Article
Multidisciplinary Sciences
Chun-Ping Yu, Chen-Hao Kuo, Chase W. Nelson, Chi-An Chen, Zhi Thong Soh, Jinn-Jy Lin, Ru-Xiu Hsiao, Chih-Yao Chang, Wen-Hsiung Li
Summary: By developing a computational pipeline for analyzing ChIP-seq data, this study discovered and characterized a large number of previously unknown TFBSs, providing insights into the biological and genomic features of TFBSs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Oncology
Peng Huang, Mengxiang Xu, Haijun Han, Xinyi Zhao, Ming D. Li, Zhongli Yang
Summary: DNA methylation plays a crucial role in regulating gene expression in hepatocellular carcinoma (HCC). This study identified a large number of differentially methylated CpG sites in HCC and highlighted the activation of cell cycle-related pathways and repression of metabolic pathways.
FRONTIERS IN ONCOLOGY
(2021)
Article
Plant Sciences
Maaike R. Boersma, Ryan M. Patrick, Sonia L. Jillings, Nur Fariza M. Shaipulah, Pulu Sun, Michel A. Haring, Natalia Dudareva, Ying Li, Robert C. Schuurink
Summary: ODO1 has been identified as a key regulator in controlling the production of floral scents in Petunia spp., by activating specific metabolic pathways to generate floral volatile compounds.
Article
Biochemistry & Molecular Biology
Len Taing, Ariaki Dandawate, Sehi LYi, Nils Gehlenborg, Myles Brown, Clifford A. Meyer
Summary: Cistrome Data Browser is a resource that provides genome-wide location maps of transcription factors, chromatin remodelers, and more in humans and mice. It has a large collection of datasets and diverse search tools, allowing users to find and visualize data effectively.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Maria Osmala, Gokcen Eraslan, Harri Lahdesmaki
Summary: ChromDMM is a mixture model based on multiple chromatin features, which accurately clusters genomic regions and discovers distinctive patterns of epigenetic signals at regulatory elements. Validated with simulated data and ENCODE data, ChromDMM demonstrates higher accuracy and robustness.
Article
Biochemistry & Molecular Biology
Haoyang Zhou, Viorel Simion, Jacob B. Pierce, Stefan Haemmig, Alex F. Chen, Mark W. Feinberg
Summary: Chronic vascular inflammation in atherosclerosis is influenced by a novel long non-coding RNA, lncRNA-MAP3K4, which regulates inflammation through the p38 MAPK signaling pathway. The expression of lncRNA-MAP3K4 is modulated during chronic and acute inflammatory conditions, and knockdown of this lncRNA can reduce inflammatory factor expression in various vascular cells. Cooperation between lncRNA-MAP3K4 and MAP3K4 in reducing inflammation in endothelial cells has also been demonstrated.
Article
Biochemical Research Methods
Musu Yuan, Liang Chen, Minghua Deng
Summary: The research introduces a robust deep learning-based single-cell Multiple Reference Annotator that effectively transfers knowledge from multiple insufficient reference datasets to unlabeled target data, while also removing batch effects.
Article
Biochemical Research Methods
Melanie Kirsche, Arun Das, Michael C. Schatz
Summary: This paper introduces Sapling, an algorithm for sequence alignment that uses a learned data model to enhance the suffix array and enable faster queries. By investigating different types of data models, providing an analysis of various neural network models, and offering an open-source aligner with a compact, practical piecewise linear model, the authors demonstrate that Sapling outperforms both optimized binary search techniques and multiple widely used read aligners across a variety of genomes. The algorithm achieves a speedup of more than two times while only adding <1% to the memory footprint of the suffix array.
Article
Biochemistry & Molecular Biology
Guanjue Xiang, Yuchun Guo, David Bumcrot, Alla Sigova
Summary: This article introduces a new method, JMnorm, which can simultaneously normalize multiple epigenetic features, better preserving feature correlations and improving data consistency, as well as enhancing the performance of downstream analyses.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Rhys Newell, Richard Pienaar, Brad Balderson, Michael Piper, Alexandra Essebier, Mikael Boden
Summary: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a primary protocol for detecting DNA-protein interactions, and the adapted ChIP-R method statistically evaluates reproducibility from experimental replicates, improving the identification of transcription factor binding events. By re-analyzing existing datasets, ChIP-R can reconstruct reproducible peaks from fragments with enhanced biological enrichment compared to current strategies.
