Article
Biochemistry & Molecular Biology
Daniel S. Saxton, Jasper Rine
Summary: Genetically identical cells can have different transcriptional states. Inheritance of silenced states relies not only on the inheritance of modified histones, but also on the presence of silencers. Strong silencers recruit Sir proteins and silence the locus in all cells, while weakening silencers can result in stable silencing in some cells but with a probability of conversion to an expressed state lacking Sir protein recruitment. The presence of different silencer states and variations in silencer-bound proteins or the concentration of a structural Sir protein can modulate the probability of a locus exhibiting the silenced or expressed state.
Article
Neurosciences
Yeya Yu, Xiaoyu Wei, Qiuting Deng, Qing Lan, Yiping Guo, Lei Han, Yue Yuan, Peng Fan, Peiying Wu, Shuncheng Shangguan, Yang Liu, Yiwei Lai, Giacomo Volpe, Miguel A. Esteban, Chuanyu Liu, Yong Hou, Longqi Liu
Summary: In this study, single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq) was used to profile chromatin accessibility in rat brains, identifying 16 distinct cell types across different cortex regions. The research revealed diversity in both cellular compositions and gene regulatory regions among the cortex regions, as well as the important roles of specific transcription factors in the pathogenesis of neurological diseases. This single-nucleus atlas of rat cortex provides valuable insights into understanding the regulatory mechanisms underlying diverse cortex cell fates and neuropathogenesis networks.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Walter Muskovic, Eve Slavich, Ben Maslen, Dominik C. C. Kaczorowski, Joseph Cursons, Edmund Crampin, Maria Kavallaris
Summary: The advent of massively parallel sequencing has revealed the existence of long noncoding RNAs (lncRNAs) and their potential broad regulatory roles. By analyzing the expression dynamics of lncRNAs and protein-coding genes using high temporal resolution RNA-seq, it was found that lncRNAs are expressed synchronously with adjacent protein-coding genes. These findings suggest that the cis-regulatory roles of lncRNAs may not be common and they may originate as transcriptional by-products from active protein-coding gene promoters and enhancers.
Article
Biochemistry & Molecular Biology
Emily L. Petty, Lorraine Pillus
Summary: Studies on suppressor screens of gcn5 phenotypes in yeast have provided unique insights into the balance of counteracting chromatin activities in regulating transcription, as well as the roles of Gcn5 in early cell cycle gene expression and chromosome segregation during mitosis.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2021)
Article
Cell Biology
Gloria Mas, Fabio Santoro, Enrique Blanco, Gianni Paolo Gamarra Figueroa, Francois Le Dily, Gianmaria Frige, Enrique Vidal, Francesca Mugianesi, Cecilia Ballare, Arantxa Gutierrez, Aleksandra Sparavier, Marc A. Marti-Renom, Saverio Minucci, Luciano Di Croce
Summary: In this study, the researchers used primary hematopoietic stem and progenitor cells (HSPCs) and leukemic blasts expressing the fusion protein PML-RARα to investigate the dynamic changes in epigenome, transcriptome, and genome architecture during oncogenic transformation. They identified Klf4 as an early down-regulated gene in PML-RARα-driven leukemogenesis and characterized the dynamic alterations in the Klf4 cis-regulatory network during APL progression. Ectopic overexpression of Klf4 was found to suppress self-renewal and reverse the differentiation block induced by PML-RARα.
GENES & DEVELOPMENT
(2022)
Article
Genetics & Heredity
Shary N. Shelton, Sarah E. Smith, Jay R. Unruh, Sue L. Jaspersen
Summary: The INM proteome differs between gametes and mitotic cells, with gametes requiring a unique set of INM proteins for gamete formation, synthesized de novo. This suggests changes in the nuclear permeability barrier and inheritance pattern of INM components during gametogenesis.
G3-GENES GENOMES GENETICS
(2021)
Article
Genetics & Heredity
Shary N. Shelton, Sarah E. Smith, Jay R. Unruh, Sue L. Jaspersen
Summary: By analyzing the differences in the inner nuclear membrane (INM) proteome between mitotic cells and gametes, the study found that gametes contain a distinct INM proteome that needs to be newly synthesized in order to complete gamete formation. Additionally, it was observed that INM components in gametes are generated de novo rather than inherited, showcasing changes in the INM proteome during gametogenesis.
