Article
Neurosciences
Amanda R. Burmeister, Juozas Gordevicius, Emmanuel N. Paul, Christina Houck, Sonia George, Martha L. Escobar Galvis, Qiong Sha, Patrik Brundin, J. Andrew Pospisilik, Karen Racicot, Lena Brundin
Summary: In this study, a mouse maternal infection model was used to investigate the impact of maternal herpesvirus infection on the development and physiology of midbrain dopaminergic neurons in adult offspring. The results suggested that maternal infection with Herpesviridae, specifically MHV68, can trigger changes in midbrain development that affect dopamine neuron physiology in adulthood. This study is important for understanding the neuronal susceptibility underlying neurodegenerative diseases, particularly Parkinson's disease.
NEUROBIOLOGY OF DISEASE
(2022)
Article
Cell Biology
Aurore Tourville, David Akbar, Olga Corti, Jochen H. M. Prehn, Ronald Melki, Stephane Hunot, Patrick P. Michel
Summary: The researchers established a model system to study alpha-Synuclein aggregation and neurodegeneration in Parkinson's disease. They found that F91 fibrils have a strong propensity to induce aggregation in DA neurons, leading to subsequent loss of these neurons. This neuronal loss can be prevented by treatment with GDNF.
Article
Chemistry, Analytical
Wenbin Liu, Wei-dong Zhang, Tongzhou Li, Zhiwei Zhou, Mingdu Luo, Xi Chen, Yuping Cai, Zheng-Jiang Zhu
Summary: This study developed a four-dimensional untargeted technology based on ion mobility-mass spectrometry (IM-MS) for comprehensive analysis of N-Acylethanolamines (NAE) lipids. By employing picolinyl derivatization and establishing a four-dimensional library, multiple NAE lipids were successfully identified, and age-associated changes in NAE lipids in the mouse brain were discovered.
ANALYTICAL CHEMISTRY
(2022)
Article
Developmental Biology
Marcella Birtele, Petter Storm, Yogita Sharma, Janko Kajtez, Jenny Nelander Wahlestedt, Edoardo Sozzi, Fredrik Nilsson, Simon Stott, Xiaoling L. He, Bengt Mattsson, Daniella Rylander Ottosson, Roger A. Barker, Alessandro Fiorenzano, Malin Parmar
Summary: This study used single-cell RNA sequencing to analyze the transcriptional profile of human fetal VM during the generation and differentiation of dopamine neurons, revealing that 3D culture conditions are superior to monolayer conditions. These findings can guide stem cell-based therapies and disease modeling in Parkinson's disease.
Article
Neurosciences
Judit Pallos, Sophia Jeng, Shannon McWeeney, Ian Martin
Summary: LRRK2 mutations are the most common genetic cause of late-onset Parkinson's disease, enhancing kinase activity and causing neurodegeneration. Using TRAP and RNA-seq, researchers profiled gene expression changes specifically in dopamine neurons induced by LRRK2 G2019S in Drosophila, uncovering a range of differentially expressed genes.
NEUROBIOLOGY OF DISEASE
(2021)
Article
Cell Biology
Daniel Dautan, Adrienn Kovacs, Tsogbadrakh Bayasgalan, Miguel A. Diaz-Acevedo, Balazs Pal, Juan Mena-Segovia
Summary: CnF and PPN neurons in the MLR demonstrate distinct physiological properties and connectivity patterns, contributing to short-lasting muscle activation and long-lasting muscle tone increase in motor behavior, respectively.
