Results 1 to 10 of about 78,844 (296)

Calibrated ribosome profiling assesses the dynamics of ribosomal flux on transcripts [PDF]

Nature Communications
Ribosome profiling, which is based on deep sequencing of ribosome footprints, has served as a powerful tool for elucidating the regulatory mechanism of protein synthesis.
Kotaro Tomuro, Mari Mito, Hirotaka Toh, Naohiro Kawamoto, Takahito Miyake, Siu Yu A. Chow, Masao Doi, Yoshiho Ikeuchi, Yuichi Shichino, Shintaro Iwasaki   +9 more
doaj   +4 more sources

Ribosome signatures aid bacterial translation initiation site identification [PDF]

BMC Biology, 2017
Background While methods for annotation of genes are increasingly reliable, the exact identification of translation initiation sites remains a challenging problem.
Adam Giess, Veronique Jonckheere, Elvis Ndah, Katarzyna Chyżyńska, Petra Van Damme, Eivind Valen   +5 more
doaj   +3 more sources

Ribosome profiling: a powerful tool in oncological research [PDF]

Biomarker Research
Neoplastic cells need to adapt their gene expression pattern to survive in an ever-changing or unfavorable tumor microenvironment. Protein synthesis (or mRNA translation), an essential part of gene expression, is dysregulated in cancer.
Dan Su, Chen Ding, Jiangdong Qiu, Gang Yang, Ruobing Wang, Yueze Liu, Jinxin Tao, Wenhao Luo, Guihu Weng, Taiping Zhang   +9 more
doaj   +2 more sources

Common cell lysis procedures distort ribosome profiling analyses of gene expression [PDF]

Genome Biology
Ribosome profiling is a powerful technique used to study gene expression on a transcriptome-wide scale. It involves sequencing of mRNA fragments protected by ribosomes from ribonuclease digestion. The initial steps commonly involve cell lysis followed by
Aoife O’Connell, Alla D. Fedorova, Patrick B. F. O’Connor, Alexander V. Zhdanov, Pavel V. Baranov, Gary Loughran, Dmitry E. Andreev   +6 more
doaj   +2 more sources

Ribosome profiling reveals downregulation of UMP biosynthesis as the major early response to phage infection [PDF]

Microbiology Spectrum
Bacteria have evolved diverse defense mechanisms to counter bacteriophage attacks. Genetic programs activated upon infection characterize phage–host molecular interactions and ultimately determine the outcome of the infection.
Patrick B. F. O’Connor, Jennifer Mahony, Eoghan Casey, Pavel V. Baranov, Douwe van Sinderen, Martina M. Yordanova   +5 more
doaj   +2 more sources

A tool for analyzing and visualizing ribo-seq data at the isoform level

BMC Bioinformatics, 2021
Background Translational regulation is one important aspect of gene expression regulation. Dysregulation of translation results in abnormal cell physiology and leads to diseases.
Wei-Sheng Wu, Yi-Hong Tsao, Sheng-Cian Shiue, Ting-Yu Chen, Yan-Yuan Tseng, Joseph T. Tseng   +5 more
doaj   +1 more source

Genome-wide Survey of Ribosome Collision

Cell Reports, 2020
Summary: Ribosome movement is not always smooth and is rather often impeded. For ribosome pauses, fundamental issues remain to be addressed, including where ribosomes pause on mRNAs, what kind of RNA/amino acid sequence causes this pause, and the ...
Peixun Han, Yuichi Shichino, Tilman Schneider-Poetsch, Mari Mito, Satoshi Hashimoto, Tsuyoshi Udagawa, Kenji Kohno, Minoru Yoshida, Yuichiro Mishima, Toshifumi Inada, Shintaro Iwasaki   +10 more
doaj   +1 more source

Humans and other commonly used model organisms are resistant to cycloheximide-mediated biases in ribosome profiling experiments

Nature Communications, 2021
Ribosome profiling has become the gold standard to analyze mRNA translation dynamics, and the translation inhibitor cycloheximide (CHX) is often used in its application.
Puneet Sharma, Jie Wu, Benedikt S. Nilges, Sebastian A. Leidel   +3 more
doaj   +1 more source

Ribosome profiling of HEK293T cells overexpressing codon optimized coagulation factor IX [version 2; peer review: 1 approved, 2 approved with reservations]

F1000Research, 2020
Ribosome profiling provides the opportunity to evaluate translation kinetics at codon level resolution. Here, we describe ribosome profiling data, generated from two HEK293T cell lines.
Aikaterini Alexaki, Jacob Kames, Gaya K. Hettiarachchi, John C. Athey, Upendra K. Katneni, Ryan C. Hunt, Nobuko Hamasaki-Katagiri, David D. Holcomb, Michael DiCuccio, Haim Bar, Anton A. Komar, Chava Kimchi-Sarfaty   +11 more
doaj   +1 more source

Quantitative Modeling of Protein Synthesis Using Ribosome Profiling Data

Frontiers in Molecular Biosciences, 2021
Quantitative prediction on protein synthesis requires accurate translation initiation and codon translation rates. Ribosome profiling data, which provide steady-state distribution of relative ribosome occupancies along a transcript, can be used to ...
Vandana Yadav, Inayat Ullah Irshad, Hemant Kumar, Ajeet K. Sharma   +3 more
doaj   +1 more source