A genome is more than just an abstract sequence of nucleotides – it is a collection of DNA molecules packaged inside of our cells. Epigenomic technologies allow us to look beyond the genome sequence, revealing information about how the genome actually exists in individual cells: bound by proteins, modified by enzymes, and folded inside the dynamic 3-dimensional space of the cell's nucleus. This epigenetic information is critical for understanding how each cell type in the human body functions during normal development, and how their function goes awry in disease.
Current research at the Center for Epigenomics focuses on exploring the function of multiple aspects of the epigenome in the context of human biology and disease; these aspects include chromatin accessibility, transcription factor binding, histone modification, and 3D chromatin architecture, in both bulk samples and in single-cell resolution. Specific technologies and associated analytical tools routinely employed at the Center for Epigenomics include, but are not limited to the following.
We use Chromatin Immunoprecipitation coupled with next-generation sequencing ("ChIP-seq") to measure how proteins bind to the genome. The genome is most closely associated with packaging proteins called histones, which can be post-translationally modified by enzymes in the cell. These histone modifications are core components of a cell's epigenome. They influence the activity of functional sequences in the genome, and are maintained through cell division to pass on gene activity states from mother cell to daughter cells.
Our ChIP-seq data from the ENCODE and NIH Roadmap Epigenomics projects can be found here: https://www.encodeproject.org/search/?type=Experiment&lab.title=Bing+Ren%2C+UCSD&assay_title=ChIP-seq
We use Assay for Transposase-Accessible Chromatin coupled with high-throughput sequencing ("ATAC-seq") to identify regions of the genome with regulatory activity. These regulatory regions are accessible to the binding of regulatory proteins that influence gene expression, and thus also accessible to the transposaseenzyme used in ATAC-seq.
Our ENCODE ATAC-seq data can be found here: https://www.encodeproject.org/search/?type=Experiment&lab.title=Bing+Ren%2C+UCSD&assay_title=ATAC-seq
We use High-throughput Chromatin Conformation Capture, or "Hi-C", to map the 3-dimensional organization of chromatin inside the nucleus. Hi-C can profile features of higher-order chromatin organization, such as Topologically Associating Domains ("TADs"), chromatin compartments, and chromatin "looping" interactions. Hi-C data is also useful for assembling genomes, discovering structural variations, and long-range phasing of sequence variants.
Proximity Ligation-Assisted ChIP-seq ("PLAC-seq") combines the proximity ligation procedure of Hi-C with the immunoprecipitation procedure of ChIP-seq, to map 3D chromatin interactions between regions bound by a particular factor or modified histone. PLAC-seq is a powerful and cost-efficient method for identifying targeted chromatin interactions - such as those between enhancer and promoter elements.
Check out our recent manuscript describing this method in Cell Research: Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq. Fang R, Yu M, Li G, Chee S, Liu T, Schmitt AD, Ren B. Cell Res. 2016 Dec;26(12):1345-1348. doi: 10.1038/cr.2016.137. Epub 2016 Nov 25. PMID: 27886167
To resolve cellular heterogeneity and delineate transcriptional regulatory sequences in the constituent cell types, we analyze the transposase-accessible chromatin in single nuclei that have been isolated from tissue samples. Our single-cell strategy is based on an assay for transposase-accessible chromatin with combinatorial barcoding. It is optimized for nuclei extracted from fresh or flash-frozen tissue samples.
Check out our pre-print manuscript on bioRxiv: Single-nucleus analysis of the chromatin landscape in mouse forebrain development. Preissl S, Fang R, Zhao Y, Raviram R, Zhang Y, Sos BC, Huang H, Gorkin DU, Afzal V, Dickel DE, Kuan S, Visel S, Pennacchio LA, Zhang K, Ren B. http://www.biorxiv.org/content/early/2017/07/06/159137.
To identify and characterize distinct cell types from heterogeneous biological samples (including frozen tissue biopsies), we use single-cell and single-nucleus RNA-seq. By combining flow cytometry with the 10x Genomics Chromium Platform, we can profile the RNA expression profile of thousands of cells or nuclei.