ArticleNucleic acids research2017
Automatic identification of informative regions with epigenomic changes associated to hematopoiesis.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- chromIDEAS reveals epigenetic dynamics via multi-dimensional clustering of chromatin states.Nucleic acids research · 2026Article
- PLAMseq enables the proteo-genomic characterization of chromatin-associated proteins and protein interactions in a single workflow.Science advances · 2025Article
- Epilogos: information-theoretic navigation of multi-tissue functional genomic annotations.bioRxiv : the preprint server for biology · 2025Article
- Evolutionarily conserved enhancer-associated features within theFrontiers in cell and developmental biology · 2024Article
- Esearch3D: propagating gene expression in chromatin networks to illuminate active enhancers.Nucleic acids research · 2023Article
- Computational methods to explore chromatin state dynamics.Briefings in bioinformatics · 2022Review
- Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers.Genome research · 2022Article
- Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas.Leukemia · 2021Article
- Fast detection of differential chromatin domains with SCIDDO.Bioinformatics (Oxford, England) · 2021Article
- Article
- Blueprint of human thymopoiesis reveals molecular mechanisms of stage-specific TCR enhancer activation.The Journal of experimental medicine · 2020Article
- Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks.Nucleic acids research · 2020Article
- Article
- Epigenetic Priming in Childhood Acute Lymphoblastic Leukemia.Frontiers in cell and developmental biology · 2019Review
- Automatic detection of genomic regions with informative epigenetic patterns.BMC genomics · 2018Article
- Dynamics of Transcription Regulation in Human Bone Marrow Myeloid Differentiation to Mature Blood Neutrophils.Cell reports · 2018Article
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8 authors.
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Abstract
Hematopoiesis is one of the best characterized biological systems but the connection between chromatin changes and lineage differentiation is not yet well understood. We have developed a bioinformatic workflow to generate a chromatin space that allows to classify 42 human healthy blood epigenomes from the BLUEPRINT, NIH ROADMAP and ENCODE consortia by their cell type. This approach let us to distinguish different cells types based on their epigenomic profiles, thus recapitulating important aspects of human hematopoiesis. The analysis of the orthogonal dimension of the chromatin space identify 32,662 chromatin determinant regions (CDRs), genomic regions with different epigenetic characteristics between the cell types. Functional analysis revealed that these regions are linked with cell identities. The inclusion of leukemia epigenomes in the healthy hematological chromatin sample space gives us insights on the healthy cell types that are more epigenetically similar to the disease samples. Further analysis of tumoral epigenetic alterations in hematopoietic CDRs points to sets of genes that are tightly regulated in leukemic transformations and commonly mutated in other tumors. Our method provides an analytical approach to study the relationship between epigenomic changes and cell lineage differentiation. Method availability: https://github.com/david-juan/ChromDet.
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