G3-GENES GENOMES GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Xiusheng Zhu, Qitong Huang, Lei Huang, Jing Luo, Qing Li, Dashuai Kong, Biao Deng, Yi Gu, Xueyan Wang, Chenying Li, Siyuan Kong, Yubo Zhang
Summary: Proper cell fate determination relies on precise spatial and temporal genome-wide cooperation between regulatory elements and their targeted genes. A method called MAE-seq was developed to experimentally identify functional regulatory elements at a 25-bp scale. Using this method, a large number of 25-bp enhancers were identified in mouse embryonic stem cells, C2C12, and HEK 293T. These 25-bp sequences were shown to act as functional units and contribute to gene regulation and genomic landscape exploration.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biology
Jee Min Kim, Pat Visanpattanasin, Vivian Jou, Sheng Liu, Xiaona Tang, Qinsi Zheng, Kai Yu Li, Jonathan Snedeker, Luke D. Lavis, Timothee Lionnet, Carl Wu
Summary: Conserved ATP-dependent chromatin remodelers exhibit hyperkinetic behaviors in chromatin with notably fast dissociation kinetics, requiring ATP binding or hydrolysis for enhanced dynamics. Multiple remodelers can repeatedly occupy the same promoter region on a timescale of minutes, suggesting an ongoing 'tug-of-war' that controls a shifting window of accessibility for the transcription initiation machinery.
Article
Biochemistry & Molecular Biology
Romain Forey, Antoine Barthe, Mireille Tittel-Elmer, Maxime Wery, Marie-Benedicte Barrault, Cecile Ducrot, Andrew Seeber, Nils Krietenstein, Ugo Szachnowski, Magdalena Skrzypczak, Krzysztof Ginalski, Maga Rowicka, Jennifer A. Cobb, Oliver J. Rando, Julie Soutourina, Michel Werner, Karine Dubrana, Susan M. Gasser, Antonin Morillon, Philippe Pasero, Armelle Lengronne, Jerome Poli
Summary: Mre11-Rad50-Xrs2 (MRX) plays a new role in limiting transcription in budding yeast by physically interacting and colocalizing with the transcriptional co-regulator Mediator on chromatin. MRX restricts transcription of coding and noncoding DNA by tethering transcriptionally active loci to the nuclear pore complex (NPC), promoting gene-NPC interactions, contributing to chromosome folding, and controlling gene expression. These findings suggest a distinct role for MRX in transcription and chromosome organization apart from its known function in DNA repair.
Article
Biochemistry & Molecular Biology
Aline Acke, Siska Van Belle, Boris Louis, Raffaele Vitale, Susana Rocha, Thierry Voet, Zeger Debyser, Johan Hofkens
Summary: Interactions between epigenetic readers and histone modifications are crucial in gene expression regulation. We have developed a method called Expansion Microscopy for Epigenetics (ExEpi) that preserves spatial information and improves resolution, allowing the study of epigenetic interactions and drug discovery.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Henry F. Thomas, Elena Kotova, Swathi Jayaram, Axel Pilz, Merrit Romeike, Andreas Lackner, Thomas Penz, Christoph Bock, Martin Leeb, Florian Halbritter, Joanna Wysocka, Christa Buecker
Summary: Multiple enhancers regulate the expression of Fgf5 gene, with a poised enhancer located in the first intron playing a crucial role at every time point. These elements are essential for the formation of a super-enhancer, which acts in a collaborative manner to induce Fgf5 expression.