Article
Cell Biology
Wei Yu, V. Praveen Chakravarthi, Shaon Borosha, Iman Dilower, Eun Bee Lee, Anamika Ratri, Rebekah R. Starks, Patrick E. Fields, Michael W. Wolfe, M. Omar Faruque, Geetu Tuteja, M. A. Karim Rumi
Summary: The study reveals that trophoblast-specific Satb1 expression is regulated by long-range chromatin looping mediated by an enhancer that interacts with ELF5 and SATB proteins, contributing to the maintenance of cell state.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Neurosciences
Lite Yang, Mengyi Xu, Shamsuddin A. Bhuiyan, Jia Li, Jun Zhao, Randall J. Cohrs, Justin T. Susterich, Sylvia Signorelli, Ursula Green, James R. Stone, Dan Levy, Jochen K. Lennerz, William Renthal
Summary: This study developed a cell atlas of trigeminal ganglion cells in humans and mice, providing insights into the gene expression patterns and gene regulatory elements of different cell types. The atlas identified cell types implicated in migraine and provides a valuable resource for understanding headache pathophysiology and developing more selective treatments.
Article
Cell Biology
Ana Rita Amandio, Leonardo Beccari, Lucille Lopez-Delisle, Benedicte Mascrez, Jozsef Zakany, Sandra Gitto, Denis Duboule
Summary: Understanding the diverse functions of CTCF sites within the Hox gene clusters is crucial for the formation of TAD borders and maintaining gene expression, showing significant evolutionary conservation.
GENES & DEVELOPMENT
(2021)
Article
Genetics & Heredity
Margaret G. Guo, David L. Reynolds, Cheen E. Ang, Yingfei Liu, Yang Zhao, Laura K. H. Donohue, Zurab Siprashvili, Xue Yang, Yongjin Yoo, Smarajit Mondal, Audrey Hong, Jessica Kain, Lindsey Meservey, Tania Fabo, Ibtihal Elfaki, Laura N. Kellman, Nathan S. Abell, Yash Pershad, Vafa Bayat, Payam Etminani, Mark Holodniy, Daniel H. Geschwind, Stephen B. Montgomery, Laramie E. Duncan, Alexander E. Urban, Russ B. Altman, Marius Wernig, Paul A. Khavari
Summary: Noncoding variants play a role in the heritability of neuropsychiatric diseases. A study in developing human neural cells investigated 2,221 noncoding variants associated with ten neuropsychiatric disorders and identified differentially-active single-nucleotide variants (daSNVs) in specific neural cell types. Integrating epigenomic and transcriptomic data helped identify candidate disease-relevant target genes modulated by these daSNVs.
Article
Genetics & Heredity
Ming-Kun Huang, Ling Zhang, Li-Meng Zhou, Wai-Shing Yung, Man-Wah Li, Hon-Ming Lam
Summary: Research identified 22,333 OCRs in wild soybean leaves, enriched at gene TSS and correlated with gene expression. These OCRs contained TF-binding motifs, forming a potential regulatory network. The activation histone mark H3K4me3 was closely associated with OCRs, while the repressive mark H3K27me3 was not, suggesting the importance of OCR duplication for plant genome architecture and gene regulation.
Article
Biochemistry & Molecular Biology
Christine K. Rummel, Miriam Gagliardi, Ruhel Ahmad, Alexander Herholt, Laura Jimenez-Barron, Vanessa Murek, Liesa Weigert, Anna Hausruckinger, Susanne Maidl, Barbara Hauger, Florian J. Raabe, Christina Fuerle, Lucia Trastulla, Gustavo Turecki, Matthias Eder, Moritz J. Rossner, Michael J. Ziller
Summary: This study conducted variant-to-function mapping in disease-relevant neural cell types to investigate the role of genetic variants in schizophrenia. By integrating multiple datasets, the functional variants were linked to target genes, biological processes, and alterations in neuronal physiology, providing insights into the context-dependent molecular processes modulated by schizophrenia-associated genetic variation.
