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A spectral analysis approach to detects actively translated open reading frames in high resolution ribosome profiling data

ABSTRACT: RNA sequencing protocols allow for quantifying gene expression regulation at each individual step, from transcription to protein synthesis. Ribosome Profiling (Ribo-seq) maps the positions of translating ribosomes over the entire transcriptome. Despite its great potential, a rigorous statistical approach to identify translated regions from Ribo-seq data is not yet available. To fill this gap, we developed RiboTaper, which quantifies the significance of the three-nucleotide periodicity of Ribo-seq reads via spectral analysis methods.

ORGANISM(S): Homo sapiens

PROVIDER: GSE73136 | GEO | 2015/11/12

SECONDARY ACCESSION(S): PRJNA296059

REPOSITORIES: GEO

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A spectral analysis approach to detects actively translated open reading frames in high resolution ribosome profiling data

Project description:RNA sequencing protocols allow for quantifying gene expression regulation at each individual step, from transcription to protein synthesis. Ribosome Profiling (Ribo-seq) maps the positions of translating ribosomes over the entire transcriptome. Despite its great potential, a rigorous statistical approach to identify translated regions from Ribo-seq data is not yet available. To fill this gap, we developed RiboTaper, which quantifies the significance of the three-nucleotide periodicity of Ribo-seq reads via spectral analysis methods. Examination of RNA fragments protected by ribosome

2015-11-12 | E-GEOD-73136 | biostudies-arrayexpress

SPECtre: a spectral coherence-based classifier of actively translated transcripts from ribosome profiling sequence data

Project description:Active protein translation can be assessed and measured using ribosome profiling sequencing strategies. Existing approaches make use of sequence fragment length or frame occupancy to differentiate between active translation and background noise, however they do not consider additional characteristics inherent to the technology which limits their overall accuracy. Here, we present an analytical tool that models the overall tri-nucleotide periodicity of ribosomal occupancy using a classifier based on spectral coherence. Our software, SPECtre, examines the relationship of normalized ribosome profiling read coverage over a rolling series of windows along a transcript against an idealized reference signal. A comparison of SPECtre against current methods on existing and new data shows a marked improvement in accuracy for detecting active translation and exhibits overall high sensitivity at a low false discovery rate. Classification of actively translated transcripts in ribosome profiling data derived from human neuroblastoma SH-SY5Y cells, and data previously published derived from mouse embryonic stem cells and zebrafish embryos.

2016-07-01 | E-GEOD-75947 | biostudies-arrayexpress

SPECtre: a spectral coherence-based classifier of actively translated transcripts from ribosome profiling sequence data

2016-07-01 | GSE75947 | GEO

Identification of translated small open reading frames in lymphocytes

Project description:Open reading frames (ORFs) are the genomic DNA sequences that have the potential to be translated. Genome annotation pipelines dismiss translation products of small ORFs (smORFs) of less than 100 codons (<300 nucleotides) as being unlikely to have a biological function. In this study, we systematically characterized smORFs in mouse B and T cells under different conditions and predicted a total of 5744 unique actively translated smORFs. We then extended our analysis to ORFs of 101-200 codons in length and predicted 945 of such longer translation products. Additionally, our results have suggested the existence of candidate secreted micropeptides. Furthermore, verifying their existence and identifying their functions will be essential and potentially lead to useful applications.

2021-04-28 | GSE154491 | GEO

RiboReport - Benchmarking ribosome profiling based identification of open reading frames in bacteria.

Project description:Generation of a Ribo-seq dataset for E. coli MG1655 for benchmarking Ribo-seq analysis tools

2022-05-20 | GSE131514 | GEO

RibORF: Identifying Genome-Wide Translated Open Reading Frames Using Ribosome Profiling.

Project description: Not available

| S-EPMC6168376 | biostudies-literature

Distinct types of short open reading frames are translated in plant cells.

Project description: Not available

| S-EPMC6724668 | biostudies-literature

Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling.

Project description: Not available

| S-EPMC4940163 | biostudies-literature

Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling.

Project description:Accurate annotations of protein coding regions are essential for understanding how genetic information is translated into biological functions. The recent development of ribosome footprint profiling provides an important new tool for measuring translation. Here we describe riboHMM, a new method that uses ribosome footprint data along with gene expression and sequence information to accurately infer translated sequences. We applied our method to human lymphoblastoid cell lines and identified 7,863 previously unannotated coding sequences, including 445 translated sequences in pseudogenes and 2,442 translated upstream open reading frames. We observed an enrichment of harringtonine-treated ribosome footprints at the inferred initiation sites, validating many of the novel coding sequences. In aggregate, the novel sequences exhibit significant signatures of purifying selection indicative of protein-coding function, suggesting that many of the novel sequences are functional. We observed that nearly 40% of bicistronic transcripts showed significant negative correlation in the levels of translation of their two coding sequences, suggesting a key regulatory role for these novel translated sequences. Despite evidence for their functional importance, the novel peptide sequences were detected by mass spectrometry at a lower rate than predicted based on data from annotated proteins, thus suggesting that many of the novel peptide products may be relatively short-lived. Our work illustrates the value of ribosome profiling for improving coding annotations, and significantly expands the set of known coding regions.

2015-12-25 | GSE75290 | GEO

Accurate annotation of human protein-coding small open reading frames

Project description:Protein-coding small open reading frames (smORFs) are emerging as an important class of genes, however, the coding capacity of smORFs in the human genome is unclear. By integrating de novo transcriptome assembly and Ribo-Seq, we confidently annotate thousands of novel translated smORFs in three human cell lines. We find that smORF translation prediction is noisier than for annotated coding sequences, underscoring the importance of analyzing multiple experiments and footprinting conditions. These smORFs are located within non-coding and antisense transcripts, the UTRs of mRNAs, and unannotated transcripts. Analysis of RNA levels and translation efficiency during cellular stress identifies regulated smORFs and provides an approach for identifying smORFs for further investigation. Sequence conservation and signatures of positive selection indicate that encoded microproteins are likely functional. Additionally, proteomics data from enriched human leukocyte antigen complexes validates the translation of hundreds of smORFs and positions them as a source of novel antigens. Thus, smORFs represent a significant number of important, yet unexplored human genes.

2019-07-03 | GSE125218 | GEO

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