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Environmental gene regulatory influence networks in rice (Oryza sativa):response to water deficit, high temperature and agricultural environments

View ORCID ProfileOlivia Wilkins, Christoph Hafemeister, View ORCID ProfileAnne Plessis, Meisha-Marika Holloway-Phillips, View ORCID ProfileGina M. Pham, Adrienne B. Nicotra, Glenn B. Gregorio, S.V. Krishna Jagadish, View ORCID ProfileEndang M. Septiningsih, View ORCID ProfileRichard Bonneau, Michael Purugganan
doi: https://doi.org/10.1101/042317
Olivia Wilkins
1Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York, USA, 11225
2Present address:Department of Plant Science, McGill University, Montréal, Québec, Canada, H9X 3V9
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Christoph Hafemeister
1Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York, USA, 11225
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Anne Plessis
1Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York, USA, 11225
3Present address:School of Biological Sciences, Plymouth University, Drake Circus, Plymouth,UK
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Meisha-Marika Holloway-Phillips
4Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
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Gina M. Pham
1Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York, USA, 11225
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Adrienne B. Nicotra
4Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
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Glenn B. Gregorio
5International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
6Present address:East-West Seed Company, Sampaloc, San Rafael, Bulacan, Philippines
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S.V. Krishna Jagadish
5International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
7Present address:Department of Agronomy, 3706 Throckmorton Plant Sciences Center,Kansas State University, Manhattan, Kansas, 66506
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Endang M. Septiningsih
5International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
8Present address:Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, USA
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Richard Bonneau
1Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York, USA, 11225
9Simons Center for Data Analysis, Simons Foundation, New York, New York, USA
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Michael Purugganan
1Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York, USA, 11225
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ABSTRACT

Environmental Gene Regulatory Influence Networks (EGRINs) coordinate the timing and rate of gene expression in response to environmental and developmental signals. EGRINs encompass many layers of regulation, which culminate in changes in the level of accumulated transcripts. Here we infer EGRINs for the response of five tropical Asian rice cultivars to high temperatures, water deficit, and agricultural field conditions, by systematically integrating time series transcriptome data (720 RNA-seq libraries), patterns of nucleosome-free chromatin (18 ATAC-seq libraries), and the occurrence of known cis-regulatory elements. First, we identify 5,447 putative target genes for 445 transcription factors (TFs) by connecting TFs with genes with known cis-regulatory motifs in nucleosome-free chromatin regions proximal to transcriptional start sites (TSS) of genes. We then use network component analysis to estimate the regulatory activity for these TFs from the expression of these putative target genes. Finally, we inferred an EGRIN using the estimated TFA as the regulator. The EGRIN included regulatory interactions between 4,052 target genes regulated by 113 TFs. We resolved distinct regulatory roles for members of a large TF family, including a putative regulatory connection between abiotic stress and the circadian clock, as well as specific regulatory functions for TFs in the drought response. TFA estimation using network component analysis is an effective way of incorporating multiple genome-scale measurements into network inference and that supplementing data from controlled experimental conditions with data from outdoor field conditions increases the resolution for EGRIN inference.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted July 05, 2016.
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Environmental gene regulatory influence networks in rice (Oryza sativa):response to water deficit, high temperature and agricultural environments
Olivia Wilkins, Christoph Hafemeister, Anne Plessis, Meisha-Marika Holloway-Phillips, Gina M. Pham, Adrienne B. Nicotra, Glenn B. Gregorio, S.V. Krishna Jagadish, Endang M. Septiningsih, Richard Bonneau, Michael Purugganan
bioRxiv 042317; doi: https://doi.org/10.1101/042317
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Environmental gene regulatory influence networks in rice (Oryza sativa):response to water deficit, high temperature and agricultural environments
Olivia Wilkins, Christoph Hafemeister, Anne Plessis, Meisha-Marika Holloway-Phillips, Gina M. Pham, Adrienne B. Nicotra, Glenn B. Gregorio, S.V. Krishna Jagadish, Endang M. Septiningsih, Richard Bonneau, Michael Purugganan
bioRxiv 042317; doi: https://doi.org/10.1101/042317

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