Background
In vertebrates, hematopoiesis takes place in two consecutive waves, primitive and definitive ones [
1,
2]. Primitive hematopoiesis, also known as embryonic hematopoiesis, predominantly produces erythroid and myeloid cells [
3,
4]; while definitive hematopoiesis, also called adult hematopoietic wave, generates hematopoietic stem cells (HSCs) that are capable of producing all lineages of blood [
5]. The zebrafish (Daniorerio) is an excellent genetic system for the study of hematopoietic development [
6,
7], especially by characterization of thousands of mutants isolated from large-scale forward genetic screens [
8,
9]. In zebrafish, definitive HSCs arise from the ventral wall of the dorsal aorta (VDA), the zebrafish equivalent of the aorta/gonad/mesonephros (AGM) of mammals [
10,
11], then HSCs migrate through the caudal hematopoietic tissue (CHT) to the thymus and kidney marrow [
12], where adult hematopoiesis occurs, similar to HSC migration through fetal liver and home to bone marrow in mammals.
The molecular regulation of hematopoiesis includes interactions of lineage-specific transcription factors and a series of epigenetic modifications, such as DNA methylation and covalent histone tail modifications [
13]. DNA methylation is an important epigenetic regulation mechanism that regulates normal development through influencing gene transcription, genomic imprinting, and genome stability in mammal cells [
14-
16]. In hematologic malignancies, dysregulation of DNA methylation may result in global shifts in gene expression, which frequently leads to increased self-renewal in malignant blood cells at the expense of normal differentiation [
17].
Three active DNMTs, namely DNMT1 [
18], DNMT3A, and DNMT3B [
19,
20], have been identified in mammals. DNMTs are highly evolutionarily conserved with a regulatory region attached to a catalytic domain [
21]. DNMT1 is the most abundant DNA methyltransferase in mammalian cells and considered to be the key maintenance methyltransferase [
22]. In mammals, DNMT1 null mutant embryonic stem cells are viable and contain a small percentage of methylated DNA and methyltransferase activity [
23]. Mouse embryos homozygous for a deletion of
Dnmt1 die at 10 to 11 days gestation due to development defects [
24]. Reduced Dnmt1 activity in xenopus [
25] and zebrafish [
26,
27] has similar consequences. Dnmt1 also plays important roles in HSPCs. The deletion of
Dnmt1 has no influence on the mature cells in the hematopoietic system but causes decreased niche retention and self-renewal and differentiation defects of HSPCs [
28]. In acute myeloid leukemia (AML), the expression of DNMTs is upregulated [
29]. Conditional knockout of
Dnmt1 blocks development of leukemia, and haploinsufficiency of Dnmt1 is sufficient to delay progression of leukemogenesis and impair leukemia stem cell (LSC) self-renewal without altering normal hematopoiesis [
30]. The precise mechanism of the Dnmt1 regulation of HSC function requires further investigation.
In this study, a heritable zebrafish mutant line with hematopoietic defects identified through ENU-based forward genetic screening was found defective in dnmt1 gene. Phenotype characterization of dnmt1 mutant has uncovered severely impaired definitive hematopoiesis. Further molecular mechanistic studies revealed that cebpa was a Dnmt1 downstream target gene and activated as a result from hypomethylation of its regulation regions in dnmt1 mutants, which suggested cebpa was a key downstream target of dnmt1 gene in HSPCs. We further demonstrated that the elevated C/ebpa activity was required and accounted for, at least in part, the defective definitive hematopoiesis.
Discussion
In this study, a zebrafish mutant line with definitive hematopoiesis defects was identified. The specific phenotype was caused by a premature termination codon in the
dnmt1 gene, which resulted in a truncated Dnmt1 protein lacking its catalytic domain. DNMT1 protein is an important DNA methyltransferase to silence and regulate genes by methylation of DNA regions without changing the genomic DNA sequence [
23]. Lack of Dnmt1 function resulted HSPC proliferation block and shortage of differentiated blood lineages. We demonstrated that normal Dnmt1 function was critical in regulating
cebpa gene expression, and intact C/ebpa function was required for HSPC proliferation block triggered by the absence of Dnmt1 function. Our studies provided new evidence for that
cebpa is a downstream target of Dnmt1 in regulating HSPC proliferation during normal hematopoiesis.
Many lines of evidences demonstrate that DNA methylation influences gene expression during embryogenesis [
51-
53]. In mice, a
Dnmt1 mutation led to a recessive lethal phenotype with stunted and delayed development [
24]. Similarly, two other zebrafish mutants related to
dnmt1 were shown to have defects in pancreas development at a late embryonic stage and resulted in embryonic lethality [
50]. In line with these mutant phenotypes, our ldd794 homozygous mutants usually die at 8 dpf with abnormal hematopoiesis and other organ formation such as the liver, further suggesting that reduced DNA methylation causes developmental abnormality and embryonic lethality. It is worth noting that ldd794 heterozygotes do not display any observable phenotype, implying that the mutated
dnmt1 allele does not play a dominant negative role.
Our developmental and molecular analyses showed that the lack of Dnmt1 enzymatic activity in ldd794 mutants led to severe reduction in HSPC numbers as well as impaired production of all three major lineages but accompanied by normal vascular development during early development. These observations are in an agreement with the ones from mouse studies [
28]. Bone marrow transplant assays revealed that Dnmt1 affected HSCs in a cell-autonomous manner [
28]. Our findings, together with those in mice, demonstrate that Dnmt1 has a conserved role in definitive hematopoiesis.