Article
Chemistry, Multidisciplinary
Ming-Yu Kuo, Natalia Spitha, Matthew P. Hautzinger, Pei-Lun Hsieh, Jing Li, Dongxu Pan, Yuzhou Zhao, Lih-Juann Chen, Michael H. Huang, Song Jin, Yung-Jung Hsu, John C. Wright
Summary: This study successfully prepared 2D/3D halide perovskite heterostructures through solution growth, revealing differences in carrier transfer and recombination among different types of 2D/3D heterostructures. The findings provide insights into charge transfer mechanisms in these perovskite heterostructures and offer guidelines for designing better optoelectronic devices.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biotechnology & Applied Microbiology
Fulong Yu, Liam D. Cato, Chen Weng, L. Alexander Liggett, Soyoung Jeon, Keren Xu, Charleston W. K. Chiang, Joseph L. Wiemels, Jonathan S. Weissman, Adam J. de Smith, Vijay G. Sankaran
Summary: Genome-wide association studies combined with single-cell genomic atlases can reveal the mechanisms of disease-causal genetic variations. However, sparse and noisy single-cell epigenomic data analysis often hinders the identification of disease-relevant cell types. To overcome this, the SCAVENGE algorithm uses network propagation to map causal variants to their relevant cellular context at a single-cell resolution, successfully identifying key biological mechanisms in various blood traits and diseases.
NATURE BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sriram Vijayraghavan, Latarsha Porcher, Piotr A. Mieczkowski, Natalie Saini
Summary: Acetaldehyde is a by-product of ethanol metabolism and is acutely toxic and carcinogenic. In vitro studies have shown its mutagenic effects on DNA, but there is variability in reporting its mutagenicity in vivo. This study used a yeast genetic reporter system and found that acetaldehyde treatment is highly mutagenic and leads to specific mutations on single stranded DNA.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Li Xing, Mary L. Lesperance, Xuekui Zhang
Article
Health Care Sciences & Services
Hanley J. Ho, Zoe Xiaozhu Zhang, Zhilian Huang, Aung Hein Aung, Wei-Yen Lim, Angela Chow
JOURNAL OF MEDICAL INTERNET RESEARCH
(2020)
Article
Statistics & Probability
Li Xing, Xuekui Zhang, Igor Burstyn, Paul Gustafson
Summary: The article discusses the shape of the relationship between a continuous exposure variable and a binary disease variable, investigating methods for inferring the shape in epidemiologic investigations and risk assessments, as well as the precise inference of the median effect of exposure. The study utilizes a family based on the Box-Cox transformation to address exposure-disease relationships.
CANADIAN JOURNAL OF STATISTICS-REVUE CANADIENNE DE STATISTIQUE
(2021)
Article
Mathematical & Computational Biology
Yitao Lu, Julie Zhou, Li Xing, Xuekui Zhang
Summary: Personalized medicine is a future trend in healthcare that tailors medical treatments to individual patients. Identifying subsets of patients with the best response to treatment is crucial, but designing clinical trials that incorporate discovered subsets/biomarkers is challenging. This study proposes an optimization solution based on high-dimensional integration and modern computing technologies, showing enhanced accuracy and speed compared to existing methods.
STATISTICS IN MEDICINE
(2021)
Article
Genetics & Heredity
Xiaowen Cao, Li Xing, Elham Majd, Hua He, Junhua Gu, Xuekui Zhang
Summary: The new technology of single-cell RNA sequencing can provide valuable insights into gene expression and cellular compositions. Researchers have used supervised machine learning algorithms to predict cell-level phenotypes, and this study evaluated the performance of these algorithms on datasets of different sizes. The results showed that ElasticNet with interactions performed the best on small and medium-sized datasets, NaiveBayes classifier was suitable for medium-sized datasets, and XGBoost algorithm excelled with large datasets.
FRONTIERS IN GENETICS
(2022)
Article
Biochemical Research Methods
Xuanjin Cheng, Yongxing Liu, Jiahe Wang, Yujie Chen, Andrew Gordon Robertson, Xuekui Zhang, Steven J. M. Jones, Stefan Taubert
Summary: Survival analysis is a valuable technique in cancer research for identifying prognostic biomarkers and genetic vulnerabilities. cSurvival is a newly developed analytical tool that allows for gene- and GS-level survival analysis, as well as integration of clinical and experimental data, showing great potential for applications in cancer studies.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Genetics & Heredity
Yao Dong, Shaoze Zhou, Li Xing, Yumeng Chen, Ziyu Ren, Yongfeng Dong, Xuekui Zhang
Summary: This paper examines the performance differences between deep learning (DL) and non-deep machine learning (ML) methods for analyzing genomic data. Through a benchmark study using the UK Biobank data and subsets with varying sample sizes, it is found that DL methods do not always outperform non-deep ML methods in analyzing genomic data, especially with smaller sample sizes. The results suggest that the performance advantages of DL methods decrease as the sample size of data increases.
