Article
Biochemical Research Methods
Michaela Frye, Susanne Bornelov
Summary: CONCUR is a standalone tool written in Perl for codon usage analysis in ribosome profiling experiments. It estimates codon counts at the ribosome E-, P- and A-sites using aligned reads in BAM format, and is freely available on https://github.com/susbo/concur.
Article
Developmental Biology
Linkai Zhu, Tong Zhou, Rajan Iyyappan, Hao Ming, Michal Dvoran, Yinjuan Wang, Qi Chen, R. Michael Roberts, Andrej Susor, Zongliang Jiang
Summary: By using high-resolution ribosome fractionation and low-input ribosome profiling, we have defined the translational landscapes of bovine oocytes and preimplantation embryos. We discovered four modes of translational selectivity in early embryo development and found a strong translational selection of low-abundance transcripts involved in metabolic pathways and lysosomes. These findings provide important insights into the translational regulation during bovine preimplantation development.
Article
Biochemistry & Molecular Biology
Yafen Wang, Zonggui Chen, Xiong Zhang, Xiaocheng Weng, Jikai Deng, Wei Yang, Fan Wu, Shaoqing Han, Chao Xia, Yu Zhou, Yu Chen, Xiang Zhou
Summary: This study presents a method for detecting f(5)C modifications in RNA and a transcriptome-wide f(5)C mapping technique called f(5)C-seq. Over 1000 f(5)C sites were identified in Saccharomyces cerevisiae using f(5)C-seq, and it was found that f(5)C has a preference for wobble sites in mRNA, suggesting its potential role in translation regulation.
ACS CHEMICAL BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Xiaoyu Yang, Bo Song, Jie Cui, Lina Wang, Shuoshuo Wang, Linlin Luo, Lei Gao, Beixin Mo, Yu Yu, Lin Liu
Summary: This study reveals that translational reprogramming plays an important role in rice's response to salt stress, with the salt-tolerant cultivar SR86 adopting a more flexible translational adaptive strategy compared to the salt-sensitive cultivar NB. The differences in translational dynamics under salt stress between NB and SR86 may be due to their varying levels of ribosome stalling.
Article
Biochemistry & Molecular Biology
Pedro do Couto Bordignon, Sebastian Pechmann
Summary: The translation of mRNAs into proteins by the ribosome is a crucial step in protein biosynthesis, tightly controlled to maintain cellular homeostasis. Ribosome profiling has provided insights into translation mechanisms, yet many aspects remain mysterious due to challenges in data interpretation. The study reveals programmed translational heterogeneity in genomic sequences, impacting cellular homeostasis and highlighting the complexity of translation regulation.
Article
Gastroenterology & Hepatology
Shilin Yuan, Guanghong Liao, Menghuan Zhang, Yuanfei Zhu, Kun Wang, Weidi Xiao, Caiwei Jia, Minhui Dong, Na Sun, Axel Walch, Ping Xu, Jiming Zhang, Qiang Deng, Ronggui Hu
Summary: This study identified multiple self-restricting HBV-host interactions, including a negative feedback mechanism of SRSF2-HpZ/P'. Targeting host splicing machinery might represent a strategy to intervene in HBV-host interactions.
JOURNAL OF HEPATOLOGY
(2021)
Article
Biochemical Research Methods
Rick Gelhausen, Teresa Mueller, Sarah L. Svensson, Omer S. Alkhnbashi, Cynthia M. Sharma, Florian Eggenhofer, Rolf Backofen
Summary: This study aimed to evaluate the performance of tools using Ribo-seq data to detect bacterial ORFs. The results showed that DeepRibo and REPARATION_blast accurately predicted translated ORFs, while start codon predictions with smORFer improved the sensitivity of ORF prediction tools in bacteria.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Biochemistry & Molecular Biology
Vandana Yadav, Inayat Ullah Irshad, Hemant Kumar, Ajeet K. Sharma
Summary: This passage discusses the methods used to extract translation rate parameters from ribosome profiling data and their applications in deciphering the regulation of gene expression. The accurate rate parameters may provide new insights into the kinetic control of the process of gene expression.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Cell Biology
Saisai Wei, Wenhao Guo, Yu Qian, Jie Xiang, Kangli Liu, Xiang-Jing Gao, Xiangwei Gao, Yicheng Chen
Summary: Our study reveals that zinc oxide nanoparticles (ZnO NPs) affect the transcription of 78 genes and translation of 1,448 genes in A549 human lung cancer cells within one hour of exposure. The mitogen-activated protein kinase (MAPK) pathway is up-regulated upon ZnO NP treatment, and upstream open reading frame (uORF) plays a crucial role in the induction of up-regulated genes such as TLNRD1 and CCNB1IP1, which in turn reduces ZnO NP-induced cytotoxicity. This study characterizes the landscape of translational alteration under ZnO NPs treatment and identifies potential targets to enhance the anticancer effect of ZnO NPs.
Article
Biochemistry & Molecular Biology
Heleen M. van 't Spijker, Emily E. Stackpole, Sandra Almeida, Olga Katsara, Botao Liu, Kuang Shen, Robert J. Schneider, Fen-Biao Gao, Joel D. Richter
Summary: GGGGCC (G(4)C(2)) repeat expansion in the first intron of C9ORF72 leads to amyotrophic lateral sclerosis and frontotemporal dementia. The repeated RNA is translated into neurotoxic DPR proteins. It was found that there are three translation initiation sites in the intron upstream of the (G(4)C(2)) repeats, and ribosomes are stalled on the repeats during translocation. Additionally, the translation process is inhibited by a uORF in the preceding exon.
