DNA Methyltransferase 1 Controls Nephron.10

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org
DNA Methyltransferase 1 Controls Nephron

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Progenitor Cell Renewal and Differentiation

Nicola Wanner,1 Julia Vornweg,2,3 Alexander Combes,4,5 Sean Wilson,4 Julia Plappert,2
nYQp/IlQrHD3i3D0OdRyi7TvSFl4Cf3VC4/OAVpDDa8K2+Ya6H515kE= on 05/01/2023
Gesa Rafflenbeul,2 Victor G. Puelles,1 Raza-Ur Rahman,6 Timur Liwinski,6,7 Saskia Lindner,2
Florian Grahammer,1 Oliver Kretz,1,8 Mary E. Wlodek,9 Tania Romano,10
Karen M. Moritz,11 Melanie Boerries,12,13,14 Hauke Busch,14,15 Stefan Bonn,6,16
Melissa H. Little,5,17 Wibke Bechtel-Walz,2 and Tobias B. Huber1,2,18,19
Due to the number of contributing authors, the affiliations are listed at the end of this article.
ABSTRACT
Background Nephron number is a major determinant of long-term renal function and cardiovascular risk.
Observational studies suggest that maternal nutritional and metabolic factors during gestation contribute to
the high variability of nephron endowment. However, the underlying molecular mechanisms have been unclear.
Methods We used mouse models, including DNA methyltransferase (Dnmt1, Dnmt3a, and Dnmt3b)
knockout mice, optical projection tomography, three-dimensional reconstructions of the nephrogenic
niche, and transcriptome and DNA methylation analysis to characterize the role of DNA methylation for
kidney development.
Results We demonstrate that DNA hypomethylation is a key feature of nutritional kidney growth restriction in
vitro and in vivo, and that DNA methyltransferases Dnmt1 and Dnmt3a are highly enriched in the nephrogenic
zone of the developing kidneys. Deletion of Dnmt1 in nephron progenitor cells (in contrast to deletion of
Dnmt3a or Dnm3b) mimics nutritional models of kidney growth restriction and results in a substantial re-
duction of nephron number as well as renal hypoplasia at birth. In Dnmt1-deficient mice, optical projection
tomography and three-dimensional reconstructions uncovered a significant reduction of stem cell niches
and progenitor cells. RNA sequencing analysis revealed that global DNA hypomethylation interferes in
the progenitor cell regulatory network, leading to downregulation of genes crucial for initiation of neph-
rogenesis, Wt1 and its target Wnt4. Derepression of germline genes, protocadherins, Rhox genes, and
endogenous retroviral elements resulted in the upregulation of IFN targets and inhibitors of cell cycle
progression.
Conclusions These findings establish DNA methylation as a key regulatory event of prenatal renal pro-
gramming, which possibly represents a fundamental link between maternal nutritional factors during
gestation and reduced nephron number.
J Am Soc Nephrol 30: 63–78, 2019. doi: https://doi.org/10.1681/ASN.2018070736
In humans, the number of nephrons is highly vari-

able, ranging from 250,000 to .2 million nephrons Received July 18, 2018. Accepted October 22, 2018.
per kidney.1 A clear inverse correlation between W.B.-W. and T.B.H. contributed equally to this work.
nephron number and the risk of developing hyper- Published online ahead of print. Publication date available at
tension and secondary renal diseases has been www.jasn.org.
shown.2,3 Known factors contributing to lower
Correspondence: Dr. Nicola Wanner or Dr. Tobias B. Huber,
nephron endowment include low birth weight III. Department of Medicine, University Medical Center Hamburg-
and in utero exposure to high-glucose, low-protein Eppendorf, Martini-Strasse 52, 20246 Hamburg, Germany. E-mail:
n.wanner@uke.de or t.huber@uke.de
diet and in utero growth restriction.4–8 During de-
velopment, reciprocal interactions between the Copyright © 2019 by the American Society of Nephrology
J Am Soc Nephrol 30: 63–78, 2019 ISSN : 1046-6673/3001-63 63

BASIC RESEARCH www.jasn.org
ureteric bud (UB) tip and the surrounding cap mesenchyme

Significance Statement
(CM) lead to induction of the renal progenitor population.
The CM represents a pluripotent stem cell niche which gives This work unravels the critical role of epigenetic modification for
rise to the nephron starting from a pretubular cell aggregate, nephron formation and nephron number. Our study shows that al-
though de novo DNA methylation is dispensable for nephron de-
which ultimately elongates and segments to form into podo-
velopment, lack of maintenance DNA methylation leads to severely
cytes, parietal epithelial cells, proximal tubule, loop of Henle, hypoplastic kidneys in the mouse model. Using whole mount optical
and distal tubule.9–11 Previous studies have shown that the stem projection tomography and 3D reconstructions of embryonic and
cell niche undergoes physiologic aging by changing its preference neonatal kidneys, we identify a dysregulation of nephron stem cell
from self-renewal toward differentiation.12,13 In mice, the niche identity leading to impaired nephron differentiation. RNA se-
quencing highlights the transcriptional programs regulated in the

