Landscape of monoallelic DNA accessibility in mouse embryonic stem cells and neural progenitor cells

Abstract

We developed an allele-specific assay for transposase-accessible chromatin with high-throughput sequencing (ATAC–seq) to genotype and profile active regulatory DNA across the genome. Using a mouse hybrid F1 system, we found that monoallelic DNA accessibility across autosomes was pervasive, developmentally programmed and composed of several patterns. Genetically determined accessibility was enriched at distal enhancers, but random monoallelically accessible (RAMA) elements were enriched at promoters and may act as gatekeepers of monoallelic mRNA expression. Allelic choice at RAMA elements was stable across cell generations and bookmarked through mitosis. RAMA elements in neural progenitor cells were biallelically accessible in embryonic stem cells but premarked with bivalent histone modifications; one allele was silenced during differentiation. Quantitative analysis indicated that allelic choice at the majority of RAMA elements is consistent with a stochastic process; however, up to 30% of RAMA elements may deviate from the expected pattern, suggesting a regulated or counting mechanism.

Clonally stable Vκ allelic choice instructs Igκ repertoire

“…7b), allele-specific promoter accessibility accurately predicts the transcription state for each allele in every clone. It thus seems likely that promoter chromatin accessibility may represent an underlying mechanism for inheritable allelic gene transcription, and this has been confirmed by other studies, as well25.…”

ATAC Primer Tool for targeted analysis of accessible chromatin

“…APT can also identify custom normalization controls based on user-supplied ATAC-seq data. We tested the correlation between ATAC-qPCR and ATAC-seq, using a panel of differentially accessible elements in human fibroblasts after topoisomerase II inhibition, as well as a panel of random monoallelically accessible elements in mouse neural progenitor cells 2 (Supplementary Table 2 and 3). Systematic comparison of ATAC-qPCR with ATAC-seq showed that normalization to invariant peaks, as implemented in APT, greatly improved the correlation between ATAC-qPCR results and read counts from deeply sequenced ATAC-seq libraries (average change from R = 0.747 to R = 0.957); we obtained similar results with cell-type-specific and universal normalization controls (Supplementary Fig.…”

“…A targeted allelic ATAC assay is highly desirable because only a small fraction of DNA elements (~1%) both possess informative sequence variants and demonstrate allelic regulation 2 . Inclusion of an informative SNP between primer-binding sites allows for targeted analysis of allele-specific accessibility by ATAC-PCR, for example, to assess the effect of disease-associated variants on allele-specific accessibility.…”

“…1c, Supplementary Table 4). We further validated allelic ATAC-PCR on a panel of DNA elements with random monoallelic accessibility in hybrid mouse NPC cells 2 (Supplementary Table 5). Allele-specific quantification by ATAC-PCR correlated strongly with the allelic accessibility determined by ATAC-seq ( R = 0.962) (Supplementary Fig.…”

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

“…Recent methodological advances, such as the advent of the assay for transposase-accessible chromatin by sequencing 1 (ATAC-seq) and the application of DNase hypersensitivity sequencing (DNase-seq) to low cell numbers 2 , have enabled the generation of high-fidelity chromatin accessibility profiles for a variety of cell types 3–9 . However, certain cell types and tissues require individualized protocol optimizations 10,11 , making data difficult to compare across multiple studies.…”