Pervasive translation of circular RNAs driven by short IRES-like elements

AbstractAlthough some circular RNAs (circRNAs) were found to be translated through IRES-driven mechanism, the scope and functions of circRNA translation are unclear because endogenous IRESs are rare. To determine the prevalence and mechanism of circRNA translation, we developed a cell-based system to screen random sequences and identified 97 overrepresented hexamers that drive cap-independent circRNA translation. These IRES-like short elements are significantly enriched in endogenous circRNAs and sufficient to drive circRNA translation. We further identified multiple trans-acting factors that bind these IRES-like elements to initiate translation. Using mass-spectrometry data, hundreds of circRNA-coded peptides were identified, most of which have low abundance due to rapid degradation. As judged by mass-spectrometry, 50% of translatable endogenous circRNAs undergo rolling circle translation, several of which were experimentally validated. Consistently, mutations of the IRES-like element in one circRNA reduced its translation. Collectively, our findings suggest a pervasive translation of circRNAs, providing profound implications in translation control.

Download Full-text

Tubulin lattice in cilia is in a stressed form regulated by microtubule inner proteins

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1911119116 ◽

2019 ◽

Vol 116 (40) ◽

pp. 19930-19938 ◽

Cited By ~ 8

Author(s):

Muneyoshi Ichikawa ◽

Ahmad Abdelzaher Zaki Khalifa ◽

Shintaroh Kubo ◽

Daniel Dai ◽

Kaustuv Basu ◽

...

Keyword(s):

Mass Spectrometry ◽

De Novo ◽

Lattice Structure ◽

Mass Spectrometry Data ◽

Atomic Resolution ◽

High Frequencies ◽

Tubulin Dimer ◽

Angle Change ◽

A Cell ◽

Longitudinal Compaction

Cilia, the hair-like protrusions that beat at high frequencies to propel a cell or move fluid around are composed of radially bundled doublet microtubules. In this study, we present a near-atomic resolution map of the Tetrahymena doublet microtubule by cryoelectron microscopy. The map demonstrates that the network of microtubule inner proteins weaves into the tubulin lattice and forms an inner sheath. From mass spectrometry data and de novo modeling, we identified Rib43a proteins as the filamentous microtubule inner proteins in the protofilament ribbon region. The Rib43a–tubulin interaction leads to an elongated tubulin dimer distance every 2 dimers. In addition, the tubulin lattice structure with missing microtubule inner proteins (MIPs) by sarkosyl treatment shows significant longitudinal compaction and lateral angle change between protofilaments. These results are evidence that the MIPs directly affect and stabilize the tubulin lattice. It suggests that the doublet microtubule is an intrinsically stressed filament and that this stress could be manipulated in the regulation of ciliary waveforms.

Download Full-text

154: Integration of TPSA and High-Throughput Mass Spectrometry Data Improves Prostate Cancer Prediction

The Journal of Urology ◽

10.1016/s0022-5347(18)30419-1 ◽

2007 ◽

Vol 177 (4S) ◽

pp. 52-53

Author(s):

Stefano Ongarello ◽

Eberhard Steiner ◽

Regina Achleitner ◽

Isabel Feuerstein ◽

Birgit Stenzel ◽

...

Keyword(s):

Prostate Cancer ◽

Mass Spectrometry ◽

High Throughput ◽

Mass Spectrometry Data ◽

Cancer Prediction

Download Full-text

Mass Spectrometry Techniques: Principles and Practices for Quantitative Proteomics

Current Protein and Peptide Science ◽

10.2174/1389203721666200921153513 ◽

2020 ◽

Vol 21 ◽

Author(s):

Rocco J. Rotello ◽

Timothy D. Veenstra

Keyword(s):

Mass Spectrometry ◽

Quantitative Proteomics ◽

Protein Identification ◽

Dynamic Nature ◽

Complete Coverage ◽

The Past ◽

Proteome Level ◽

A Cell ◽

Quantitative Changes ◽

Made In

: In the current omics-age of research, major developments have been made in technologies that attempt to survey the entire repertoire of genes, transcripts, proteins, and metabolites present within a cell. While genomics has led to a dramatic increase in our understanding of such things as disease morphology and how organisms respond to medications, it is critical to obtain information at the proteome level since proteins carry out most of the functions within the cell. The primary tool for obtaining proteome-wide information on proteins within the cell is mass spectrometry (MS). While it has historically been associated with the protein identification, developments over the past couple of decades have made MS a robust technology for protein quantitation as well. Identifying quantitative changes in proteomes is complicated by its dynamic nature and the inability of any technique to guarantee complete coverage of every protein within a proteome sample. Fortunately, the combined development of sample preparation and MS methods have made it capable to quantitatively compare many thousands of proteins obtained from cells and organisms.

Download Full-text