Article
Biochemistry & Molecular Biology
Sarah L. Fong, John A. Capra
Summary: The study revealed that simple enhancers are younger, more functionally diverse, and more active across species, while complex enhancers are older, less likely to associate with human traits and biochemical activity. Transposable-element-derived sequences contribute to enhancers of both architectures, with the majority found in simple enhancers.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Megan Crow, Hamsini Suresh, John Lee, Jesse Gillis
Summary: Differences in gene regulation play a critical role in cell specialization and diversification, and the differential regulation of ancient gene programs contributes to transcriptional cell identity.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Horticulture
Yanan Cao, Hongqiang Yu, Dan Tian, E. Sun, Longgang Zuo, Daji Jiang, Cunwu Zuo, Ruiyi Fan
Summary: A study identified and classified 3718 NLR genes in Rosaceae plants, and found that some of them were significantly upregulated in response to Valsa canker infection. These findings provide insights into the evolution of NLR genes in Rosaceae and the key regulators of Valsa canker resistance.
Article
Plant Sciences
Huaxing Huang, Hongli Ji, Song Ju, Wei Lin, Jing Li, Xuanrui Lv, Lixian Lin, Lijin Guo, Dongliang Qiu, Jianyong Yan, Xiaokai Ma
Summary: This study investigated the genomic information and gene regulation network for color variation of bracts in Bougainvillea plants. It identified differentially expressed genes and co-expressed hub genes that are responsible for the color variations. These findings provide valuable insights into the molecular basis of color variation in key bracts of horticultural Bougainvillea.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Vasileios L. Zogopoulos, Georgia Saxami, Apostolos Malatras, Antonia Angelopoulou, Chih-Hung Jen, William J. Duddy, Gerasimos Daras, Polydefkis Hatzopoulos, David R. Westhead, Ioannis Michalopoulos
Summary: Gene coexpression analysis aims to identify sets of genes with similar expression patterns across multiple data sets, such as microarray experiments. The Arabidopsis Coexpression Tool (ACT) generates a coexpression tree from processed microarray data, revealing relationships between different genes. ACT offers a user-friendly interface for gene set enrichment analysis and is successful in identifying both ubiquitous and tissue-specific gene expressions.
Article
Biochemistry & Molecular Biology
Haiwei Chen, Connor E. Rosen, Jaime A. Gonzalez-Hernandez, Deguang Song, Jan Potempa, Aaron M. Ring, Noah W. Palm
Summary: The study developed a highly multiplexed screening technology called PRESTO-Salsa that can evaluate nearly all conventional GPCRs in a single well of a 96-well plate. Using this technology, researchers screened 1,041 human-associated metabolites and discovered previously unreported GPCR agonists. They also generated an atlas of microbiome-GPCR interactions across multiple body sites, revealing conserved patterns of GPCR engagement and activation. These findings contribute to a better understanding of metabolite-GPCR interactions.
Article
Multidisciplinary Sciences
Jiaojiao Hua, Zhengyi Yang, Tianzi Jiang, Shan Yu
Summary: The complexity of the human brain is determined by the orchestrated expression of thousands of genes, while pairwise interactions between genes are sufficient to predict the transcriptional pattern of the brain. This quadratic complexity of transcriptional patterns in the human brain, as revealed by the study, highlights the importance of gene-gene interactions in the functional and structural richness of the brain.
Article
Multidisciplinary Sciences
Soudeh Ghafouri-Fard, Arash Safarzadeh, Mohammad Taheri, Elena Jamali
Summary: A co-expression network of differentially expressed genes (DEGs) related to colorectal cancer (CRC) and their target genes was constructed using the weighted gene co-expression network analysis (WGCNA) algorithm. GO and KEGG pathway analysis revealed that these genes were mainly involved in the regulation of hormone levels, extracellular matrix organization, and extracellular structure organization. The study also identified DKC1, PA2G4, LYAR and NOLC1 as the key hub genes of CRC.
SCIENTIFIC REPORTS
(2023)
Article
Cell Biology
Vasileios L. Zogopoulos, Apostolos Malatras, Konstantinos Kyriakidis, Chrysanthi Charalampous, Evanthia A. Makrygianni, Stephanie Duguez, Marianna A. Koutsi, Marialena Pouliou, Christos Vasileiou, William J. Duddy, Marios Agelopoulos, George P. Chrousos, Vassiliki A. Iconomidou, Ioannis Michalopoulos
Summary: HGCA2.0 is a webtool that studies the global coexpression of human genes. It analyzes a large-scale dataset of healthy individuals' RNA samples and presents coexpressed subclades to the gene of interest, providing various enrichments analysis on gene ontologies, biological pathways, protein families, and diseases, as well as revealing enriched transcription factors. It has been successful in identifying genes with ubiquitous and tissue-specific expression patterns.
