Article
Biology
Marissa M. Gaskill, Tyler J. Gibson, Elizabeth D. Larson, Melissa M. Harrison
Summary: In Drosophila, besides Zelda, another pioneer factor GAF plays a crucial role in development during the maternal-to-zygotic transition. By activating widespread zygotic transcription and remodeling the chromatin accessibility landscape, GAF and Zelda together drive the development through this critical period.
Article
Multidisciplinary Sciences
Jinlei Han, Damar Lopez-Arredondo, Guangrun Yu, Yankun Wang, Baohua Wang, Sarah Brooke Wall, Xin Zhang, Hui Fang, Alfonso Carlos Barragan-Rosillo, Xiaoping Pan, Yanqin Jiang, Jingbo Chen, Hui Zhang, Bao-Liang Zhou, Luis Herrera-Estrella, Baohong Zhang, Kai Wang
Summary: This study examined the genome-wide DNase I-hypersensitive site (DHS) and its variations in domesticated allotetraploid cotton, revealing the interplay among transposable elements, cis-regulatory elements, and histone modifications during polyploidization. These findings advance our understanding of regulatory architecture in plants.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Genetics & Heredity
Rita Jui-Hsien Lu, Yen-Ting Liu, Chih Wei Huang, Ming-Ren Yen, Chung-Yen Lin, Pao-Yang Chen
Summary: ATACgraph is a bioinformatics software designed for analyzing and visualizing ATAC-seq data, incorporating specific quality control and biological properties of chromatin accessibility. It profiles accessible chromatin regions, allows identification of differentially accessible regions, and provides an intuitive user experience for biologists.
FRONTIERS IN GENETICS
(2021)
Article
Biochemical Research Methods
Rozemarijn W. D. Kleinendorst, Guido Barzaghi, Mike L. Smith, Judith B. Zaugg, Arnaud R. Krebs
Summary: Precise gene expression control involves multiple factors working together at cis-regulatory elements. Single-molecule footprinting technology developed recently allows simultaneous resolution of protein occupancy on single DNA molecules genome-wide. The technique combines cytosine methyltransferases and bisulfite sequencing to resolve transcription factor binding patterns at cis-regulatory elements.
Article
Biochemical Research Methods
Betul Akgol Oksuz, Liyan Yang, Sameer Abraham, Sergey V. Venev, Nils Krietenstein, Krishna Mohan Parsi, Hakan Ozadam, Marlies E. Oomen, Ankita Nand, Hui Mao, Ryan M. J. Genga, Rene Maehr, Oliver J. Rando, Leonid A. Mirny, Johan H. Gibcus, Job Dekker
Summary: Chromosome conformation capture assays, such as Hi-C and Micro-C, are used to map chromatin interactions and understand chromosome folding mechanisms. Through systematic evaluation of experimental parameters, an optimized Hi-C protocol was developed for detecting loops and compartments, improving the ability to study chromosome organization.
Article
Biotechnology & Applied Microbiology
Samuel Khodursky, Eric B. Zheng, Nicolas Svetec, Sylvia M. Durkin, Sigi Benjamin, Alice Gadau, Xia Wu, Li Zhao
Summary: The study investigates the sequence determinants of chromatin accessibility in different species and tissues of Drosophila using deep neural networks. The results show that the sequence determinants are highly conserved and accessible regions are mutationally robust. The study also identifies motifs predictive of accessibility, recovering both novel and previously known motifs.
Article
Biotechnology & Applied Microbiology
Aileen R. Ferraro, Abigail J. Ameri, Zefu Lu, Masayuki Kamei, Robert J. Schmitz, Zachary A. Lewis
Summary: Regulation of chromatin accessibility and transcription are coordinated processes. This study characterizes accessible chromatin regions in Neurospora crassa, revealing molecular features and histone modifications associated with accessibility and inaccessibility. H3K27 acetylation is the most predictive histone modification for open chromatin in N. crassa, while H3K36 methylation is a key marker of inaccessible chromatin.
Article
Chemistry, Analytical
Nicolas Cetraro, Joanne Y. Yew
Summary: Lipid pheromones play a crucial role in insect behavior and ecology. Researchers have developed a method using real-time mass spectrometry to analyze lipid molecules from single fruit fly pheromone glands, and found that it can accurately categorize species. This method has direct applications in chemical ecology and potential uses in pharmaceutical studies.
