Article
Biology
Ian G. McLachlan, Talya S. Kramer, Malvika Dua, Elizabeth M. DiLoreto, Matthew A. Gomes, Ugur Dag, Jagan Srinivasan, Steven W. Flavell, Joshua M. Kaplan
Summary: Animals need to balance competing needs and states in order to generate adaptive behavioral responses to the environment. This study found that various states and stimuli converge on a single olfactory neuron in Caenorhabditis elegans to modulate food-seeking behavior. The expression of olfactory receptor genes in this neuron is influenced by feeding state, physiological stress, and recent sensory cues. The study also revealed the molecular and neural circuit pathways through which external sensory information and internal nutritional state are integrated. This provides a general model for how sensory and state-dependent changes in gene expression at the sensory periphery modulate animals' sensorimotor responses to meet their ongoing needs and states.
Review
Biochemistry & Molecular Biology
Felicity J. Emerson, Siu Sylvia Lee
Summary: This review discusses the current state of research on chromatin and aging, with a focus on chromatin factors related to longevity that have been discovered in model organisms. High-resolution genomics tools have allowed researchers to study the chromatin environment and its impact on lifespan with greater precision.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Review
Neurosciences
Iris Marchal, Baris Tursun
Summary: The review summarizes the current knowledge regarding cell fate safeguarding mechanisms in the germline, focusing on the molecular mechanisms underlying neuronal induction from germ cells upon TF-mediated reprogramming. It briefly discusses the specific characteristics that might make germ cells especially fit to change cellular fate and become neurons. The potential of C. elegans research in advancing knowledge of the mechanisms regulating cellular identity and implications for therapeutic approaches such as regenerative medicine are also highlighted.
FRONTIERS IN NEUROSCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Haiyan Gong, Yi Yang, Xiaotong Zhang, Minghong Li, Sichen Zhang, Yang Chen
Summary: CASPIAN is a method based on spatial density clustering algorithm for accurately identifying chromatin TAD boundaries and enriching factors related to gene expression. It is implemented using HDBSCAN and adapts well to Hi-C contact matrices of different resolutions.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Multidisciplinary Sciences
Gholamali Jafari, Liakot A. Khan, Hongjie Zhang, Edward Membreno, Siyang Yan, Graham Dempsey, Verena Gobel
Summary: Recent research has shown that intracellular vesicular trafficking can determine the position of the apical domain independent of membrane-based polarity cues. Actin dynamics play a crucial role in the polarized distribution of apical membrane components, PARs, and itself. Using photomodulation, it has been demonstrated that F-actin travels towards the future apical domain. These findings suggest an alternative polarity model where actin-directed trafficking asymmetrically inserts the nascent apical domain into the growing epithelial membrane.
Article
Biotechnology & Applied Microbiology
Marie Zufferey, Yuanlong Liu, Daniele Tavernari, Marco Mina, Giovanni Ciriello
Summary: The study shows that gene co-regulation is only observed in a minority of chromatin domains across multiple human cancers, which are enriched in the less active B sub-compartments and for genes with similar function. Differential activation of chromatin domains is not associated with major changes of domain boundaries, but rather with changes of sub-compartments and intra-domain contacts.
Article
Biology
Ni Ji, Vivek Venkatachalam, Hillary Denise Rodgers, Wesley Hung, Taizo Kawano, Christopher M. Clark, Maria Lim, Mark J. Alkema, Mei Zhen, Aravinthan D. T. Samuel
Summary: Animals, including Caenorhabditis elegans, exhibit persistent behavioral and neural responses to stimuli. In this study, it was found that the worm uses feedback from the motor circuit to sustain its motor state during thermotactic navigation. The AIY interneuron encodes both temperature and motor state information, representing a corollary discharge signal for sustained neural activity and behavioral patterns.
Article
Biochemical Research Methods
Jiankang Wang, Ryuichiro Nakato
Summary: This study reviews the currently available one-dimensional (1D) metrics for analyzing individual Hi-C samples or comparisons between two samples, discussing their validity and suitable analysis scenarios. The authors also propose several new 1D metrics to identify unique features of chromosome structures. They emphasize the reproducibility and robustness of 1D metrics for comparing and visualizing multiple Hi-C samples, as well as their ease of integration with epigenome tracks for detailed chromatin state annotation. The development of the HiC1Dmetrics framework provides a valuable resource for chromosome organization researchers.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Cell Biology
Stefano Giustino Manzo, Lise Dauban, Bas van Steensel
Summary: This article reviews recent advances in the study of LAD-NL interactions, discussing molecular tethers and looseners of LADs, and their link to transcription regulation and genome replication. It also provides a brief summary of technological advances that may uncover new aspects of LAD biology.
CURRENT OPINION IN CELL BIOLOGY
(2022)
Article
Biology
Abigail R. R. Guillermo, Karolina Chocian, Gavriil Gavriilidis, Julien Vandamme, Anna Elisabetta Salcini, Jane Mellor, Alison Woollard
Summary: This study identifies chromatin modifiers as key regulators of longevity, with interactions between different factors such as expression levels and tissue specificity influencing lifespan outcomes. When considering molecular and tissue-specific effects, the heterochromatin loss model of ageing may be too simplistic to fully explain organismal ageing.
Article
Biology
Ni Ji, Gurrein K. Madan, Guadalupe Fabre, Alyssa Dayan, Casey M. Baker, Talya S. Kramer, Ijeoma Nwabudike, Steven W. Flavell
Summary: The neural circuit controlling the choice between roaming and dwelling states in C. elegans shows stereotyped changes in circuit activity corresponding to each behavioral state. Mutual inhibition between two antagonistic neuromodulatory systems underlies the persistence and mutual exclusivity of neural activity patterns observed in each state, enabling flexible, sensory-driven control of persistent behavioral states.
