Profiling histone modifications in the normal mouse kidney and after unilateral ureteric obstruction

Multi-omic approaches to acute kidney injury and repair

The kidney has a remarkable regenerative capacity. In response to ischemic or toxic injury, proximal tubule cells can proliferate to rebuild damaged tubules and restore kidney function. However, severe acute kidney injury (AKI) or recurrent AKI events can lead to maladaptive repair and disease progression from AKI to chronic kidney disease (CKD). The application of single cell technologies has identified injured proximal tubule cell states weeks after AKI, distinguished by a pro-inflammatory senescent molecular signature. Epigenetic studies highlighted dynamic changes in the chromatin landscape of the kidney following AKI and described key transcription factors linked to the AKI response. The integration of multi-omic technologies opens new possibilities to improve our understanding of AKI and the driving forces behind the AKI-to-CKD transition, with the ultimate goal of designing tailored diagnostic and therapeutic strategies to improve AKI outcomes and prevent kidney disease progression.

Epigenomics and the kidney

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.