Conserved non-coding regulatory signatures in Arabidopsis co-expressed gene modules.
Complex traits and other polygenic processes require coordinated gene expression. Co-expression networks model mRNA co-expression: the product of gene regulatory networks. To identify regulatory mechanisms underlying coordinated gene expression in a tissue-enriched context, ten Arabidopsis thaliana...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3443200?pdf=render |
| _version_ | 1798045537236156416 |
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| author | Jacob B Spangler Stephen P Ficklin Feng Luo Michael Freeling F Alex Feltus |
| author_facet | Jacob B Spangler Stephen P Ficklin Feng Luo Michael Freeling F Alex Feltus |
| author_sort | Jacob B Spangler |
| collection | DOAJ |
| description | Complex traits and other polygenic processes require coordinated gene expression. Co-expression networks model mRNA co-expression: the product of gene regulatory networks. To identify regulatory mechanisms underlying coordinated gene expression in a tissue-enriched context, ten Arabidopsis thaliana co-expression networks were constructed after manually sorting 4,566 RNA profiling datasets into aerial, flower, leaf, root, rosette, seedling, seed, shoot, whole plant, and global (all samples combined) groups. Collectively, the ten networks contained 30% of the measurable genes of Arabidopsis and were circumscribed into 5,491 modules. Modules were scrutinized for cis regulatory mechanisms putatively encoded in conserved non-coding sequences (CNSs) previously identified as remnants of a whole genome duplication event. We determined the non-random association of 1,361 unique CNSs to 1,904 co-expression network gene modules. Furthermore, the CNS elements were placed in the context of known gene regulatory networks (GRNs) by connecting 250 CNS motifs with known GRN cis elements. Our results provide support for a regulatory role of some CNS elements and suggest the functional consequences of CNS activation of co-expression in specific gene sets dispersed throughout the genome. |
| first_indexed | 2024-04-11T23:22:35Z |
| format | Article |
| id | doaj.art-cbf831013cb44e6b89d19e8757b96233 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-11T23:22:35Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-cbf831013cb44e6b89d19e8757b962332022-12-22T03:57:25ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-0179e4504110.1371/journal.pone.0045041Conserved non-coding regulatory signatures in Arabidopsis co-expressed gene modules.Jacob B SpanglerStephen P FicklinFeng LuoMichael FreelingF Alex FeltusComplex traits and other polygenic processes require coordinated gene expression. Co-expression networks model mRNA co-expression: the product of gene regulatory networks. To identify regulatory mechanisms underlying coordinated gene expression in a tissue-enriched context, ten Arabidopsis thaliana co-expression networks were constructed after manually sorting 4,566 RNA profiling datasets into aerial, flower, leaf, root, rosette, seedling, seed, shoot, whole plant, and global (all samples combined) groups. Collectively, the ten networks contained 30% of the measurable genes of Arabidopsis and were circumscribed into 5,491 modules. Modules were scrutinized for cis regulatory mechanisms putatively encoded in conserved non-coding sequences (CNSs) previously identified as remnants of a whole genome duplication event. We determined the non-random association of 1,361 unique CNSs to 1,904 co-expression network gene modules. Furthermore, the CNS elements were placed in the context of known gene regulatory networks (GRNs) by connecting 250 CNS motifs with known GRN cis elements. Our results provide support for a regulatory role of some CNS elements and suggest the functional consequences of CNS activation of co-expression in specific gene sets dispersed throughout the genome.http://europepmc.org/articles/PMC3443200?pdf=render |
| spellingShingle | Jacob B Spangler Stephen P Ficklin Feng Luo Michael Freeling F Alex Feltus Conserved non-coding regulatory signatures in Arabidopsis co-expressed gene modules. PLoS ONE |
| title | Conserved non-coding regulatory signatures in Arabidopsis co-expressed gene modules. |
| title_full | Conserved non-coding regulatory signatures in Arabidopsis co-expressed gene modules. |
| title_fullStr | Conserved non-coding regulatory signatures in Arabidopsis co-expressed gene modules. |
| title_full_unstemmed | Conserved non-coding regulatory signatures in Arabidopsis co-expressed gene modules. |
| title_short | Conserved non-coding regulatory signatures in Arabidopsis co-expressed gene modules. |
| title_sort | conserved non coding regulatory signatures in arabidopsis co expressed gene modules |
| url | http://europepmc.org/articles/PMC3443200?pdf=render |
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