Parker C Wilson1, Nicolas Ledru, Benjamin D Humphreys. 1. Department of Pathology and Immunology Division of Nephrology, Department of Medicine Department of Developmental Biology, Washington University in St. Louis, St. Louis, Missouri, USA.
Abstract
PURPOSE OF REVIEW: Epigenetic modifications are reversible changes to a cell's DNA or histones that alter gene expression but not DNA sequence. The present review will explore epigenomic profiling and bioinformatics techniques for the study of kidney development and disease. RECENT FINDINGS: Reversible DNA and histone modifications influence chromatin accessibility and can be measured by a variety of recent techniques including DNase-seq, ATAC-seq, and single cell ATAC-seq. These approaches have been used to demonstrate that DNA methylation is critical for nephron progenitor maturation, for example. New bioinformatics techniques allow the prediction of chromatin loops that connect regulatory elements to target genes. Recent studies have demonstrated that DNA elements regulate transcription in the kidney via long-range physical interactions and create a new framework for understanding how genome wide association studies risk loci contribute to kidney disease. Increasingly, epigenomic approaches are being combined with transcriptomic analyses to generate multimodal datasets. SUMMARY: Epigenomics has expanded our knowledge of gene architecture and regulation. Novel tools and techniques have led to the emergence of 'multiomics' in which epigenomic profiling, transcriptomics, and additional methods complement each other to improve our understanding of kidney disease and development.
PURPOSE OF REVIEW: Epigenetic modifications are reversible changes to a cell's DNA or histones that alter gene expression but not DNA sequence. The present review will explore epigenomic profiling and bioinformatics techniques for the study of kidney development and disease. RECENT FINDINGS: Reversible DNA and histone modifications influence chromatin accessibility and can be measured by a variety of recent techniques including DNase-seq, ATAC-seq, and single cell ATAC-seq. These approaches have been used to demonstrate that DNA methylation is critical for nephron progenitor maturation, for example. New bioinformatics techniques allow the prediction of chromatin loops that connect regulatory elements to target genes. Recent studies have demonstrated that DNA elements regulate transcription in the kidney via long-range physical interactions and create a new framework for understanding how genome wide association studies risk loci contribute to kidney disease. Increasingly, epigenomic approaches are being combined with transcriptomic analyses to generate multimodal datasets. SUMMARY: Epigenomics has expanded our knowledge of gene architecture and regulation. Novel tools and techniques have led to the emergence of 'multiomics' in which epigenomic profiling, transcriptomics, and additional methods complement each other to improve our understanding of kidney disease and development.
Authors: Hannah A Pliner; Jonathan S Packer; José L McFaline-Figueroa; Darren A Cusanovich; Riza M Daza; Delasa Aghamirzaie; Sanjay Srivatsan; Xiaojie Qiu; Dana Jackson; Anna Minkina; Andrew C Adey; Frank J Steemers; Jay Shendure; Cole Trapnell Journal: Mol Cell Date: 2018-08-02 Impact factor: 17.970
Authors: Jason D Buenrostro; Beijing Wu; Ulrike M Litzenburger; Dave Ruff; Michael L Gonzales; Michael P Snyder; Howard Y Chang; William J Greenleaf Journal: Nature Date: 2015-06-17 Impact factor: 49.962