Article
Biochemistry & Molecular Biology
Tiebin Wang, Nathan Tague, Stephen A. Whelan, Mary J. Dunlop
Summary: Transcription factor decoys can effectively regulate gene expression, with tunability through changes in copy number or modifications to the DNA decoy site sequence. Introducing the decoy system can significantly increase arginine production in metabolic flux steering, without affecting growth compared to wild type strains.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Microbiology
H. Martin Kramer, David E. Cook, Michael F. Seidl, Bart P. H. J. Thomma
Summary: Through the association of protein complexes to DNA, the eukaryotic nuclear genome is organized into open euchromatin that is accessible and condensed heterochromatin that is inaccessible. Chromatin alterations impact its organization and functionality and are important regulators of nuclear processes. Studies in fungal plant pathogens uncover the association between chromatin organization and the expression of in planta-induced genes that are important for pathogenicity.
Article
Biochemistry & Molecular Biology
Shue Chen, Leah F. Rosin, Gianluca Pegoraro, Nellie Moshkovich, Patrick J. Murphy, Guoyun Yu, Elissa P. Lei
Summary: NURF301 is identified as a novel regulator of gypsy insulator body localization, promoting insulator barrier activity. It physically interacts with insulator proteins and co-localizes with them genome-wide. NURF301 functions through nucleosome repositioning and promoting 3D contact between insulator bodies and DNA binding sites.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Horticulture
Yaqiong Wu, Tianyu Han, Lianfei Lyu, Weilin Li, Wenlong Wu
Summary: Anthocyanins are important secondary metabolites in plants, which determine the color of flowers and fruits. They have various nutritional and medicinal functions, such as antioxidant, anticancer, and cardiovascular disease prevention. This review discusses the biosynthesis pathway of plant anthocyanins, the key structural genes involved, the impact of transcription factors and microRNAs, the influence of environmental factors, and the effects of six major exogenous hormones on anthocyanin synthesis and metabolism. Future research directions and trends in anthocyanins are also considered to provide a reference for future studies and applications.
SCIENTIA HORTICULTURAE
(2023)
Review
Biochemistry & Molecular Biology
Arina O. Degtyareva, Elena Antontseva, Tatiana Merkulova
Summary: Many genetic variants affecting gene expression are found in the noncoding part of the genome, mainly through alterations in transcription factor binding. Advanced methods such as eQTL analysis and searching for allele-specific events in various sequencing data are used to identify regulatory variants and understand their functionality.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Elisa Kreibich, Rozemarijn Kleinendorst, Guido Barzaghi, Sarah Kaspar, Arnaud R. Krebs
Summary: Enhancers are cis-regulatory elements that control cell identity during development. This study reveals that DNA demethylation is necessary for the activation of a specific class of enhancers, where DNA methylation antagonizes the binding of transcription factors. This finding suggests that DNA methylation directly controls transcription factor occupancy at active enhancers, in addition to protecting the genome from spurious activation.
Article
Biochemistry & Molecular Biology
Jingwen Song, Syed Nabeel-Shah, Shuye Pu, Hyunmin Lee, Ulrich Braunschweig, Zuyao Ni, Nujhat Ahmed, Edyta Marcon, Guoqing Zhong, Debashish Ray, Kevin C. H. Ha, Xinghua Guo, Zhaolei Zhang, Timothy R. Hughes, Benjamin J. Blencowe, Jack F. Greenblatt
Summary: Alternative polyadenylation (APA) enhances gene regulatory potential by increasing the diversity of mRNA transcripts. A study found that the transcription factor Sp1 binds RNA and is a common repressor of distal poly(A) site usage. Sp1 inhibits cleavage at distal sites by interacting with the subunits of the core cleavage and polyadenylation (CPA) machinery.
Article
Biochemistry & Molecular Biology
Matthew Dyer, Quy Xiao Xuan Lin, Sofiia Shapoval, Denis Thieffry, Touati Benoukraf
Summary: MethMotif is a publicly available database that provides a comprehensive repository of transcription factor-binding profiles with DNA methylation patterns. The latest release includes over 700 position weight matrices, segregated based on their cofactors and DNA methylation status. The database also offers precomputed GO annotations for human TFs and TF-co-TF complexes, allowing for a comprehensive analysis of TF functions in their context with cofactors. Furthermore, MethMotif has been expanded to include data for two additional species, increasing its applicability and value to the scientific community.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Robert J. Schmitz, Erich Grotewold, Maike Stam
Summary: This review discusses the characteristics, identification technologies, and role of cis-regulatory sequences in plant biology. Despite advances in sequence assembly and genome annotation, there are still challenges in identifying and understanding cis-regulatory modules.