Article
Biotechnology & Applied Microbiology
Fei Zhang, Deborah Velez-Irizarry, Catherine W. Ernst, Wen Huang
Summary: In this study, genome-wide analysis of alternative splicing in skeletal muscle of a Duroc x Pietrain F2 pig population was performed. It was found that the heritability of alternative splicing scores was lower than that of overall gene expression. Additionally, there was little correlation between alternative splicing and overall gene expression. Integration of splice QTL mapping with phenotype QTL mapping identified potential mediators of phenotype QTL effects through alternative splicing.
Article
Cell Biology
Lorena Suarez-Artiles, Tilman Breiderhoff, Rossana Girardello, Hannes Gonschior, Sophie Rodius, Antoine Lesur, Ulf Reimer, Evelyn Ramberger, Daniel Perez-Hernandez, Dominik Muller, Philipp Mertins, Gunnar Dittmar
Summary: This study investigates the interaction of the C-terminal tails of the Claudin family with other proteins, revealing their potential involvement in specific biological processes in epithelial cells and their regulation by post-translational modifications.
Article
Biochemistry & Molecular Biology
Li Guo, Yihao Kang, Yiqi Xiong, Lin Jia, Xiaoqiang Yan, Daoliang Xia, Jiafeng Yu, Jun Wang, Tingming Liang
Summary: This study identified key genes and RNAs associated with prostate adenocarcinoma (PRAD) and constructed a risk model that could potentially serve as a biomarker for cancer prognosis. The study also revealed potential interactions among different RNAs and surveyed the landscape of isomiRs in homologous miRNA loci. Furthermore, the study characterized TK1, miR-222-3p, and SNHG3 as crucial RNAs with correlations to poor survival outcomes.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemical Research Methods
Javier Pardo-diaz, Mariano Beguerisse-diaz, Philip S. Poole, Charlotte M. Deane, Gesine Reinert
Summary: In this study, a pipeline combining novel scores from gene coexpression network analysis is presented to identify genes associated with specific growth conditions or highly coexpressed with a predefined set of genes of interest. This association may lead to putative functional annotation or a prioritized list of genes for further study.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2022)
Article
Pediatrics
Wangkai Liu, Yihua Su, Sitao Li, Haitian Chen, Yumei Liu, Xiaoyu Li, Wei Shen, Xinqi Zhong, Fan Wu, Qiong Meng, Xiaoyun Jiang
Summary: This study identified a significantly downregulated coexpression module related to the bronchopulmonary dysplasia (BPD) phenotype, enriched in genes associated with human T-cell leukemia virus infection and the mitogen-activated protein kinase pathway. The decreased expression of hub genes FOS, BTG2, JUN, and EGR1 in infants with BPD could serve as biomarkers for early diagnosis of BPD.
PEDIATRIC PULMONOLOGY
(2021)
Article
Microbiology
Min Jin Kwon, Charlotte Steiniger, Timothy C. Cairns, Jennifer H. Wisecaver, Abigail L. Lind, Carsten Pohl, Carmen Regner, Antonis Rokas, Vera Meyer
Summary: Fungal secondary metabolites are important for drug discovery, but their biosynthetic pathways are often transcriptionally silent in typical laboratory conditions. Utilizing gene coexpression network approaches can predict global and pathway-specific transcription factors, advancing the discovery and activation of fungal secondary metabolic pathways.
MICROBIOLOGY SPECTRUM
(2021)
Editorial Material
Medicine, General & Internal
Mukesh K. Jain, Vivian G. Cheung, Paul J. Utz, Brian K. Kobilka, Tadataka Yamada, Robert Lefkowitz
NEW ENGLAND JOURNAL OF MEDICINE
(2019)
Article
Genetics & Heredity
Jason A. Watts, Joshua Burdick, Jillian Daigneault, Zhengwei Zhu, Christopher Grunseich, Alan Bruzel, Vivian G. Cheung
AMERICAN JOURNAL OF HUMAN GENETICS
(2019)
Article
Clinical Neurology
Christopher Grunseich, Aneesh Patankar, Joshua Amaya, Jason A. Watts, Dongjun Li, Prisila Ramirez, Alice B. Schindler, Kenneth H. Fischbeck, Vivian G. Cheung
ANNALS OF NEUROLOGY
(2020)
Article
Multidisciplinary Sciences
Yaojuan Liu, Yesenia Rodriguez, Robert L. Ross, Ruoxia Zhao, Jason A. Watts, Christopher Grunseich, Alan Bruzel, Dongjun Li, Joshua T. Burdick, Rajendra Prasad, Robert J. Crouch, Patrick A. Limbach, Samuel H. Wilson, Vivian G. Cheung
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Editorial Material
Medicine, General & Internal
Vivian G. Cheung
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
(2020)
Article
Multidisciplinary Sciences
Prisila Ramirez, Robert J. Crouch, Vivian G. Cheung, Christopher Grunseich
Summary: The three-stranded nucleic acid structure known as R-loop is being increasingly recognized for its role in gene regulation. Recent findings suggest that R-loops have functional roles in human cells and understanding their abundance is critical. Challenges in the field include quantifying R-loops accurately.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Editorial Material
Genetics & Heredity
Juan D. Alfonzo, Jessica A. Brown, Peter H. Byers, Vivian G. Cheung, Richard J. Maraia, Robert L. Ross
Summary: While DNA sequences are available for most organisms, complete RNA sequences remain elusive. Therefore, there is a call for the development of technologies capable of sequencing full-length RNAs along with all their modifications.
