Single-cell atlas of the transcriptome and chromatin accessibility in the human retina.

Single-cell sequencing has revolutionized the scale and resolution of molecular profiling of tissues and organs. Here, we present an integrated multimodal reference atlas of the most accessible portion of the mammalian central nervous system, the retina. We compiled around 2.4 million cells from 55 donors, including 1.4 million unpublished data points, to create a comprehensive human retina cell atlas (HRCA) of transcriptome and chromatin accessibility, unveiling over 110 types. Engaging the retina community, we annotated each cluster, refined the Cell Ontology for the retina, identified distinct marker genes, and characterized cis-regulatory elements and gene regulatory networks (GRNs) for these cell types. Our analysis uncovered intriguing differences in transcriptome, chromatin, and GRNs across cell types. In addition, we modeled changes in gene expression and chromatin openness across gender and age. This integrated atlas also enabled the fine-mapping of GWAS and eQTL variants. Accessible through interactive browsers, this multimodal cross-donor and cross-lab HRCA, can facilitate a better understanding of retinal function and pathology.

Editor's evaluation: Shared enhancer gene regulatory networks between wound and oncogenic programs

Decision letter: Shared enhancer gene regulatory networks between wound and oncogenic programs

Mapping the Effects of Genetic Variation on Chromatin State and Gene Expression Reveals Loci That Control Ground State Pluripotency.

Decision letter: The single-cell chromatin accessibility landscape in mouse perinatal testis development

Tuberculosis, a deadly infectious lung disease caused by Mycobacterium tuberculosis (Mtb), remains the leading cause of bacterial disease-related deaths worldwide. Mtb reprograms and disables key antibacterial response pathways, many of which are regulated by epigenetic mechanisms that control the accessibility of chromatin to the transcriptional machinery. Recent reports suggest that host phosphatases, such as PPM1A, contribute to regulating chromatin accessibility during bacterial infections. However, changes in genome-wide chromatin accessibility during Mtb infection and whether PPM1A plays a role in this process remains unknown. Herein, we use combinatorial chromatin accessibility (ATAC-seq) and transcriptomic (RNA-seq) profiling of wild-type, PPM1A knockout and PPM1A overexpressing macrophages to demonstrate that Mtb infection induces global chromatin remodelling consistent with changes in gene expression. The strongest concordant changes to chromatin accessibility and gene expression triggered by Mtb infection were enriched for genes involved in type I interferon (IFN) signalling pathways. A panel of 15 genes with the strongest concordant changes in chromatin accessibility and gene expression were validated to be significantly upregulated in Mtb-infected human monocyte-derived macrophages. PPM1A expression affects chromatin accessibility profiles during Mtb infection that are reflected in the total number, chromosome location, and directionality of change. Transcription factor binding motif analysis revealed enrichment for transcription factors involved in the type I IFN pathway during Mtb infection, including members of the IRF, MEF2, and AP-1 families. Our study shows that altered type I IFN responses in Mtb-infected macrophages occur due to genome-wide changes in chromatin accessibility, and that PPM1A could influence a subset of these signatures.

Author response: Heritability enrichment in context-specific regulatory networks improves phenotype-relevant tissue identification

The interaction of mammals with a novel environment (NE) results in structural and functional changes in multiple brain areas, including the hippocampus. This experience-dependent circuit reorganization is driven in part by changes in gene expression however, the dynamic sensory experience-driven chromatin states and the diverse cell type specific gene expression programs that are regulated by novel experiences are not well described. We employed single- nucleus multiomics (snRNA- and ATAC-seq) and bulk RNA-seq of the hippocampal DG, CA3, and CA1 regions to characterize the temporal evolution of cell-type-specific chromatin accessibility and gene expression changes that occur in 14 different cell types of the hippocampus upon exposure of mice to a novel environment. We observe strong hippocampal regional specificity in excitatory neuron chromatin accessibility and gene expression as well as great diversity in the inhibitory neuron and non-neuronal transcriptional responses. The novel environment-regulated genes in each cell type were enriched for genes that encode secreted factors, and cell-type-specific expression of their cognate receptors identified promising candidates for the modulation of learning and memory processes. Our characterization of the effect of novel experience on chromatin revealed thousands of cell-type-specific changes in chromatin accessibility. Coordinated analysis of chromatin accessibility and gene expression changes within individual cell types identified Fos/AP-1 as a key driver of novel experience-induced changes in chromatin accessibility and cell-type-specific gene expression. Together, these data provide a rich resource of hippocampal chromatin accessibility and gene expression profiles across diverse cell types in response to novel experience, a physiological stimulus that affects learning and memory.

Decision letter: CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo

Transcriptional reprogramming by oxidative stress occurs within a predefined chromatin accessibility landscape

BackgroundThe three-dimensional spatial organization of the genome plays important roles in chromatin accessibility and gene expression in multiple biological processes and has been reported to be altered in response to environmental stress. However, the functional changes in spatial genome organization during environmental changes in crop plants are poorly understood.ResultsHere we perform Hi-C, ATAC-seq, and RNA-seq in two agronomically important rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica), to report a comprehensive profile of nuclear dynamics during heat stress (HS). We show that heat stress affects different levels of chromosome organization, including A/B compartment transition, increase in the size of topologically associated domains, and loss of short-range interactions. The chromatin architectural changes were associated with chromatin accessibility and gene expression changes. Comparative analysis revealed that 93-11 exhibited more dynamic gene expression and chromatin accessibility changes, including HS-related genes, consistent with observed higher HS tolerance in this cultivar.ConclusionsOur data uncovered higher-order chromatin architecture as a new layer in understanding transcriptional regulation in response to heat stress in rice.

