Using dHMM to reveal nucleosome breathing in methylation-seq

Gene expression is regulated by the organization of DNA in chromatin. Chromatin consists of 147 bp DNA wrapped nucleosomes and linker DNA. Transient unwrapping of DNA from nucleosomes is known as nucleosome breathing and experimental methods quantifying nucleosome breathing are limited. Therefore nucleosomal breathing is not well-understood in vivo. Here we used long read methylation-seq data that provides nucleosome footprints in chromatin extracted from yeast. Using novel dHMM analysis, we assigned nucleosome positions with near base pair accuracy. Nucleosomes feature breathing of several dozens of base pairs and a sequence analysis of the assigned nucleosomes showed dinucleotide dependence. Compared to previous MNase nucleosome mapping, methylation-seq is less sequence dependent and compared to chemical cleavage nucleosome mapping we can observe and quantify the extent of nucleosome breathing and we have a larger dataset. Moreover, by keeping the connectivity, there is potential...Show moreGene expression is regulated by the organization of DNA in chromatin. Chromatin consists of 147 bp DNA wrapped nucleosomes and linker DNA. Transient unwrapping of DNA from nucleosomes is known as nucleosome breathing and experimental methods quantifying nucleosome breathing are limited. Therefore nucleosomal breathing is not well-understood in vivo. Here we used long read methylation-seq data that provides nucleosome footprints in chromatin extracted from yeast. Using novel dHMM analysis, we assigned nucleosome positions with near base pair accuracy. Nucleosomes feature breathing of several dozens of base pairs and a sequence analysis of the assigned nucleosomes showed dinucleotide dependence. Compared to previous MNase nucleosome mapping, methylation-seq is less sequence dependent and compared to chemical cleavage nucleosome mapping we can observe and quantify the extent of nucleosome breathing and we have a larger dataset. Moreover, by keeping the connectivity, there is potential to detect long range correlations in nucleosome positioning and breathing. Being able to uncover such long range chromatin organization with base pair accuracy, is indispensable for mechanistic insights into gene regulation. Using third-generation sequencing for nucleosome mapping may help diagnosis and treatment of chromatin related diseases, such as specific forms of cancer.Show less

Leiden University Student Repository

Documents

In Collections

Using dHMM to reveal nucleosome breathing in methylation-seq