Sci-bioinformatics
Welcome to Stellenbosch University

Research

​Prof. Hugh Patterton

(+27 21 808 2774, hpatterton@sun.ac.za)

Bioinformatics of the epigenome

DNA is packaged into chromatin in eukaryotes to fit the enormous length of DNA (approximately 2m in humans) into a cell nucleus of about 10um diameter.  This is achieved by the repetitive packaging of the DNA into structures known as nucleosomes.  Although this achieves the packaging requirement, it introduces a significant problem in terms of access of the DNA molecule to proteins that are required interact with it to fulfil its genetic function.  The eukaryotic cell has evolved numerous mechanisms that take advantage of the repressive effect of chromatin to regulate DNA function.  This includes ATP-dependent chromatin remodellers, swapping in/out of histone isotypes into the nucleosome, chemical modification of specific residues in the N-terminal histone tails, and chemical modification of the DNA bases. Some of these modifications are trans-generationally heritable, and such modifications form part of the epigenome. The epigenome contains the signatures of many environmental factors, including nutrition, stress, etc.

Prof. Patterton’s research in bioinformatics is focused on the development of methods and coding of programs to investigate the role of the epigenome in the regulation of DNA function. This includes software for the analysis of physical clustering of co-regulated genes, the genome-wide distribution of nucleosomes and signals involved in precise positioning of nucleosomes at select genomic loci, and the distribution and function of specific epigenetic histone marks. 

Dr. Anandi Bierman

(anandie@sun.ac.za)

From junk to functional DNA: how transposable elements impact eukaryotic genomes

Transposable elements are repetitive DNA motifs that can move from one position to another in chromosomes. Originally discovered by Nobel laureate, Barbara McClintock in maize, these elements were thought of as "junk" DNA, with no specific function, for a long time. McClintock had the insight to suggest that these elements might serve a purpose in contributing to the dynamic and plastic nature of our genomes, helping organisms to cope with environmental change. Today, transposable elements are thought of as being both beneficial, as in the generation of novel mutations that drive evolution, but also detrimental, in their association with epigenetic control mechanisms that lead to cancer. Through bioinformatic tools, genomic features such as transposable elements can be studied on a scale previously unattainable, and further insight into their abundance and functions in the genomes of eukaryotic organisms can be attained.