Article
Biochemical Research Methods
Xin Dong, Ke Chen, Wenbo Chen, Jun Wang, Liuping Chang, Jin Deng, Lei Wei, Leng Han, Chunhua Huang, Chunjiang He
Summary: This article introduces a novel algorithm, circRIP, for identifying circRNA-RBP interactions from RIP-Seq and eCLIP data. The algorithm successfully identified multiple circRNAs binding to different RBPs, which is of great significance for further exploring the functions of circRNAs.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Virology
Alejandro Casco, Akansha Gupta, Mitchell Hayes, Reza Djavadian, Makoto Ohashi, Eric Johannsen
Summary: Herpesviruses employ extensive bidirectional transcription of overlapping genes to overcome length constraints. Traditional methods struggle to accurately measure this complexity. The study introduces UCDS and UTS methods to estimate gene abundance from RNA-seq data, with UTS showing the highest accuracy and compatibility with overlapping genes.
JOURNAL OF VIROLOGY
(2022)
Article
Biochemical Research Methods
Anushua Biswas, Leelavati Narlikar
Summary: The study introduces ExoDiversity, which uses a model-based framework to learn a joint distribution over footprints and motifs, resolving the mixture of ChIP-exo footprints into diverse binding modes. It automatically learns the number of different modes from the data and can identify co-factor TF motifs.
Article
Cell Biology
Anna Balcerak, Ewelina Macech-Klicka, Maciej Wakula, Rafal Tomecki, Krzysztof Goryca, Malgorzata Rydzanicz, Mateusz Chmielarczyk, Malgorzata Szostakowska-Rodzos, Marta Wisniewska, Filip Lyczek, Aleksandra Helwak, David Tollervey, Grzegorz Kudla, Ewa A. Grzybowska
Summary: This study characterizes the RNA targets of HAX1 and reveals its involvement in translation, ribosome biogenesis, and rRNA processing. Knockouts of HAX1 show downregulation of transcripts partially overlapping with HAX1 RNA targets, suggesting a role in mRNA stabilization. The study also demonstrates a functional connection between HAX1 and ribosome biogenesis.
Article
Cell Biology
Kaoru Sato, Ken-ichi Takayama, Satoshi Inoue
Summary: Environmental and physiological stresses can accelerate Alzheimer's disease (AD) pathogenesis. Stress granules (SGs), cytoplasmic membraneless structures, are associated with neurodegenerative disorders, including AD. SGs contain translationally arrested mRNAs, suggesting a role of impaired RNA metabolism in AD progression. This study identifies specific mRNAs and long non-coding RNAs targeted by SG core proteins G3BP1 and G3BP2, and demonstrates the accumulation of AD-associated gene transcripts within SGs, indicating a direct regulatory role of SGs in AD development.
Article
Plant Sciences
Saman Maqbool, Suhaib Ahmad, Zarnishal Kainat, Muhammad Ibrar Khan, Ammarah Maqbool, Muhammad Adeel Hassan, Awais Rasheed, Zhonghu He
Summary: This study evaluated the root system architecture (RSA) of 58 historical spring wheat cultivars from Pakistan and found a positive historic change in RSA after 1965. The research also identified root depth and steep angle as promising traits to withstand water-limited environments.
Article
Developmental Biology
Rebecca Chowdhury, Yue Wang, Melissa Campbell, Susan K. Goderie, Francis Doyle, Scott A. Tenenbaum, Gretchen Kusek, Thomas R. Kiehl, Suraiya A. Ansari, Nathan C. Boles, Sally Temple
Summary: STAU2 is a double-stranded RNA-binding protein enriched in the nervous system. It distributes into intermediate progenitor cells during asymmetric divisions in the developing mouse cortex, delivering RNA molecules that impact IPC behavior. Through RIP-seq over four stages of mouse cortical development, a comprehensive cargo profile for STAU2 was generated, revealing both stable and dynamic subsets of cargo with different functions in corticogenesis.
