Cis-Regulatory Code for Predicting Plant Cell-Type Transcriptional Response to High Salinity

Uygun, Sahra; Azodi, Christina B.; Shiu, Shin-Han

doi:10.1104/pp.19.00653

Title: Cis-Regulatory Code for Predicting Plant Cell-Type Transcriptional Response to High Salinity

Full Record
Other Related Research

Authors:

^[1];

^[2];

^[3]

Genetics Program, Michigan State University, East Lansing, Michigan 48824
Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
Genetics Program, Michigan State University, East Lansing, Michigan 48824, Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, Department of Computational, Mathematics, Science, and Engineering, Michigan State University, East Lansing, Michigan 48824

Publication Date:: 2019-09-24

Sponsoring Org.:: USDOE

OSTI Identifier:: 1566208

Grant/Contract Number:: SC0018409

Resource Type:: Published Article

Journal Name:: Plant Physiology (Bethesda)

Additional Journal Information:: Journal Name: Plant Physiology (Bethesda) Journal Volume: 181 Journal Issue: 4; Journal ID: ISSN 0032-0889

Publisher:: Oxford University Press

Country of Publication:: United States

Language:: English

Citation Formats


                    Uygun, Sahra, Azodi, Christina B., and Shiu, Shin-Han. Cis-Regulatory Code for Predicting Plant Cell-Type Transcriptional Response to High Salinity.  United States: N. p., 2019. 
Web.  doi:10.1104/pp.19.00653.

Copy to clipboard


                    Uygun, Sahra, Azodi, Christina B., & Shiu, Shin-Han. Cis-Regulatory Code for Predicting Plant Cell-Type Transcriptional Response to High Salinity.  United States.  https://doi.org/10.1104/pp.19.00653

Copy to clipboard


                    Uygun, Sahra, Azodi, Christina B., and Shiu, Shin-Han. Tue .  
"Cis-Regulatory Code for Predicting Plant Cell-Type Transcriptional Response to High Salinity".  United States.  https://doi.org/10.1104/pp.19.00653.

Copy to clipboard


                    
@article{osti_1566208,

  title        = {Cis-Regulatory Code for Predicting Plant Cell-Type Transcriptional Response to High Salinity},

  author       = {Uygun, Sahra and Azodi, Christina B. and Shiu, Shin-Han},

  abstractNote = {},

  doi          = {10.1104/pp.19.00653},

  journal      = {Plant Physiology (Bethesda)},

  number       = 4,

  volume       = 181,

  place        = {United States},

  year         = {2019},

  month        = {9}

}

Copy to clipboard

Journal Article:

Free Publicly Available Full Text

Publisher's Version of Record
https://doi.org/10.1104/pp.19.00653

Other availability

Search WorldCat to find libraries that may hold this journal

Citation Metrics:

Cited by: 3 works

Citation information provided by
Web of Science

Save / Share:

Export Metadata

Save to My Library

Similar Records in DOE PAGES and OSTI.GOV collections:

Cis-Regulatory Code for Predicting Plant Cell-Type Transcriptional Response to High Salinity

Journal Article Uygun, Sahra ; Azodi, Christina B. ; Shiu, Shin-Han - Plant Physiology (Bethesda)

Not provided.
https://doi.org/10.1104/pp.19.00653
The cis-regulatory codes of response to combined heat and drought stress in Arabidopsis thaliana

Journal Article Azodi, Christina B. ; Lloyd, John P. ; Shiu, Shin-Han - NAR Genomics and Bioinformatics

Abstract Plants respond to their environment by dynamically modulating gene expression. A powerful approach for understanding how these responses are regulated is to integrate information about cis-regulatory elements (CREs) into models called cis-regulatory codes. Transcriptional response to combined stress is typically not the sum of the responses to the individual stresses. However, cis-regulatory codes underlying combined stress response have not been established. Here we modeled transcriptional response to single and combined heat and drought stress in Arabidopsis thaliana. We grouped genes by their pattern of response (independent, antagonistic and synergistic) and trained machine learning models to predict their response usingmore »« less
https://doi.org/10.1093/nargab/lqaa049
Putative cis-Regulatory Elements Predict Iron Deficiency Responses in Arabidopsis Roots

Journal Article Schwarz, Birte ; Azodi, Christina B. ; Shiu, Shin-Han ; ... - Plant Physiology (Bethesda)
Cited by 2
https://doi.org/10.1104/pp.19.00760
Putative cis-Regulatory Elements Predict Iron Deficiency Responses in Arabidopsis Roots

Journal Article Schwarz, Birte ; Azodi, Christina B. ; Shiu, Shin-Han ; ... - Plant Physiology (Bethesda)

Not provided.
https://doi.org/10.1104/pp.19.00760
A cis-regulatory module activating transcription in the suspensor contains five cis-regulatory elements

Journal Article Henry, Kelli F. ; Kawashima, Tomokazu ; Goldberg, Robert B. - Plant Molecular Biology

Little is known about the molecular mechanisms by which the embryo proper and suspensor of plant embryos activate specific gene sets shortly after fertilization. We analyzed the upstream region of the Scarlet Runner Bean (Phaseolus coccineus) G564 gene in order to understand how genes are activated specifically in the suspensor during early embryo development. Previously, we showed that a 54-bp fragment of the G564 upstream region is sufficient for suspensor transcription and contains at least three required cis-regulatory sequences, including the 10-bp motif (5'-GAAAAGCGAA-3'), the 10 bp-like motif (5'-GAAAAACGAA-3'), and Region 2 motif (partial sequence 5'-TTGGT-3'). Here, we use site-directedmore »« less
Cited by 1
https://doi.org/10.1007/s11103-015-0308-z

Full Text Available

Similar Records