Review
Biochemistry & Molecular Biology
S. A. Antonov, E. Novosadova
Summary: Human induced pluripotent stem cells offer new possibilities for Parkinson's disease research, allowing for investigation of disease pathogenesis, drug development, and personalized therapy. Despite the wide coverage of benefits in current literature, the drawbacks of the current model, particularly in differentiation protocols, are often overlooked. Further research is needed to improve differentiation conditions and increase efficiency for PD drug development using iPS cell-derived neurons.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Neurosciences
Renchao Chen, Timothy R. Blosser, Mohamed N. Djekidel, Junjie Hao, Aritra Bhattacherjee, Wenqiang Chen, Luis M. Tuesta, Xiaowei Zhuang, Yi Zhang
Summary: The authors utilized single-cell RNA sequencing and multiplexed error-robust FISH to generate a cell census of the mouse nucleus accumbens, revealing a high level of cell heterogeneity. This study demonstrates that the transcriptional and spatial diversity of neuron subtypes underlie the anatomic and functional heterogeneity of the nucleus accumbens.
NATURE NEUROSCIENCE
(2021)
Article
Neurosciences
Manli Zhong, Yuhan Wang, Geng Lin, Francesca-Fang Liao, Fu-Ming Zhou
Summary: This study found that in mice, the medium spiny neurons responsible for motor control and cognition in the striatum are not affected by dopamine loss, contrary to previous theories.
NEUROBIOLOGY OF DISEASE
(2023)
Review
Genetics & Heredity
Valentina Snetkova, Len A. Pennacchio, Axel Visel, Diane E. Dickel
Summary: This review examines the reasons behind the minor phenotypic consequences of disrupting ultraconserved sequences and discusses the broader implications for gene regulation and human variant interpretation. Ultraconserved elements, predominantly non-coding regions in the human genome, play roles as enhancers activating tissue-specific gene expression during embryonic development. Researchers continue to be intrigued by the extreme conservation of these non-coding elements, which have been found to be dispensable for viability.
NATURE REVIEWS GENETICS
(2022)
Article
Cell Biology
Tanvi Sinha, Kelly Lammerts van Bueren, Diane E. Dickel, Ivana Zlatanova, Reuben Thomas, Carlos O. Lizama, Shan-Mei Xu, Ann C. Zovein, Kohta Ikegami, Ivan P. Moskowitz, Katherine S. Pollard, Len A. Pennacchio, Brian L. Black
Summary: This study investigates the initiation of gene-regulatory networks (GRNs) for endothelial and erythropoietic development by analyzing a hypomorphic Etv2 mutant. The researchers find that Etv2 has different threshold requirements for initiating the downstream GRNs for each lineage, directly regulating the endothelial GRN and indirectly activating Tal1 for erythropoietic development.
Article
Clinical Neurology
Paolo Reho, Shunsuke Koga, Zalak Shah, Ruth Chia, Rosa Rademakers, Clifton L. Dalgard, Bradley F. Boeve, Thomas G. Beach, Dennis W. Dickson, Owen A. Ross, Sonja W. Scholz
Summary: This study aimed to evaluate pathogenic variants in GRN among Lewy body dementia (LBD) patients and found an enrichment of GRN loss-of-function mutations in the cases.
MOVEMENT DISORDERS
(2022)
Article
Clinical Neurology
Franziska Hopfner, Anja K. Tietz, Viktoria C. Ruf, Owen A. Ross, Shunsuke Koga, Dennis Dickson, Adriano Aguzzi, Johannes Attems, Thomas Beach, Allison Beller, William P. Cheshire, Vivianna van Deerlin, Paula Desplats, Guenther Deuschl, Charles Duyckaerts, David Ellinghaus, Valentin Evsyukov, Margaret Ellen Flanagan, Andre Franke, Matthew P. Frosch, Marla Gearing, Ellen Gelpi, Jay A. van Gerpen, Bernardino Ghetti, Jonathan D. Glass, Lea T. Grinberg, Glenda Halliday, Ingo Helbig, Matthias Hollerhage, Inge Huitinga, David John Irwin, Dirk C. Keene, Gabor G. Kovacs, Edward B. Lee, Johannes Levin, Maria J. Marti, Ian Mackenzie, Ian McKeith, Catriona Mclean, Brit Mollenhauer, Manuela Neumann, Kathy L. Newell, Alex Pantelyat, Manuela Pendziwiat, Annette Peters, Laura Molina Porcel, Alberto Rabano, Radoslav Matej, Alex Rajput, Ali Rajput, Regina Reimann, William K. Scott, William Seeley, Sashika Selvackadunco, Tanya Simuni, Christine Stadelmann, Per Svenningsson, Alan Thomas, Claudia Trenkwalder, Claire Troakes, John Q. Trojanowski, Ryan J. Uitti, Charles L. White, Zbigniew K. Wszolek, Tao Xie, Teresa Ximelis, Justo Yebenes, Ulrich Mueller, Gerard D. Schellenberg, Jochen Herms, Gregor Kuhlenbaumer, Gunter Hoeglinger
Summary: Multiple System Atrophy is a rare neurodegenerative disease characterized by alpha-synuclein aggregation in glial cytoplasmic inclusions. By studying autopsy-confirmed cases, it was found that rs16859966 on chromosome 3, rs7013955 on chromosome 8, and rs116607983 on chromosome 4 are the most strongly disease-associated markers.
