Nucleosome Organization in Human Embryonic Stem Cells

Abstract

The fundamental repeating unit of eukaryotic chromatin is the nucleosome. Besides being involved in packaging DNA, nucleosome organization plays an important role in transcriptional regulation and cellular identity. Currently, there is much debate about the major determinants of the nucleosome architecture of a genome and its significance with little being known about its role in stem cells. To address these questions, we performed ultra-deep sequencing of nucleosomal DNA in two human embryonic stem cell lines and integrated our data with numerous epigenomic maps. Our analyses have revealed that the genome is a determinant of nucleosome organization with transcriptionally inactive regions characterized by a “ground state” of nucleosome profiles driven by underlying DNA sequences. DNA sequence preferences are associated with heterogeneous chromatin organization around transcription start sites. Transcription, histone modifications, and DNA methylation alter this “ground state” by having distinct effects on both nucleosome positioning and occupancy. As the transcriptional rate increases, nucleosomes become better positioned. Exons transcribed and included in the final spliced mRNA have distinct nucleosome profiles in comparison to exons not included at exon-exon junctions. Genes marked by the active modification H3K4m3 are characterized by lower nucleosome occupancy before the transcription start site compared to genes marked by the inactive modification H3K27m3, while bivalent domains, genes associated with both marks, lie exactly in the middle. Combinatorial patterns of epigenetic marks (chromatin states) are associated with unique nucleosome profiles. Nucleosome organization varies around transcription factor binding in enhancers versus promoters. DNA methylation is associated with increasing nucleosome occupancy and different types of methylations have distinct location preferences within the nucleosome core particle. Finally, computational analysis of nucleosome organization alone is sufficient to elucidate much of the circuitry of pluripotency. Our results, suggest that nucleosome organization is associated with numerous genomic and epigenomic processes and can be used to elucidate cellular identity.

NUCOME: A Comprehensive Database of Nucleosome Organizations in Mammalian Genomes

“…The better nucleosome positioning pattern exhibits an increased nucleosome depletion level (Figure 2d) and reduced nucleosome fuzziness (Figure 2e). Many previous studies have reported similar observations using specific cell cultured systems or tissues (24)(25)(26)(27)(28)(29)(30). Here, we showed that the regulation manner is conserved among various human and mouse tissues and cell types by performing this analysis in multiple samples stored in NUCOME (Supplementary Figure 2b-e).…”

Biophysical characterization of the association of histones with single-stranded DNA

“…In contrast to the well-established fact that the dsDNA sequences in a genome are a determinant of nucleosome organization and positioning [60,61], to the best of our knowledge there are no studies on the possible differential affinity of ssDNA sequences for histones. However, we have found that for a short DNA of 148 base pairs like the NX1 fragment each of the two complementary strands has different affinities for histones.…”

Enhancers predominantly regulate gene expression in vivo via transcription initiation

“…To examine initiation and pausing simultaneously and across a larger window, we modified the Start-seq assay. First, we isolated much larger RNA transcripts (<=300nt compared to ~100nt), enriching for nascent RNA and enabling us to identify the distribution of RNA 3' ends far beyond the predicted range of Pol II pausing (+30-60bps relative to the TSS), and also beyond the boundary of the +1 nucleosome (+ ~150bps) (Jonkers and Lis 2015;Mieczkowski et al 2016;Voong et al 2016;Yazdi et al 2015). Second, we used paired-end sequencing to identify both ends of each nascent RNA transcript capturing individual episodes of transcriptional initiation and pausing from single molecules.…”