Deciphering Transcriptional Dynamics In Vivo by Counting Nascent RNA Molecules.
Deciphering how the regulatory DNA sequence of a gene dictates its expression in response to intra and extracellular cues is one of the leading challenges in modern genomics. The development of novel single-cell sequencing and imaging techniques, as well as a better exploitation of currently availab...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2015-11-01
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| Series: | PLoS Computational Biology |
| Online Access: | http://europepmc.org/articles/PMC4636183?pdf=render |
| _version_ | 1819042252961349632 |
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| author | Sandeep Choubey Jane Kondev Alvaro Sanchez |
| author_facet | Sandeep Choubey Jane Kondev Alvaro Sanchez |
| author_sort | Sandeep Choubey |
| collection | DOAJ |
| description | Deciphering how the regulatory DNA sequence of a gene dictates its expression in response to intra and extracellular cues is one of the leading challenges in modern genomics. The development of novel single-cell sequencing and imaging techniques, as well as a better exploitation of currently available single-molecule imaging techniques, provides an avenue to interrogate the process of transcription and its dynamics in cells by quantifying the number of RNA polymerases engaged in the transcription of a gene (or equivalently the number of nascent RNAs) at a given moment in time. In this paper, we propose that measurements of the cell-to-cell variability in the number of nascent RNAs provide a mostly unexplored method for deciphering mechanisms of transcription initiation in cells. We propose a simple kinetic model of transcription initiation and elongation from which we calculate nascent RNA copy-number fluctuations. To demonstrate the usefulness of this approach, we test our theory against published nascent RNA data for twelve constitutively expressed yeast genes. Rather than transcription being initiated through a single rate limiting step, as it had been previously proposed, our single-cell analysis reveals the presence of at least two rate limiting steps. Surprisingly, half of the genes analyzed have nearly identical rates of transcription initiation, suggesting a common mechanism. Our analytical framework can be used to extract quantitative information about dynamics of transcription from single-cell sequencing data, as well as from single-molecule imaging and electron micrographs of fixed cells, and provides the mathematical means to exploit the quantitative power of these technologies. |
| first_indexed | 2024-12-21T09:37:57Z |
| format | Article |
| id | doaj.art-8fa5f622964b49e7a1ca6b56233ef424 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-21T09:37:57Z |
| publishDate | 2015-11-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-8fa5f622964b49e7a1ca6b56233ef4242022-12-21T19:08:34ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582015-11-011111e100434510.1371/journal.pcbi.1004345Deciphering Transcriptional Dynamics In Vivo by Counting Nascent RNA Molecules.Sandeep ChoubeyJane KondevAlvaro SanchezDeciphering how the regulatory DNA sequence of a gene dictates its expression in response to intra and extracellular cues is one of the leading challenges in modern genomics. The development of novel single-cell sequencing and imaging techniques, as well as a better exploitation of currently available single-molecule imaging techniques, provides an avenue to interrogate the process of transcription and its dynamics in cells by quantifying the number of RNA polymerases engaged in the transcription of a gene (or equivalently the number of nascent RNAs) at a given moment in time. In this paper, we propose that measurements of the cell-to-cell variability in the number of nascent RNAs provide a mostly unexplored method for deciphering mechanisms of transcription initiation in cells. We propose a simple kinetic model of transcription initiation and elongation from which we calculate nascent RNA copy-number fluctuations. To demonstrate the usefulness of this approach, we test our theory against published nascent RNA data for twelve constitutively expressed yeast genes. Rather than transcription being initiated through a single rate limiting step, as it had been previously proposed, our single-cell analysis reveals the presence of at least two rate limiting steps. Surprisingly, half of the genes analyzed have nearly identical rates of transcription initiation, suggesting a common mechanism. Our analytical framework can be used to extract quantitative information about dynamics of transcription from single-cell sequencing data, as well as from single-molecule imaging and electron micrographs of fixed cells, and provides the mathematical means to exploit the quantitative power of these technologies.http://europepmc.org/articles/PMC4636183?pdf=render |
| spellingShingle | Sandeep Choubey Jane Kondev Alvaro Sanchez Deciphering Transcriptional Dynamics In Vivo by Counting Nascent RNA Molecules. PLoS Computational Biology |
| title | Deciphering Transcriptional Dynamics In Vivo by Counting Nascent RNA Molecules. |
| title_full | Deciphering Transcriptional Dynamics In Vivo by Counting Nascent RNA Molecules. |
| title_fullStr | Deciphering Transcriptional Dynamics In Vivo by Counting Nascent RNA Molecules. |
| title_full_unstemmed | Deciphering Transcriptional Dynamics In Vivo by Counting Nascent RNA Molecules. |
| title_short | Deciphering Transcriptional Dynamics In Vivo by Counting Nascent RNA Molecules. |
| title_sort | deciphering transcriptional dynamics in vivo by counting nascent rna molecules |
| url | http://europepmc.org/articles/PMC4636183?pdf=render |
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