population exists until shortly after birth, when a last burst of
nephron progenitor cell pool and links DNA methylation to the
differentiation into nephrons leads to its depletion.14 upregulation of germline genes and endogenous retroviral ele-
Nephron development is known to be influenced by ments, leading to an IFN response and cell cycle inhibition.
prenatal exposure to environmental conditions, which in
turn can induce changes in epigenetic patterns such as
Metanephric Organ Culture
DNA methylation and histone modification. However, there
is a paucity of information related to the role of DNA meth- Timed matings were set up with hNPHS2Cre;mT/mG (Gt
ylation for nephron development and function. During em- (ROSA)26Sortm4(ACTB-tdTomato,2EGFP)Luo/J) mice.27 Metanephric
bryonic development, DNA methylation is a dynamic yet kidneys were microdissected from the embryos at embryonic day
tightly controlled process, which contributes to the regulation 12.5 (E12.5) and cultured in MEM containing 10% FCS and 1%
of cell fate transitions.15,16 It is widely acknowledged that penicillin and streptomycin with 55 mM a-D-glucose or 5.5 mM
DNA methylation can lead to changes in DNA conformation, a-D-glucose and 55 mM mannitol, at 37°C and 5% CO2 on
thus influencing transcription factor binding.17 In mammals, 0.4-mm transwell inserts. The medium was replaced every
DNA methylation occurs mostly at CpG sites of which 48 hours. Kidney cultures were harvested after 7 days in culture.
60%–80% are methylated.18 CpG islands at promoters of
constitutively active genes are usually hypomethylated, Intrauterine Growth Restriction
whereas long-term silencing of gene expression can be estab- Wistar Kyoto rats were obtained from the Australian Resource
lished by hypermethylated promoter CpG islands. Addition- Centre (Murdoch, Western Australia, Australia) and fed stan-
ally, methylation at enhancers and insulators is crucial for dard food pellets and tap water ad libitum. Rats were housed
the silencing of imprinted loci, which confer parent allele- in a 12-hour light/dark cycle and a temperature-controlled
specific gene expression.19 Importantly, methylation at peri- room. All experiments were approved by the University of
centromeric regions leads to the repression of endogenous Melbourne Animal Ethics Committee and the La Trobe ani-
transposable elements, which make up 37.5% of the murine mal ethics committee before commencement following the
and 45% of the human genome.20,21 DNA methylation is National Health and Medical Research Council Australian
catalyzed by DNA methyltransferases using S-adenosyl-l- code for the care and use of animals for scientific purposes.
methionine as a substrate to convert cytosine into 5-methyl- Bilateral uterine vessel ligation to induce intrauterine growth
cytosine.22 DNA methyltransferase 1 (Dnmt1) preferentially restriction or sham surgery was performed on day 18 of ges-
binds to hemimethylated DNA and is crucial for restoring tation according to Wlodek et al.7,8,28 Kidneys were collected
DNA methylation patterns at replication foci, therefore ac- on postnatal day 1 from male pups.
counting for maintenance of DNA methylation during
S-phase.23–25 In contrast, Dnmt3 family members Dnmt3a Urinary and Serum Measurements
and Dnmt3b are not only essential for de novo DNA methyl- Urinary albumin and creatinine were measured at E19.5/
ation at specific sites in early postimplantation embryos, postnatal day 1 and then once per week using mouse albumin-
but also for subsequent embryonic development and tissue specific (Mikrofluoral Mikroalbumin Test; Progen) and cre-
differentiation.26 atinine kits (Creatinine PAP LT-SYS; LABOR1TECHNIK;
In this study, we investigate the link between environment, Eberhard Lehmann GmbH) according to the manufacturer’s
epigenetics, and nephron formation. instructions. Albumin-to-creatinine ratio was calculated and
expressed as milligrams of albumin per milligram of creatinine.
Serum urea was measured on E19.5/postnatal day 1 using LA-
METHODS BOR+TECHNIK (LT-SYS; Eberhard Lehmann GmbH, Berlin)
Urea Kit according to the manufacturer’s instruction using a
Animals photometer.
All animal experiments were conducted according to the
guidelines of the American Physiologic Society, as well as Histologic Analysis
the German law for the welfare of animals, and were approved Kidneys were dissected, fixed in 4% paraformaldehyde, and
by local authorities (G11/51, X13/04A, G16/85, G16/148). embedded in paraffin. For periodic acid–Schiff (PAS) and acid
64 Journal of the American Society of Nephrology J Am Soc Nephrol 30: 63–78, 2019
www.jasn.org BASIC RESEARCH
A B D
p<0.0001 p=0.0010
Low glucose
4 0.05
total kidney weight (g)

kidney area (mm2 )
0.04
0.03
2
0.02
High glucose
1
0.01
0 0.00
Low glucose High glucose Control Restricted
C E
p=0.0022 p=0.0022 p=0.0430
1.2
100
DNA methylation/ Control

1.0
% methylated CpGs
75
0.8
50 0.6
0.4
25 Low glucose
High glucose 0.2
0 0.0
LINE-1 major satellite Control Restricted
F G
E15.5
adult
H
E19.5
adult
cap mesenchyme
nephrogenic
ureteric zone
bud
pretubular
aggregate I
renal vesicle
comma-
E19.5
adult
shaped body
s-shaped
body
glomerulus
J Am Soc Nephrol 30: 63–78, 2019 DNA Methyltransferase 1 in Kidney Development 65

fuchsin–Orange G stainings, 3-mm sections were cut on a mouse anti-Pancytokeratin (1:100, ab11213; Abcam), mouse anti-
Leica microtome and analyzed and photographed with an Ax- pHH3 (1:100, Ser10 6G3; Cell Signaling Techology), anti-BrdU
ioplan 2 microscope (Zeiss) and an AxioCam camera (Zeiss). (1:100; AbdSerotec), and rabbit anti-active caspase 3 (1:1000,
AF835; R&D). Secondary antibodies and nuclear staining reagents
Transmission Electron Microscopy were obtained from Invitrogen.
For ultrastructural analysis, kidneys were fixed in 4% PFA/
0.01% glutaraldehyde for 24 hours (Serva, Heidelberg, Whole Mount Staining and Optical Projection
Germany). Samples were postfixed in 1% osmium tetroxide Tomography
in the same buffer for 1 hour and stained en bloc in 1% uranyl Kidneys were dissected from E15.5 embryos and E19.5 pups
acetate in 70% ethanol for 1 hour, dehydrated in ethanol, and and fixed and stained as described previously.29 Optical pro-
embedded in Durcopan (Plano, Wetzlar, Germany). Thin sec- jection tomography (OPT) and niche counts were performed
tions were stained with lead citrate and examined in a Zeiss as described29 with the following variations: Some whole
Leo-906 transmission electron microscope. kidney samples scanned for niche counts by OPT contained
regions where the niches were damaged and unable to be
Nephron Count counted. The surface area of these regions was estimated
Sections of 8 mm were cut from paraffin-embedded kidneys. and niche number adjusted accordingly (two samples, approx-
Because the glomerular diameter equals approximately imately 5% damage to each). Confocal imaging and cell counts
60 mm, every fourth section was stained with PAS (E19.5) or per niche were performed as described.29
anti-Nephrin immunofluorescence (E14.5, E15.5). The glo-
meruli on all sections were counted. DNA Methylation
DNA from E15.5 FACS-sorted Six2Cre, Tomato/EGFP hetero-
Immunofluorescence Staining of Kidney Sections zygous, or homozygous Dnmt1 KO animals was bisulfite
Kidneys were fixed in 4% paraformaldehyde overnight, de- converted using EpiTect Bisulfite Kit from Qiagen according
hydrated, and embedded in paraffin. The embedded tissue to the manufacturer’s instructions. Converted DNA (20 ng)
was sectioned at 6 mm with a Leica Microtome. The sections was used as template in a PCR reaction using AmpliTaq Gold
were deparaffinized in xylol/histoclear and rehydrated. (Invitrogen). PCR products were ligated into a pCR4-TOPO-
Heat-mediated antigen retrieval was performed using citrate Vector using the TOPO TA Cloning Kit for sequencing (Invi-
buffer pH 6 or Tris buffer pH 9 (caspase-3) in a steamer. The trogen) and transformed into DH10 bacteria. Clones were
sections were blocked with PBS containing 5% BSA, and in- sent for sequencing (GATC, Konstanz). Inspection, align-
cubated for 1 hour with primary antibodies. After three PBS ment, visualization, and statistics were performed with
rinses, fluorophore-conjugated Alexa secondary antibodies QUMA: quantification tool for methylation analysis.30 DNA
(Invitrogen) were applied for 30 minutes. Microscopy and from growth-restricted rats was used for global DNA methyl-
acquisition of images were performed using a Zeiss ation analysis using a 5mC DNA ELISA Kit (Zymo Research)
microscope. according to the manufacturer’s instructions.
Antibodies RNA-Seq and Data Analysis

