Identification of target genes regulated by transcription factor SSH1 in sugarcane, using ChIP-Seq assay

• Grant number: 12/20486-2
• Support Opportunities: Scholarships abroad - Research Internship - Post-doctor
• Start date: February 11, 2013
• End date: January 10, 2014
• Field of knowledge: Agronomical Sciences - Agronomy - Crop Science
• Principal Investigator: Paulo Mazzafera
• Grantee: Michael dos Santos Brito
• Supervisor: Erich Grotewold
• Host Institution: Instituto de Biologia (IB). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
• Institution abroad: Ohio State University, Columbus, United States
• Associated to the scholarship: 10/11476-8 - IDENTIFICATION AND VALIDATION OF TRANSCRIPTION FACTORS INVOLVED WITH LIGNIN BIOSYNTHESIS IN SUGAR CANE, BP.PD

Abstract

The search for renewable fuels has become an increasing challenge. In this scenario, the construction of transgenic plants have been a major alternative in the attempt to reduce the amount and/or to change structure of lignin for obtaining ethanol from cellulosic origin. One of the main targets to construct these transgenic plants have been the Transcription Factors (TFs). In the last years, many TFs had been characterized as regulators of lignin biosynthesis in different organisms. An interesting feature shared between these TFs is that some of them seem to have different target-genes and even different mechanisms of interactions in a species-specific manner. Among these TFs, AtSHN2 has been characterized in Arabidopsis and rice, as an inhibitor of lignin biosynthesis and an activator of the cellulose biosynthesis, being considered as an important target for manipulation. Until now, nothing was known about these TFs and their roles during the regulation process of lignin biosynthesis in sugarcane. The work associated with this proposal was the first to draw a sketch containing some TFs and their expression profiles in two contrasting sugarcane genotypes for lignin content. Among these TFs analyzed, one of them is the homolog of AtSHN2 gene. In an initial search, it was not possible to identify the presence of the homologous of AtSHN2 in SUCEST database. Nevertheless, we found the homologous AtSHN2 gene in our RNA-Seq database. In sugarcane this gene was called ShSHN1. qPCR analysis showed a differential expression of the ShSHN1 gene in that genotype with more lignin, as well as showed by the most of TFs here analyzed, indicating that the whole machinery (repressors and inducers) should operate proportionally in order to ensure a perfect operation of this pathway. Identify the targets of regulation of these TFs is extremely important, aiming points and mapping which routes could be altered by manipulating a given TF. Thus, it would be extremely important to check, in sugarcane, which targets-genes were regulated by ShSHN1. Among the approaches applied for this purpose, chromatin immunoprecipitation coupled with large-scale sequencing (ChIP-SEQ) has been the most used. Thus, this study aims to identify the potential targets of regulation of the ShSHN1 using ChIP-SEQ. (AU)

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

BURDO, BRETT; GRAY, JOHN; GOETTING-MINESKY, MARY P.; WITTLER, BETTINA; HUNT, MATTHEW; LI, TAI; VELLIQUETTE, DAVID; THOMAS, JULIE; GENTZEL, IRENE; BRITO, MICHAEL DOS SANTOS; et al. The Maize TFome - development of a transcription factor open reading frame collection for functional genomics. Plant Journal, v. 80, n. 2, p. 356-366, OCT 2014. (12/20486-2)