The Epigenetics of Acute and Chronic Kidney Disease
The Epigenetics of Acute and Chronic Kidney Disease
Epigenetics research has been spurred by the development of highly sensitive techniques and advances in genome sequencing that have aided in detecting epigenetic modifications such as histone modifications and DNAme, chromatin structure (open or condensed), as well as long-range interaction of enhancers in transcription regulation. Utility of these approaches to detect epigenetic changes at candidate genes has been extended to unbiased genome-wide location analyses by using microarrays and NGS. Whole transcriptome profiling by NGS (for coding and noncoding genes) and epigenome-wide association studies, which combine immunoisolation of epigenetic marks and NGS, can yield information on genome-scale dynamic changes (Table 1), whereas sophisticated bioinformatic tools can analyze the emanating terabytes of data. Such approaches have made it possible to predict different regulatory elements in chromatin, identify long noncoding RNAs and alternate splicing based on specific genome locations of epigenetic modifications. Notably, epigenomic profiling led to the characterization of enhancers in mammalian cells, including 'super enhancers', enhancer-derived RNAs and stimulus-specific 'latent enhancers'. Chromatin conformation capture (3C) assays followed by sequencing (4C-seq) demonstrate long-range enhancer interactions and regulation of promoters several 100 kilobases away. Epigenome-wide association study also revealed that single-nucleotide polymorphisms in noncoding regions may regulate chromatin structure and possibly enhancer functions in disease conditions. Each of the methods used for epigenetic profiling has strengths and weaknesses. A major advantage of NGS-based studies such as RNA-seq, ChIP-seq, bisulfite-seq, and others (Table 1) is that these unbiased approaches provide genome-wide and quantitative information unlike microarrays. However, nucleotide resolution and differences in costs, as well as the complexity of data analyses, are also key factors to be considered. In particular, there is a lot of interest in examining DNAme in clinical cohorts and choice of the specific technique among those available for the analysis of DNAme patterns (Table 1) would weigh in these specific advantages and disadvantages. Genome-wide quantification of sodium bisulfite conversion–based cytosine DNAme is the most commonly used method that can be performed by either NGS platforms or the Infinium Human Methylation 450K Bead-chips (San Diego, CA). 450K is widely used, especially for large-scale clinical projects, as an easy and relatively affordable platform with base resolution and coverage of most CpG loci and islands. Bisulfite-seq provides better resolution and genome-wide coverage compared with affinity-based methods such as Methylated DNA immunoprecipitation-seq (MeDIP-seq) or MBD-seq, but it is more expensive and it involves more complex bioinformatics analysis. Heterogeneity of cell types in renal tissues also poses a challenge in Epigenome-wide association studies, as epigenomes and transcriptomes are cell-type specific. With the rapid advent in better technologies and reduced costs, epigenome-wide association studies are increasingly being performed in wide-ranging experimental and clinical studies. Advances in epigenomics platforms and data analysis tools, as well as publicly available data sets, can therefore be exploited to gain new insights into the pathologies of common kidney diseases and uncover targets for novel epigenetic therapies.
Tools to Study Epigenetic Modifications and the Epigenome
Epigenetics research has been spurred by the development of highly sensitive techniques and advances in genome sequencing that have aided in detecting epigenetic modifications such as histone modifications and DNAme, chromatin structure (open or condensed), as well as long-range interaction of enhancers in transcription regulation. Utility of these approaches to detect epigenetic changes at candidate genes has been extended to unbiased genome-wide location analyses by using microarrays and NGS. Whole transcriptome profiling by NGS (for coding and noncoding genes) and epigenome-wide association studies, which combine immunoisolation of epigenetic marks and NGS, can yield information on genome-scale dynamic changes (Table 1), whereas sophisticated bioinformatic tools can analyze the emanating terabytes of data. Such approaches have made it possible to predict different regulatory elements in chromatin, identify long noncoding RNAs and alternate splicing based on specific genome locations of epigenetic modifications. Notably, epigenomic profiling led to the characterization of enhancers in mammalian cells, including 'super enhancers', enhancer-derived RNAs and stimulus-specific 'latent enhancers'. Chromatin conformation capture (3C) assays followed by sequencing (4C-seq) demonstrate long-range enhancer interactions and regulation of promoters several 100 kilobases away. Epigenome-wide association study also revealed that single-nucleotide polymorphisms in noncoding regions may regulate chromatin structure and possibly enhancer functions in disease conditions. Each of the methods used for epigenetic profiling has strengths and weaknesses. A major advantage of NGS-based studies such as RNA-seq, ChIP-seq, bisulfite-seq, and others (Table 1) is that these unbiased approaches provide genome-wide and quantitative information unlike microarrays. However, nucleotide resolution and differences in costs, as well as the complexity of data analyses, are also key factors to be considered. In particular, there is a lot of interest in examining DNAme in clinical cohorts and choice of the specific technique among those available for the analysis of DNAme patterns (Table 1) would weigh in these specific advantages and disadvantages. Genome-wide quantification of sodium bisulfite conversion–based cytosine DNAme is the most commonly used method that can be performed by either NGS platforms or the Infinium Human Methylation 450K Bead-chips (San Diego, CA). 450K is widely used, especially for large-scale clinical projects, as an easy and relatively affordable platform with base resolution and coverage of most CpG loci and islands. Bisulfite-seq provides better resolution and genome-wide coverage compared with affinity-based methods such as Methylated DNA immunoprecipitation-seq (MeDIP-seq) or MBD-seq, but it is more expensive and it involves more complex bioinformatics analysis. Heterogeneity of cell types in renal tissues also poses a challenge in Epigenome-wide association studies, as epigenomes and transcriptomes are cell-type specific. With the rapid advent in better technologies and reduced costs, epigenome-wide association studies are increasingly being performed in wide-ranging experimental and clinical studies. Advances in epigenomics platforms and data analysis tools, as well as publicly available data sets, can therefore be exploited to gain new insights into the pathologies of common kidney diseases and uncover targets for novel epigenetic therapies.