Article
Biochemistry & Molecular Biology
Juan Deng, Ya-Jing Liu, Wen-Tian Wei, Qi-Xuan Huang, Li-Ping Zhao, Ling-Yun Luo, Qi Zhu, Lin Zhang, Yuan Chen, Yan-Ling Ren, Shan-Gang Jia, Yu-Luan Lin, Ji Yang, Feng-Hua Lv, Hong-Ping Zhang, Feng-E Li, Li Li, Meng-Hua Li
Summary: We characterized the developmental changes of the rumen in sheep and goats by profiling single-cell transcriptomes. Through comprehensive transcriptome and metagenome atlases, we identified key transitional signatures associated with the development of ruminal cells, microbiota, and core transcriptional regulatory networks. We also revealed potential cross-talk between host cells and microbiomes and their roles in modulating gene expression in ruminal cells.
Review
Genetics & Heredity
Sarthak Sinha, Ansuman T. Satpathy, Weiqiang Zhou, Hongkai Ji, Jo A. Stratton, Arzina Jaffer, Nizar Bahlis, Sorana Morrissy, Jeff A. Biernaskie
Summary: The review outlines the molecular methods and bioinformatic tools for capturing cell-to-cell chromatin variation using scATAC-seq in a scalable fashion. It also covers joint profiling of chromatin with transcriptome/proteome measurements, computational strategies for multi-omic integration, and predictive bioinformatic tools for inferring chromatin accessibility from single-cell transcriptomic datasets. Methodological refinements that increase power for cell discovery and integrate measurements from multiple modalities will further expand understanding of gene regulation during homeostasis and disease.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Haoran Duan, Siqiong Zhang, Yoram Zarai, Rupert Ollinger, Yanmeng Wu, Li Sun, Cheng Hu, Yaohui He, Guiyou Tian, Roland Rad, Xiangquan Kong, Yabin Cheng, Tamir Tuller, Dieter A. Wolf
Summary: eIF3k and eIF3l play an important role in maintaining translational capacity during cellular stress by regulating ribosome synthesis.
Article
Microbiology
Dengwei Zhang, Jian Zhang, Shanthini Kalimuthu, Jing Liu, Zhi-Man Song, Bei-bei He, Peiyan Cai, Zheng Zhong, Chenchen Feng, Prasanna Neelakantan, Yong-Xin Li
Summary: This study systematically investigates the biosynthetic potential of lactic acid bacteria (LAB) and their profiles in the human microbiome, linking them to their antagonistic contributions to microbiome homeostasis. The research discovers diverse and prevalent antibacterial secondary metabolites produced by LAB, suggesting their potential therapeutic applications.
Article
Cardiac & Cardiovascular Systems
Virginia Smit, Jill de Mol, Frank H. Schaftenaar, Marie A. C. Depuydt, Rimke J. Postel, Diede Smeets, Fenne W. M. Verheijen, Laurens Bogers, Janine van Duijn, Robin A. F. Verwilligen, Hendrika W. Grievink, Mireia N. A. Bernabe Kleijn, Eva van Ingen, Maaike J. M. de Jong, Lauren Goncalves, Judith A. H. M. Peeters, Harm J. Smeets, Anouk Wezel, Julia K. Polansky, Menno P. J. de Winther, Christoph J. Binder, Dimitrios Tsiantoulas, Ilze Bot, Johan Kuiper, Amanda C. Foks
Summary: This study found that aging promotes advanced atherosclerosis in mice and induces immunological alterations. The expression of genes involved in atherogenic processes shifted with age, and age-associated T- and B-cells emerged in atherosclerotic plaques and blood. Further research on age-associated immunity may contribute to novel diagnostic and therapeutic tools for cardiovascular disease.
CARDIOVASCULAR RESEARCH
(2023)
Article
Cell Biology
Fuad Mohammad, Christopher J. Woolstenhulme, Rachel Green, Allen R. Buskirk
Article
Biochemistry & Molecular Biology
Aishwarya G. Jacob, Ravi K. Singh, Fuad Mohammad, Thomas W. Bebee, Dawn S. Chandler
JOURNAL OF BIOLOGICAL CHEMISTRY
(2014)
Article
Biochemistry & Molecular Biology
Bhalchandra S. Rao, Fuad Mohammad, Michael W. Gray, Jane E. Jackman
NUCLEIC ACIDS RESEARCH
(2013)
Article
Multidisciplinary Sciences
Aishwarya G. Jacob, Ravi K. Singh, Daniel F. Comiskey, Matthew F. Rouhier, Fuad Mohammad, Thomas W. Bebee, Dawn S. Chandler
Article
Oncology
Aishwarya G. Jacob, Dennis O'Brien, Ravi K. Singh, Daniel F. Comiskey, Robert M. Littleton, Fuad Mohammad, Jordan T. Gladman, Maria C. Widmann, Selvi C. Jeyaraj, Cheryl Bolinger, James R. Anderson, Donald A. Barkauskas, Kathleen Boris-Lawrie, Dawn S. Chandler
Article
Microbiology
Jeremy Weaver, Fuad Mohammad, Allen R. Buskirk, Gisela Storz