Review
Biochemistry & Molecular Biology
Akio Masuda, Toshihiko Kawachi, Kinji Ohno
Summary: This article discusses the importance of protein-RNA interactions in mRNA transcription and processing, as well as the methods for detecting these interactions and their applications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Microbiology
Ayoub Maachi, Covadonga Torre, Raquel N. Sempere, Yolanda Hernando, Miguel A. Aranda, Livia Donaire
Summary: High-throughput sequencing was used to identify seven virus species on tomato samples from the Iberian Peninsula, with pepino mosaic virus being the most abundant. Double-stranded RNA input provided better coverage and read depth. In silico analyses determined the minimum sequencing depth required for virus detection in samples.
Article
Biochemistry & Molecular Biology
Arun B. Dutta, Daniel S. Lank, Roza K. Przanowska, Piotr Przanowski, Lixin Wang, Bao Nguyen, Ninad M. Walavalkar, Fabiana M. Duarte, Michael J. Guertin
Summary: Adipocytes have a significant role in metabolic disorders and understanding their differentiation process is crucial. By integrating chromatin accessibility and nascent transcription data, a temporally resolved network describing transcription factor binding events and target gene expression has been generated. This study reveals the cooperation and antagonism between different transcription factor families in regulating adipogenesis. Additionally, the mechanistic contributions of individual transcription factors in distinct steps of transcription have been quantified. The identification of Twist2 as a negative regulator of adipocyte differentiation and its impact on lipid storage provides insight into adipogenesis. This network inference framework has wide applications in interpreting complex biological phenomena.
Article
Multidisciplinary Sciences
Linyu Zuo, Guanwei Zhang, Matthew Massett, Jun Cheng, Zicong Guo, Liang Wang, Yifei Gao, Ru Li, Xu Huang, Pilong Li, Zhi Qi
Summary: FUS/EWS/TAF15 (FET) fusion oncoproteins, containing low complexity domain, form biomolecular condensates that recruit RNA polymerase II, promoting gene transcription. Through the development of a single-molecule assay, a causal relationship between the formation of condensates on DNA and gene transcription is supported, along with the identification of a threshold number of fusion-binding DNA elements required for the formation of FET protein condensates.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Aziz M. Al'Khafaji, Jonathan T. Smith, Kiran V. Garimella, Mehrtash Babadi, Victoria Popic, Moshe Sade-Feldman, Michael Gatzen, Siranush Sarkizova, Marc A. Schwartz, Emily M. Blaum, Allyson Day, Maura Costello, Tera Bowers, Stacey Gabriel, Eric Banks, Anthony A. Philippakis, Genevieve M. Boland, Paul C. Blainey, Nir Hacohen
Summary: Full-length RNA-sequencing methods using long-read technologies are limited in throughput. We introduce MAS-ISO-seq, a technique that programmably concatenates cDNAs for long-read sequencing, increasing throughput by >15-fold to nearly 40 million cDNA reads per run. Applied to single-cell RNA sequencing of tumor-infiltrating T cells, MAS-ISO-seq showed a 12- to 32-fold increase in the discovery of differentially spliced genes.
NATURE BIOTECHNOLOGY
(2023)
Article
Cell Biology
Xiao Yang, Yang Lu, Hang Zhou, Hai-Tao Jiang, Lei Chu
Summary: This study identified potential biomarkers for different grades of intervertebral disc degeneration (IDD) through an integrated analysis of proteome sequencing, bulk RNA sequencing, and single-cell RNA sequencing data. SERPINA1 was identified as a biomarker involved in regulating or predicting the progress of disc degeneration.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Genetics & Heredity
Peter Gergics, Cathy Smith, Hironori Bando, Alexander A. L. Jorge, Denise Rockstroh-Lippold, Sebastian A. Vishnopolska, Frederic Castinetti, Mariam Maksutova, Luciani Renata Silveira Carvalho, Julia Hoppmann, Julian Martinez Mayer, Frederique Albarel, Debora Braslavsky, Ana Keselman, Ignacio Bergada, Marcelo A. Marti, Alexandru Saveanu, Anne Barlier, Rami Abou Jamra, Michael H. Guo, Andrew Dauber, Marilena Nakaguma, Berenice B. Mendonca, Sajini N. Jayakody, A. Bilge Ozel, Qing Fang, Qianyi Ma, Jun Z. Li, Thierry Brue, Maria Ines Perez Millan, Ivo J. P. Arnhold, Roland Pfaeffle, Jacob O. Kitzman, Sally A. Camper
Summary: This study identified new variants that affect transcription and splicing of the POU1F1 gene, which may lead to pituitary hormone deficiency. The research underscores the importance of evaluating the impact of splicing on variants for interpreting unknown significance variants in POU1F1.
