The role of genomic imprinting in Arabidopsis thaliana.
Fertilization in plants generates the seed, that consists of three genetically distinct components: I) the diploid embryo with one genome copy from each of the parents, II) the triploid endosperm with two maternal and one paternal copy, and III) a seed-coat having the same genotype as the diploid mother-plant. The importance of balanced parental gene expression for development of offspring has been demonstrated in both mammals and flowering plants. In plants, the endosperm - a structure with functions similar to the mammalian placenta, is the main site for genomic imprinting. Imprinting is an epigenetic phenomenon, where parent-of-origin dependent gene expression takes place due to epigenetic regulatory marks already established in the male and female germline.
Imprinting has evolved in mammals and plants independently. Over the past few years, many imprinted genes have been identified in plants, but surprisingly mutations of these genes often do not have a mutant phenotype. The biological role of imprinted genes is therefore not known and it is also not known why imprinting has evolved.
The master student will be involved in two different projects that aim to understand function and biological role of genomic imprinting. The first and main project involves a mutant, capulet2, that has been identified as a potential imprinted gene mutant with a phenotype caused by a single nucleotide polymorphism (SNP). Its current identity is unknown, but several candidate SNPs, and their corresponding genes, have been identified. The focus will be on the identification and characterization of these candidate SNPs and verification that they are responsible for the capulet2 phenotype. The second project aims to understand the function of the different domains/regions of the plant endosperm and what role imprinting play in different domains. Using FACS assisted nuclear sorting, domain specific nuclei have been captured and used for RNA sequencing. Currently, we are using bioinformatics to identify genes that are imprinted in a domain specific manner.
During the thesis, the student will be supervised and trained in basic molecular techniques, including PCR and realtime PCR, molecular cloning and generation of transgenic plants, bioinformatics and statistical analyses, confocal and light microscopy as well as CRISPR and FACS nuclear sorting. Furthermore, regular lab meetings, presentations and conference participation will be utilized to train scientific skills, such as presenting, writing and project planning.
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