Ribomaps | Four Interesting Preprints Uploaded to bioRxiv in January 2020 that Feature Ribosome Profiling (and One that Does Not)
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Four Interesting Preprints Uploaded to bioRxiv in January 2020 that Feature Ribosome Profiling (and One that Does Not)

  1. FMRP Control of Ribosome Translocation Promotes Chromatin Modifications and Alternative Splicing of Neuronal Genes Linked to Autism | Posted 27th January 2020

By: Sneha Shah, Gemma Molinaro, Botao Liu, Ruijia Wang, Kimberly M. Huber, Joel D. Richter

Loss of the FMR1 gene product FMRP, an RNA binding protein which inhibits polypeptide elongation, results in Fragile X Syndrome. Here, the Richter Lab out of @UMassMedical detail how they have performed ribosome profiling run off experiments on hippocampal brain slices from wild-type and Fmr-1 KO mice, finding that loss of FMRP leads to a decline of ribosome stalling on specific mRNAs.

Our study demonstrates that a reduction in ribosome stalling in the Fmr1-deficient brain results in a cascade of epigenetic and RNA processing changes that likely contribute to neurologic disease.

 

  1. Exhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes | Posted 26th January 2020

By: Hiro Takahashi, Shido Miyaki, Hitoshi Onouchi, Taichiro Motomura, Nobuo Idesako, Anna Takahashi, Masataka Murase, Shuichi Fukuyoshi, Toshinori Endo, Kenji Satou, Satoshi Naito, Motoyuki Itoh

Up until now, uORFs with conserved peptide sequences (CPuORFs) have only been identified for animals by comparing uORF sequences between a limited number of closely related species (mostly human and mouse). Researchers from the Itoh Lab out of @Chiba_Univ_PR conducted exhaustive genome-wide searches for animal uORFs conserved in various taxonomic ranges, identifying 1,425 novel CPuORFs. They subsequently carried out dual luciferase reporter assays in 17 of the CPuORFs identified in humans, finding seven of them to exert regulatory control over translation of the main protein coding ORF in a sequence dependent manner.

The data from the current study may be useful for selection of CPuORFs as potential targets for pharmaceutical drugs and for identification of regulatory CPuORFs.

 

  1. Multi-faceted deregulation of gene expression and protein synthesis with age | Posted 19th January 2020

By: Aleksandra S. Anisimova, Mark B. Meerson, Maxim V. Gerashchenko, Ivan V. Kulakovskiy, Sergey E. Dmitriev, Vadim N. Gladyshev

How protein synthesis is affected by aging and how this in turn impacts cell function remains largely unexplored. This paper, from the Gladyshev Lab out of @harvardmed used Ribo-seq to characterize age-related changes in both the transcriptome and translatome of mouse tissues over the entire lifespan, finding dozens of transcripts encoding ribosome biogenesis and protein synthesis machinery components to be down-regulated with age at the translational level. Interestingly, Ribo-Seq analyses also revealed a transcriptome-wide redistribution of footprints from the beginning to the end of mRNA coding regions.

Another important observation in our study concerns changes in the metagene profile of ribosome coverage along coding regions, pointing to a systemic alteration of translation with age.

 

  1. Ribo-ODDR: Ribo-seq focused Oligo Design pipeline for experiment-specific Depletion of Ribosomal RNAs | Posted 14th January 2020

By: Ferhat Alkan, Joana Silva, Eric Pintó Barberà, William J. Faller

The discontinuation of Illumina’s Ribo-Zero Kit for ribosomal RNA depletion was a major disruption to the ribosome profiling community, forcing researchers to come up with alternative solution for the removal of these contaminating reads. One solution is to use custom-designed biotinylated oligos complementary to the most abundant rRNA fragments. Here, the Faller Lab out of @NKI_nl present Ribo-ODDR an oligo design pipeline integrated with a user-friendly interface that assists in oligo selection for efficient experiment-specific rRNA depletion.

Ribo-ODDR gives experimenters a platform to assess the most optimal oligos, allowing for increased depth of mRNA fragment sequencing, and maximizing the information gained in Ribo-seq experiments.

 

Bonus: Quantifying the spatiotemporal dynamics of IRES versus Cap translation with single-molecule resolution in living cells | Posted 9th January 2020

By: Amanda Koch, Luis Aguilera, Tatsuya Morisaki, Brian Munsky, Timothy J. Stasevich

Although not a ribosome profiling paper, this work from the Stasevich Lab out of @ColoradoStateU is a must read for anyone interested in the study of translational dynamics. The paper describes development of a real-time biosensor to quantify IRES-mediated translation dynamics with single-molecule resolution in living cells. The authors anticipate this technology will find broad application, not just to better understand viral replication, but also in screens to help identify and develop novel therapeutics that selectively perturb IRES-mediated translation.

Overall, our technology to visualize when, where, and to what degree IRES-mediated translation occurs at the single-molecule level in the natural setting of living cells provides a new angle on viral translation that will complement technologies like ribosome profiling and in vitro single-molecule assays.