Article
Biology
Maximilian Sprang, Matteo Krueger, Miguel A. Andrade-Navarro, Jean -Fred Fontaine
Summary: Traditional quality guidelines and features are found to be too limited for accurately assessing the quality of NGS data in this study. New data-driven guidelines, derived from statistical analysis of public datasets using quality features calculated by bioinformatics tools, are proposed. Genome mapping statistics are confirmed to be highly relevant for quality assessment, while some quality features are shown to have limited relevance across all conditions.
LIFE SCIENCE ALLIANCE
(2021)
Article
Biology
Claudia Caudai, Monica Zoppe, Anna Tonazzini, Ivan Merelli, Emanuele Salerno
Summary: The three-dimensional structure of chromatin in the cellular nucleus is crucial for physiological and pathological functions, and researchers use experimental and computational methods to study the spatial organization of DNA in cells. Different experimental techniques provide complementary information that is challenging to integrate.
Article
Biology
Roberto Vera Alvarez, Lorinc Pongor, Leonardo Marino-Ramirez, David Landsman
Summary: PM4NGS is a project management framework for NGS data analysis, providing a standard organizational structure, bioinformatics tool management, and data analysis pipelines. It is easy to install and use on personal computers and laptops, aiming to bridge the gap between researchers in experimental laboratories and data analysis workflows.
Article
Biochemistry & Molecular Biology
Anna Macioszek, Bartek Wilczynski
Summary: The article describes a new method for genome-wide data analysis called HERON, which can detect DNA regions enriched for a certain feature even in long DNA domains, demonstrating good interpretative ability for difficult data such as modified histone variants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Microbiology
Canfeng Hua, Jiadai Huang, Tingting Wang, Yue Sun, Jingui Liu, Linfeng Huang, Xin Deng
Summary: This study reveals that bacterial transcription factors have the same binding pattern in both coding and promoter regions. Additionally, three regulatory mechanisms of CDS-bound transcription factors are identified, demonstrating the complexity of bacterial TF regulation and the prevalence of internal cryptic promoters in CDS.
Article
Genetics & Heredity
Adam M. Bournazos, Lisa G. Riley, Shobhana Bommireddipalli, Lesley Ades, Lauren S. Akesson, Mohammad Al-Shinnag, Stephen Alexander, Alison D. Archibald, Shanti Balasubramaniam, Yemima Berman, Victoria Beshay, Kirsten Boggs, Jasmina Bojadzieva, Natasha J. Brown, Samantha J. Bryen, Michael F. Buckley, Belinda Chong, Mark R. Davis, Ruebena Dawes, Martin Delatycki, Liz Donaldson, Lilian Downie, Caitlin Edwards, Matthew Edwards, Amanda Engel, Lisa J. Ewans, Fathimath Faiz, Andrew Fennell, Michael Field, Mary-Louise Freckmann, Lyndon Gallacher, Russell Gear, Himanshu Goel, Shuxiang Goh, Linda Goodwin, Bernadette Hanna, James Harraway, Megan Higgins, Gladys Ho, Bruce K. Hopper, Ari E. Horton, Matthew F. Hunter, Aamira J. Huq, Sarah Josephi-Taylor, Himanshu Joshi, Edwin Kirk, Emma Krzesinski, Kishore R. Kumar, Frances Lemckert, Richard J. Leventer, Suzanna E. Lindsey-Temple, Sebastian Lunke, Alan Ma, Steven Macaskill, Amali Mallawaarachchi, Melanie Marty, Justine E. Marum, Hugh J. McCarthy, Manoj P. Menezes, Alison McLean, Di Milnes, Shekeeb Mohammad, David Mowat, Aram Niaz, Elizabeth E. Palmer, Chirag Patel, Shilpan G. Patel, Dean Phelan, Jason R. Pinner, Sulekha Rajagopalan, Matthew Regan, Jonathan Rodgers, Miriam Rodrigues, Richard H. Roxburgh, Rani Sachdev, Tony Roscioli, Ruvishani Samarasekera, Sarah A. Sandaradura, Elena Savva, Tim Schindler, Margit Shah, Ingrid B. Sinnerbrink, Janine M. Smith, Richard J. Smith, Amanda Springer, Zornitza Stark, Samuel P. Strom, Carolyn M. Sue, Kenneth Tan, Tiong Y. Tan, Esther Tantsis, Michel C. Tchan, Bryony A. Thompson, Alison H. Trainer, Karin Van Spaendonck-Zwarts, Rebecca Walsh, Linda Warwick, Stephanie White, Susan M. White, Mark G. Williams, Meredith J. Wilson, Wui Kwan Wong, Dale C. Wright, Patrick Yap, Alison Yeung, Helen Young, Kristi J. Jones, Bruce Bennetts, Sandra T. Cooper
Summary: The study aims to provide standardized practices for PCR-based RNA diagnostics using clinically accessible specimens. The results show that RNA diagnostics can provide meaningful data for most genetic cases, allowing for variant reclassification and important applications in genetic counseling, clinical care, and prenatal counseling.