The following primary antibodies were used: anti-5- RNA from E18.5 sorted CM (n=3) was extracted using the
methylcytosine (5mC) (1:100, ab10805; Abcam), rabbit anti-Six2 chloroform/phenol method. Then, 50 ng was sent to the
(1:200, 11562–1-AP; Proteintech), rabbit anti-Pax2 (1:100, ab37129; DKFZ (Heidelberg) for ultra-low RNA sequencing. Fastq
Abcam), guinea pig anti-Nephrin (1:200, GP-N2; Progen), rabbit reads were pseudoaligned to the mm10 genome assembly us-
anti-Jag1 (1:100, #2620; Cell Signaling Technology), rabbit anti- ing Kallisto31 and transcript read counts were aggregated to
WT1 (1:300, ab15249; Abcam), mouse anti-WT1 (1:300, clone Ensembl Gene IDs for further analysis. Differential gene ex-
6F-H2, Millipore), rabbit anti-Podocin (1:600, P0372; Sigma), pression was analyzed using the DESeq2 R library.32 P values
Figure 1. DNA methyltransferases are enriched in the nephrogenic zone of the developing kidney. (A) E12.5 metanephric kidneys
from Nphs2Cre;mT/mG (Gt(ROSA)26Sortm4(ACTB-tdTomato,2EGFP)Luo/J) reporter mice (mEGFP: podocytes, mTomato: all other cells) were
treated with 5.5 or 55 mM glucose. (B) Kidney area after 7 days of glucose treatment. n=27. Paired t test. (C) Bisulfite-sequencing
quantitation shows a reduction in DNA methylation levels of LINE-1 and major satellite elements. n$6. Mann–Whitney U test. (D) Total
kidney weight of postnatal day 1 rats with intrauterine growth restriction. (E) ELISA quantification of DNA methylation of control and
growth-restricted rat kidneys. (F) Schematic of renal development. (G) In situ hybridization shows prominent expression of Dnmt1 in the
nephrogenic zone of embryonic kidney sections and reduced expression in 8-week adult tissue. (H) In situ hybridization shows ex-
pression of Dnmt3a in the nephrogenic zone of embryonic kidney sections and reduced expression in adult tissue. (I) In situ hybrid-
ization of embryonic and adult kidney sections of Dnmt3b shows weak overall expression. Left column: scale bar, 500 mm. Middle
column: scale bar, 50 mm. Right column: scale bar, 100 mm.
A B
merge Six2 5mC
Dnmt1fl/fl
Six2Cre Dnmt1 fl/fl
merge Six2 5mC
Six2Cre;Dnmt1fl/fl
Six2 Promoter
Cre X Dnmt1
loxP loxP
C D E I
major satellite LINE-1 IAP
KO
KO
KO
HET
HET
HET
F G H
p=0.0012 p=0.0064 p=0.013
100 100 100
% methylated CpGs
% methylated CpGs
% methylated CpGs
75 75 75
50 50 50
25 25 25
0 0 0
ET
ET
KO
KO
ET
KO
H
H
J K L
p<0.00001
8
Dnmt1fl/fl
WT
kidney weight (mg)/
6
body weight (g)
4
KO
Six2Cre;Dnmt1fl/fl
0 mm 0 1 2 3 4
T
KO
W
Figure 2. Deletion of Dnmt1, but not Dnmt3a or Dnmt3b, in nephron progenitor cells results in reduced kidney mass. (A) Six2Cre mice
were bred with Dnmt1 floxed mice. (B) anti-5-methylcytosine (5mC) colocalizes with Six2 in WT cells but is absent in Dnmt1 KO cells.

were adjusted (q-values) for the false-discovery rate according methylation in the kidney, we determined the expression pat-
to Benjamini and Hochberg. GEO accession number: terns of Dnmt1, Dnmt3a, and Dnmt3b during renal develop-
GSE94089. ment. Analysis of RNA-seq data showed high expression of
Preliminary link: https://www.ncbi.nlm.nih.gov/geo/ Dnmt1 and Dnmt3a in developing kidneys, whereas Dnmt3b
query/acc.cgi?acc=GSE94089. showed lower expression levels (Supplemental Figure 2). In
adult kidneys, expression levels of all Dnmts were low. To de-

