Epigenetic States of nephron progenitors and epithelial differentiation

Abstract

In mammals, formation of new nephrons ends perinatally due to consumption of mesenchymal progenitor cells. Premature depletion of progenitors due to prematurity or postnatal loss of nephrons due to injury causes chronic kidney disease and hypertension. Intensive efforts are currently invested in designing regenerative strategies to form new nephron progenitors from pluripotent cells, which upon further differentiation provide a potential source of new nephrons. To know if reprogramed renal cells can maintain their identity and fate requires knowledge of the epigenetic states of native nephron progenitors and their progeny. In this article, we summarize current knowledge and gaps in the epigenomic landscape of the developing kidney. We now know that Pax2/PTIP/H3K4 methyltransferase activity provides the initial epigenetic specification signal to the metanephric mesenchyme. During nephrogenesis, the cap mesenchyme housing nephron progenitors is enriched in bivalent chromatin marks; as tubulogenesis proceeds, the tubular epithelium acquires H3K79me2. The latter mark is uniquely induced during epithelial differentiation. Analysis of histone landscapes in clonal metanephric mesenchyme cell lines and in Wilms tumor and normal fetal kidney has revealed that promoters of poised nephrogenesis genes carry bivalent histone signatures in progenitors. Differentiation or stimulation of Wnt signaling promotes resolution of bivalency; this does not occur in Wilms tumor cells consistent with their developmental arrest. The use of small cell number ChIP-Seq should facilitate the characterization of the chromatin landscape of the metanephric mesenchyme and various nephron compartments during nephrogenesis. Only then we will know if stem and somatic cell reprogramming into kidney progenitors recapitulates normal development.

Keywords: CHROMATIN SIGNATURE; EPIGENETICS; KIDNEY DEVELOPMENT; NEPHROGENESIS; NEPHRON PROGENITORS.

Figure 1

Major post-translational histone modifications on Histone H3 tail are schematized. Genomic regions or activity that associated with each modification is indicated in writings. For example, tri-methylation H3 Lysine 4 position (H3K4me3) is associated with transcriptional initiation, whereas tri-methylation of Lysine 27 position (H3 K27me3) is associated with Polycomb mediation repression.

Figure 2

Chromatin states of regulatory genomic regions are tabulated. Whole-genome mapping of histone modifications reveals specific epigenomic features at regulatory genomic regions. Integrative analysis of these marks in a given cell type allows identification cell type specific chromatin states at regulatory genomic regions such as promoters and enhancers.

Figure 3

(A) Epigenetic specification of the metanephric mesenchyme in the intermediate mesoderm prior to the onset of metanephric development (embryonic day 10). Regulatory elements of the earliest renal developmental genes carry bivalent histone marks. The transcription factor Pax2 specifies the nephric lineage by recruiting an activating histone methyltransferase complex (PTIP/MLL) thus activating nephric lineage genes [Dressler and Patel, 2014; Patel and Dressler, 2013]. (B) The histone H3 signature of Six2 stem cells and progeny as assessed by section immunofluorescence at embryonic day 15.5. Repressive histone marks are abundant in the cap mesenchyme, whereas H3K79me2 is more abundant in differentiated tubules and podocytes [McLaughlin et al., 2013a]. ND, nephric duct; NC: nephrogenic cord; PTA: pre-tubular aggregate; RV: renal vesicle; CB: C-shaped body; SB: S- shaped body; G: glomerulus; UB: ureteric bud.

Figure 4

ChIP-Seq tracks of renal progenitor genes (A) and nephrogenesis genes (B) in mouse clonal undifferentiated mK3 (Six2^high; Wnt4^low) and differentiating mK4 (Six2^low;Wnt4^high) metanephric mesenchyme-like cells. Repression of renal progenitor genes is generally achieved by loss of activating histone marks (H3K4me3) in the proximal promoters. In the case of Six2, gain of H3K9me2 also occurs (not shown). In comparison, nephrogenesis genes undergo a gain of H3K4me3, depletion of H3K27me3 or both during differentiation.

Figure 5

(A) Working model for the epigenetic regulation of nephron progenitor cell differentiation. Six2^high stem cells express high levels of HDAC1/2, Ezh2 and G9a. Histone deacetylation and methylation on H3K9 and K27 of nephrogenic genes keeps them silent yet poised for differentiation (paused PolII). Downregulation of Six2 and upregulation of β-catenin, in response to Wnt signaling, promotes the remodeling of local chromatin into an accessible state allowing the displacement of the repressive epigenetic machinery and the binding of the transcription factor-active PolII complexes. (B) In response to Wnt signaling, nephrogenesis genes are induced; this is accompanied by enhanced promoter occupancy with β-catenin, H3K4me3 and reciprocal depletion of H3K27me3/Ezh2 [McLaughlin et al., 2013b].