Project description:Many animals have polka dot patterns on their body surface, some of which are known to have signalling functions; however, their evolutionary origins remain unclear. Dot patterns can trigger a fear response (trypophobia) in humans and are known to function as aposematic signals in non-human animals, suggesting that dots may deserve attention for biological reasons. Interestingly in many birds, plumage dot patterns serve for social/sexual signalling. To understand their evolution, we have focused on the sensory bias hypothesis, which predicts the role of pre-existing sensory preference driven by natural selection in shaping signal design. Our previous phylogenetic comparative study supported the hypothesis and showed that diet-driven visual preference promoted the evolution of plumage patterns, as there was an evolutionary correlation between termite-eating (white roundish gregarious prey) and the presence of plumage dot patterns in species of the family Estrildidae. This suggests that these species possess an intrinsic preference for dots. To test this, we compared the responses of an Estrildid species with dot plumage pattern (star finch Neochmia ruficauda) towards simultaneously presented monochrome-printed white dot vs white stripe patterns under both food-deprived and -supplied conditions. Overall, star finches preferred dots to stripes. They showed foraging-like behaviours almost only toward dots when hungry and gazed at dots frequently even when food was available, suggesting both hunger-related and hunger-neutral dot preferences. These results are rather surprising, given how strongly the subjects were attracted to abstract dot patterns without organic structure, but provided good support for the sensory bias hypothesis.
Project description:This study aims to investigate the DNA methylation patterns at transcription factor binding regions and their evolutionary conservation with respect to binding activity divergence. We combined newly generated bisulfite-sequencing experiments in livers of five mammals (human, macaque, mouse, rat and dog) and matched publicly available ChIP-sequencing data for five transcription factors (CEBPA, HNF4a, CTCF, ONECUT1 and FOXA1). To study the chromatin contexts of TF binding subjected to distinct evolutionary pressures, we integrated publicly available active promoter, active enhancer and primed enhancer calls determined by profiling genome wide patterns of H3K27ac, H3K4me3 and H3K4me1.
Project description:Whole genome sequencing of the Arabidopsis thaliana dot5-1 transposon insertion line described in Petricka et al 2008 The Plant Journal 56(2): 251-263.
Project description:The analysis identifies differentially occupied genomic regions of H2Bub1, H3K79me3, and H3K27ac by RNF40 silencing in HCC1806 cells
Project description:This study aims to investigate the interactions of mutagenic lesions from diethylnitrosamine (DEN) treatment of mouse livers with such processes as replication, transcription, and interaction of DNA with proteins. Liver samples of 15-day old (P15) untreated C3H/HeOuJ mice were isolated and flash-frozen. ChIP-seq was performed to identify CTCF binding sites in livers of ten pooled individuals. The experiment was done with five biological replicates with a matched input library.