Article
Biochemical Research Methods
Daniel Osorio, Marieke L. Kuijjer, James J. Cai
Summary: This study introduces rPanglaoDB, an R package for downloading and merging uniformly processed scRNA-seq data to collect rare cell types by integrating multiple public datasets. By characterizing a set of 157 fibrocytes, the study demonstrates the potential and utility of rPanglaoDB in enabling the collection of rare cell types for transcriptomic profiling.
Article
Biotechnology & Applied Microbiology
Federico Agostini, Julian Zagalak, Jan Attig, Jernej Ule, Nicholas M. Luscombe
Summary: The study investigates the transcriptional activity of unannotated regions in the human genome, revealing that most transcripts originate from fuzzy transcription of known genes and a small portion from putative long non-coding RNA loci. The transcriptional activity and sensitivity of intergenic RNAs were validated using various methods, providing insights into their processing and degradation pathways.
Article
Mathematics
Gines Almagro-Hernandez, Juana-Maria Vivo, Manuel Franco, Jesualdo Tomas Fernandez-Breis
Summary: Computational genomics focuses on understanding the impact of genome functionality by analyzing the genetic sequence, structure, and interactions with other factors. The study develops a method based on multivariate models for analyzing ChIP-seq data, providing a novel approach for characterizing and comparing experiments. By using a multivariate hypergeometric distribution, the method is able to handle biological data complexity and uncertainty more effectively than existing dichotomous models.
Article
Biotechnology & Applied Microbiology
Dongyuan Song, Jingyi Jessica Li
Summary: PseudotimeDE is a differential gene expression identification method that adapts to various pseudotime inference methods, considers pseudotime inference uncertainty, and provides well-calibrated p-values. Comprehensive simulations and real-data applications confirm that PseudotimeDE outperforms existing methods in controlling false discovery rate and power.
Article
Dentistry, Oral Surgery & Medicine
Libo Liang, Yi Li, Binwu Ying, Xinyan Huang, Shenling Liao, Jiajin Yang, Ga Liao
Summary: This study aimed to understand the molecular mechanisms of tongue squamous cell carcinoma better by combining whole-genome sequencing, whole-genome methylation, and whole-transcriptome analyses. Through multi-omics sequencing, we identified differentially methylated intervals, methylated loop sites, methylated promoters, and transcripts associated with tongue squamous cell carcinoma. We found mutated methylation promoters significantly associated with mRNA and lncRNA expression levels, which are involved in triggering the mitogen-activated protein kinase cascade and affecting the prognosis of tongue squamous cell carcinoma patients.
INTERNATIONAL JOURNAL OF ORAL SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Loryn P. Byres, Marat Mufteev, Kyoko E. Yuki, Wei Wei, Alina Piekna, Michael D. Wilson, Deivid C. Rodrigues, James Ellis
Summary: The study identified specific mRNA targets regulated by TIA1 during human neurodevelopment in hESCs, NPCs, and neurons, indicating that translation repression is a key process targeted by TIA1 binding.
MOLECULAR BIOLOGY REPORTS
(2021)
Article
Engineering, Aerospace
Valber Cesar Cavalcanti Roza, Octavian Postolache
Summary: Research shows that takeoff, approach, and landing during flight correspond to the highest brain activities, and experienced and confident volunteers exhibit lower brain activities compared to less experienced volunteers. Furthermore, experienced and confident volunteers display different patterns of brain activities compared to less experienced volunteers.
Article
Plant Sciences
Yuki Monden, Hirona Tanaka, Ryota Funakoshi, Seiya Sunayama, Kiyotaka Yabe, Eri Kimoto, Kentaro Matsumiya, Takanori Yoshikawa
Summary: This study identified two rice lines with higher protein content by analyzing the insertion sites of mPing transposons and the transcriptome. The results provide insights into the mechanism behind increased protein content in rice and contribute to solving malnutrition and health problems by improving rice protein content.
FRONTIERS IN PLANT SCIENCE
(2022)