MOVEMENT DISORDERS
(2022)
Article
Biochemistry & Molecular Biology
Joseph F. Thole, Christopher A. Waudby, Gary J. Pielak
Summary: The biophysical characterization of protein-protein interactions involving disordered proteins is challenging. Although simplifications can be made, such as measuring the thermodynamics and kinetics using peptides with minimum residues, these methods do not provide a complete understanding of the interactions.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
I-Min A. Chen, Ken Chu, Krishnaveni Palaniappan, Anna Ratner, Jinghua Huang, Marcel Huntemann, Patrick Hajek, Stephan J. Ritter, Cody Webb, Dongying Wu, Neha J. Varghese, T. B. K. Reddy, Supratim Mukherjee, Galina Ovchinnikova, Matt Nolan, Rekha Seshadri, Simon Roux, Axel Visel, Tanja Woyke, Emiley A. Eloe-Fadrosh, Nikos C. Kyrpides, Natalia N. Ivanova
Summary: The Integrated Microbial Genomes & Microbiomes system (IMG/M) at the Department of Energy Joint Genome Institute (JGI) provides support for comparative analysis of various genomes, metagenomes, and metatranscriptomes. It includes datasets from JGI, as well as imported datasets from public sources and user-submitted datasets. In recent years, efforts have been made to improve annotation pipeline, upgrade reference database versions, and add new analysis functionalities.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Ferdinand Marletaz, Elisa de la Calle-Mustienes, Rafael D. Acemel, Christina Paliou, Silvia Naranjo, Pedro Manuel Martinez-Garcia, Ildefonso Cases, Victoria A. Sleight, Christine Hirschberger, Marina Marcet-Houben, Dina Navon, Ali Andrescavage, Ksenia Skvortsova, Paul Edward Duckett, Alvaro Gonzalez-Rajal, Ozren Bogdanovic, Johan H. Gibcus, Liyan Yang, Lourdes Gallardo-Fuentes, Ismael Sospedra, Javier Lopez-Rios, Fabrice Darbellay, Axel Visel, Job Dekker, Neil Shubin, Toni Gabaldon, Tetsuya Nakamura, Juan J. Tena, Dario G. Lupianez, Daniel S. Rokhsar, Jose Luis Gomez-Skarmeta
Summary: Through the analysis of the little skate Leucoraja erinacea genome, it was found that the enlarged pectoral fins of skates are attributed to genomic rearrangements in the planar cell polarity pathway. Functional inhibition of planar cell polarity signaling resulted in a reduction in fin size, confirming its role in skate fin morphology.
Review
Genetics & Heredity
Paul W. Hook, Winston Timp
Summary: Hook and Timp describe the flexible uses of single-molecule sequencing technologies in genome analysis, including targeted sequencing, chromatin state analysis, and sequencing of short reads. The matured high-throughput short-read sequencing technology has shaped the way genomes are studied. Recently, single-molecule, long-read sequencing has emerged as an essential tool in deciphering genome structure and function, leading to a more accessible era of nucleic acid sequencing.