Article
Biotechnology & Applied Microbiology
Henry A. Ertl, Mark S. Hill, Patricia J. Wittkopp
Summary: This study reveals the role of chromatin remodeling factors and their relationship with gene expression and chromatin structure in gene regulatory mechanisms. The findings suggest that variations in chromatin accessibility and Grainy head binding contribute to the evolution of gene expression, shedding light on the complex interactions among molecular layers in gene regulation.
Article
Biochemistry & Molecular Biology
Olga V. Andreenkova, Olga D. Shishkina, Alexandra I. Klimenko, Aleksandra E. Korenskaia, Margarita A. Bobrovskikh, Natalja V. Shatskaya, Gennady V. Vasiliev, Nataly E. Gruntenko
Summary: Several methods for extracting Wolbachia DNA from insect hosts have been described, but the low quantity of the bacteria made these techniques labor-intensive. This paper proposes a simplified and accelerated method for isolating high-purity Wolbachia DNA from Drosophila melanogaster, using centrifugation, filtration, and a modified version of the Livak buffer protocol. The proportion of Wolbachia DNA in total DNA was quantified using sequencing and bioinformatic analysis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Jeroen Dobbelaere, Tiffany Y. Su, Balazs Erdi, Alexander Schleiffer, Alexander Dammermann
Summary: Cilia are cellular projections that perform sensory and motile functions in eukaryotic cells. In this study, a set of 386 human genes associated with cilium assembly or motility were identified by analyzing the presence and absence pattern in the genomes of diverse eukaryotes. The novel genes were further characterized and found to be related to cilium defects in fruit flies and nematodes. This dataset defines the core set of genes required for cilium assembly and motility across eukaryotes and provides a valuable resource for future studies.
Article
Biochemistry & Molecular Biology
Tian Lu, Cheen Euong Ang, Xiaowei Zhuang
Summary: The recent development of spatial omics methods has advanced our understanding of spatial regulation of cell and tissue functions. In this study, a new method for spatially resolved epigenomic profiling of single cells was introduced, allowing for high-resolution spatial mapping. This approach has the potential to enhance our understanding of how gene expression is temporally and spatially regulated.
Article
Biochemistry & Molecular Biology
Christopher J. Benway, Jiangyuan Liu, Feng Guo, Fei Du, Scott H. Randell, Michael H. Cho, Edwin K. Silverman, Xiaobo Zhou
Summary: This study identified potential causal variants for COPD risk by integrating fine mapping in GWAS loci with cell-specific regulatory profiling. By prioritizing variants in putative regulatory elements with potential functional effects and revealing cell type-specific regulatory effects of COPD variants in lung epithelium, endothelium, and immune cells, the importance of leveraging chromatin status in relevant cell types to predict the molecular effects of risk variants in lung disease was highlighted.
AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY
(2021)
Article
Genetics & Heredity
Qiao Liu, Kui Hua, Xuegong Zhang, Wing Hung Wong, Rui Jiang
Summary: DeepCAGE is a deep learning framework that accurately predicts chromatin accessible regions in a variety of cell types, and exhibits superior performance in the classification and regression of chromatin accessibility signals.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Fuqing Jiang, Xin Zhou, Yingying Qian, Miao Zhu, Li Wang, Zhuxia Li, Qingmei Shen, Minhan Wang, Fangfang Qu, Guizhong Cui, Kai Chen, Guangdun Peng
Summary: The study describes a microfluidic indexing-based spatial assay (MISAR-seq) that combines spatial-ATAC-seq and RNA-seq to simultaneously profile chromatin accessibility and gene expression in the developing mouse brain. This method provides insights into tissue organization and spatiotemporal regulatory logics during brain development.
Review
Genetics & Heredity
Stepanka Zverinova, Victor Guryev
Summary: This review discusses the significance of properly performed variant calling in various genetics studies, highlighting the challenges in method and algorithm selection due to the diversity in genomics protocols, techniques, and platforms. The article outlines considerations for study design and preparation, types of variants detected through sequencing, and recent developments enabling variant calling in genomics field applications. Technological and algorithmic advances are also examined for their potential to revolutionize DNA variant calling in the near future.
