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Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
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The technique...
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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
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Related Experiment Video

Updated: Jul 25, 2025

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
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Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

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Transcriptional and proteomic analysis.

Liu Xiao-Jing1, Xing Bao1, Wang Meng-Yu1

  • 1Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, MARA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Beijing, China.

GM Crops & Food
|June 30, 2023
PubMed
Summary
This summary is machine-generated.

Gene editing in rice using CRISPR-Cas9 and adenine base editor (ABE) showed minimal unintended effects. Omics analyses revealed no new genes or proteins, indicating safety for gene-edited crops.

Keywords:
Gene editproteometranscriptomeunintended effects

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Area of Science:

  • Agricultural Science
  • Molecular Biology
  • Biotechnology

Background:

  • Gene editing technologies like CRISPR-Cas9 and adenine base editor (ABE) offer precise crop modification.
  • Assessing unintended effects of gene editing is crucial for crop safety and regulatory approval.
  • Omics approaches provide comprehensive molecular insights into biological systems.

Purpose of the Study:

  • To evaluate the unintended molecular consequences of CRISPR-Cas9 and ABE gene editing in rice.
  • To compare the transcriptomic and proteomic profiles of gene-edited rice with wild-type Nipponbare.
  • To determine if gene editing introduces novel genes or proteins, impacting crop safety.

Main Methods:

  • Transcriptome analysis (RNA sequencing) was performed on CRISPR-Cas9 and ABE-edited rice and wild-type Nipponbare.
  • Proteomics analysis (mass spectrometry) was conducted on the same rice samples.
  • Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was used to interpret differentially expressed genes and proteins.

Main Results:

  • Transcriptome analysis identified 520 and 566 differentially expressed genes (DEGs) in Cas9/Nip and ABE/Nip comparisons, respectively.
  • Proteomics analysis identified 298 and 54 differentially expressed proteins (DEPs) in Cas9/Nip and ABE/Nip comparisons, respectively.
  • Integrated analysis revealed no newly generated transcripts or proteins in gene-edited rice, with minimal impact on overall transcription levels.

Conclusions:

  • CRISPR-Cas9 and ABE gene editing in rice have limited unintended effects on the transcriptome and proteome.
  • The identified DEGs were primarily involved in environmental adaptation pathways, such as plant-pathogen interactions and signal transduction.
  • Gene-edited rice lines analyzed in this study are considered safe, as no novel genes or proteins were detected.