Barcoded DNA-tag reporters for multiplex cis-regulatory analysis.
Cis-regulatory DNA sequences causally mediate patterns of gene expression, but efficient experimental analysis of these control systems has remained challenging. Here we develop a new version of "barcoded" DNA-tag reporters, "Nanotags" that permit simultaneous quantitative analys...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3339872?pdf=render |
| _version_ | 1818250957062930432 |
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| author | Jongmin Nam Eric H Davidson |
| author_facet | Jongmin Nam Eric H Davidson |
| author_sort | Jongmin Nam |
| collection | DOAJ |
| description | Cis-regulatory DNA sequences causally mediate patterns of gene expression, but efficient experimental analysis of these control systems has remained challenging. Here we develop a new version of "barcoded" DNA-tag reporters, "Nanotags" that permit simultaneous quantitative analysis of up to 130 distinct cis-regulatory modules (CRMs). The activities of these reporters are measured in single experiments by the NanoString RNA counting method and other quantitative procedures. We demonstrate the efficiency of the Nanotag method by simultaneously measuring hourly temporal activities of 126 CRMs from 46 genes in the developing sea urchin embryo, otherwise a virtually impossible task. Nanotags are also used in gene perturbation experiments to reveal cis-regulatory responses of many CRMs at once. Nanotag methodology can be applied to many research areas, ranging from gene regulatory networks to functional and evolutionary genomics. |
| first_indexed | 2024-12-12T16:00:38Z |
| format | Article |
| id | doaj.art-0d213c13f62f4f93b892b579a6b12b24 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-12T16:00:38Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-0d213c13f62f4f93b892b579a6b12b242022-12-22T00:19:24ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-0174e3593410.1371/journal.pone.0035934Barcoded DNA-tag reporters for multiplex cis-regulatory analysis.Jongmin NamEric H DavidsonCis-regulatory DNA sequences causally mediate patterns of gene expression, but efficient experimental analysis of these control systems has remained challenging. Here we develop a new version of "barcoded" DNA-tag reporters, "Nanotags" that permit simultaneous quantitative analysis of up to 130 distinct cis-regulatory modules (CRMs). The activities of these reporters are measured in single experiments by the NanoString RNA counting method and other quantitative procedures. We demonstrate the efficiency of the Nanotag method by simultaneously measuring hourly temporal activities of 126 CRMs from 46 genes in the developing sea urchin embryo, otherwise a virtually impossible task. Nanotags are also used in gene perturbation experiments to reveal cis-regulatory responses of many CRMs at once. Nanotag methodology can be applied to many research areas, ranging from gene regulatory networks to functional and evolutionary genomics.http://europepmc.org/articles/PMC3339872?pdf=render |
| spellingShingle | Jongmin Nam Eric H Davidson Barcoded DNA-tag reporters for multiplex cis-regulatory analysis. PLoS ONE |
| title | Barcoded DNA-tag reporters for multiplex cis-regulatory analysis. |
| title_full | Barcoded DNA-tag reporters for multiplex cis-regulatory analysis. |
| title_fullStr | Barcoded DNA-tag reporters for multiplex cis-regulatory analysis. |
| title_full_unstemmed | Barcoded DNA-tag reporters for multiplex cis-regulatory analysis. |
| title_short | Barcoded DNA-tag reporters for multiplex cis-regulatory analysis. |
| title_sort | barcoded dna tag reporters for multiplex cis regulatory analysis |
| url | http://europepmc.org/articles/PMC3339872?pdf=render |
| work_keys_str_mv | AT jongminnam barcodeddnatagreportersformultiplexcisregulatoryanalysis AT erichdavidson barcodeddnatagreportersformultiplexcisregulatoryanalysis |