Article
Biology
Florian Geisler, Sanne Remmelzwaal, Vera Jankowski, Ruben Schmidt, Mike Boxem, Rudolf E. Leube
Summary: Using Caenorhabditis elegans, researchers have identified the IF polypeptide IFB-2 as an efficient suppressor of structural and functional deficiencies in mutants that disrupt the organization of the intestinal IF cytoskeleton. This rescue capability is specific to IF isotypes and extends to mutants that disrupt the function of other cytoskeletal proteins. The findings provide strong evidence for the adverse consequences of deranged IF networks, with implications for diseases characterized by altered IF network organization.
Article
Biochemistry & Molecular Biology
Zhongyang Lin, Yichun Xie, Wenyan Nong, Xiaoliang Ren, Runsheng Li, Zhongying Zhao, Jerome Ho Lam Hui, Karen Wing Yee Yuen
Summary: Research shows that AT-poor sequences can delay the acquisition of segregation competency in ACs; co-injection of fragmented yeast genomic DNA can build a more complex AC structure; CENP-A(HCP-3) binds to unexpressed genes and fragmented yeast sequences on the AC, while being excluded from high-AT-content areas.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Haiyan Gong, Dawei Zhang, Xiaotong Zhang
Summary: TADs play a crucial role in disease detection. This study introduces a novel approach named TOAST, which utilizes graph auto-encoders and clustering techniques to identify TADs. By conceptualizing genomic bins as graph nodes and using the Hi-C contact matrix as the graph's adjacency matrix, TOAST can quickly and accurately identify TADs, outperforming existing algorithms in experimental analysis.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biology
Samuel J. P. Taylor, Laura Bel Borja, Flavie Soubigou, Jack Houston, Dhanya K. Cheerambathur, Federico Pelisch
Summary: Phosphorylation is an important post-translational modification used for regulating protein localization and activity. Polo-like kinase 1 (PLK-1) is crucial for mitotic and meiotic cell divisions, but its specific roles and regulation in meiosis have been unclear. In this study, using C. elegans oocytes, we demonstrate that PLK-1 is involved in spindle assembly, chromosome alignment and segregation, and polar body extrusion during meiosis I. We also uncover the mechanisms of PLK-1 recruitment to meiotic chromosomes. Our findings reveal the essential functions of PLK-1 in oocyte meiosis and provide insights into its targeting mechanisms.
Article
Cell Biology
Jennifer K. Heppert, Daniel J. Dickinson, Ariel M. Pani, Christopher D. Higgins, Annette Steward, Julie Ahringer, Jeffrey R. Kuhn, Bob Goldstein
MOLECULAR BIOLOGY OF THE CELL
(2016)
Article
Microbiology
Melanie Tanguy, Louise Veron, Przemyslaw Stempor, Julie Ahringer, Peter Sarkies, Eric A. Miska
Article
Biology
Alicia N. McMurchy, Przemyslaw Stempor, Tessa Gaarenstroom, Brian Wysolmerski, Yan Dong, Darya Aussianikava, Alex Appert, Ni Huang, Paulina Kolasinska-Zwierz, Alexandra Sapetschnig, Eric A. Miska, Julie Ahringer
Article
Genetics & Heredity
Julie Ahringer, Susan M. Gasser
Article
Genetics & Heredity
Julie Ahringer, Susan M. Gasser
Article
Biology
Sundar Ram Naganathan, Sebastian Fuerthauer, Josana Rodriguez, Bruno Thomas Fievet, Frank Juelicher, Julie Ahringer, Carlo Vittorio Cannistraci, Stephan W. Grill
Article
Genetics & Heredity
Ting Deng, Przemyslaw Stempor, Alex Appert, Michael Daube, Julie Ahringer, Alex Hajnal, Evelyn Lattmann
Article
Biochemistry & Molecular Biology
Jacques Serizay, Yan Dong, Jurgen Janes, Michael Chesney, Chiara Cerrato, Julie Ahringer
Article
Biochemistry & Molecular Biology
Ni Huang, Wei Qiang Seow, Alex Appert, Yan Dong, Przemyslaw Stempor, Julie Ahringer
Summary: Nuclear organization and chromatin interactions are crucial for genome function, but accurately determining chromatin connections at a high resolution remains challenging. This study introduces a new tool called ARC-C, which allows for the analysis of interactions between regulatory elements throughout the entire genome, while also providing insights into the structure and domain-level architecture of chromatin.
Article
Multidisciplinary Sciences
Francesco Nicola Carelli, Chiara Cerrato, Yan Dong, Alex Appert, Abby Dernburg, Julie Ahringer
Summary: The movement of selfish DNA elements can lead to widespread genomic alterations and rewiring of germline transcriptional regulation. This study found that transposon expansions in Caenorhabditis nematodes led to the acquisition of germline-specific promoters from miniature inverted repeat transposable elements (TEs). These promoters are regulated by a transcription factor related to a transposase. Comparative analyses revealed evolutionary conservation and species-specificity of the co-opted promoters.
Article
Biochemistry & Molecular Biology
Francesco N. Carelli, Garima Sharma, Julie Ahringer
Article
Cell Biology
Josana Rodriguez, Florent Peglion, Jack Martin, Lars Hubatsch, Jacob Reich, Nisha Hirani, Alicia G. Gubieda, Jon Roffey, Artur Ribeiro Fernandes, Daniel St Johnston, Julie Ahringer, Nathan W. Goehring
DEVELOPMENTAL CELL
(2017)