Statistical Analyses termine the localization of Dnmt expression, we performed in
Data are presented as mean6SEM throughout the text unless situ hybridization on embryonic and adult kidney sections.
otherwise specified. Statistical comparisons were performed Dnmt1-, Dnmt3a-, and Dnmt3b-positive cells were mainly lo-
using unpaired two-tailed t test where applicable and unless calized to the highly proliferative nephrogenic zone of the de-
otherwise specified. A value of P,0.05 was considered to rep- veloping kidney (Figure 1, G–I). Dnmt1 expression could be
resent statistically significant differences. Analyses were done detected in cells of the nephrogenic niche (CM), UB tips, and
using GraphPad Prism. early stages of the developing nephrons, such as renal vesicles
and comma-shaped and s-shaped bodies, but not in mature
podocytes and tubules (Figure 1G). It was also evident in the
RESULTS stromal elements of the nephrogenic zone. Expression pat-
terns for Dnmt3a were equally enriched in the nephrogenic
DNA Methylation Is Reduced in Models of zone and nephron precursors, whereas Dnmt3b was only
Environmental and Intrauterine Growth Restriction weakly expressed (Figure 1, H and I). After cessation of neph-
In utero exposure to environmental stressors such as gesta- rogenesis, expression of all Dnmts was greatly reduced,
tional diabetes and dietary restriction has been shown to in- resulting in only residual expression in the adult renal tissue
fluence renal growth.33 To gain understanding of the effect of (Figure 1, G–I).
the environment on DNA methylation, E12.5 metanephric
organs were cultured under low- and high-glucose conditions Deletion of Dnmt1, but Not Dnmt3a or Dnmt3b,
(Figure 1A). After 7 days, the kidney size and nephron number in Nephron Progenitor Cells Results in Reduced
showed a significant reduction under high-glucose conditions Kidney Mass
(Figure 1B, Supplemental Figure 1). At the same time, DNA To investigate the role of Dnmts for nephron formation, we
methylation at two repetitive sequences, long interspersed nu- generated conditional transgenic Six2-TGC tg (Six2Cre);
clear element-1 (LINE-1) and major satellite elements, Dnmt1fl/fl KO mice and Six2-TGCtg(Six2Cre);Dnmt3afl/fl;
showed partial DNA demethylation of 20% and 28%, respec- Dnmt3bfl/fl KO mice (Figure 2A, Supplemental Figure 3A).35
tively, suggesting global DNA methylation changes in the renal Utilizing the Cre-loxP system, the catalytic domains are ex-
tissue (Figure 1C). cised resulting in loss of Dnmt1 and Dnmt3a/b function, re-
As an additional in vivo model of renal hypoplasia, the spectively, in the CM and its derivatives starting from about
kidneys of postnatal day 1 rat offspring were analyzed. This E10.5. Deletion of Dnmt3a/b in the nephron progenitor cells re-
model of intrauterine growth restriction mimicking uteropla- sulted in normal renal development and function, as indicated by
cental insufficiency has been previously shown to lead to a kidney size, long-term follow-up kidney morphology, body
decreased nephron number.7,8,34 Corresponding to a reduc- weight, and urinary analysis (Supplemental Figure 3, B–F).
tion in kidney weight of the same animals, analysis of global Dnmt1 is crucial for maintaining DNA methylation pat-
DNA methylation also showed a decreased methylation rate in terns after cell division. Therefore, we verified passive deme-
the kidneys 8,34 (Figure 1, D and E). thylation caused by Dnmt1 deletion from nephron progenitor
cells in the kidney by immunofluorescence staining using an
DNA Methyltransferases Are Enriched in the antibody against methylated cytosine (5mC) on E19.5 kidneys
Nephrogenic Zone of the Developing Kidney sections. In Dnmt1 conditional knockout (cKO) tissues, 5mC
During renal development, the metanephric mesenchyme un- intensity was drastically reduced in cells of the CM and their
dergoes dynamic changes in the nephrogenic zone, where UB descendants, whereas the surrounding stromal cells and cells
branching, induction of the CM, and the births of new neph- from the ureter showed a specific nuclear staining (Figure 2B).
rons take place (Figure 1F). To understand the role of DNA Intensity of 5mC was also reduced in more mature, medullary
Scale bar, 50 mm. (C–E) Bisulfite sequencing of major satellite regions, LINE-1 elements, and intracisternal A particles (IAPs). (F–H) quan-
tification of methylation levels of major satellite regions, LINE-1, and IAP elements. Statistical significance was evaluated using Mann–
Whitney U test. (I) Production of retrotransposon particles can be seen in electron microscopy. Scale bars: top, 2.5 mm; middle, 1 mm;
bottom, 250 nm. Arrows, particle-producing cells. (J) Kidney-to–body weight ratio is reduced in Dnmt1 cKO mice at E19.5 (WT: n=45 and
KO: n=19). (K) Macroscopic images of E19.5 WT and Dnmt1 KO kidneys. (L) PAS staining of E19.5 kidney sections shows increased stroma
and lack of epithelial structures in Dnmt1 cKO. Scale bars: left, 500 mm; right, 50 mm. HET, heterozygous; KO, knockout; WT, wildtype.
A Dnmt1fl/fl Six2Cre;Dnmt1fl/fl B
1500 p=0.030
1250
E14.5
1000
750
# of glomeruli
500 p=0.040
80
60
40 p=0.031
E15.5
20
10
0
KO
KO
KO
T
T
W
W
E14.5 E15.5 E19.5
E19.5
C 15 p<0.0001
Weight (mg)
10
Pax2 Nephrin
D Dnmt1fl/fl Six2Cre;Dnmt1fl/fl 5 n.s.
0.6
Volume (mm3)
renal vesicle
0.4 n.s.
0.2
0.0
KO
KO
KO
T
T
W
W
E14.5 E15.5 E19.5
comma-shaped body
E Dnmt1fl/fl Six2Cre;Dnmt1fl/fl
Nephrin Podocin
s-shaped body
F
immature glomerulus
Jag1 WT1