NATURE REVIEWS GENETICS
(2023)
Article
Biology
Sudha Rajderkar, Iros Barozzi, Yiwen Zhu, Rong Hu, Yanxiao Zhang, Bin Li, Ana Alcaina Caro, Yoko Fukuda-Yuzawa, Guy Kelman, Adyam Akeza, Matthew J. Blow, Quan Pham, Anne N. Harrington, Janeth Godoy, Eman M. Meky, Kianna von Maydell, Riana D. Hunter, Jennifer A. Akiyama, Catherine S. Novak, Ingrid Plajzer-Frick, Veena Afzal, Stella Tran, Javier Lopez-Rios, Michael E. Talkowski, K. C. Kent Lloyd, Bing Ren, Diane E. Dickel, Axel Visel, Len A. Pennacchio
Summary: Topologically associating domain (TAD) boundaries partition the genome and disruptions of these boundaries can interfere with normal gene expression and cause developmental phenotypes. In this study, targeted deletions of TAD boundaries in mice resulted in phenotypic changes, including altered chromatin interactions, gene expression, viability, and anatomical phenotypes. These findings emphasize the importance of TAD boundary sequences for proper genome function and the need to consider the potential pathogenicity of noncoding deletions affecting TAD boundaries in clinical genetics screening.
COMMUNICATIONS BIOLOGY
(2023)
Article
Developmental Biology
Magdalena Schindler, Marco Osterwalder, Izabela Harabula, Lars Wittler, Athanasia C. Tzika, Dina K. N. Dechmann, Martin Vingron, Axel Visel, Stefan A. Haas, Francisca M. Real
Summary: Changes in gene expression play a critical role in phenotypic innovation. This study reveals the co-option of SALL1 expression through changes in enhancer activity as a mechanism for the development of masculinizing ovotestes in female moles. The researchers identified the conservation of 3D organization at the SALL1 locus but an evolutionary divergence of enhancer activity. Interspecies reporter assays support the activation of mole-specific enhancers in urogenital tissues. Overexpression experiments in transgenic mice further demonstrate the capability of SALL1 to induce kidney-related gene programs associated with mole ovotestes.
Article
Multidisciplinary Sciences
Arang Rhie, Sergey Nurk, Monika Cechova, Savannah J. Hoyt, Dylan J. Taylor, Nicolas Altemose, Paul W. Hook, Sergey Koren, Mikko Rautiainen, Ivan A. Alexandrov, Jamie Allen, Mobin Asri, Andrey V. Bzikadze, Nae-Chyun Chen, Chen-Shan Chin, Mark Diekhans, Paul Flicek, Giulio Formenti, Arkarachai Fungtammasan, Carlos Garcia Giron, Erik Garrison, Ariel Gershman, Jennifer L. Gerton, Patrick G. S. Grady, Andrea Guarracino, Leanne Haggerty, Reza Halabian, Nancy F. Hansen, Robert Harris, Gabrielle A. Hartley, William T. Harvey, Marina Haukness, Jakob Heinz, Thibaut Hourlier, Robert M. Hubley, Sarah E. Hunt, Stephen Hwang, Miten Jain, Rupesh K. Kesharwani, Alexandra P. Lewis, Heng Li, Glennis A. Logsdon, Julian K. Lucas, Wojciech Makalowski, Christopher Markovic, Fergal J. Martin, Ann M. Mc Cartney, Rajiv C. Mccoy, Jennifer Mcdaniel, Brandy M. Mcnulty, Paul Medvedev, Alla Mikheenko, Katherine M. Munson, Terence D. Murphy, Hugh E. Olsen, Nathan D. Olson, Luis F. Paulin, David Porubsky, Tamara Potapova, Fedor Ryabov, Steven L. Salzberg, Michael E. G. Sauria, Fritz J. Sedlazeck, Kishwar Shafin, Valery A. Shepelev, Alaina Shumate, Jessica M. Storer, Likhitha Surapaneni, Angela M. Taravella Oill, Francoise Thibaud-Nissen, Winston Timp, Marta Tomaszkiewicz, Mitchell R. Vollger, Brian P. Walenz, Allison C. Watwood, Matthias H. Weissensteiner, Aaron M. Wenger, Melissa A. Wilson, Samantha Zarate, Yiming Zhu, Justin M. Zook, Evan E. Eichler, Rachel J. O'Neill, Michael C. Schatz, Karen H. Miga, Kateryna D. Makova, Adam M. Phillippy
Summary: The Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y), which corrects errors in the reference sequence and adds additional sequence information. This new reference sequence provides a comprehensive view of the Y chromosome and contributes to the complete understanding of the human genome.
