Terminome-seq

Terminome-seq is a protocol to systematically map transcript ends in the chloroplast transcriptome of Arabidopsis thaliana. The method allows for identifying and cataloging primary 5' ends (transcription start sites), processed 5' ends, and 3' ends of RNA transcripts.

By applying Terminome-seq, the researchers discovered a surprising diversity of RNA termini, with abundant ends in intergenic regions, coding regions, and introns. The study also revealed a clustering pattern of 5' and 3' ends, suggesting imprecision in the transcription and RNA processing machinery. Many of the identified termini correlated with the extremities of small RNA footprints or predicted stem-loop structures, supporting the model of passive RNA protection.

Topic

Gene transcripts;Plant biology;Gene expression;Functional, regulatory and non-coding RNA;Protein secondary structure

Detail

  • Operation: Protein secondary structure comparison;RNA binding site prediction;RNA structure prediction

  • Software interface: Command-line user interface

  • Language: Shell

  • License: Not stated

  • Cost: Free of charge

  • Version name: -

  • Credit: The US Department of Energy, the LabEx Saclay Plant Sciences-SPS.

  • Input: -

  • Output: -

  • Contact: David B Stern ds28@cornell.edu

  • Collection: -

  • Maturity: -

Publications

  • Systematic sequencing of chloroplast transcript termini from Arabidopsis thaliana reveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures.
  • Castandet B, et al. Systematic sequencing of chloroplast transcript termini from Arabidopsis thaliana reveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures. Systematic sequencing of chloroplast transcript termini from Arabidopsis thaliana reveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures. 2019; 47:11889-11905. doi: 10.1093/nar/gkz1059
  • https://doi.org/10.1093/NAR/GKZ1059
  • PMID: 31732725
  • PMC: PMC7145512

Download and documentation

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