ArticleNucleic acids research2019
Optimization of ribosome profiling using low-input brain tissue from fragile X syndrome model mice.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 27 citations in OpenAlex.
- RiboBA: a bias-aware probabilistic framework for robust ORF identification across diverse ribosome profiling protocols.Nucleic acids research · 2026Article
- Ribo-ITP enables identification of translons from limited input samples.Nature communications · 2026Article
- The use of Benzonase to produce ribosome footprints simplifies translational levels quantification by Ribo-seq.NAR genomics and bioinformatics · 2026Article
- How tailored Ribo-seq methods probe unique translation events.RNA (New York, N.Y.) · 2026Review
- Metabolic reprogramming during human neuron differentiation indicates glutaminase as a key determinant in Fragile X syndrome.Cell reports · 2026Article
- Transcriptome-wide mapping of small ribosomal subunits elucidates scanning mechanisms of translation initiation in the mammalian brain.Communications biology · 2025Article
- Principles, challenges, and advances in ribosome profiling: from bulk to low-input and single-cell analysis.Advanced biotechnology · 2023Review
- Development of nanoRibo-seq enables study of regulated translation by cortical neuron subtypes, showing uORF translation in synaptic-axonal genes.Cell reports · 2023Article
- Ribosomes in RNA Granules Are Stalled on mRNA Sequences That Are Consensus Sites for FMRP Association.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2023Article
- Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation.Genome research · 2022Article
- Ribosome profiling reveals novel regulation ofRNA (New York, N.Y.) · 2022Article
- The molecular biology of FMRP: new insights into fragile X syndrome.Nature reviews. Neuroscience · 2021Review
- Taming human brain organoids one cell at a time.Seminars in cell & developmental biology · 2021Review
- Optimization of Ribosome Footprinting Conditions for Ribo-Seq in Human andFrontiers in molecular biosciences · 2021Article
- FMRP Control of Ribosome Translocation Promotes Chromatin Modifications and Alternative Splicing of Neuronal Genes Linked to Autism.Cell reports · 2020Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Dysregulated protein synthesis is a major underlying cause of many neurodevelopmental diseases including fragile X syndrome. In order to capture subtle but biologically significant differences in translation in these disorders, a robust technique is required. One powerful tool to study translational control is ribosome profiling, which is based on deep sequencing of mRNA fragments protected from ribonuclease (RNase) digestion by ribosomes. However, this approach has been mainly applied to rapidly dividing cells where translation is active and large amounts of starting material are readily available. The application of ribosome profiling to low-input brain tissue where translation is modest and gene expression changes between genotypes are expected to be small has not been carefully evaluated. Using hippocampal tissue from wide type and fragile X mental retardation 1 (Fmr1) knockout mice, we show that variable RNase digestion can lead to significant sample batch effects. We also establish GC content and ribosome footprint length as quality control metrics for RNase digestion. We performed RNase titration experiments for low-input samples to identify optimal conditions for this critical step that is often improperly conducted. Our data reveal that optimal RNase digestion is essential to ensure high quality and reproducibility of ribosome profiling for low-input brain tissue.
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