Navigating the transcriptional roadmap regulating plant secondary cell wall deposition
The current status of lignocellulosic biomass as an invaluable resource in industry, agriculture and health has spurred increased interest in understanding the transcriptional regulation of secondary cell wall (SCW) biosynthesis. The last decade of research has revealed an extensive network of NAC,...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2013-08-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2013.00325/full |
| _version_ | 1818695308811436032 |
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| author | Steven Grant Hussey Eshchar eMizrachi Nicky M. Creux Alexander A. Myburg |
| author_facet | Steven Grant Hussey Eshchar eMizrachi Nicky M. Creux Alexander A. Myburg |
| author_sort | Steven Grant Hussey |
| collection | DOAJ |
| description | The current status of lignocellulosic biomass as an invaluable resource in industry, agriculture and health has spurred increased interest in understanding the transcriptional regulation of secondary cell wall (SCW) biosynthesis. The last decade of research has revealed an extensive network of NAC, MYB and other families of transcription factors regulating Arabidopsis SCW biosynthesis, and numerous studies have explored SCW-related transcription factors in other dicots and monocots. Whilst the general structure of the Arabidopsis network has been a topic of several reviews, they have not comprehensively represented the detailed protein-DNA and protein-protein interactions described in the literature, and an understanding of network dynamics and functionality has not yet been achieved for SCW formation. Furthermore the methodologies employed in studies of SCW transcriptional regulation have not received much attention, especially in the case of non-model organisms. In this review, we have reconstructed the most exhaustive literature-based network representations to date of SCW transcriptional regulation in Arabidopsis. We include a manipulable Cytoscape representation of the Arabidopsis SCW transcriptional network to aid in future studies, along with a list of supporting literature for each documented interaction. Amongst other topics, we discuss the various components of the network, its evolutionary conservation in plants, putative modules and dynamic mechanisms that may influence network function, and the approaches that have been employed in network inference. Future research should aim to better understand network function and its response to dynamic perturbations, whilst the development and application of genome-wide approaches such as ChIP-seq and systems genetics are in progress for the study of SCW transcriptional regulation in non-model organisms. |
| first_indexed | 2024-12-17T13:43:25Z |
| format | Article |
| id | doaj.art-1f27f7cc65744edb8fa9efcf0a8a0863 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-17T13:43:25Z |
| publishDate | 2013-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-1f27f7cc65744edb8fa9efcf0a8a08632022-12-21T21:46:13ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2013-08-01410.3389/fpls.2013.0032556749Navigating the transcriptional roadmap regulating plant secondary cell wall depositionSteven Grant Hussey0Eshchar eMizrachi1Nicky M. Creux2Alexander A. Myburg3University of PretoriaUniversity of PretoriaUniversity of PretoriaUniversity of PretoriaThe current status of lignocellulosic biomass as an invaluable resource in industry, agriculture and health has spurred increased interest in understanding the transcriptional regulation of secondary cell wall (SCW) biosynthesis. The last decade of research has revealed an extensive network of NAC, MYB and other families of transcription factors regulating Arabidopsis SCW biosynthesis, and numerous studies have explored SCW-related transcription factors in other dicots and monocots. Whilst the general structure of the Arabidopsis network has been a topic of several reviews, they have not comprehensively represented the detailed protein-DNA and protein-protein interactions described in the literature, and an understanding of network dynamics and functionality has not yet been achieved for SCW formation. Furthermore the methodologies employed in studies of SCW transcriptional regulation have not received much attention, especially in the case of non-model organisms. In this review, we have reconstructed the most exhaustive literature-based network representations to date of SCW transcriptional regulation in Arabidopsis. We include a manipulable Cytoscape representation of the Arabidopsis SCW transcriptional network to aid in future studies, along with a list of supporting literature for each documented interaction. Amongst other topics, we discuss the various components of the network, its evolutionary conservation in plants, putative modules and dynamic mechanisms that may influence network function, and the approaches that have been employed in network inference. Future research should aim to better understand network function and its response to dynamic perturbations, whilst the development and application of genome-wide approaches such as ChIP-seq and systems genetics are in progress for the study of SCW transcriptional regulation in non-model organisms.http://journal.frontiersin.org/Journal/10.3389/fpls.2013.00325/fullArabidopsistranscription factorwood formationsecondary cell walltranscriptional network |
| spellingShingle | Steven Grant Hussey Eshchar eMizrachi Nicky M. Creux Alexander A. Myburg Navigating the transcriptional roadmap regulating plant secondary cell wall deposition Frontiers in Plant Science Arabidopsis transcription factor wood formation secondary cell wall transcriptional network |
| title | Navigating the transcriptional roadmap regulating plant secondary cell wall deposition |
| title_full | Navigating the transcriptional roadmap regulating plant secondary cell wall deposition |
| title_fullStr | Navigating the transcriptional roadmap regulating plant secondary cell wall deposition |
| title_full_unstemmed | Navigating the transcriptional roadmap regulating plant secondary cell wall deposition |
| title_short | Navigating the transcriptional roadmap regulating plant secondary cell wall deposition |
| title_sort | navigating the transcriptional roadmap regulating plant secondary cell wall deposition |
| topic | Arabidopsis transcription factor wood formation secondary cell wall transcriptional network |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2013.00325/full |
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