Project description:The potentially devastating effects of climate change have raised awareness of the need to understand how the biology of wild animals is influenced by extreme-weather events. We investigate how a wild arctic-breeding bird, the Lapland longspur (Calcarius lapponicus), responds to different environmental perturbations and its coping strategies. We explore the transcriptomic response to environmental adversity during the transition from arrival at the breeding grounds to incubation on the Arctic tundra. The effects of an extremely cold spring on arrival and a severe storm during incubation are examined through RNA-seq analysis of pertinent tissues sampled across the breeding cycle. The stress response, circadian rhythms, reproduction, and metabolism are all affected. A key gene of the Hypothalamic-Pituitary-Adrenal axis, FKBP5, was significantly up-regulated in hypothalamus. The genome assembly and gene expression profiles provide comprehensive resources for future studies. Our findings on different coping strategies to chronic and acute stressors will contribute to understanding the interplay between changing environments and genomic regulation.
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.
