Spatial expression of transcription factors in Drosophila embryonic organ development
Background: Site-specific transcription factors (TFs) bind DNA regulatory elements to control expression of target genes, forming the core of gene regulatory networks. Despite decades of research, most studies focus on only a small number of TFs and the roles of many remain unknown. Results: We p...
| Main Authors: | , , , , , , , , , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Language: | English |
| Published: |
BioMed Central Ltd
2014
|
| Online Access: | http://hdl.handle.net/1721.1/85995 |
| _version_ | 1826217820638150656 |
|---|---|
| author | Hammonds, Ann S. Fisher, William W. Weiszmann, Richard Wu, Siqi Hartenstein, Volker Kellis, Manolis Yu, Bin Frise, Erwin Celniker, Susan E. Bristow, Christopher A. |
| author2 | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory |
| author_facet | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Hammonds, Ann S. Fisher, William W. Weiszmann, Richard Wu, Siqi Hartenstein, Volker Kellis, Manolis Yu, Bin Frise, Erwin Celniker, Susan E. Bristow, Christopher A. |
| author_sort | Hammonds, Ann S. |
| collection | MIT |
| description | Background:
Site-specific transcription factors (TFs) bind DNA regulatory elements to control expression of target genes, forming the core of gene regulatory networks. Despite decades of research, most studies focus on only a small number of TFs and the roles of many remain unknown.
Results:
We present a systematic characterization of spatiotemporal gene expression patterns for all known or predicted Drosophila TFs throughout embryogenesis, the first such comprehensive study for any metazoan animal. We generated RNA expression patterns for all 708 TFs by in situ hybridization, annotated the patterns using an anatomical controlled vocabulary, and analyzed TF expression in the context of organ system development. Nearly all TFs are expressed during embryogenesis and more than half are specifically expressed in the central nervous system. Compared to other genes, TFs are enriched early in the development of most organ systems, and throughout the development of the nervous system. Of the 535 TFs with spatially restricted expression, 79% are dynamically expressed in multiple organ systems while 21% show single-organ specificity. Of those expressed in multiple organ systems, 77 TFs are restricted to a single organ system either early or late in development. Expression patterns for 354 TFs are characterized for the first time in this study.
Conclusions:
We produced a reference TF dataset for the investigation of gene regulatory networks in embryogenesis, and gained insight into the expression dynamics of the full complement of TFs controlling the development of each organ system. |
| first_indexed | 2024-09-23T17:09:23Z |
| format | Article |
| id | mit-1721.1/85995 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T17:09:23Z |
| publishDate | 2014 |
| publisher | BioMed Central Ltd |
| record_format | dspace |
| spelling | mit-1721.1/859952022-09-30T00:03:57Z Spatial expression of transcription factors in Drosophila embryonic organ development Hammonds, Ann S. Fisher, William W. Weiszmann, Richard Wu, Siqi Hartenstein, Volker Kellis, Manolis Yu, Bin Frise, Erwin Celniker, Susan E. Bristow, Christopher A. Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Bristow, Christopher A. Kellis, Manolis Background: Site-specific transcription factors (TFs) bind DNA regulatory elements to control expression of target genes, forming the core of gene regulatory networks. Despite decades of research, most studies focus on only a small number of TFs and the roles of many remain unknown. Results: We present a systematic characterization of spatiotemporal gene expression patterns for all known or predicted Drosophila TFs throughout embryogenesis, the first such comprehensive study for any metazoan animal. We generated RNA expression patterns for all 708 TFs by in situ hybridization, annotated the patterns using an anatomical controlled vocabulary, and analyzed TF expression in the context of organ system development. Nearly all TFs are expressed during embryogenesis and more than half are specifically expressed in the central nervous system. Compared to other genes, TFs are enriched early in the development of most organ systems, and throughout the development of the nervous system. Of the 535 TFs with spatially restricted expression, 79% are dynamically expressed in multiple organ systems while 21% show single-organ specificity. Of those expressed in multiple organ systems, 77 TFs are restricted to a single organ system either early or late in development. Expression patterns for 354 TFs are characterized for the first time in this study. Conclusions: We produced a reference TF dataset for the investigation of gene regulatory networks in embryogenesis, and gained insight into the expression dynamics of the full complement of TFs controlling the development of each organ system. National Institutes of Health (U.S.). Ruth L. Kirschstein National Research Service Award 2014-04-03T16:41:59Z 2014-04-03T16:41:59Z 2013-12 2013-09 2014-04-02T14:58:27Z Article http://purl.org/eprint/type/JournalArticle 1465-6906 1474-7596 http://hdl.handle.net/1721.1/85995 Hammonds, Ann S et al. “Spatial Expression of Transcription Factors in Drosophila Embryonic Organ Development.” Genome Biology 14.12 (2013): R140. en http://dx.doi.org/10.1186/gb-2013-14-12-r140 Genome Biology Creative Commons Attribution http://creativecommons.org/licenses/by/2.0 Ann S Hammonds et al.; licensee BioMed Central Ltd. application/pdf BioMed Central Ltd BioMed Central Ltd |
| spellingShingle | Hammonds, Ann S. Fisher, William W. Weiszmann, Richard Wu, Siqi Hartenstein, Volker Kellis, Manolis Yu, Bin Frise, Erwin Celniker, Susan E. Bristow, Christopher A. Spatial expression of transcription factors in Drosophila embryonic organ development |
| title | Spatial expression of transcription factors in Drosophila embryonic organ development |
| title_full | Spatial expression of transcription factors in Drosophila embryonic organ development |
| title_fullStr | Spatial expression of transcription factors in Drosophila embryonic organ development |
| title_full_unstemmed | Spatial expression of transcription factors in Drosophila embryonic organ development |
| title_short | Spatial expression of transcription factors in Drosophila embryonic organ development |
| title_sort | spatial expression of transcription factors in drosophila embryonic organ development |
| url | http://hdl.handle.net/1721.1/85995 |
| work_keys_str_mv | AT hammondsanns spatialexpressionoftranscriptionfactorsindrosophilaembryonicorgandevelopment AT fisherwilliamw spatialexpressionoftranscriptionfactorsindrosophilaembryonicorgandevelopment AT weiszmannrichard spatialexpressionoftranscriptionfactorsindrosophilaembryonicorgandevelopment AT wusiqi spatialexpressionoftranscriptionfactorsindrosophilaembryonicorgandevelopment AT hartensteinvolker spatialexpressionoftranscriptionfactorsindrosophilaembryonicorgandevelopment AT kellismanolis spatialexpressionoftranscriptionfactorsindrosophilaembryonicorgandevelopment AT yubin spatialexpressionoftranscriptionfactorsindrosophilaembryonicorgandevelopment AT friseerwin spatialexpressionoftranscriptionfactorsindrosophilaembryonicorgandevelopment AT celnikersusane spatialexpressionoftranscriptionfactorsindrosophilaembryonicorgandevelopment AT bristowchristophera spatialexpressionoftranscriptionfactorsindrosophilaembryonicorgandevelopment |