Editorial Material
Genetics & Heredity
Douglas H. Phanstiel, Gang Greg Wang
Summary: In this study, Winick-Ng et al. used immunoGAM to investigate chromatin structure in different brain cell types, revealing cell type-specific chromatin topologies, long gene decompaction, and the involvement of transcription factors.
TRENDS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Jessica M. Halow, Rachel Byron, Megan S. Hogan, Raquel Ordonez, Mark Groudine, M. A. Bender, John A. Stamatoyannopoulos, Matthew T. Maurano
Summary: The study investigates the genetic effects on DNA accessibility in vivo across multiple cell and tissue types using highly diverged hybrid mice, providing a foundation for quantitatively predicting the cell-type specific effects of non-coding variation on TF activity.
NATURE COMMUNICATIONS
(2021)
Article
Computer Science, Artificial Intelligence
Shushan Toneyan, Ziqi Tang, Peter K. Koo
Summary: This study introduces a unified evaluation framework and uses it to compare different binary and quantitative models for predicting chromatin accessibility data. The results show that quantitative modeling improves the generalizability and interpretability of the models, and a robustness metric is introduced to enhance model selection and variant effect predictions.
NATURE MACHINE INTELLIGENCE
(2022)
Article
Genetics & Heredity
Bernardo P. de Almeida, Franziska Reiter, Michaela Pagani, Alexander Stark
Summary: A deep-learning model called DeepSTARR accurately predicts enhancer activity based on DNA sequence in both Drosophila and human, and the model learns relevant TF motifs and syntax rules that determine enhancer activity.
Article
Cell Biology
Ashish Kumar, Yuanzhi Lyu, Yuichi Yanagihashi, Chanikarn Chantarasrivong, Vladimir Majerciak, Michelle Salemi, Kang-Hsin Wang, Tomoki Inagaki, Frank Chuang, Ryan R. Davis, Clifford G. Tepper, Kazushi Nakano, Chie Izumiya, Michiko Shimoda, Ken-ichi Nakajima, Alexander Merleev, Zhi-Ming Zheng, Mel Campbell, Yoshihiro Izumiya
Summary: This study reveals the nuclear microenvironment of Kaposi sarcoma-associated herpesvirus (KSHV) and its role in regulating the latency-lytic replication switch. Viral long non-coding RNAs interact with CHD4 to control KSHV reactivation.
Article
Biochemistry & Molecular Biology
Tao Wan, Magdalena Horova, Daisy Guiza Beltran, Shanren Li, Huey-Xian Wong, Li-Mei Zhang
Summary: WhiB7 is a distinct subclass of transcription factors in the WhiB-Like (Wbl) family, interacting with the primary sigma factor (sigma(A)(4)) in RNA polymerase holoenzyme to regulate gene expression through its DNA-binding motif, the AT-hook. This study reveals the structural basis of functional divergence between the two subclasses of Wbl proteins in Mycobacterium tuberculosis through high-resolution structural analysis and molecular approaches.
Article
Plant Sciences
Konstantin O. Kutashev, Michal Franek, Klev Diamanti, Jan Komorowski, Marie Olsinova, Martina Dvorackova
Summary: Arabidopsis thaliana's 45S ribosomal genes are located on the termini of chromosomes 2 and 4, encoding rRNA. Not all intranucleolar rDNA is active, with some forming condensed foci marked with repressive histone marks. The condensed foci relate to rDNA folding and contain typical modifications of inactive rDNA.
Article
Biochemical Research Methods
Mateusz Garbulowski, Klev Diamanti, Karolina Smolinska, Nicholas Baltzer, Patricia Stoll, Susanne Bornelov, Aleksander Ohrn, Lars Feuk, Jan Komorowski
Summary: The R.ROSETTA package is an R wrapper of the ROSETTA framework, allowing for the construction and analysis of non-linear interpretable machine learning models. It gathers combinatorial statistics via rule-based modelling for transparent results, suitable for adoption within the wider scientific community. The package also provides statistical and visualization tools to minimize analysis bias and noise.