nephrons, with very few cells retaining the 5mC signal (Sup- counted. In cKO animals, the number of glomeruli was re-
plemental Figure 4). To further quantify demethylation levels duced to almost half of the numbers measured in WT animals
in DNA from FACS-sorted CM cells, specific loci in the mouse at E14.5, E15.5, and E19.5 (Figure 3, A and B). Because kidney
chromosomes were tested for methylation by bisulfite PCR. size was still equal between cKO and WT animals at E14.5 and
Major satellite regions around mouse centromeres showed the E15.5, the reduction of nephrogenesis seemed to precede the
most severe changes in their methylation patterns (87% de- retardation of renal growth in cKO mice (Figure 3C). At E19.5,
methylation) (Figure 2, C and F). Likewise, transposable ret- nephron number was reduced even in relation to kidney
roviral elements such as LINE-1 and intracisternal A particles weight. To confirm that the process of nephron differentiation
(IAPs) were also partially demethylated in the absence of itself was not impaired but followed the normal developmen-
Dnmt1 (26% and 41%, respectively; Figure 2, D, E, G, and tal program, cKO and WT kidney sections were stained for the
H). Electron microscopic analysis on E19.5 (postnatal day 0) proximal nephron marker WT1 and the distal/intermediate
confirmed a partial lack of transcriptional silencing of repet- marker Jag1. All precursor stages of the nephron, such as renal
itive elements such as IAPs in cells originating from the CM vesicles, comma-shaped bodies, s-shaped bodies, and imma-
such as nephron precursors, as well as tubular cells and podo- ture/mature glomeruli, were found in the Dnmt1 cKO animals
cytes, by showing pseudoviral vesicle production (Figure 2I). with correct polarization (Figure 3D). The filtration unit of the
For the phenotypic analysis, Dnmt1 cKO mice and their nephron, the glomerulus, from Dnmt1 cKO animals expressed
littermates were examined at E19.5. The pups were born at mature markers of the slit diaphragm, such as Nephrin and
the expected Mendelian rates and no differences could be Podocin, and mature podocyte foot processes and slit dia-
found in the body weights (Supplemental Figure 5, A and phragms could be seen in electron microscopy, indicating nor-
B). However, analysis of the kidneys showed a 42% reduction mal glomerular development (Figure 3, E and F).
of kidney weight–to–body weight ratio in homozygous cKO
animals compared with wildtype (WT) animals (Figure 2, J Dnmt1 Depletion Leads to Reduced Self-Renewal of
and K). Histologic analysis of sectioned E19.5 kidneys the Progenitor Pool
showed a reduction of epithelial structures in the Dnmt1 The differentiation of nephrons is initiated by condensation of
cKO kidneys. PAS-positive proximal tubules were decreased, cells from the CM. To analyze the nephron progenitor pool in
whereas stromal tissue increased substantially (Figure 2L, Sup- detail, we performed whole mount stainings of Dnmt1 hetero-
plemental Figure 5D). Nevertheless, no fibrotic regions were zygous and homozygous KO kidneys for the niche marker Six2
detectable. Furthermore, renal functional parameters, such as and the ureter marker Pancytokeratin and analyzed 3D recon-
albuminuria and serum urea, did not differ from WT litter- structions of the kidneys from OPT and confocal imaging.29,36
mate controls (Supplemental Figure 5, E and F). In E15.5 kidneys, kidney length, niche number, and cells
In order to understand the role of maintenance and de novo per niche were the same in Dnmt1 cKO and heterozygous
DNA methylation in differentiated renal cells, such as podo- animals (Figure 4A). However, at E19.5 the morphology of
cytes, we crossed Nphs2Cre mice with Dnmt1 floxed, Dnmt3a the caps was changed in the Dnmt1 cKO animals (Figure 4B,
floxed, and Dnmt3b floxed mice to generate podocyte-specific Supplemental Movies 1 and 2). The total niche number of
Dnmt1 single, Dnmt3a/b double, and Dnmt1/3a/3b triple 3D-reconstructed kidneys at E19.5 indicated a reduction of
knockout mice (Supplemental Figure 6, A–C). None of these 20% in the cKO animals (Figure 4C). This indicates a reduction
mouse lines showed impaired renal development and func- in ureteric branching. Furthermore, at E19.5, the cap cell num-
tion, as indicated by their renal morphology after 9 months bers per niche were reduced in cKO mice (Figure 4D).
and long-term urinary follow-up (Supplemental Figure 6, To investigate whether changes in the proliferation rate were
D–M). responsible for the reduced nephron progenitor cell number
in Dnmt1 cKO, Dnmt1 heterozygous and cKO kidneys were
Dnmt1 Is Required for Efficient Nephron Formation tested for Bromodeoxyuridine (BrdU) incorporation. For this,
The decrease of epithelial structures in the Dnmt1 cKO kidneys the number of Six2Hi cells representing the nephron progen-
indicated a reduced number of nephrons. Therefore, kidneys itor cell population was counted and the percentage of cells
of WTand cKO animals were examined with podocyte marker that had incorporated BrdU quantified at E18.5 (Figure 4E,
Nephrin and the total number of glomeruli of each kidney was Supplemental Figure 7A). A significant difference was found
Figure 3. Dnmt1 is required for efficient nephron formation. (A) Pax2 and Nephrin immunofluorescence stainings of Six2Cre;Dnmt1
WT and KO E14.5, E15.5, and E19.5 kidney sections. Scale bar, 50 mm. (B) Total number of glomeruli determined from kidney cross-
sections at E14.5 (n=3), E15.5 (n=6), and E19.5 (n=3). (C) Volume of E14.5 (n=3) and E15.5 (n=6) WT and KO kidneys determined from
sections, weight of E19.5 kidneys (WT: n=45 and KO: n=19). (D) Immunofluorescence staining of distal/intermediate nephron marker
Jag1 and proximal marker WT1 showing all stages of nephron precursor stadiums. Scale bar, 10 mm. (E) Immunofluorescence stainings
of slit diaphragm markers Nephrin and Podocin, showing mature podocytes. Scale bar, 10 mm. (F) Electron microscopy of the glo-
merular filtration barrier showing mature podocyte foot processes. Scale bar, 250 nm. KO, knockout; WT, wildtype.
A C
p=0.027
3000
Six2Cre;Dnmt1fI/+
HET
KO
2500
Number of niches
2000
p=0.165
1500
600
400
Six2Cre;Dnmt1fI/fI
200
.5
.5
5
9
E1
E1
Six2 Six2 Pancytokeratin
B D
200
p=0.061 HET
Six2Cre;Dnmt1fI/+
KO
Number of cells per niche
150
100
p=0.028
50
Six2Cre;Dnmt1fI/fI
0
5
5
5.
9.
E1
E1
Six2 Six2 Pancytokeratin
E F G
p=0.047 p=0.876 p=0.00015
0.40 0.8
% BrdU-pos Six2Lo cells
% BrdU-pos Six2Hi cells
150000
Estimated number of
total progenitor cells
HET
0.6 KO
0.35 100000
0.4
0.30 50000
0.2
0.25 0.0 0
ET
ET
KO
KO
5
5.
9.
H
H
E1
E1
Figure 4. Dnmt1 depletion leads to reduced self-renewal of the progenitor pool. (A) OPT 3D reconstruction of the Six2-positive
nephron progenitor niches and Six2 and pan-cytokeratin confocal images of Six2Cre;Dnmt1 HET and KO kidneys at E15.5. Scale bars,
300 and 50 mm, respectively. (B) OPT 3D reconstruction of the Six2-positive nephron progenitor niches and Six2 and pan-cytokeratin

between heterozygous and homozygous Dnmt1 cKO niche DNA Hypomethylation Leads to Transcriptional
populations, indicating that loss of Dnmt1 led to a reduction Derepression of Germline Genes and ERVs
in CM proliferation. Furthermore, the number of Six2Lo cells, To understand the direct effect of Dnmt1 cKO–dependent hy-
representing cells undergoing differentiation into renal vesi- pomethylation, we compared the differentially expressed
cles, was quantified for BrdU incorporation. However, no dif- genes with DNA methylation data from Dnmt1 cKO versus
ferences in the proliferation rate could be detected between WT (external data36). From the 1716 upregulated genes, the
heterozygous and cKO animals (Figure 4F). promoter regions of 481 genes were found to be significantly
Estimation of the total progenitor numbers at E15.5 and hypomethylated in the external data set (28%, P,6.01e211;
E19.5 from niche number and cell counts shows that the lower Figure 6A). From the downregulated genes, only 28 were
found to be hypermethylated (P,2.85e204; Figure 6B). In
niche number and reduced cell count add up to an overall