GENETICS IN MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Gerald F. Spath, Giovanni Bussotti
Summary: The article highlights the importance of genome instability as a key factor in microbial and cancer adaptation, as well as the development of a novel bioinformatic pipeline called GIP to study genetic changes. Through application to various genome sequencing datasets, GIP was shown to validate biological discoveries in Leishmania, Plasmodium, Candida, and cancer, indicating its potential in driving disease biomarker discovery.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Cell Biology
Marina Reixachs-Sole, Eduardo Eyras
Summary: High-throughput sequencing of cellular RNAs has revealed the wide-ranging impact of alternative splicing on the transcriptome, and differential production of transcript isoforms is recognized as a critical mechanism in cell differentiation, organismal development, and disease. However, the extent of the effect of alternative splicing on protein production and cellular function is still a matter of debate. Recent advances in experimental and computational approaches have shed light on how molecular changes in the RNA processing pathway can affect protein production and function.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2022)
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
Medical Laboratory Technology
Juan M. Jimenez-Vacas, Antonio J. Montero-Hidalgo, Enrique Gomez-Gomez, Prudencio Saez-Martinez, Antonio C. Fuentes-Fayos, Adria Closa, Teresa Gonzalez-Serrano, Ana Martinez-Lopez, Rafael Sanchez-Sanchez, Pedro P. Lopez-Casas, Andre Sarmento-Cabral, David Olmos, Eduardo Eyras, Justo P. Castano, Manuel D. Gahete, Raul M. Luque
Summary: Prostate cancer is a major cause of cancer-related deaths in men, and there is a need for novel molecular targets for treatment. The study found that RB22, a key spliceosome component, is down-regulated in prostate cancer and is associated with tumor aggressiveness. Overexpression of RB22 can reduce the aggressiveness of prostate cancer by impacting the splicing of numerous genes and the regulation of cell cycle. Targeting negative regulators of RB22 expression/activity could be a novel therapeutic strategy for prostate cancer.
TRANSLATIONAL RESEARCH
(2023)
Article
Biology
Alba Navarro-Romero, Lorena Galera-Lopez, Paula Ortiz-Romero, Alberto Llorente-Ovejero, Lucia De los Reyes-Ramirez, Iker Bengoetxea de Tena, Anna Garcia-Elias, Aleksandra Mas-Stachurska, Marina Reixachs-Sole, Antoni Pastor, Rafael de la Torre, Rafael Maldonado, Begona Benito, Eduardo Eyras, Rafael Rodriguez-Puertas, Victoria Campuzano, Andres Ozaita
Summary: Williams-Beuren syndrome (WBS) is a rare genetic disorder characterized by intellectual disability and hypersocial behavior. This study suggests that modulation of the endocannabinoid system could be a potential therapeutic approach for treating WBS, as it improves both social and cognitive phenotypes in a mouse model.
Article
Developmental Biology
Olga Zaytseva, Naomi C. Mitchell, Damien Muckle, Caroline Delandre, Zuqin Nie, Janis K. Werner, John T. Lis, Eduardo Eyras, Ross D. Hannan, David L. Levens, Owen J. Marshall, Leonie M. Quinn
Summary: FUBP1 and Psi, members of the FUSE Binding Protein family, regulate gene transcription by binding to single-stranded DNA and RNA, promoting cell growth and division. Psi activates Myc and stg to promote cell proliferation, while repressing the transcription of tok, a growth inhibitor.