BMC BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Ammar Zaghlool, Adnan Niazi, Asa K. Bjorklund, Jakub Orzechowski Westholm, Adam Ameur, Lars Feuk
Summary: The study revealed significant differences in RNA expression between cytosol and nucleus, with nuclear-encoded mitochondrial proteins showing enrichment in the cytosol. Differential expression analysis between fetal and adult brains using cytosolic and nuclear RNA yielded differing results in transcript types and number of differentially expressed genes.
SCIENTIFIC REPORTS
(2021)
Article
Clinical Neurology
Luiz Eduardo Mateus Brandao, Daniel Espes, Jakub Orzechowski Westholm, Teemu Martikainen, Nestori Westerlund, Lauri Lampola, Alexandru Popa, Heike Vogel, Annette Schurmann, Suzanne L. Dickson, Christian Benedict, Jonathan Cedernaes
Summary: This study demonstrated that acute sleep loss leads to increased circulating levels of FGF21 in healthy young men, independent of tissue-based stress response in metabolic peripheral tissues. DNA methylation in the FGF21 promoter region increased in adipose tissue, while muscle showed adverse transcriptional changes.
JOURNAL OF SLEEP RESEARCH
(2022)
Article
Cell Biology
Helena Sork, Mariana Conceicao, Giulia Corso, Joel Nordin, Yi Xin Fiona Lee, Kaarel Krjutskov, Jakub Orzechowski Westholm, Pieter Vader, Marie Pauwels, Roosmarijn E. Vandenbroucke, Matthew J. A. Wood, Samir EL Andaloussi, Imre Mager
Summary: The study found that most miRNAs were secreted in the non-EV fraction, with over 96% of total miRNA found in non-EVs. Despite containing only a fraction of the secreted miRNAs, EVs were stable at 37 degrees Celsius in a serum-containing environment.
Article
Biology
Husen M. Umer, Karolina Smolinska, Jan Komorowski, Claes Wadelius
Summary: Regulatory mutations affecting noncoding sequences in cancer genomes were found to have downstream effects on gene regulation that contribute to cancer progression. Analysis of 2,515 cancer genomes identified a significant enrichment of regulatory mutations associated with deamination signature overlapping a CpG site in multiple cancer types. Overall, 5,749 mutated regulatory elements were identified in 1,844 tumor samples from 39 cohorts.
LIFE SCIENCE ALLIANCE
(2021)
Article
Biology
Gang Pan, Klev Diamanti, Marco Cavalli, Ariadna Lara Gutierrez, Jan Komorowski, Claes Wadelius
Summary: YY1 plays a pivotal role in liver diseases by regulating genes involved in hepatic lipid metabolism in cooperation with key transcription factors. Knockdown of YY1 disrupts this cooperation, leading to dysregulated expression of key enzymes involved in lipogenesis.
LIFE SCIENCE ALLIANCE
(2021)
Correction
Multidisciplinary Sciences
Karolina Stepniak, Magdalena A. Machnicka, Jakub Mieczkowski, Anna Macioszek, Bartosz Wojtas, Bartlomiej Gielniewski, Katarzyna Poleszak, Malgorzata Perycz, Sylwia K. Krol, Rafal Guzik, Michal J. Dabrowski, Michal Draminski, Marta Jardanowska, Ilona Grabowicz, Agata Dziedzic, Hanna Kranas, Karolina Sienkiewicz, Klev Diamanti, Katarzyna Kotulska, Wieslawa Grajkowska, Marcin Roszkowski, Tomasz Czernicki, Andrzej Marchel, Jan Komorowski, Bozena Kaminska, Bartek Wilczynski
NATURE COMMUNICATIONS
(2021)
Article
Oncology
Mateusz Garbulowski, Karolina Smolinska, Ugur Cabuk, Sara A. Yones, Ludovica Celli, Esma Nur Yaz, Fredrik Barrenas, Klev Diamanti, Claes Wadelius, Jan Komorowski
Summary: This study developed a methodology that corrected batch effects in glioma data and identified co-enrichment mechanisms for glioma grading using machine learning. The findings suggest potential therapeutic targets and validate the usefulness of the approach for future studies.
