Long-Range Chromatin Interactions in the Kidney

Chromatin architecture reveals cell type-specific target genes for kidney disease risk variants

BACKGROUND

Cell type-specific transcriptional programming results from the combinatorial interplay between the repertoire of active regulatory elements. Disease-associated variants disrupt such programming, leading to altered expression of downstream regulated genes and the onset of pathological states. However, due to the non-linear regulatory properties of non-coding elements such as enhancers, which can activate transcription at long distances and in a non-directional way, the identification of causal variants and their target genes remains challenging. Here, we provide a multi-omics analysis to identify regulatory elements associated with functional kidney disease variants, and downstream regulated genes.

RESULTS

In order to understand the genetic risk of kidney diseases, we generated a comprehensive dataset of the chromatin landscape of human kidney tubule cells, including transcription-centered 3D chromatin organization, histone modifications distribution and transcriptome with HiChIP, ChIP-seq and RNA-seq. We identified genome-wide functional elements and thousands of interactions between the distal elements and target genes. The results revealed that risk variants for renal tumor and chronic kidney disease were enriched in kidney tubule cells. We further pinpointed the target genes for the variants and validated two target genes by CRISPR/Cas9 genome editing techniques in zebrafish, demonstrating that SLC34A1 and MTX1 were indispensable genes to maintain kidney function.

CONCLUSIONS

Our results provide a valuable multi-omics resource on the chromatin landscape of human kidney tubule cells and establish a bioinformatic pipeline in dissecting functions of kidney disease-associated variants based on cell type-specific epigenome.

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

Posttranslational modification of nucleosomal histones is a major determinant of chromatin structure and gene activity. In the present study, we hypothesized that unilateral ureteric obstruction (UUO), a widely used model of tubulointerstitial injury, would be associated with a distinct pattern of histone modifications (marks) in the kidney. Mass spectrometry was used to profile 63 different histone marks in normal mouse kidneys and those after 10 days of UUO. A subsequent histochemical analysis further examined examples of specific marks that changed significantly after UUO for which antisera are available. Histone marks were much more widely distributed and abundant in the normal kidney than is usually appreciated. Although aggregate analysis of the mass spectrometry results revealed net differences between control and UUO groups, residue-specific variations were subtle. Of the 16/63 significant changes ( P < 0.05), only 8 changes were quantitatively different by >5%. Nevertheless, we identified several that are not usually examined in the kidney, including marks in the globular domain of core histones (H3:K79), linker histones (H1.4), and histone variants (H3.1:K27 and H3.3:K27). In several cases, there were complementary changes in different marks on the same amino acid. Using H3:K79ME2 as an example, mark enrichment was heterogeneous but largely colocalized with active transcription in a subset of tubular pathology. In conclusion, our study highlights the importance of unbiased screening in examining histone marks. Simultaneous changes in multiple marks on the same amino acid indicate a coordinated histone mark signature. The heterogeneous enrichment of marks, even within the same tubule, highlights the importance of regulatory context.