Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules
Comparative functional genomics studies the evolution of biological processes by analyzing functional data, such as gene expression profiles, across species. A major challenge is to compare profiles collected in a complex phylogeny. Here, we present Arboretum, a novel scalable computational algorith...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | en_US |
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Cold Spring Harbor Laboratory Press
2014
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| Online Access: | http://hdl.handle.net/1721.1/84953 https://orcid.org/0000-0001-8567-2049 |
| _version_ | 1811075799796678656 |
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| author | Kellis, Manolis Regev, Aviv Roy, Sushmita Wapinski, Ilan Pfiffner, Jenna French, Courtney Socha, Amanda Konieczka, Jay Habib, Naomi Thompson, Dawn |
| author2 | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory |
| author_facet | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Kellis, Manolis Regev, Aviv Roy, Sushmita Wapinski, Ilan Pfiffner, Jenna French, Courtney Socha, Amanda Konieczka, Jay Habib, Naomi Thompson, Dawn |
| author_sort | Kellis, Manolis |
| collection | MIT |
| description | Comparative functional genomics studies the evolution of biological processes by analyzing functional data, such as gene expression profiles, across species. A major challenge is to compare profiles collected in a complex phylogeny. Here, we present Arboretum, a novel scalable computational algorithm that integrates expression data from multiple species with species and gene phylogenies to infer modules of coexpressed genes in extant species and their evolutionary histories. We also develop new, generally applicable measures of conservation and divergence in gene regulatory modules to assess the impact of changes in gene content and expression on module evolution. We used Arboretum to study the evolution of the transcriptional response to heat shock in eight species of Ascomycota fungi and to reconstruct modules of the ancestral environmental stress response (ESR). We found substantial conservation in the stress response across species and in the reconstructed components of the ancestral ESR modules. The greatest divergence was in the most induced stress, primarily through module expansion. The divergence of the heat stress response exceeds that observed in the response to glucose depletion in the same species. Arboretum and its associated analyses provide a comprehensive framework to systematically study regulatory evolution of condition-specific responses. |
| first_indexed | 2024-09-23T10:12:04Z |
| format | Article |
| id | mit-1721.1/84953 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T10:12:04Z |
| publishDate | 2014 |
| publisher | Cold Spring Harbor Laboratory Press |
| record_format | dspace |
| spelling | mit-1721.1/849532022-09-30T19:33:36Z Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules Kellis, Manolis Regev, Aviv Roy, Sushmita Wapinski, Ilan Pfiffner, Jenna French, Courtney Socha, Amanda Konieczka, Jay Habib, Naomi Thompson, Dawn Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology. Department of Biology Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Kellis, Manolis Regev, Aviv Comparative functional genomics studies the evolution of biological processes by analyzing functional data, such as gene expression profiles, across species. A major challenge is to compare profiles collected in a complex phylogeny. Here, we present Arboretum, a novel scalable computational algorithm that integrates expression data from multiple species with species and gene phylogenies to infer modules of coexpressed genes in extant species and their evolutionary histories. We also develop new, generally applicable measures of conservation and divergence in gene regulatory modules to assess the impact of changes in gene content and expression on module evolution. We used Arboretum to study the evolution of the transcriptional response to heat shock in eight species of Ascomycota fungi and to reconstruct modules of the ancestral environmental stress response (ESR). We found substantial conservation in the stress response across species and in the reconstructed components of the ancestral ESR modules. The greatest divergence was in the most induced stress, primarily through module expansion. The divergence of the heat stress response exceeds that observed in the response to glucose depletion in the same species. Arboretum and its associated analyses provide a comprehensive framework to systematically study regulatory evolution of condition-specific responses. Howard Hughes Medical Institute Broad Institute of MIT and Harvard National Institutes of Health (U.S.) (Pioneer Award) National Institutes of Health (U.S.) (R01 2R01CA119176-01) Burroughs Wellcome Fund (Career Award at the Scientific Interface) Alfred P. Sloan Foundation 2014-02-14T16:59:33Z 2014-02-14T16:59:33Z 2013-05 2013-02 Article http://purl.org/eprint/type/JournalArticle 1088-9051 http://hdl.handle.net/1721.1/84953 Roy, S., I. Wapinski, J. Pfiffner, C. French, A. Socha, J. Konieczka, N. Habib, M. Kellis, D. Thompson, and A. Regev. “Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules.” Genome Research 23, no. 6 (June 1, 2013): 1039-1050. © 2013, Published by Cold Spring Harbor Laboratory Press https://orcid.org/0000-0001-8567-2049 en_US http://dx.doi.org/10.1101/gr.146233.112 Genome Research Creative Commons Attribution‐NonCommercial License http://creativecommons.org/licenses/by-nc/3.0/ application/pdf Cold Spring Harbor Laboratory Press Genome Research |
| spellingShingle | Kellis, Manolis Regev, Aviv Roy, Sushmita Wapinski, Ilan Pfiffner, Jenna French, Courtney Socha, Amanda Konieczka, Jay Habib, Naomi Thompson, Dawn Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules |
| title | Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules |
| title_full | Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules |
| title_fullStr | Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules |
| title_full_unstemmed | Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules |
| title_short | Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules |
| title_sort | arboretum reconstruction and analysis of the evolutionary history of condition specific transcriptional modules |
| url | http://hdl.handle.net/1721.1/84953 https://orcid.org/0000-0001-8567-2049 |
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