AMERICAN JOURNAL OF HUMAN GENETICS
(2021)
Article
Immunology
Son H. McLaren, Nischay Mishra, Nobuko Hijiya, James Ng, Cheng Guo, Susan Whittier, Erica Mariani, Laura Glaser, Irene Frantzis, Marc T. Vindas, Cheng-Shiun Leu, Peter S. Dayan
Summary: In this pilot study, we found that a novel high-throughput sequencing platform, called BacCapSeq, had moderate agreement with blood culture in diagnosing bacteremia among children with cancer presenting with fever. There were discordant organisms, some of which were clinically irrelevant.
PEDIATRIC INFECTIOUS DISEASE JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Shiyan Wang, Chi Chun Wong, Yanquan Zhang, Junzhe Huang, Chuangen Li, Jianning Zhai, Guoping Wang, Hong Wei, Xueji Zhang, Housheng Hansen He, Jun Yu
Summary: ZNF545 suppresses colorectal cancer by repressing rRNA transcription and protein translation. Deletion of Znf545 promotes gene expression and cell growth, leading to accelerated CRC development. Experimental evidence demonstrates the tumor-suppressive role of ZNF545 in CRC.
Article
Biochemical Research Methods
Jared Brown, Zijian Ni, Chitrasen Mohanty, Rhonda Bacher, Christina Kendziorski
Summary: Dino is a normalization method based on a flexible negative-binomial mixture model of gene expression, which improves downstream analysis performance in various settings.
Article
Biochemistry & Molecular Biology
Xiang Gao, Weipeng Mo, Junpeng Shi, Ning Song, Pei Liang, Jian Chen, Yiting Shi, Weilong Guo, Xinchen Li, Xiaohong Yang, Beibei Xin, Haiming Zhao, Weibin Song, Jinsheng Lai
Summary: HITAC-seq is a novel sequencing technology that enables efficient and large-scale DNA sequencing. It offers high-quality contiguous sequences at a lower cost, suitable for various sequencing and genotyping applications.
JOURNAL OF GENETICS AND GENOMICS
(2021)
Article
Biochemical Research Methods
Guo-Hua Yuan, Ying Wang, Guang-Zhong Wang, Li Yang
Summary: In this study, a machine learning model called RNAlight was developed to identify nucleotide features related to the subcellular localizations of mRNAs and lncRNAs. By extracting nucleotide features and mapping them to RBPs, the sequence basis for distinct RNA subcellular localizations was revealed. Furthermore, RNAlight could also predict the subcellular localizations of other types of RNAs, highlighting its generality in RNA subcellular localization prediction.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Guo-Hua Yuan, Ying Wang, Guang-Zhong Wang, Li Yang
Summary: Different types of RNAs have distinct subcellular localizations, and the nucleotide features determining these localizations are not fully understood. This study presents RNAlight, a machine learning model based on LightGBM, to identify nucleotide k-mers that contribute to the subcellular localizations of mRNAs and lncRNAs. By analyzing these nucleotide features and their association with RBPs, the sequence basis for different RNA subcellular localizations is revealed. RNAlight is also proven to be effective in predicting the subcellular localizations of other types of RNAs, indicating its potential for general application in RNA localization prediction.
BRIEFINGS IN BIOINFORMATICS
(2023)
Review
Microbiology
Amy H. Fitzpatrick, Agnieszka Rupnik, Helen O'Shea, Fiona Crispie, Sinead Keaveney, Paul Cotter
Summary: This review assesses and recommends approaches for targeted and agnostic High Throughput Sequencing of RNA viruses, highlighting the challenges and biases that method choice can impart to sequencing results. Methodology choices from RNA extraction to library preparation have a significant impact on the detection or characterization of RNA viruses.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Aly Atef Shoun, Rania Abozahra, Kholoud Baraka, Mai Mehrez, Sarah M. Abdelhamid
Summary: This study investigated the genotype and structural analysis of patients with genotype 4a hepatitis C virus (HCV) infections who failed to respond to sofosbuvir treatment. The presence of mutation sites and amino acid substitutions associated with resistance to sofosbuvir was identified. The results highlight the significant impact of these mutations on the resistance of the HCV NS5B RNA-dependent RNA polymerase to direct-acting antivirals.