Article
Biochemistry & Molecular Biology
Sara A. Yones, Rajmund Csombordi, Jan Komorowski, Klev Diamanti
Summary: Small-compound databases provide abundant information on metabolites and pathways, but face issues with analysis and standardization due to redundancy. MetaFetcheR, an open-source R package, outperforms existing methods and databases by linking metabolite data, resolving inconsistencies, and covering various data fetching use-cases.
Article
Hematology
Svea Stratmann, Sara A. Yones, Mateusz Garbulowski, Jitong Sun, Aron Skaftason, Markus Mayrhofer, Nina Norgren, Morten Krogh Herlin, Christer Sundstrom, Anna Eriksson, Martin Hoglund, Josefine Palle, Jonas Abrahamsson, Kirsi Jahnukainen, Monica Cheng Munthe-Kaas, Bernward Zeller, Katja Pokrovskaja Tamm, Lucia Cavelier, Jan Komorowski, Linda Holmfeldt
Summary: Numerous studies have been conducted to understand the genomic and transcriptomic lesions driving acute myeloid leukemia (AML) initiation. However, there is limited knowledge about the molecular characteristics of longitudinal AML samples and the challenges of relapse and therapy resistance. Our study identified differentially expressed genes associated with short event-free survival and AML relapse, providing insights into AML progression and potential personalized drug targets.
Article
Multidisciplinary Sciences
Sara A. Yones, Alva Annett, Patricia Stoll, Klev Diamanti, Linda Holmfeldt, Carl Fredrik Barrenas, Jennifer R. S. Meadows, Jan Komorowski
Summary: This study applies rule-based machine learning methods to analyze blood expression data in pediatric SLE, aiming to develop gene networks for disease activity classification. The resulting model shows high accuracy and reveals gene sets correlated with clinical variables, providing insights into disease progression and potential clinical applications.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Analytical
Salvador Daniel Rivas-Carrillo, Evgeny E. E. Akkuratov, Hector Valdez Ruvalcaba, Angel Vargas-Sanchez, Jan Komorowski, Daniel San-Juan, Manfred G. G. Grabherr
Summary: Electroencephalogram (EEG) interpretation is crucial in assessing neurological conditions, especially epilepsy. Manual analysis of EEG recordings is time-consuming and expensive. Automatic detection, like MindReader, offers the potential to shorten diagnosis time and optimize resource allocation. MindReader utilizes an autoencoder network, hidden Markov model (HMM), and generative component to generate labels for pathological and non-pathological phases, reducing the search space for trained personnel. Evaluation on 686 recordings showed MindReader's high sensitivity in detecting epileptic events (99.45%).
Article
Cell Biology
Klev Diamanti, Marco Cavalli, Maria J. Pereira, Gang Pan, Casimiro Castillejo-Lopez, Chanchal Kumar, Filip Mundt, Jan Komorowski, Atul S. Deshmukh, Matthias Mann, Olle Korsgren, Jan W. Eriksson, Claes Wadelius
Summary: Environmental and genetic factors contribute to defects in pancreatic islets and insulin resistance in type 2 diabetes (T2D). Through proteomic analysis of multiple metabolic tissues, we identified tissue-specific metabolic dysregulations in T2D, including inflammatory, immune, and vascular alterations.
CELL REPORTS MEDICINE
(2022)
Meeting Abstract
Veterinary Sciences
Fredrik Barrenas, Scott Hansen, Lynn Law, Connor Driscoll, Richard Green, Elise Smith, Jean Chang, Inah Golez, Taryn Urion, Xinxia Peng, Leanne Whitmore, Daniel Newhouse, Colette Hughes, David Morrow, Kurt Randall, Andrea Selseth, Julia Ford, Roxanne Gilbride, Bryan Randall, Emily Ainslie, Kelli Oswald, Rebecca Shoemaker, Randy Fast, William Bosche, Michael Axthelm, Yoshinori Fukazawa, George Pavlakis, Barbara Felber, Slim Fourati, Sekaly Rafick-Pierre, Jeffrey Lifson, Jan Komorowski, Ewelina Kosmider, Danica Shao, Wenjun Song, Paul Edlefsen, Louis Picker, Michael Gale
JOURNAL OF MEDICAL PRIMATOLOGY
(2022)