Project description:Chromatin profiling at locus resolution uncovers gene regulatory features that define cell types and developmental trajectories, but it remains challenging to map and compare distinct chromatin-associated proteins within the same sample. Here we describe a scalable antibody barcoding approach for profiling multiple chromatin features simultaneously in the same individual cells, Multiple Target Identification by Tagmentation (MulTI-Tag). MulTI-Tag is optimized to retain high sensitivity and specificity of enrichment for multiple chromatin targets in the same assay. We use MulTI-Tag to resolve distinct cell types using multiple chromatin features on a commercial single-cell platform, and to distinguish unique, coordinated patterns of active and repressive element regulatory usage in the same individual cells. Multifactorial profiling has allowed us to detect novel associations between histone marks in single cells and holds promise for comprehensively characterizing cell-specific gene regulatory landscapes in development and disease.
Project description:Chromatin organization and enhancer-promoter contacts are critical for establishing unique spatiotemporal gene expression patterns in distinct cell types. Non-coding genetic variants can influence cellular phenotypes by modifying higher-order transcriptional hubs and consequently gene expression. To elucidate transcriptional regulation by non-coding genome in human retina, we mapped chromatin contacts at high resolution and integrated this data with histone marks and super-enhancers (SEs). Retinal SEs exhibited abundant local interactions and reside in topologically associated domains (TADs) with weak boundary insulation. Notably, intra-TAD positioning of SEs correlated with the biological function of their target genes in the retina. We also identified regulatory landscapes of retinopathy genes and uncovered candidate genes for risk variants associated with age-related macular degeneration and glaucoma. Our studies of high-resolution genomic architecture of the human retina provide new insights into genetic control of tissue-specific functions, suggest paradigms for missing heritability, and enable the dissection of multifactorial disease phenotypes.
Project description:Chromatin organization and enhancer-promoter contacts are critical for establishing unique spatiotemporal gene expression patterns in distinct cell types. Non-coding genetic variants can influence cellular phenotypes by modifying higher-order transcriptional hubs and consequently gene expression. To elucidate transcriptional regulation by non-coding genome in human retina, we mapped chromatin contacts at high resolution and integrated this data with histone marks and super-enhancers (SEs). Retinal SEs exhibited abundant local interactions and reside in topologically associated domains (TADs) with weak boundary insulation. Notably, intra-TAD positioning of SEs correlated with the biological function of their target genes in the retina. We also identified regulatory landscapes of retinopathy genes and uncovered candidate genes for risk variants associated with age-related macular degeneration and glaucoma. Our studies of high-resolution genomic architecture of the human retina provide new insights into genetic control of tissue-specific functions, suggest paradigms for missing heritability, and enable the dissection of multifactorial disease phenotypes.
Project description:Chromatin organization and enhancer-promoter contacts are critical for establishing unique spatiotemporal gene expression patterns in distinct cell types. Non-coding genetic variants can influence cellular phenotypes by modifying higher-order transcriptional hubs and consequently gene expression. To elucidate transcriptional regulation by non-coding genome in human retina, we mapped chromatin contacts at high resolution and integrated this data with histone marks and super-enhancers (SEs). Retinal SEs exhibited abundant local interactions and reside in topologically associated domains (TADs) with weak boundary insulation. Notably, intra-TAD positioning of SEs correlated with the biological function of their target genes in the retina. We also identified regulatory landscapes of retinopathy genes and uncovered candidate genes for risk variants associated with age-related macular degeneration and glaucoma. Our studies of high-resolution genomic architecture of the human retina provide new insights into genetic control of tissue-specific functions, suggest paradigms for missing heritability, and enable the dissection of multifactorial disease phenotypes.
Project description:Chromatin states are functionally defined by a complex combination of histone modifications, transcription factor binding, DNA accessibility, and other factors. However, most current single-cell-resolution methods are unable to measure more than one aspect of chromatin state in a single experiment, limiting our ability to accurately measure chromatin states. Here, we introduce nanobody-tethered transposition followed by sequencing (NTT-seq), a new assay capable of measuring the genome-wide presence of multiple histone modifications and protein-DNA binding sites at single-cell resolution. NTT-seq utilizes recombinant Tn5 transposase fused to a set of secondary nanobodies (nb). Each nb-Tn5 fusion protein specifically binds to different immunoglobulin-G antibodies, enabling a mixture of primary antibodies binding different epitopes to be used in a single experiment. We apply bulk- and single-cell NTT-seq to generate high-resolution multimodal maps of chromatin states in cell culture and cells of the human immune system, demonstrating the high accuracy and sensitivity of the method. We further extend NTT-seq to enable simultaneous profiling of cell-surface protein expression alongside multimodal chromatin states to study cells of the immune system.