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TRS: a method for determining transcript termini from RNAtag-seq sequencing data
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DOI：10.1038/s41467-023-43534-2.png)
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摘要
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In bacteria, determination of the 3' termini of transcripts plays an essential role in regulation of gene expression, affecting the functionality and stability of the transcript. Several experimental approaches were developed to identify the 3' termini of transcripts, however, these were applied only to a limited number of bacteria and growth conditions. Here we present a straightforward approach to identify 3' termini from widely available RNA-seq data without the need for additional experiments. Our approach relies on the observation that the RNAtag-seq sequencing protocol results in overabundance of reads mapped to transcript 3' termini. We present TRS (Termini by Read Starts), a computational pipeline exploiting this property to identify 3' termini in RNAtag-seq data, and show that the identified 3' termini are highly reliable. Since RNAtag-seq data are widely available for many bacteria and growth conditions, our approach paves the way for studying bacterial transcription termination in an unprecedented scope. TRS is a new method for determining 3' transcript termini in bacteria, using data generated by the RNAtag-seq protocol. This methodology opens the door to study the evolution of transcription termini and their condition-dependent dynamics.
Keyword:
ESCHERICHIA-COLI
GENE-EXPRESSION
RNAS
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15.7
论文数:
9.3W
被引数:
91.2W
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