progenitor deficit of 46% in the organ as a whole (Figure 4G). comparison, transcriptome data from whole kidney Six2Cre;
To exclude enhanced apoptosis as a cause for the reduced Dnmt1 cKO animals showed little overlap (upregulated and
CM population and nephrogenesis upon differentiation of the hypomethylated genes, P,0.06; downregulated and hyperme-
nephron progenitors, E19.5 renal sections were stained for the thylated genes, P,0.002). In the nephron progenitor cells, the
apoptosis marker active caspase-3 and the number of positive upregulated and hypermethylated genes were involved in mei-
cells in the nephrogenic zone was quantified. Here, no differ- osis, immune response, adhesion, and metabolism (Figure
ences were detectable between WT and cKO (Supplemental 6C). Among the upregulated and hypermethylated genes
Figure 7, B–D). were many genes normally not expressed in the kidney, such
as the germline genes Dazl, Sohlh2, Mov10l1, Tex19.1, and
Absence of Dnmt1 Disrupts Transcriptional Programs Tuba3a,38 which have been described to be upregulated during
Regulating Progenitor Identity DNA hypomethylation in cancer. Furthermore, protocadher-
The consequences of DNA hypomethylation on transcriptional ins, Rhox homeobox genes, and heat shock proteins were up-
activity were examined by next generation RNA sequencing of regulated and hypomethylated. The upregulation of several
FACS-sorted cells from the nephrogenic niche. Of all genes, 2626 genes was validated by RT-qPCR analysis (Supplemental
genes (12.52%) were differentially regulated (q-value ,0, 1), Figure 8) and demethylation of the promoter region of Tuba3a
1716 genes (65.35%) were upregulated, and only 910 genes was validated by bisulfite sequencing, showing global loss of
(34.65%) were downregulated (Figure 5A). Pathway analysis methylation in an otherwise fully methylated locus (Figure
on the basis of the REACTOME database was performed with 6D). Alignment of the RNA-seq reads also showed expression
differentially regulated genes to explore the functional impli- of endogenous retroviral transcripts, specifically IAPs,
cations of the alterations observed (Figure 5B). Collagen for- whereas LINE elements were not derepressed (Figure 6E, Sup-
mation and extracellular matrix organization as well as Wnt plemental Figure 9). Transcription of endogenous retroviral
signaling pathways were downregulated, suggesting a crucial DNA was accompanied by the enrichment of gene upregula-
role of stromal formation and Wnt communication in renal tion in response to interferon (IFN) type I in gene set enrich-
development. Upregulated genes were involved in carbohy- ment analysis (P=8310212) (Figure 6F), including genes
drate and amino acid metabolism as well as inflammatory transmitting an antiviral response, such as Irf1, Il15, Ifit1,
response (neutrophil deg ranulation) (Figure 5B). and Oas1a. Cell cycle regulators p53 (Trp53) and p21 (Cdkn1a)
Strikingly, a gene set of the top 500 enriched genes in the P0 were upregulated, but not hypomethylated. Altogether, the
CM showed a strong negative correlation (P=931024) and data indicate that Dnmt1 deficiency leads to global DNA hy-
downregulation in KO cells (Figure 5C). Whereas CM marker pomethylation and upregulation of ectopic gene and retroviral
genes such as Cited1, Hoxd11, Hoxc8, Wt1, and Meox2 were elements, interfering with the progenitor cell regulatory net-
significantly downregulated, other markers, such as Six2, work (Figure 6, G and H).
Eya1, or Osr1, showed only slight declines in expression levels
(Figure 5D). Validation of CM markers Cited1 and Wt1
mRNA showed a lack of expression of both genes in the DISCUSSION
CM, whereas Wt1 seemed to be re-expressed in the developing
nephron (Figure 5, E and F, Supplemental Figure 7B). Overall, Environmental influences, such as low-protein diet and dietary
these data suggest that key developmental programs are dys- restriction, have been shown to lead to renal hypoplasia and
regulated in the nephron progenitor cells. lower nephron endowment in utero. 7,8,39 Because DNA
confocal images of HET and KO kidneys at E19.5. Scale bars, 400 and 50 mm, respectively. (C) Total number of niches at E15.5 and E19.5
using OPT analysis (n=8 and n=5, respectively). One-tailed P value. (D) Number of cells per niche, determined by confocal imaging (E15.5, HET:
n=7, KO: n=8, and E19.5: n=5). One-tailed P value. (E) Quantification of BrdU-positive Six2Hi cells on E18.5 kidney sections (HET: n=5 and
KO: n=4). (F) Quantification of BrdU-positive Six2Lo cells on E18.5 kidney sections (HET: n=5 and KO: n=4). (G) Estimated total progenitor cell
number at E15.5 and E19.5 from niche number and cell number per niche (HET: n=7 and KO: n=5). HET, heterozygous; KO, knockout.
A B
Total Diff. regulated SLC−mediated transmembrane transport
Upregulated Downregulated Metabolism of amino acids and derivatives
Transport of small molecules
20979 Metabolism of carbohydrates
910 34.65 %
2626 Neutrophil degranulation

1716 Collagen formation
65.35 % Signaling by WNT
Collagen biosynthesis and modifying enzymes
Extracellular matrix organization
–2 0 2 4 6
Signal strength
C D
Cited1
CM top 500
Six2
p=9*10-4
CM Cited1
0.8 Six2
2 RV Meox1
Six2
Wnt4 Eya1
Eya1
Scaled expression
0.4
Wnt4
log2 fold change
0 0
-0.4
-2
-0.8
* * * * *
* * * * * *
-1.2 * * * * * * *
* * * * * * * * * * *
Cited1
Hoxd11
Hoxc8
Hoxc6
Wt1
Meox2
Hoxc4
Foxd2
Wnt4
Osr1
Eya1
Gas1
Hoxa11
Six2
Sall1
Crym
Meis2
Gdnf
Pax2
Spock2
Fgf1
Bmp7
Meox1
HET2
HET1
HET3
KO1
KO2
KO3
E F
Dnmt1fl/fl Six2Cre;Dnmt1fl/fl Dnmt1fl/fl Six2Cre;Dnmt1fl/fl
CM UB
CM
UB
UB
Cited1
WT1
CM
UB
CM
Figure 5. DNA methylation controls transcriptional programs regulating progenitor identity and differentiation. (A) Pie chart of
differentially regulated genes (q-value,0.1) (B) Top up- and downregulated REACTOME pathways. (C) Heatmap of P0 CM-specific
genes ranked top 500 and corresponding gene set enrichment analysis score. (D) Log2 fold-change of CM marker genes. Asterisks,
differentially regulated genes. (E) In situ hybridization of Cited1 and (F) Wt1 in WT and KO kidney sections. Scale bar, 50 mm. Diff.,
differentially; RV, renal vesicle.
methyltransferases rely on substrates derived from folate and in nephron progenitor cell renewal and nephron formation.
methionine, a direct link between environmental conditions Our own data confirmed decreased methylation levels under
and epigenetic regulation has been established.40 Several stud- in vitro high-glucose conditions, as well as in an intrauterine
ies show the effect of nutrition, such as dietary or protein growth restriction model of placental insufficiency. Condi-
restriction, on the expression of Dnmts and global DNA tional depletion of DNA maintenance methyltransferase
methylation.41,42 Here, we report the role of DNA methylation Dnmt1 but not de novo methyltransferases Dnmt3a and

A C
GO Biological Process
8
7
Upregulated Hypomethylated
6
-LOG10[qval]
1235 481 6001 5

