A Method to Study the Epigenetic Chromatin States of Rare Hematopoietic Stem and Progenitor Cells; MiniChIP–Chip

A unique and defining property for any stem cell population is intrinsic self-renewal throughout the process of cell division, whilst maintaining the capacity to form multiple differentiated and mature cell types over the lifetime of an organism. Stem cells undergo dramatic changes in morphology, cell cycle status and gene expression during differentiation into specialized progenitor subsets. Such alterations are proposed to result from chromatin reorganization of the genome, allowing for the establishment and maintenance of lineage-specific transcriptional networks [1,2]. Therefore, cellular differentiation can be viewed as a product of heritable chromatin states, which in turn, are induced and maintained by specific epigenetic chromatin modifications [3].Chromatin structure defines the higher order structure by which DNA is organized within the cell nucleus [4]. It consists of a chain of nucleosomes, representing about 146–147 bp of DNA wrapped around a core of histone octamers [5]. The precise degree of nucleosome compaction at genomic regions influences the accessibility of transcription factor binding to gene promoters and enhancer regions critical for transcriptional regulation [6]. Accordingly, genomic regions are packaged into euchromatin, which forms a relaxed structure of large genomic distances between nucleosomes, or a higher degree of DNA compaction known as heterochromatin [7]. Euchromatin is also referred to as active chromatin and is linked to actively transcribed regions of the genome, while genes located in heterochromatin (inactive chromatin) are usually transcriptionally silent.In mammals, the most studied epigenetic chromatin modifications are DNA methylation and covalent modifications at the N-terminal tails of histone proteins [8,9]. DNA cytosine methylation, as mediated by the DNA methyltransferases, is thus far the only epigenetic mechanism known to directly modify DNA [10,11]. DNA methylation occurs mainly on cytosine–phosphate–guanine dinu