Understanding the control of nuclear-gene-expression by the cytoplasmic genomes using maize isonuclear lines


Funding
This work is being funded through grant no. PN-II-RU-TE-2014-4-1767-41/2015, of the Romanian National Authority for Scientific Research, CNDI-UEFISCDI

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Summary

Nuclear genome is outnumbered by organellar genomes (plastid and mitochondria) by as much as 1 to 5,000. Retrograde signaling pathways (RSP) exist, which model nuclear gene expression (NGE) according to signals received from both organelles. Only mutants that are defective in the RSP have been used so far in trying to untangle how organelles control NGE. Therefore it still remains unclear what other molecular adjustments come into play in a non-mutant cell environment, which could change the paradigm we use to explain organelle-to-nucleus communication. To circumvent the problem of using the less informative mutants we propose the use of maize isonuclear lines, whose agronomic/morphologic traits were shown to be linked to the RSP. No other study has used the NGS technology (i.e., RNAseq) to sequence whole transcriptomes in order to assess NGE in isonuclear lines. In this context, we want to delve into the fundamental aspect of retrograde signaling pathways and couple the acquired knowledge to important agronomic traits in maize. We’ll also be the first to use bisulfite sequencing of nuclear genes in order to answer the question whether or not methylation plays a role in controlling NGE in a foreign cytoplasmic environment. In addition, we’ll sequence the organellar genomes (by means of NGS) of the isonuclear lines used above in order to explain changes in NGE; which could be the result of the existing polymorphism in these much smaller genomes.

Objectives


2015 - 2016

Objective 1. 
1.1. RNA/DNA extraction and library preparations for NGS. 
1.2. Transcriptome sequencing of maize isonuclear lines and sequencing of their plastid and mitochondrial genomes.
                    Status: Done

Objective 2. 
Bioinformatics analysis - identifying key players/molecular switches that respond to retrograde signalling.
                    Status: Done 
- intermediate results published: 


2017

Objective 3. 
Functional analysis of the genes identified as part of objective #2 

Objective 4. 
Sequencing and bisulfite sequencing of the genes of interest to gain new insights into the role of methylation in controlling NGE.