4
3
28% p < 6.007e-11 2

1
B 0
is s e n n s s ity n t
Downregulated Hypermethylated os es ns s io s io es es iv tio en
ei ro
c
sp
o
he he ro
c
ro
c
ac
t
un
c
pm
m d p p
rp re la la
d
m m tic ar
f
el
o
882 28 la e l a e e y l v
420
llu un ce ic st st tal cu de
ce m og sy sy ca ol
e re
im ol e e of tu
bi un un
m c
m m on of tru
ti n s
im im la io al
3% p < 2.847e-04 of u lat ic
eg gu
i on r om
l at re at
D gu an
re
Tuba3a ve
s iti
po
KO
F Alpha interferon response

HET
Scaled expression
p=8*10-12 -2 0 2
E
IAPLTR1_Mm#LTR/ERVK
KO
HET2
HET1
HET
HET3
chr16:11,679,000-11,686,000 KO3
KO1
G
KO2
Ep300
Osr1
H
Dnmt1
Dnmt1 WT Dnmt1 KO
Nr2f2
Eya1 Cell cycle
DNA hypomethylation
Pax2 Trp53
Six2 Cdkn1a Genes, ERV... Genes, ERV...
Gdnf
Wt1 Transcription dsRNA
factors, germline transcriptional IAPs
Hoxd11 regulator
Ret Wnt4 genes etc
Wnt11 RV Progenitor Immune

CM survival and Wnt9b WT1 IFN
induction & cell markers response
UB induction
Lef1 differentiation
log2FC
Wnt4 Differentiation
Wnt4 p53/p21 Cell cycle
inductors repressors
-2 -1 0 1 2
up
down differentiation cell cycle
Dnmt3b in the murine nephron progenitor population led to Cited1,48 Eya1, and Meox2, as well as many genes from the Hox
hypoplastic kidneys, with reduced nephrogenesis and tran- gene cluster, was significantly downregulated, an overall shift in
scriptional changes in the CM population. gene expression of marker genes such as Six2,49 Osr1, and Sall1
Although Dnmt1 depletion clearly affects nephron devel- was detectable, indicating a broad dysregulation of progenitor
opment, de novo DNA methylation seems to be dispensable for cell identity. Because initiation of nephron differentiation is
nephron development because deletion of both Dnmt3a and likely dependent on a threshold in expression levels, this
Dnmt3b did not perturb nephrogenesis and long-term renal might be the cause of delay in nephrogenesis under
function, despite the fact that Dnmt3a is highly expressed in Dnmt1 cKO conditions. Of the genes responsible for neph-
the nephrogenic zone and both have been shown to play im- ron induction and activation of mesenchymal-to-epithelial
portant roles in stem cell differentiation and stem cell prolif- transition, expression of Wt1 and its target Wnt4, crucial for
eration.43 Furthermore, loss of Dnmt3a and Dnmt3b has initiation of nephrogenesis, were reduced. 50,51 However,
previously been shown to lead to demethylation due to a mi- because DNA hypomethylation usually results in derepres-
nor contribution to maintenance methylation.26 Therefore, sion of gene activation, downregulated gene expression is
the lack of phenotype indicates that at this stage of nephro- most likely a secondary effect of gene dysregulation. Besides
genesis de novo DNA methylation might not be further re- the diminished capacity for nephrogenesis, the capacity for
quired for cell fate decisions of the nephrogenic niche. cap mesenchymal proliferation in Dnmt1 cKO renal pro-
Likewise, our analysis of Dnmt1-deficient differentiated po- genitor cells was also decreased, leading to gradual changes
docytes showed that these cells were not functionally depen- in CM morphology and reduced niche numbers. Even
dent on Dnmt1 activity under physiologic conditions. Because though the effect on cell proliferation is subtle, the immense
they are terminally differentiated, there seems to be no require- proliferative activity of the progenitor cells causes an accu-
ment for maintenance of DNA methylation, which concords mulative reduction and premature exhaustion of the niche,
with the low Dnmt1 expression status. Furthermore, Dnmt3a/b which also affects ureteric branching. Upregulated as a re-
function in podocytes was dispensable, as is the loss of function sponse to endogenous retrovirus-like particle production,
of all three Dnmts together. The stable renal function observed IFN signaling is known to have a strong antiproliferative/
until 9 months of age in Dnmt cKO animals indicates no phys- antitumoral effect via activation of p53/p21.52–56 Overall,
iologic long-term adverse effects, although a change in sensi- the derepression of genes and endogenous retroviral ele-
tivity to renal injury cannot be excluded and is an interesting ments seems to result in the activation of pathways dealing
line for future investigation.44 Indeed, several studies indicate with changes in cell cycle, immune system, and metabolism,
that DNA methylation plays a role in diabetic nephropathy or thereby changing the regulation of proliferation and differ-
hypertensive nephrosclerosis, both of which are known to be entiation.57 Thus, our study on the role of DNA methyl-
podocyte dependent.45,46 transferases in kidney development describes a possible
In contrast to differentiated cells, we show that maintenance mediating role for DNA methylation between gestational
of DNA methylation plays a key role during nephron develop- environmental stressors, such as metabolic influences, and
ment. Loss of Dnmt1 in nephron progenitor cells led to a strong renal hypoplasia.
reduction of DNA methylation in all cells originating from the To our knowledge, this study is the first comprehensive
CM. This is in accordance with previous reports showing a analysis of the regulatory function of DNA methylation during
global approximately 80% decrease of DNA methylation after renal development and podocyte homeostasis showing that
deletion of Dnmt1.47 Furthermore, decreased DNA methylation Dnmt1, but not Dnmt3a or Dnmt3b, is a key regulator of the
greatly influenced the behavior of the nephron progenitor pop- renal stem cell niche during glomerular development,
ulation. First of all, we observed a greatly diminished capacity for whereas long-term podocyte homeostasis and function do
nephrogenesis starting as early as E14.5, and hence before any not depend on DNA methyltransferase activity. Our study
detectable slowdown in branching or niche reduction. This re- indicates that DNA demethylation results in derepression
sulted in a decrease of nephron generation of about 50% at birth. and transcriptional activation of genes and endogenous ret-
Although the expression of only a few CM-specific genes, such as roviral particles in the CM, leading to reduced progenitor cell
Figure 6. DNA hypomethylation leads to transcriptional derepression of germline genes and ERVs. (A) Overlap of upregulated genes
in the Dnmt1 KO progenitor cells and DNA hypomethylated regions. (B) Overlap of downregulated genes in the Dnmt1 KO progenitor
cells and hypermethylated regions. (C) GO terms “Biological Process” of upregulated and hypomethylated genes. (D) Bisulfite se-
quencing of the Tuba3a promoter region shows DNA hypomethylation. (E) RNA sequencing shows transcription of reads aligning to
IAP elements. ERVK, endogenous retrovirus-K; LTR, long terminal repeat; Mm, Mus musculus. (F) Heatmap of genes upregulated in
response to a-IFN proteins and corresponding GSEA score. (G) Regulatory network of the CM with potentially inhibited cellular
functions. RV, renal vesicle. (H) Dnmt1 KO results in reactivation of genes and endogenous retrovirus-like particles (ERVs) inducing an
IFN response, influencing cell cycle progression and Wt1 gene expression and resulting in reduced differentiation of nephrons. FC, fold
change; GO, gene ontology; HET, heterozygous; IAP, intracisternal A particle; KO, knockout; WT, wildtype.