Gene regulatory networks (GRNs), consisting of transcription factors and their target cis-regulatory sequences, control neurogenesis and cell fate specification in the developing central nervous system, but their organization is poorly characterized. In this study, we performed integrated single-cell RNA- and scATAC-seq analysis in both mouse and human retina to profile dynamic changes in gene expression, chromatin accessibility and transcription factor footprinting during retinal neurogenesis. We identified multiple interconnected, evolutionarily-conserved GRNs consisting of cell type-specific transcription factors that both activate expression of genes within their own network and often inhibit expression of genes in other networks. These GRNs control state transitions within primary retinal progenitors that underlie temporal patterning, regulate the transition from primary to neurogenic progenitors, and drive specification of each major retinal cell type. We confirmed the prediction of this analysis that the NFI transcription factors Nfia, Nfib, and Nfix selectively activate expression of genes that promote late-stage temporal identity in primary retinal progenitors. We also used GRNs to identify additional transcription factors that promote (Insm1/2) and inhibit (Tbx3 and Tcf7l1/2) rod photoreceptor specification in postnatal retina. This study provides an inventory of cis- and trans-acting factors that control retinal development, identifies transcription factors that control the temporal identity of retinal progenitors and cell fate specification, and will potentially guide cell-based therapies aimed at replacing retinal neurons lost due to disease.

Background: While many studies have uncovered genetic mutations that drive tumorigenesis, far fewer have described epigenetic changes, such as nucleosome positioning and DNA methylation, which lead to the development of cancer. Therefore, accurately mapping these changes between normal and tumor tissue will provide novel information to identify genes that undergo epigenetic changes that drive tumorigenesis (“epigenetic driver genes”). In this study, we used an assay developed in our laboratory to investigate the epigenetic changes between clear cell renal cell carcinoma (ccRCC, the most common subtype of renal carcinoma) tumors and normal tissue to uncover genes that contribute to ccRCC tumorigenesis. Methods: Current methods to investigate epigenomic changes in clinical samples are expensive and require abundant biological sample material for analysis. We have developed a novel assay (“AcceSssIble”) to simultaneously determine DNA methylation and chromatin accessibility in clinical samples. It is rapid and cost-effective, only requiring 20 mg of tissue, the Infinium HumanMethylation450 BeadChip platform, and the CpG methyltransferase M.SssI. We used this method to measure the changes in DNA methylation and chromatin accessibility in 9 matched pairs of ccRCC tumors and adjacent normal tissue from different patients, and intersected this data with RNA-seq data of 72 matched ccRCC samples and DNA methylation data of 160 matched ccRCC samples from The Cancer Genome Atlas (TCGA). Genes that were revealed to have the most changes in chromatin structure and expression were then targeted by siRNA knockdown for functional validation in ccRCC. Results: From the AcceSssIble assay on 9 pairs of ccRCC patient tumor/normal samples, we uncovered 438 genes whose promoters change in chromatin accessibility in at least 2 ccRCC samples, both dependent and independent of DNA methylation changes, and have an accompanying change in gene expression in TCGA RNA-seq data. The results produce a striking figure in which chromatin accessibility changes are inversely correlated with DNA methylation but directly correlated with gene expression changes. Interestingly, loss of (DNA methylation change-dependent) accessibility preferentially occurred within CpG islands, while gain of (DNA methylation change-dependent) accessibility was strongly biased towards non-CpG islands. Meanwhile, chromatin accessibility changes independent of DNA methylation changes do not show preference in CpG content. Furthermore, pathway analyses reveal involvement of HIF1α signaling, cAMP-mediated signaling, and G-protein Coupled Receptor Signaling in the development of ccRCC. Lastly, we performed siRNA knockdown experiments on several top genes most changing in expression and accessibility, which revealed two genes, encoding type IV collagen and an RNA-binding protein, whose knockdown resulted in a significant increase in proliferation in normal kidney epithelial cells. Conclusions: Our study revealed a vast number of chromatin accessibility and accompanying gene expression changes that occur in gene promoters in the development of ccRCC, both dependent and independent of DNA methylation changes. Each individual tumor has a unique profile of epigenetic alterations. Moreover, almost none of the genes that were found to undergo epigenetic and resulting gene expression changes overlap with TCGA's findings of commonly mutated genes in ccRCC. Overall, these studies represent novel approaches that can help identify new therapeutic target genes and treatment strategies for ccRCC, including personalized approaches. Citation Format: Elinne Coral Becket, Christopher Duymich, Yin-Wei Chang, Kurinji Pandiyan, Peter Nichols, Peter Jones, Inderbir Gill, Gangning Liang. Elucidation of epigenetic driver genes in clear cell renal cell carcinoma using a newly developed assay, AcceSssIble. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A1-05.

Lens differentiation is characterized by stage-specific changes in chromatin accessibility correlating with differentiation state-specific gene expression

Decision letter: Single-cell RNA sequencing of the Strongylocentrotus purpuratus larva reveals the blueprint of major cell types and nervous system of a non-chordate deuterostome