SUMMARYEmbryogenesis requires epigenetic information that allows each cell to respond appropriately to developmental cues. Histone modifications are core components of a cell’s epigenome, giving rise to chromatin states that modulate genome function. Here, we systematically profile histone modifications in a diverse panel of mouse tissues at 8 developmental stages from 10.5 days post conception until birth, performing a total of 1,128 ChIP-seq assays across 72 distinct tissue-stages. We combine these histone modification profiles into a unified set of chromatin state annotations, and track their activity across developmental time and space. Through integrative analysis we identify dynamic enhancers, reveal key transcriptional regulators, and characterize the role of chromatin-based repression in developmental gene regulation. We also leverage these data to link enhancers to putative target genes, revealing connections between coding and non-coding sequence variation in disease etiology. Our study provides a compendium of resources for biomedical researchers, and achieves the most comprehensive view of embryonic chromatin states to date.

Genome-wide analysis of chromatin accessibility in primary tissues has uncovered millions of candidate regulatory sequences in the human and mouse genomes [1][2][3][4] . However, the heterogeneity of biological samples used in previous studies has prevented a precise understanding of the dynamic chromatin landscape in specific cell types. Here, we show that analysis of the transposase-accessible-chromatin in single nuclei isolated from frozen tissue samples can resolve cellular heterogeneity and delineate transcriptional regulatory sequences in the constituent cell types. Our strategy is based on a combinatorial barcoding assisted single cell assay for transposase-accessible chromatin 5 and is optimized for nuclei from flash-frozen primary tissue samples (snATACseq). We used this method to examine the mouse forebrain at seven development stages and in adults. From snATAC-seq profiles of more than 15,000 high quality nuclei, we identify 20 distinct cell populations corresponding to major neuronal and non-neuronal cell-types in foetal and adult forebrains. We further define cell-type specific cis regulatory sequences and infer potential master transcriptional regulators of each cell population.Our results demonstrate the feasibility of a general approach for identifying cell-typespecific cis regulatory sequences in heterogeneous tissue samples, and provide a rich resource for understanding forebrain development in mammals. MAINA significant fraction of the non-coding DNA in the mammalian genome encodes transcriptional regulatory elements that play fundamental roles in mammalian development and human disease 3,6 . Identification of these sequences and characterizing their dynamic activities in specific cell types is a major goal in biology. Analysis of chromatin accessibility in primary tissues using assays such as DNase-seq 2,4 and ATACseq 7,8 has led to annotation of millions of candidate cis regulatory elements in the human and mouse genomes 1,3 . Yet, the catalogue of current cis regulatory elements, based primarily on analysis of bulk, heterogeneous biological samples, lacks precise information regarding cell-type-and developmental-stage-specific activities of each element. In-vivo lineage tracing using INTACT mouse models 8,9 and isolation of particular cell types based peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/159137 doi: bioRxiv preprint first posted online Jul. 4, 2017; 3 on specific protein markers can address this limitation to some degree and in limited cell types 10,11 . But a more general strategy is necessary to study primary tissues from all stages of development in human as well as in other species.In theory, single cell based chromatin accessibility studies can be used for unbiased identification of subpopulations in a heterogeneous population, and proof of principle has been reported using cultured mammalian cells and cryopreserved blood cell-types 5,12,...