Article
Multidisciplinary Sciences
Cassie L. Kemmler, Jana Smolikova, Hannah R. Moran, Brandon J. Mannion, Dunja Knapp, Fabian Lim, Anna Czarkwiani, Viviana Hermosilla Aguayo, Vincent Rapp, Olivia E. Fitch, Seraina Boetschi, Licia Selleri, Emma Farley, Ingo Braasch, Maximina Yun, Axel Visel, Marco Osterwalder, Christian Mosimann, Zbynek Kozmik, Alexa Burger
Summary: In this study, researchers identified the enhancers responsible for the specific expression of Brachyury/T/TBXT in the notochord of mammals. These enhancers act as auto-regulatory shadow enhancers, controlling the development of the notochord.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Marta Losa, Iros Barozzi, Marco Osterwalder, Viviana Hermosilla-Aguayo, Angela Morabito, Brandon H. Chacon, Peyman Zarrineh, Ausra Girdziusaite, Jean Denis Benazet, Jianjian Zhu, Susan Mackem, Terence D. Capellini, Diane Dickel, Nicoletta Bobola, Aimee Zuniga, Axel Visel, Rolf Zeller, Licia Selleri
Summary: This study investigates how transcription factors with widespread distribution in vertebrate embryos can perform tissue-specific functions. The researchers demonstrate that PBX TALE homeoproteins interact with the transcriptional regulator HAND2 to regulate a gene regulatory network (GRN) in subsets of hindlimb mesenchymal cells, revealing principles of cooperation between promiscuous and tissue-specific regulators in developmental programs.
NATURE COMMUNICATIONS
(2023)
Correction
Multidisciplinary Sciences
Jay Devine, Marta Vidal-Garcia, Wei Liu, Amanda Neves, Lucas D. Lo Vercio, Rebecca M. Green, Heather A. Richbourg, Marta Marchini, Colton M. Unger, Audrey C. Nickle, Bethany Radford, Nathan M. Young, Paula N. Gonzalez, Robert E. Schuler, Alejandro Bugacov, Campbell Rolian, Christopher J. Percival, Trevor Williams, Lee Niswander, Anne L. Calof, Arthur D. Lander, Axel Visel, Frank R. Jirik, James M. Cheverud, Ophir D. Klein, Ramon Y. Birnbaum, Amy E. Merrill, Rebecca R. Ackermann, Daniel Graf, Myriam Hemberger, Wendy Dean, Nils D. Forkert, Stephen A. Murray, Henrik Westerberg, Ralph S. Marcucio, Benedikt Hallgrimsson
Article
Clinical Neurology
Hiroaki Sekiya, Shunsuke Koga, Aya Murakami, Michael Deture, Owen A. Ross, Ryan J. Uitti, William P. Cheshire, Zbigniew K. Wszolek, Dennis W. Dickson
Summary: Comorbid pathologies are uncommon in multiple system atrophy (MSA), even in advanced age, indicating its uniqueness among neurodegenerative disorders. These comorbid pathologies have minimal clinical impact on MSA.
MOVEMENT DISORDERS
(2023)