Publications

Evolutionary Analysis of Regulatory Sequences (EARS) in Plants, Emma Picot, Peter Krusche, Alexander Tiskin, Isabelle Carré, Sascha Ott, The Plant Journal, 64: 165-176, 2010.

Evolutionarily conserved regulatory motifs in the promoter of the Arabidopsis clock gene LATE ELONGATED HYPOCOTYL, Mark Spensley, Jae-Yean Kim, Emma Picot, Sascha Ott, John Reid, Chris Helliwell, Isabelle A. Carré, Plant Cell, 21: 2606-2623, 2009.

External Conferences Attended

UK Clock Club (Edinburgh 2008)

Plant Genomes: Genes Networks & Applications (Cold Spring Harbor 2009)

Understanding promoter architecture is necessary to form a complete understanding of gene regulation. It is known that there are regions of non-coding DNA containing transcription factor binding sites that act together in order to regulate the transcription of genes, these regions are termed “Regulatory Modules” (ReMos). Currently to discover which areas have a regulatory role costly and time consuming experiments must be performed. We present a refinement to an existing vertebrate tool used to identify ReMos that can be successfully employed to identify key regulatory regions in Arabidopsis.

View poster presented here

UK Clock Club (Oxford 2009)

UK Clock Club (UCL 2009)

View poster presented here .

ICAR 2010: International Conference of Arabidopsis Research (Yokohama 2010).

Comparative genomics is a powerful method to elucidate which bases in DNA sequences are important for transcription factor binding. the rationale behind these approaches is that random mutations are unlikely to be maintained during evolution if they affect functional regions of a genome; therefore bases that are conserved across species are likely to correspond to functionally important regions.
We have developed a novel alignment-based comparative genomics tool called EARS (Evolutionary Analysis of Regulatory Sequences) that is specifically tuned for the analysis of plant genomes. This method compares two sequences by breaking them into windows of a fixed length, and computes the optimal alignment score between all possible window pairs. Therefore, to align two 2kb sequences, approximately four million individual window alignments are performed. As all alignments are optimal global alignments, rather than heuristic, a loss-free comparison of the sequences is achieved. A conservation profile is generated showing the p-value of the maximum alignment score for each given window to its best matching window in the other sequence. Peaks above the significance threshold identify putative conserved sequences. The conservation profile allows a rapid assessment of whether or not two promoters may exhibit regions of sequence similarity.
We demonstrate the power of this method by discovering evolutionarily conserved sequences in the promoters of Arabidopsis circadian clock genes, including TOC1, LHY, CCA1 and LUX (PCL1). Within these sequences we demonstrate conservation of known transcription factor binding sites, and uncover putative novel elements. to test whether the elements detected are involved in the rhythmic transcription of these genes, we have developed software that performs a statistical test for over-representation of motifs in groups of genes with similar temporal patterns of expression.

View poster presented here