Review
Biochemical Research Methods
Pablo Acera Mateos, You Zhou, Kathi Zarnack, Eduardo Eyras
Summary: The development of new high-throughput techniques has played a crucial role in discovering the properties of RNA modifications with the help of machine learning. Despite the challenges, this review provides a comprehensive survey of machine learning methods for detecting RNA modifications and strategies for training and testing these methods. The review also highlights current challenges and open questions in RNA modification analysis, and emphasizes the potential of machine learning in addressing these limitations.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Giovanni Bussotti, Blaise Li, Pascale Pescher, Barbora Vojtkova, Isabelle Louradour, Katerina Pruzinova, Jovana Sadlova, Petr Volf, Gerald F. Spath
Summary: This study investigates the genomic adaptation of the parasitic pathogen Leishmania donovani during sand fly infection. The findings suggest that oxidative DNA damage and DNA repair processes contribute to haplotype and allelic selection in the parasite.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Statistics & Probability
Michael Greenacre, Eric Grunsky, John Bacon-Shone, Ionas Erb, Thomas Quinn
Summary: This article traces the development of John Aitchison's compositional data analysis approach, introduces his logratio approach for working with data with a fixed-sum constraint, and summarizes and reassesses its properties. It argues that subcompositional coherence, the main property on which this approach was built, is not strictly necessary, and quasi-coherence is sufficient for practical purposes. The article also discusses the importance of isometric and related logratio transformations, as well as alternative quasi-coherent transformations.
STATISTICAL SCIENCE
(2023)
Article
Microbiology
Alicia Vachon, Grace E. Seo, Nishi H. Patel, Carla S. Coffin, Eric Marinier, Eduardo Eyras, Carla Osiowy
Summary: This study evaluated the composition and proportionality of serum hepatitis B virus (HBV) RNA transcripts in chronic hepatitis B (CHB) infection patients using PCR-cDNA nanopore sequencing. The results showed that HBV pregenomic RNA (pgRNA) was the most frequently observed transcript isoform, followed by other pgRNA spliced variants, 3' truncated variants and HBx mRNA. The type and proportion of transcripts were influenced by HBV genotype and HBeAg status. The study demonstrated the utility of long-read sequencing for studying the serum HBV transcriptome.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Cell Biology
Paloma Sola, Elisabetta Mereu, Julia Bonjoch, Marta Casado-Pelaez, Neus Prats, Monica Aguilera, Oscar Reina, Enrique Blanco, Manel Esteller, Luciano Di Croce, Holger Heyn, Guiomar Solanas, Salvador Aznar Benitah
Summary: Skin aging is characterized by changes in structure and function, which contribute to age-related frailty. In this study, the authors found a higher expression of IL-17 in aged skin and demonstrated that blocking IL-17 signaling can reduce inflammation and delay age-related traits. The results suggest that targeting IL-17 signaling could potentially prevent skin aging.
Article
Biochemistry & Molecular Biology
Adria Closa, Marina Reixachs-Sole, Antonio C. Fuentes-Fayos, Katharina E. Hayer, Juan L. Melero, Fabienne R. S. Adriaanse, Romy S. Bos, Manuel Torres-Diz, Stephen P. Hunger, Kathryn G. Roberts, Charles G. Mullighan, Ronald W. Stam, Andrei Thomas-Tikhonenko, Justo P. Castano, Raul M. Luque, Eduardo Eyras
Summary: This study conducted a comprehensive multicohort analysis to explore the molecular mechanisms underlying the poor prognosis in infant B-cell acute lymphoblastic leukemia (B-ALL) patients. They identified gene fusions and RNA splicing alterations that may contribute to the observed outcomes. Specifically, they found that upregulation of the splicing factor SRRM1 is associated with high risk and affects cell survival, proliferation, and invasion. These findings suggest a potential convergent mechanism of aberrant RNA processing in infant B-ALL.
Meeting Abstract
Hematology
Talia Velasco, Juan Trincado, Meritxell Vinyoles, Adria Closa, Oscar Molina, Clara Bueno, Eduardo Eyras, Holger Heyn, Pablo Menendez
EXPERIMENTAL HEMATOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Ivan de la Rubia, Akanksha Srivastava, Wenjing Xue, Joel A. Indi, Silvia Carbonell-Sala, Julien Lagarde, M. Mar Alba, Eduardo Eyras
Summary: Nanopore sequencing enables efficient and unbiased measurement of transcriptomes. RATTLE, a tool that performs reference-free reconstruction and quantification of transcripts using only Nanopore reads, accurately determines transcript sequences and abundances. It demonstrates good scalability with the number of transcripts, based on simulated and experimental data from multiple sources.