Award Abstract # 1051654
Collaborative Research: The Epigenetic Regulatory Role of the Maize Ufo1 Gene

NSF Org: MCB
Division of Molecular and Cellular Biosciences
Recipient: THE PENNSYLVANIA STATE UNIVERSITY
Initial Amendment Date: March 23, 2011
Latest Amendment Date: November 20, 2018
Award Number: 1051654
Award Instrument: Standard Grant
Program Manager: Karen Cone
kccone@nsf.gov
 (703)292-4967
MCB
 Division of Molecular and Cellular Biosciences
BIO
 Directorate for Biological Sciences
Start Date: July 1, 2011
End Date: December 31, 2019 (Estimated)
Total Intended Award Amount: $595,908.00
Total Awarded Amount to Date: $736,919.00
Funds Obligated to Date: FY 2011 = $595,908.00
FY 2012 = $6,000.00

FY 2013 = $18,000.00

FY 2015 = $117,011.00
History of Investigator:
  • Surinder Chopra (Principal Investigator)
Recipient Sponsored Research Office: Pennsylvania State Univ University Park
201 OLD MAIN
UNIVERSITY PARK
PA  US  16802-1503
(814)865-1372
Sponsor Congressional District: 15
Primary Place of Performance: Pennsylvania State Univ University Park
201 OLD MAIN
UNIVERSITY PARK
PA  US  16802-1503
Primary Place of Performance
Congressional District:
15
Unique Entity Identifier (UEI): NPM2J7MSCF61
Parent UEI:
NSF Program(s): Genetic Mechanisms,
Plant Genome Research Project
Primary Program Source: 01001112DB NSF RESEARCH & RELATED ACTIVIT
01001213DB NSF RESEARCH & RELATED ACTIVIT

01001314DB NSF RESEARCH & RELATED ACTIVIT

01001516DB NSF RESEARCH & RELATED ACTIVIT
Program Reference Code(s): 1112, 1329, 7465, 7577, 9109, 9178, 9179, 9183, 9251, BIOT
Program Element Code(s): 111200, 132900
Award Agency Code: 4900
Fund Agency Code: 4900
Assistance Listing Number(s): 47.074

ABSTRACT

Intellectual Merit: One of the mechanisms that allow diversification of form and function is epigenetic regulation. Epigenetic changes are alterations in the DNA or protein components of chromatin that affect gene expression. Epigenetic modifications that are of transient nature are widespread in the plant kingdom, but are rarely isolated or identified because the associated phenotypes are not easy to see and the modifications are not stable from generation to generation. Using the pericarp color1 (p1) gene and its red pigmentation as a marker in maize, allelic variation at the p1 locus has been shown to be a function of gene structure and organization, which is further regulated by epigenetic mechanisms. To understand the basis of allelic diversity modulated through epigenetic regulation of gene expression, molecular and genetic characterization of a dominant mutation called Ufo1 (Unstable factor for orange1) has been performed. Plants with a particular p1 allele, called P1-wr, produce ears with colorless kernel pericarps and red cob glumes, and this silent pericarp phenotype is stable; however, in the presence of Ufo1 the P1-wr allele confers variably enhanced pigmentation phenotypes in several tissues. Expression studies demonstrated that the gain of pigmentation is associated with increased steady state levels of P1 transcript. Enhanced P1 expression in P1-wr;Ufo1 plants was shown to correlate with a decrease in DNA methylation at the promoter and coding sequence of the P1-wr allele. In the current project, map based cloning of ufo1 gene will be carried out. New alleles of ufo1 will be generated using transposon mutagenesis. Evidence for Ufo1-mediated effects on epigenetic regulation will be analyzed using high throughput sequencing methods for global profiling of chromatin, transcript (mRNA and small RNA), and DNA methylation of Ufo1 mutant and wild type plants. A database will be developed to visualize and analyze data generated from ChIP-seq, RNA-seq and bisulfite sequencing. The results will establish the role of the Ufo1 mutation (and wild type ufo1 gene) in effecting global changes in transposons, DNA methylation, histone modifications and RNA profiles. Because Ufo1 does not appear to act in the same way as other known epigenetic regulators in maize, this project will expand understanding of how overlapping epigenetic pathways regulate gene expression in this important crop plant.

