federico De Masi, Kirstine Belling, Lars J. Jensen, Soren Brunak, Marco Pellegrini, Alfredo Ferro
NUCLEIC ACIDS RESEARCH
(2018)
Article
Biochemical Research Methods
Maria Luisa Matey-Hernandez, Soren Brunak, Jose M. G. Izarzugaza
BMC BIOINFORMATICS
(2018)
Article
Genetics & Heredity
Jonas Andreas Sibbesen, Lasse Maretty, Anders Krogh
Article
Cell Biology
Sofia Boeg Winge, Marlene Danner Dalgaard, Kirstine G. Belling, Jacob Malte Jensen, John Erik Nielsen, Lise Aksglaede, Mikkel Heide Schierup, Soren Brunak, Niels Erik Skakkebaek, Anders Juul, Ewa Rajpert-De Meyts, Kristian Almstrup
CELL DEATH & DISEASE
(2018)
Article
Genetics & Heredity
Isabella Friis Jorgensen, Francesco Russo, Anders Boeck Jensen, David Westergaard, Mette Lademann, Jessica Xin Hu, Soren Brunak, Kirstine Belling
GENETICS IN MEDICINE
(2019)
Article
Cell Biology
Kristoffer Niss, Cristina Gomez-Casado, Jessica X. Hjaltelin, Thorsten Joeris, William W. Agace, Kirstine G. Belling, Soren Brunak
Article
Public, Environmental & Occupational Health
Cristina Leal Rodriguez, Benjamin Skov Kaas-Hansen, Robert Eriksson, Jorge Hernansanz Biel, Kirstine G. Belling, Stig Ejdrup Andersen, Soren Brunak
Summary: This study aimed to investigate potential drug-drug interactions and their associated adverse outcomes in Danish hospital prescriptions, and identify patient types that are more affected. The results showed that certain drug combinations may lead to adverse outcomes, including increased mortality rates. Therefore, caution should be exercised to avoid these unsafe drug combinations during prescribing.
PHARMACOEPIDEMIOLOGY AND DRUG SAFETY
(2022)
Article
Cell Biology
Kristoffer Niss, Magnus E. Jakobsson, David Westergaard, Kirstine G. Belling, Jesper Olsen, Soren Brunak
MOLECULAR AND CELLULAR ENDOCRINOLOGY
(2020)
Article
Mathematical & Computational Biology
Soren Brunak, Catherine Bjerre Collin, Katharina Eva O. Cathaoir, Martin Golebiewski, Marc Kirschner, Ingrid Kockum, Heike Moser, Dagmar Waltemath
JOURNAL OF INTEGRATIVE BIOINFORMATICS
(2020)
Article
Medical Informatics
Hans-Christian Thorsen-Meyer, Annelaura B. Nielsen, Anna P. Nielsen, Benjamin Skov Kaas-Hansen, Palle Toft, Jens Schierbeck, Thomas Strom, Piotr J. Chmura, Marc Heimann, Lars Dybdahl, Lasse Spangsege, Patrick Hulsen, Kirstine Belling, Soren Brunak, Anders Perner
LANCET DIGITAL HEALTH
(2020)
Article
Medical Informatics
Annelaura B. Nielsen, Hans-Christian Thorsen-Meyer, Kirstine Belling, Anna P. Nielsen, Cecilia E. Thomas, Piotr J. Chmura, Mette Lademann, Pope L. Moseley, Marc Heimann, Lars Dybdahl, Lasse Spangsege, Patrick Hulsen, Anders Perner, Soren Brunak
LANCET DIGITAL HEALTH
(2019)
Meeting Abstract
Biochemistry & Molecular Biology
F. Russo, I. Friis Jorgensen, D. Westergaard, A. Boeck Jensen, J. Xin Hu, K. Belling, S. Brunak
EUROPEAN JOURNAL OF HUMAN GENETICS
(2018)