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Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE
Perturbation and time-course data sets, in combination with computational approaches, can be used to infer transcriptional regulatory networks which ultimately govern the developmental pathways and responses of cells. Here, we individually knocked down the four transcription factors PU.1, IRF8, MYB...
Autores principales: | , , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2010
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3001087/ https://www.ncbi.nlm.nih.gov/pubmed/20724440 http://dx.doi.org/10.1093/nar/gkq729 |
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author | Vitezic, Morana Lassmann, Timo Forrest, Alistair R. R. Suzuki, Masanori Tomaru, Yasuhiro Kawai, Jun Carninci, Piero Suzuki, Harukazu Hayashizaki, Yoshihide Daub, Carsten O. |
author_facet | Vitezic, Morana Lassmann, Timo Forrest, Alistair R. R. Suzuki, Masanori Tomaru, Yasuhiro Kawai, Jun Carninci, Piero Suzuki, Harukazu Hayashizaki, Yoshihide Daub, Carsten O. |
author_sort | Vitezic, Morana |
collection | PubMed |
description | Perturbation and time-course data sets, in combination with computational approaches, can be used to infer transcriptional regulatory networks which ultimately govern the developmental pathways and responses of cells. Here, we individually knocked down the four transcription factors PU.1, IRF8, MYB and SP1 in the human monocyte leukemia THP-1 cell line and profiled the genome-wide transcriptional response of individual transcription starting sites using deep sequencing based Cap Analysis of Gene Expression. From the proximal promoter regions of the responding transcription starting sites, we derived de novo binding-site motifs, characterized their biological function and constructed a network. We found a previously described composite motif for PU.1 and IRF8 that explains the overlapping set of transcriptional responses upon knockdown of either factor. |
format | Text |
id | pubmed-3001087 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-30010872010-12-13 Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE Vitezic, Morana Lassmann, Timo Forrest, Alistair R. R. Suzuki, Masanori Tomaru, Yasuhiro Kawai, Jun Carninci, Piero Suzuki, Harukazu Hayashizaki, Yoshihide Daub, Carsten O. Nucleic Acids Res Genomics Perturbation and time-course data sets, in combination with computational approaches, can be used to infer transcriptional regulatory networks which ultimately govern the developmental pathways and responses of cells. Here, we individually knocked down the four transcription factors PU.1, IRF8, MYB and SP1 in the human monocyte leukemia THP-1 cell line and profiled the genome-wide transcriptional response of individual transcription starting sites using deep sequencing based Cap Analysis of Gene Expression. From the proximal promoter regions of the responding transcription starting sites, we derived de novo binding-site motifs, characterized their biological function and constructed a network. We found a previously described composite motif for PU.1 and IRF8 that explains the overlapping set of transcriptional responses upon knockdown of either factor. Oxford University Press 2010-12 2010-08-19 /pmc/articles/PMC3001087/ /pubmed/20724440 http://dx.doi.org/10.1093/nar/gkq729 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Genomics Vitezic, Morana Lassmann, Timo Forrest, Alistair R. R. Suzuki, Masanori Tomaru, Yasuhiro Kawai, Jun Carninci, Piero Suzuki, Harukazu Hayashizaki, Yoshihide Daub, Carsten O. Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE |
title | Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE |
title_full | Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE |
title_fullStr | Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE |
title_full_unstemmed | Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE |
title_short | Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE |
title_sort | building promoter aware transcriptional regulatory networks using sirna perturbation and deepcage |
topic | Genomics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3001087/ https://www.ncbi.nlm.nih.gov/pubmed/20724440 http://dx.doi.org/10.1093/nar/gkq729 |
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