renewal and differentiation capacity by the nephrogenic DISCLOSURES

niche. None.
This article contains the following supplemental material online at http://

ACKNOWLEDGMENTS jasn.asnjournals.org/lookup/suppl/doi:10.1681/ASN.2018070736/-/
DCSupplemental.
We thank L. Hein for providing Dnmt3a/bfl/fl mice. We thank Betina
Kiefer, Charlotte Meyer, and Barbara Joch for expert technical as-
sistance and all members of our laboratory for helpful discussions SUPPLEMENTAL MATERIAL
and support. The authors greatly acknowledge the Genomics and

Proteomics Core Facility, German Cancer Research Center/DKFZ,
Supplemental Figure 1. Nephrin number is decreased in kidneys grown on
Heidelberg, Germany for their sequencing service. high glucose medium.
The Galaxy server that was used for some calculations is in part Supplemental Figure 2. Dnmt1 and Dnmt3a are highly expressed during
funded by Collaborative Research Centre 992 Medical Epigenetics kidney development.
(Deutsche Forschungsgesellschaft [DFG] grant SFB 992/1 2012) and Supplemental Figure 3. Dnmt3a/b function is dispensable for nephron
the German Federal Ministry of Education and Research (Bundes- development.
ministerium für Bildung und Forschung [BMBF] grants 031 A538A/ Supplemental Figure 4. Lineage tracing of Dnmt1 KO cells using 5mC.
A538C RBC, 031L0101B/031L0101C de.NBI-epi, 031L0106 de.STAIR Supplemental Figure 5. Renal parameters of Dnmt1 KO animals.
[de.NBI]). This work is supported by a Marie Curie European Union Supplemental Figure 6. Podocyte function does not rely on DNA methyl-
transferase activity.
grant (CIG 293568) (to W.B.-W.), the Margarete von Wrangell Habil-
Supplemental Figure 7. Proliferation and survival rate of renal progenitor
itationsprogramm (Ministerium für Wissenschaft Baden-Württemberg)
cells.
(to W.B.-W.), and the Mathilde-Wagner-Habilitationspreis (to W.B.-W.).
Supplemental Figure 8. Germline genes are upregulated in the Dnmt1 KO
Furthermore, this study was supported by the German Research kidney.
Foundation (DFG): CRC 1140 (to T.B.H.), CRC 1192 (to T.B.H.), Supplemental Figure 9. IAPs are specifically expressed upon loss of Dnmt1.
CRC 992 (to T.B.H.), EXE306 (to H.B.), and CRC 850 (to M.B.); by
the Heisenberg program (to T.B.H.); by the European Research
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AFFILIATIONS
2
Faculty of Medicine, Department of Medicine IV, Medical Center–University of Freiburg, and 8Department of Neuroanatomy, University of
Freiburg, Freiburg, Germany; 1III. Department of Medicine, 6Institute of Medical Systems Biology, Center for Molecular Neurobiology, and
7
I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; 3Faculty of Biology, 14Institute of
Molecular Medicine and Cell Research, 18Centre for Biological Signalling Studies (BIOSS) and Center for Biological Systems Analysis
(ZBSA), and 19Freiburg Institute for Advanced Studies, Albert Ludwig University of Freiburg, Freiburg, Germany; Departments of 4Anatomy
and Neuroscience, 9Physiology, and 17Pediatrics, University of Melbourne, Melbourne, Australia; 5Cell Biology Theme, Murdoch Children’s
Research Institute, Melbourne, Australia; 10Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Victoria,
Australia; 11Child Health Research Centre and School of Biomedical Sciences, University of Queensland, St. Lucia, Queensland, Australia;
12
German Cancer Consortium, Heidelberg, Germany; 13German Cancer Research Center, Heidelberg, Germany; 15Lübeck Institute of
Experimental Dermatology, Lübeck, Germany; and 16Laboratory of Computational Systems Biology, German Center for
Neurodegenerative Diseases (DZNE), Tübingen, Germany

DNA Methyltransferase 1 Controls Nephron.10

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DNA Methyltransferase 1 Controls Nephron

Progenitor Cell Renewal and Differentiation

J Am Soc Nephrol 30: 63–78, 2019. doi: https://doi.org/10.1681/ASN.2018070736

In humans, the number of nephrons is highly vari-

J Am Soc Nephrol 30: 63–78, 2019 ISSN : 1046-6673/3001-63 63

ureteric bud (UB) tip and the surrounding cap mesenchyme

quencing highlights the transcriptional programs regulated in the

total kidney weight (g)

DNA methylation/ Control

J Am Soc Nephrol 30: 63–78, 2019 DNA Methyltransferase 1 in Kidney Development 65

Antibodies RNA-Seq and Data Analysis

merge Six2 5mC

J Am Soc Nephrol 30: 63–78, 2019 DNA Methyltransferase 1 in Kidney Development 67

adult kidneys, expression levels of all Dnmts were low. To de-

D Dnmt1fl/fl Six2Cre;Dnmt1fl/fl 5 n.s.

J Am Soc Nephrol 30: 63–78, 2019 DNA Methyltransferase 1 in Kidney Development 69

Six2 Six2 Pancytokeratin

J Am Soc Nephrol 30: 63–78, 2019 DNA Methyltransferase 1 in Kidney Development 71

niche number and reduced cell count add up to an overall

2626 Neutrophil degranulation

Extracellular matrix organization

J Am Soc Nephrol 30: 63–78, 2019 DNA Methyltransferase 1 in Kidney Development 73

1235 481 6001 5

28% p < 6.007e-11 2

F Alpha interferon response

Wnt11 RV Progenitor Immune

J Am Soc Nephrol 30: 63–78, 2019 DNA Methyltransferase 1 in Kidney Development 75

renewal and differentiation capacity by the nephrogenic DISCLOSURES

This article contains the following supplemental material online at http://

and support. The authors greatly acknowledge the Genomics and

J Am Soc Nephrol 30: 63–78, 2019 DNA Methyltransferase 1 in Kidney Development 77

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