Article
Multidisciplinary Sciences
Yuliya A. Veryaskina, Sergei E. Titov, Mikhail K. Ivanov, Pavel S. Ruzankin, Anton S. Tarasenko, Sergei P. Shevchenko, Igor B. Kovynev, Evgenij Stupak, Tatiana Pospelova, Igor F. Zhimulev
Summary: miRNAs are important biomarkers in cancer research, and qPCR is the most commonly used technique for measuring miRNA expression levels, but normalization against reference genes is required. This study identified miRNAs with stable expression in different tissues, which may serve as promising reference genes for miRNA quantification in qPCR in the future.
Article
Biochemistry & Molecular Biology
Tatyana D. Kolesnikova, Galina V. Pokholkova, Viktoria V. Dovgan, Igor F. Zhimulev, Veit Schubert
Summary: This study examines the probability distribution and dynamics of replication initiation using Drosophila polytene chromosomes and super-resolution microscopy. The analysis reveals significant differences in the probability of initiation across different regions, and identifies stochasticity in the process. Additionally, the study finds that certain regions exhibit faster replication initiation, while others are slower.
CHROMOSOME RESEARCH
(2022)
Review
Medicine, General & Internal
Yulia Andreevna Veryaskina, Sergei Evgenievich Titov, Igor Fyodorovich Zhimulev
Summary: MicroRNAs (miRNAs) show promise as biomarkers for disease diagnosis and prognosis, but the lack of validated reference genes can introduce bias in results. Selecting the most stable reference genes is common practice in each experiment.
MEDICAL PRINCIPLES AND PRACTICE
(2022)
Article
Biotechnology & Applied Microbiology
Irina Zakharova, Shoraan Saaya, Alexander Shevchenko, Alena Stupnikova, Maria Zhiven', Pavel Laktionov, Alena Stepanova, Alexander Romashchenko, Lyudmila Yanshole, Alexander Chernonosov, Alexander Volkov, Elena Kizilova, Evgenii Zavjalov, Alexander Chernyavsky, Alexander Romanov, Andrey Karpenko, Suren Zakian
Summary: This study demonstrates the potential use of discarded cardiac tissue for regenerative medicine and tissue engineering. The researchers investigated the benefits of using cardiac explants to repair vascular defects and tested a method to prevent cell division using mitomycin C. The results showed that the cell-containing patches engrafted successfully and did not interfere with normal patency. Mitomycin C-treated cells exhibited no tumorigenic effect and retained their specific cell markers, extracellular matrix production, and ability to stimulate angiogenesis. This approach may contribute to the development of safe cell products for regenerative medicine.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Plant Sciences
Ulyana S. Zubairova, Aleksandra Yu. Kravtsova, Alexander V. Romashchenko, Anastasiia A. Pushkareva, Alexey V. Doroshkov
Summary: Water flows in plants are crucial for growth and play a significant role in the life cycle. This paper explores hydrodynamics using methods that track small particles within water flows. The authors used contrast-enhanced MRI and laser scanning microscopy to analyze the structural and dimensional characteristics of the xylem bundles in maize stems.
Review
Genetics & Heredity
Vincent C. T. Hanlon, Peter M. Lansdorp, Victor Guryev
Summary: Polymorphic inversions are common in humans and have been linked to adaptation and disease. Various methods have been developed for the detection and genotyping of inversions, utilizing complex wet lab protocols or sophisticated bioinformatic analyses.
Article
Biochemistry & Molecular Biology
Tatyana Ivanovna Babochkina, Ludmila Alekseevna Gerlinskaya, Margarita Vladimirovna Anisimova, Galina Vladimirovna Kontsevaya, Natalia Aleksandrovna Feofanova, Aliya Konstantinovna Stanova, Mikhail Pavlovich Moshkin, Yuri Mikhailovich Moshkin
Summary: Developmental instability (DI) is inversely related to an organism's ability to buffer its development against genetic and environmental perturbations. DI is represented by inter- and intra-individual variabilities of a trait. This study investigated the impact of mother-fetus MHC interaction on gene expression noise and developmental stability. A statistical framework was used to analyze the extrinsic and intrinsic components of trait variance/noise using PCA projection and GAMLSS modeling. The results showed that MHC combinations could decrease extrinsic and intrinsic gene noise and positively influence embryonic growth stability.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Annelies Van Hemelryk, Ingrid Tomljanovic, Corrina M. A. de Ridder, Debra C. Stuurman, Wilma J. Teubel, Sigrun Erkens-Schulze, Esther Verhoef, Sebastiaan Remmers, Amrish J. Mahes, Geert J. L. H. van Leenders, Martin E. van Royen, Harmen J. G. van de Werken, Magda Grudniewska, Guido W. Jenster, Wytske M. van Weerden
Summary: This study presents patient-derived xenografts (PDXs) and matching PDX-derived organoids (PDXOs) as new models for studying castration-resistant prostate cancer (CRPC). These models accurately reflect donor tumors and can predict patient responses to different treatments. The study provides valuable insights into the genomic and transcriptomic features of CRPC and offers a resource for studying treatment-induced resistance mechanisms.
