Epigenetic Optical Mapping of 5-Hydroxymethylcytosine in Nanochannel Arrays.
Tslil GabrieliHila SharimGil NifkerJonathan JeffetTamar ShahalRani AriellyMichal Levi-SakinLily HochNissim ArbibYael MichaeliYuval EbensteinPublished in: ACS nano (2018)
The epigenetic mark 5-hydroxymethylcytosine (5-hmC) is a distinct product of active DNA demethylation that is linked to gene regulation, development, and disease. In particular, 5-hmC levels dramatically decline in many cancers, potentially serving as an epigenetic biomarker. The noise associated with next-generation 5-hmC sequencing hinders reliable analysis of low 5-hmC containing tissues such as blood and malignant tumors. Additionally, genome-wide 5-hmC profiles generated by short-read sequencing are limited in providing long-range epigenetic information relevant to highly variable genomic regions, such as the 3.7 Mbp disease-related Human Leukocyte Antigen (HLA) region. We present a long-read, highly sensitive single-molecule mapping technology that generates hybrid genetic/epigenetic profiles of native chromosomal DNA. The genome-wide distribution of 5-hmC in human peripheral blood cells correlates well with 5-hmC DNA immunoprecipitation (hMeDIP) sequencing. However, the long single-molecule read-length of 100 kbp to 1 Mbp produces 5-hmC profiles across variable genomic regions that failed to show up in the sequencing data. In addition, optical 5-hmC mapping shows a strong correlation between the 5-hmC density in gene bodies and the corresponding level of gene expression. The single-molecule concept provides information on the distribution and coexistence of 5-hmC signals at multiple genomic loci on the same genomic DNA molecule, revealing long-range correlations and cell-to-cell epigenetic variation.
Keyphrases
- single molecule
- dna methylation
- genome wide
- gene expression
- copy number
- single cell
- living cells
- atomic force microscopy
- high resolution
- peripheral blood
- endothelial cells
- high density
- induced apoptosis
- healthcare
- stem cells
- cell therapy
- young adults
- mesenchymal stem cells
- cell death
- machine learning
- endoplasmic reticulum stress
- cell free
- social media
- electronic health record
- genome wide association study