Inferring changes in histone modification during cell differentiation by ancestral state estimation based on phylogenetic trees of cell types: Human hematopoiesis as a model case
| Autor: | Kanako O. Koyanagi |
|---|---|
| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
Er erythroblast Mo monocyte Cellular differentiation TSS transcription start sites 0302 clinical medicine DNA deoxyribonucleic acid CRISPR clustered regularly interspaced short palindromic repeat Ne neutrophil skin and connective tissue diseases Epigenomics Me megakaryocyte H3K9me3 trimethylations of histone H3 at lysine 9 Phylogenetic tree biology T T cell General Medicine Eo eosinophil L lymphoid lineage Haematopoiesis Histone 030220 oncology & carcinogenesis Histone modification ChIP-seq chromatin immunoprecipitation sequencing Cell type lcsh:QH426-470 H3K4me3 trimethylation of histone H3 at lysine 4 H3K36me3 trimethylation of histone H3 at lysine 36 M myeloid lineage Article 03 medical and health sciences kb kilobase(s) H3K27ac acetylation of histone H3 at lysine 27 Genetics KEGG Kyoto encyclopedia of genes and genomes Epigenetics Gene Ancestral state estimation Cell lineage Cell-type tree B B cell BED browser extensible data Nk natural killer cell H3K27me3 trimethylations of histone H3 at lysine 27 lcsh:Genetics 030104 developmental biology H3K4me1 monomethylation of histone H3 at lysine 4 Evolutionary biology biology.protein sense organs Phyloepigenetics |
| Zdroj: | Gene: X Gene: X, Vol 3, Iss, Pp-(2019) |
| ISSN: | 2590-1583 |
| Popis: | Revealing the landscape of epigenetic changes in cells during differentiation is important for understanding the development of organisms. In this study, to infer such epigenetic changes during human hematopoiesis, ancestral state estimation based on a phylogenetic tree was applied to map the epigenomic changes in six kinds of histone modifications onto the hierarchical cell differentiation process of hematopoiesis using epigenomes of eight types of differentiated hematopoietic cells. The histone modification changes inferred during hematopoiesis showed that changes that occurred on the branches separating different cell types reflected the characteristics of hematopoiesis in terms of genomic position and gene function. These results suggested that ancestral state estimation based on phylogenetic analysis of histone modifications in differentiated hematopoietic cells could reconstruct an appropriate landscape of histone modification changes during hematopoiesis. Since integration of the inferred changes of different histone modifications could reveal genes with specific histone marks such as active histone marks and bivalent histone marks on each internal branch of cell-type trees, this approach could provide valuable information for understanding the cell differentiation steps of each cell lineage. Highlights • Ancestral state estimation was used to infer epigenetic changes in cells during hematopoiesis. • Six histone modification types and eight hematopoietic cell types were used. • The landscape of histone modification changes could be reconstructed in terms of genomic position and gene function. |
| Databáze: | OpenAIRE |
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