Letter
Respiratory System
Tessa M. Kole, Simon D. Pouwels, Rene Bults, Marlies E. Ketelaar, Victor Guryev, Lisanne Koll, Huib A. M. Kerstjens, Martijn C. Nawijn, Alen Faiz, Maarten van den Berge
Article
Physiology
Nicolaas J. Bekker, Alienke van Pijkeren, Justina C. Wolters, Alejandro Sanchez Brotons, Victor Guryev, Roy R. Woldhuis, Rainer Bischoff, Wynand Alkema, Peter Horvatovich, Johannes L. L. van Nijnatten, Maarten van den Berge, Wim Timens, Corry-Anke Brandsma
Summary: This study compared COPD and non-COPD fibroblasts using proteomic and transcriptomic analysis, and identified 40 differentially expressed proteins, including previously described COPD proteins and new COPD research targets. Lack of overlap and correlation between gene and protein data supports the use of unbiased proteomics analysis.
AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY
(2023)
Article
Multidisciplinary Sciences
Claudio Novella-Rausell, Magda Grudniewska, Dorien J. M. Peters, Ahmed Mahfouz
Summary: Researchers created the Mouse Kidney Atlas (MKA), a comprehensive atlas of the healthy adult mouse kidney, by integrating 140,000 cells and nuclei from 59 publicly available single-cell and single-nuclei RNA-sequencing datasets. They also built a hierarchical model of the cell populations, allowing them to predict missing cell annotations and identify reproducible markers for poorly understood cell types and transitional states. The MKA provides valuable insights into the cellular diversity of the kidney.
Article
Cardiac & Cardiovascular Systems
Jude Taylor, Anna C. Y. Yeung, Anthony Ashton, Alen Faiz, Victor Guryev, Bernard Fang, Sean Lal, Mark Grosser, Cristobal G. dos Remedios, Filip Braet, Craig S. McLachlan, Amy Li
Summary: Peripartum cardiomyopathy (PPCM) is a rare form of acute onset heart failure that can occur in otherwise healthy pregnant women around the time of delivery. This study compared the gene expression profiles of end-stage PPCM patients to female dilated cardiomyopathy (DCM) patients and healthy donors, revealing commonalities in metabolic pathways and extracellular matrix remodeling between PPCM and DCM. However, there were also unique gene expression patterns in PPCM related to golgi vesicles biogenesis and immune cell populations, suggesting potential targets for disease-specific interventions.
JOURNAL OF CARDIOVASCULAR DEVELOPMENT AND DISEASE
(2023)
Review
Biochemistry & Molecular Biology
Dorothea Tholl, Zarley Rebholz, Alexandre V. Morozov, Paul E. O'Maille
Summary: Many animals release terpenes as semiochemicals for inter- and intra-specific interactions. The biosynthetic origin of these compounds has remained unclear, but recent advances in genome and transcriptome resources have led to the identification of enzymes and pathways involved in independent terpene production. These findings have important implications for understanding terpene biosynthesis in animals and for developing applications in pharmaceuticals and agriculture.
NATURAL PRODUCT REPORTS
(2023)
Article
Physics, Multidisciplinary
Aditya Ballal, Willow B. Kion-Crosby, Alexandre Morozov
Summary: This paper presents an approach to partitioning network nodes into nonoverlapping communities, which is crucial for understanding network modularity and functional organization. By using random walks and the walk-likelihood algorithm, an optimal partition can be obtained, and the method has been successfully applied to a large-scale road and intersection map.
PHYSICAL REVIEW RESEARCH
(2022)