Albany 2015:Book of Abstracts
June 9-13 2015
©Adenine Press (2012)
Interplay of nucleosome repositioning, DNA methylation and transcription factor binding during stem cell development
Cell fate is controlled by complex networks that link chromatin features like DNA methylation, histone modifications, nucleosome positioning and transcription factor (TF) binding. A particular interesting aspect are changes of the competitive binding of the histone octamer and TFs during differentiation and resulting effects on the cell's active transcription program. In our recent studies we have combined high-throughput sequencing with theoretical modeling to decipher nucleosome repositioning as a novel mechanism that connects DNA methylation/demethylation with transcription factor binding. As an example of a transcription factor utilizing this mechanism we have specifically investigated the CCCTC-binding factor CTCF. We found that during differentiation of mouse embryonic stem cells (ESCs) DNA methylation (5mC), hydroxymethylation (5hmC), nucleosome repositioning and CTCF binding are linked in a context-dependent manner. The mostly unmethylated CpG islands displayed reduced nucleosome occupancy and were enriched in cell type-independent binding sites for CTCF. The few remaining methylated CpG dinucleotides were preferentially associated with nucleosomes. In contrast, outside of CpG islands most CpGs were methylated and the average methylation density oscillated so that it was highest in the linker region between nucleosomes. Outside CpG islands binding of TET1, an enzyme that converts 5mC to 5hmC, was associated with labile nucleosomes. Such nucleosomes were poised for eviction in ESCs and became stably bound in differentiated cells upon reduction of TET1 and 5hmC levels. This process regulates a class of CTCF binding sites outside CpG islands that were occupied by CTCF in ESCs but lost the protein during differentiation. This cell type dependent targeting of CTCF can be rationalized with a quantitative biophysical model of competitive binding with the histone octamer in dependence of the TET1, 5hmC and 5mC state. Extensions of this model to include combinatorial cooperative binding of multiple TFs as well as the formation of differentially regulated chromatin territories will be also discussed.
Beshnova D.A., Cherstvy A.G. Vainshtein Y. and Teif V.B. (2014). Regulation of the nucleosome repeat length in vivo by the DNA sequence, protein concentrations and long-range interactions. PLoS Comput. Biol. 10(7):e1003698.
Teif V.B., Erdel F., Beshnova D.A., Vainshtein Y., Mallm J.-P., Rippe K. (2013) Taking into account nucleosomes for predicting gene expression. Methods 62, 26-38.