Hypomethylated domain-enriched DNA motifs prepattern the accessible nucleosome organization in teleosts

Abstract

BackgroundGene promoters in vertebrate genomes show distinct chromatin features such as stably positioned nucleosome array and DNA hypomethylation. The nucleosomes are known to have certain sequence preferences, and the prediction of nucleosome positioning from DNA sequence has been successful in some organisms such as yeast. However, at gene promoters where nucleosomes are much more stably positioned than in other regions, the sequence-based model has failed to work well, and sequence-independent mechanisms have been proposed.ResultsUsing DNase I-seq in medaka embryos, we demonstrated that hypomethylated domains (HMDs) specifically possess accessible nucleosome organization with longer linkers, and we reassessed the DNA sequence preference for nucleosome positioning in these specific regions. Remarkably, we found with a supervised machine learning algorithm, k-mer SVM, that nucleosome positioning in HMDs is accurately predictable from DNA sequence alone. Specific short sequences (6-mers) that contribute to the prediction are specifically enriched in HMDs and distribute periodically with approximately 200-bp intervals which prepattern the position of accessible linkers. Surprisingly, the sequence preference of the nucleosome and linker in HMDs is opposite from that reported previously. Furthermore, the periodicity of specific motifs at hypomethylated promoters was conserved in zebrafish.ConclusionThis study reveals strong link between nucleosome positioning and DNA sequence at vertebrate promoters, and we propose hypomethylated DNA-specific regulation of nucleosome positioning.Electronic supplementary materialThe online version of this article (doi:10.1186/s13072-017-0152-2) contains supplementary material, which is available to authorized users.

Recapitulation-like developmental transitions of chromatin accessibility in vertebrates

“…For each biological replicate, ATAC-seq was performed as previously described [47, 48], with some modifications. In brief, embryos were minced as required by using a razor blade, placed in homogenization buffer (25 mM D-sucrose, 20 mM tricine [pH 7.8], 15 mM NaCl, 60 mM KCl, 2 mM MgCl 2 , 0.5 mM spermidine, and cOmplete Protease Inhibitor Cocktail Tablet [Roche]), and homogenized in an ice-cold Dounce tissue grinder with a loose-fitting pestle, according to the methods of Yue et al [49].…”

Targeted in vivo epigenome editing of H3K27me3

“…These target promoters do not show any particular characteristics in terms of CpG contents compared to others. sgRNAs were designed to target DNase I hypersensitive sites using DNase I-seq data from medaka blastula [ 28 ], because previous genome-wide Cas9 binding studies showed that chromatin inaccessibility prevents sgRNA/Cas9 complex binding [ 29 , 30 ]. We used a set of sgRNAs targeting a single promoter region because previous studies showed that multiple sgRNAs at each target promoter increased the efficiency of epigenome editing [ 17 , 31 , 32 ].…”

“…c , g , k , n The epigenetic modification patterns around Arhgap35, Kita , Nanos3 and Dcx , sgRNAs (blue bars) and ChIP-qPCR product (black bars) positions. H3K27me3 (red) and H3K27ac (blue) ChIP-seq [ 27 ], DNase I-seq (black) [ 28 ] and DNA methylation [ 34 ] enrichment at the blastula stage are shown. d , e , h , i , l , m , o , p The results of ChIP-qPCR using anti-FLAG antibody ( d , h , l , o ) and anti-H3K27me3 antibody ( e , i , l , m ).…”

Unlinking the methylome pattern from nucleotide sequence, revealed by large-scale in vivo genome engineering and methylome editing in medaka fish

“…In order to relate the methylation state of the integrated fragments to possible binding or recognition by DNA-binding proteins (e.g., transcription factors), we identified DNase I hypersensitive sites (DHS) by remapping the publicly available DNase-seq dataset of drR medaka blastula embryos (accession number: SRX1032807 [ 83 ]) to the medaka genome assembly v2.2.4. Adaptor trimming and alignment was accomplished using BBmap v37.36 [ 76 ] with default parameters.…”