TRS: a method for determining transcript termini from RNAtag-seq sequencing data
Abstract 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 ap...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-11-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-023-43534-2 |
| _version_ | 1797414705487151104 |
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| author | Amir Bar Liron Argaman Michal Eldar Hanah Margalit |
| author_facet | Amir Bar Liron Argaman Michal Eldar Hanah Margalit |
| author_sort | Amir Bar |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-03-09T05:37:26Z |
| format | Article |
| id | doaj.art-19808b9c93444d2eac040ba7e96891f6 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-03-09T05:37:26Z |
| publishDate | 2023-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-19808b9c93444d2eac040ba7e96891f62023-12-03T12:27:21ZengNature PortfolioNature Communications2041-17232023-11-0114111410.1038/s41467-023-43534-2TRS: a method for determining transcript termini from RNAtag-seq sequencing dataAmir Bar0Liron Argaman1Michal Eldar2Hanah Margalit3Department of Microbiology and Molecular Genetics IMRIC, Faculty of Medicine, The Hebrew University of JerusalemDepartment of Microbiology and Molecular Genetics IMRIC, Faculty of Medicine, The Hebrew University of JerusalemDepartment of Microbiology and Molecular Genetics IMRIC, Faculty of Medicine, The Hebrew University of JerusalemDepartment of Microbiology and Molecular Genetics IMRIC, Faculty of Medicine, The Hebrew University of JerusalemAbstract 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.https://doi.org/10.1038/s41467-023-43534-2 |
| spellingShingle | Amir Bar Liron Argaman Michal Eldar Hanah Margalit TRS: a method for determining transcript termini from RNAtag-seq sequencing data Nature Communications |
| title | TRS: a method for determining transcript termini from RNAtag-seq sequencing data |
| title_full | TRS: a method for determining transcript termini from RNAtag-seq sequencing data |
| title_fullStr | TRS: a method for determining transcript termini from RNAtag-seq sequencing data |
| title_full_unstemmed | TRS: a method for determining transcript termini from RNAtag-seq sequencing data |
| title_short | TRS: a method for determining transcript termini from RNAtag-seq sequencing data |
| title_sort | trs a method for determining transcript termini from rnatag seq sequencing data |
| url | https://doi.org/10.1038/s41467-023-43534-2 |
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