Editorial Material
Cell Biology
Paul J. Utz, Mukesh K. Jain, Vivian G. Cheung, Brian K. Kobilka, Robert Lefkowitz, Tadataka Yamada, Victor J. Dzau
SCIENCE TRANSLATIONAL MEDICINE
(2022)
Article
Public, Environmental & Occupational Health
Bolajoko Olusanya, Nem Yun Boo, M. K. C. Nair, Maureen E. Samms-Vaughan, Mijna Hadders-Algra, Scott M. Wright, Cecilia Breinbauer, Nihad A. Almasri, Marisol Moreno-Angarita, Jalal Arabloo, Narendra K. Arora, Sandra S. Block, Brad D. Berman, Gwen Burchell, Olaf K. de Camargo, Gwen Carr, Christie del Castillo-Hegyi, Vivian G. Cheung, Ricardo Halpern, Rosa A. Hoekstra, Paul Lynch, Mphelekedzeni C. Mulaudzi, Angelina Kakooza-Mwesige, Felix A. Ogbo, Jacob O. Olusanya, Valeria Rojas-Osorio, Amira Shaheen, Andrew N. Williams, Chiara Servili, Melissa Gladstone, Hannah Kuper, Donald Wertlieb, Adrian C. Davis, Charles R. J. Newton
Summary: This paper highlights the urgent need to prioritize early childhood development for children with lifelong disabilities, particularly in low-income and middle-income countries as part of the Sustainable Development Goals agenda. Disability-focused programming, monitoring approaches, economic analysis of interventions, and substantial funding are required to address the current inequalities among this group of children by 2030.
LANCET GLOBAL HEALTH
(2022)
Article
Biochemistry & Molecular Biology
Jason A. Watts, Christopher Grunseich, Yesenia Rodriguez, Yaojuan Liu, Dongjun Li, Joshua T. Burdick, Alan Bruzel, Robert J. Crouch, Robert W. Mahley, Samuel H. Wilson, Vivian G. Cheung
Summary: RNA can regulate cellular processes through modifications and folding, and dysregulation of RNA sequence and structure can contribute to diseases. In this study, a new mechanism was uncovered, where RNA abasic sites in R-loops regulate transcription by pausing RNA polymerase II. Additionally, a noncoding RNA called AANCR was found to regulate the expression of APOE, and its folding and modification were associated with different cell types and stress conditions. Furthermore, DNA sequence variations in AANCR were significantly linked to APOE expression and Alzheimer's Disease, highlighting the potential role of AANCR as a modifier of the disease.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Pediatrics
Bolajoko O. Olusanya, Claudine Storbeck, Vivian G. Cheung, Mijna Hadders-Algra
Summary: Before the launch of the SDGs in 2015, childhood disability was not considered important in global health. The SDGs now require identification and support for children under 5 who are at risk of not benefiting from inclusive quality education. UNICEF has developed a tool for identifying children who are not developmentally on track, but it has limited sensitivity for detecting children with disabilities.
Article
Genetics & Heredity
Joshua T. Burdick, Annelise Comai, Alan Bruzel, Guangxin Sun, Peter C. Dedon, Vivian G. Cheung
Summary: RNA undergoes complex posttranscriptional processing, including chemical modifications, which must be considered in RNA biology and therapeutics. Current RNA-sequencing methods primarily capture complementary DNA, missing the modifications in RNA. Direct RNA-sequencing technology aims to address this limitation, but it still has a high error rate and cannot fully detect all modifications. There is a need for comprehensive sequencing technologies and analysis methods for RNA complexity. The RNA sequences obtained in this study are provided as a benchmark for analysis methods.
G3-GENES GENOMES GENETICS
(2023)
Meeting Abstract
Clinical Neurology
Govind Nair, Myoung-Hwa Lee, Stephen Dodd, Daniel P. Perl, Wenxue Li, Dragan Maric, Helen Murray, Vivian G. Cheung, Jason A. Watts, Eliezer Masliah, Iren Horkayne-Szakaly, Robert V. Jones, Michelle N. Stram, Joel T. Moncur, Marco Hefti, Rebecca D. Folkerth, Alan P. Koretsky, Avindra Nath
ANNALS OF NEUROLOGY
(2022)
Meeting Abstract
Environmental Sciences
Yesenia Rodriguez, Vivian G. Cheung, Samuel H. Wilson
ENVIRONMENTAL AND MOLECULAR MUTAGENESIS
(2022)
Meeting Abstract
Oncology
M. Abdulghani, N. Razavian, J. Burdick, Z. Zhu, T. C. Humphrey, V. G. Cheung
INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS
(2020)