Broader Impacts: This project will provide training opportunities in plant epigenetics and study of allelic variation of plant genes. The collaboration between Pennsylvania State University and the University Delaware will enhance professional interactions in the area of plant biology and bioinformatics. Specifically, two postdoctoral fellows and two graduate students will be cross-trained in computational biological aspects and epigenetic gene regulation. Undergraduate students, including women and minority students, will learn classical and cutting-edge plant biology techniques that are used understand and dissect the molecular basis of regulation of tissue-specific gene expression. In addition, high school students and teachers will participate in a summer biotechnology workshop to learn gene expression techniques in maize.

This project is co-funded by the Genetic Mechanisms Program in the Division of Molecular and Cellular Biosciences and by the Plant Genome Research Program in the Division of Integrative Organismal Systems.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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Chatterjee, Debamalya and Zhang, Ziru and Lin, Pei-Yu and Wang, Po-Hao and Sidhu, Gurpreet K and Yennawar, Neela H and Hsieh, Jo-Wei Allison and Chen, Pao-Yang and Song, Rentao and Meyers, Blake C and Chopra, Surinder "Maize unstable factor for orange1 encodes a nuclear protein that affects redox accumulation during kernel development" The Plant Cell , 2024 https://doi.org/10.1093/plcell/koae301 Citation Details
Kameron Wittmeyer, Jin Cui, Debamalya Chatterjee, Tzuu-fen Lee, Qixian Tan, Weiya Xue, Yinping Jiao, Po-Hao Wang, Iffa Gaffoor, Doreen Ware, Blake C. Meyers, Surinder Chopra "The Dominant and Poorly Penetrant Phenotypes of Maize Unstable factor for orange1 Are Caused by DNA MethylationChanges at a Linked Transposon" The Plant Cell , v.30 , 2018 , p.3006 www.plantcell.org/cgi/doi/10.1105/tpc.18.00546
Po-Hao Wang, Kameron Wittmeyer, Tzuu-fen Lee, Blake Meyers & Surinder Chopra. "Overlapping RdDM and non-RdDM mechanisms work together to maintain somatic repression of a paramutagenic epiallele of maize pericarp color1" PloS One , 2017
Robbins, M., Roy, A., Wang, P., Gaffoor, I., Sekhon, R., Buanafina, M., Rohila,J., and Chopra, S. "Comparative Proteomics Analysis by DIGE and iTRAQ Provides Insight into the Regulation of Phenylpropanoids in Maize. J of Proteomics." J of Proteomics , 2013 doi: 10.1016/j.jprot.2013.06.018.
Sekhon R, Sidorenko L, Chandler V, Chopra S. "Maize unstable factor for orange1 is required for maintaining silencing associated with paramutation at the pericarp color1 and booster1 loci." PLOS GENETICS, 8 (10): , v.8 , 2012 , p.e1002980

PROJECT OUTCOMES REPORT

Disclaimer

This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.

Ufo1 gene in corn produce variable patterns of pigment.

A single gene can produce different outcomes depending on when, where, and at what levels it is turned on. A classical example of this is the red pigment found in corn kernels. A single gene controls the production of this pigment when it is turned on. Many different patterns of pigment have been reported, such as red kernels and white cobs, red cobs and white kernels, and red cobs and red striped kernels. All of these patterns are produced by changing when and where the single pigment gene is turned on and off. We are interested in understanding how a single gene can produce such a wide variety of patterns. We studied another gene with a mutation that turns on the pigment gene all of the time. The mutant gene, called Unstable factor for orange1 (Ufo1), also produces a variety of patterns, hence the inclusion of ?Unstable? in its name. We identified the DNA sequence of the Ufo1 gene, which had been unknown for more than 50 years. In addition, we found that a transposon had moved into the Ufo1 gene. Transposons are pieces of DNA that copy themselves and move around the genome by jumping into and out of genes. The transposon is responsible for causing Ufo1 and the resulting pigments to be turned on all of the time. Finally, we found that the Ufo1 gene could be turned off or on by modifications to the transposon DNA that occur sporadically. We now understand that Ufo1 can be turned on or off at different stages of growth or in different tissues, explaining why it produces variable patterns of pigment. We are still interested in understanding how Ufo1 interacts with the pigment gene to turn on the production of pigments. In our study, we also found that Ufo1 turns on or off many other genes involved in responses to stress, so we are interested in identifying the underlying function of Ufo1.

 


Last Modified: 03/28/2020
Modified by: Surinder Chopra

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