FRONTIERS IN GENETICS
(2022)
Article
Business, Finance
Xuekui Zhang, Yuying Huang, Ke Xu, Li Xing
Summary: Full electronic automation in stock exchanges has led to the generation of high-frequency intraday data and the development of near real-time price forecasting methods. Researchers rarely discuss the processing of raw data for these prediction methods. In this study, we propose three novel modelling strategies that significantly improve the performance of the predictions on high-frequency data of Dow Jones 30 stocks.
FINANCIAL INNOVATION
(2023)
Article
Environmental Sciences
Shuai You, Xiaolin Huang, Li Xing, Mary Lesperance, Charles LeBlanc, L. Paul Moccia, Vincent Mercier, Xiaojian Shao, Youlian Pan, Xuekui Zhang
Summary: Canada's vast coastline supports a thriving seafood industry, including bivalve shellfish production. In order to ensure the health of shellfish harvesting habitats, the Canadian Shellfish Sanitation Program has been monitoring fecal coliform bacteria levels at marine sample sites across six coastal provinces since 1979. By applying Functional Principal Component Analysis and correlation analysis, the annual variation patterns of bacteria levels at each site in each province were identified. The magnitude of fecal contamination was associated with human and warm-blooded animal activities, while the seasonality was strongly influenced by river discharge driven by precipitation and snow melt in British Columbia.
MARINE POLLUTION BULLETIN
(2023)
Article
Mathematical & Computational Biology
Xuekui Zhang, Haijun Jia, Li Xing, Cong Chen
Summary: The 2-in-1 adaptive design allows seamless expansion of an ongoing Phase 2 trial into a Phase 3 trial to expedite drug development. It has drawn immediate attention from academic researchers and industry practitioners due to its flexibility and robustness.
STATISTICS IN BIOPHARMACEUTICAL RESEARCH
(2023)
Proceedings Paper
Computer Science, Artificial Intelligence
Shuai You, Xiaolin Huang, Li Xing, Youlian Pan, Xuekui Zhang
Summary: Fecal coliform bacteria are commonly used to assess fecal contamination in water. This study focuses on the Canadian Shellfish Sanitation Program's monitoring of fecal coliform bacteria levels at shellfish harvesting sites along Canada's coastline from 1980 to 2019. The irregular sparsity of the measurement data posed a challenge for analysis. Through preprocessing techniques, the study successfully transformed the irregularly sparse measurements into surrogate variables that represent contamination levels and seasonal variations, enabling downstream analyses.
2022 IEEE CONFERENCE ON COMPUTATIONAL INTELLIGENCE IN BIOINFORMATICS AND COMPUTATIONAL BIOLOGY (IEEE CIBCB 2022)
(2022)
Article
Medicine, General & Internal
Xiaolin Huang, Xiaojian Shao, Li Xing, Yushan Hu, Don D. Sin, Xuekui Zhang
Summary: The timing of lockdowns is crucial in controlling the spread of COVID-19, with delays leading to a significant increase in cumulative case counts. Factors such as total population, median family income, Gini index, median age, and within-county mobility also play a substantial role in influencing case counts.
Article
Microbiology
Omar Alaqeeli, Li Xing, Xuekui Zhang
Summary: In this study, the performance of various R packages for classification tree methods in single-cell RNA-Sequencing data analysis was evaluated using 22 data sets. The comparison was based on Precision, Recall, F-1-score, and AUC metrics, revealing differences in performance and complexity among the packages.
MICROBIOLOGY RESEARCH
(2021)
Review
Mathematical & Computational Biology
Xiaowen Cao, Li Xing, Hua He, Xuekui Zhang
Article
Business, Finance
Xu Ke, Zheng Xinwei, Pan Deng, Xing Li, Zhang Xuekui
JOURNAL OF FINANCIAL RESEARCH
(2020)