The phenotype with lower number of HSPCs in CHT might be due to either reduced proliferation or increased apoptosis of HSPCs. The pH3 and TUNEL assays suggested that the definitive HSPC defects are not due to increased apoptosis but likely caused by decreased proliferation of HSPCs. These results are also consistent with the fact that the frequencies of apoptotic cells in total BM, CMPs, GMPs, or MEPs remained unchanged in mouse mutants [
28].
Given the fact that C/ebpa is a critical transcription factor for granulopoiesis [
43], we have expected that its activation might induce accelerated myeloid differentiation. However, downregulated
mpx expression in
dnmt1 mutant does not support an increased myeloid differentiation process. Meanwhile, an increased number of reports have demonstrated that C/ebpa is an important modulator of HSPC function [
44-
47]. Supporting this idea, we have found that hypomethylation of the
cebpa regulatory region as a result of Dnmt1 deficiency is directly associated with HSPC impairment. Although the possibility of other negative regulators being activated cannot be excluded completely, HSPC proliferation defect caused by
dnmt1 mutation is indeed C/ebpa dependent; as in the
cebpa/
dnmt1 double null mutants, the
cmyb expression appeared to be normal. It was reported that C/EBPa negatively regulated n-myc, and the loss of C/EBPa resulted in de-repression of n-myc in mice HSCs [
47]. Indeed, our Q-PCR analysis revealed that in
cmyb-EGFP positive cells sorted from
dnmt1 MO knockdown embryos,
n-myc had a much lower expression level (data not shown), which might account for the pronounced decreased proliferation of HSPCs. Finally, one recent report revealed that a non-coding RNA arising from the
CEBPA gene locus could influence the methylation level of
CEBPA promoter by inhibiting DNMT1 protein binding to the regulatory region of
CEBPA gene [
54], which also supported our findings that Dnmt1 acts directly on
cebpa promoter.
Taken together, our findings and others point out that the regulation of C/ebpa function during hematopoiesis takes place at multi-levels, including epigenetic modification, transcriptional regulation, and post-translational modification, which allow C/ebpa to exert its distinguished role in a fine-tuned manner.
Methods
Zebrafish maintenance and ENU mutagenesis
Zebrafish were maintained and staged under standard conditions as described previously [
55]. Zebrafish embryos were cultured in “egg water” consisting of 0.03% sea salt and 0.002% methylene blue. A 0.0045% 1-phenyl-2-thiourea (Sigma-Aldrich, St. Louis, MO, USA) was used to prevent melanization and facilitate
in situ hybridization analysis of gene expression [
55]. ENU mutagenesis on Tubingen (Tu) strain was carried out as described [
56]. The WIK line was used as the mapping strain. The zebrafish maintenance and study protocols were approved by the Institutional Review Board of the Institute of Health Sciences, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences (Shanghai, China).
Whole-mount in situ hybridization (WISH)
Digoxigenin (DIG)-labeled RNA probes were synthesized with T3 or T7 polymerase (Ambion, Life Technologies, Carlsbad, CA, USA), using linearized cDNA plamid constructs. Whole-mount mRNA
in situ hybridization was performed as described previously [
57]. The DIG-labeled probes were detected using alkaline phosphatase-coupled anti-digoxigenin Fab fragment antibody (Roche, Basel, Switzerland) with BCIP/NBT staining (Vector Laboratories, Burlingame, CA, USA).
Mapping and positional cloning of ldd794
ldd794 (Tu background) carrying the mutant allele were outcrossed to the polymorphic wild-type strain WIK for positional cloning. The genome for linked SSLP (simple sequence length polymorphism) markers were scanned by bulk segregation analysis using standard methods [
58]. For fine mapping, ldd794 mutant embryos were genotyped with SSLP markers to narrow down the genetic interval. The cDNAs of candidate genes were sequenced from pooled mutant RNA, and candidate mutation was confirmed by sequencing the genomic DNA of individual mutant embryo. All primers used for positional cloning and
dnmt1 sequencing are provided in Additional file
2.
Morpholinos and mRNA microinjection
Morpholinos (MOs) and mRNA were injected into embryos at one-cell stage. Morpholino oligonucleotides were designed by and ordered from Gene Tools. The morpholino sequences are as follows: for
dnmt1 MO, 5′-ACAATGAGGTCTTGGTAGGCATTTC-3′ (4 ng/embryo) [
27]; and for
dnmt1 splicing MO, 5′-CCACCCTTCAAAACAATAACAGTGT-3′ (8 ng/embryo). Capped mRNA samples were transcribed from linearized plasmids (mMessage Machine; Ambion), purified, and diluted to 100 ng/ul (
dnmt1 and
dnmt1 mutant mRNA) or 50 ng/ul (
SUMO2-C/ebpa and
POZ-C/ebpa mRNA) for injection of embryos at one-cell stage.
Anti-phosphorylated histone H3 (pH3) immunostaining and TUNEL assay
Three days post-fertilization (dpf), Tg (cmyb:eGFP) embryos were fixed in 4% paraformaldehyde (PFA). After dehydration and rehydration, the embryos were treated with Proteinase K (10 mg/ml) for 30 min at RT and re-fixed in 4% PFA for 20 min. After blocking with blocking buffer (2 mg/ml BSA+ 10% FBS + 0.3% Triton-X100 + 1% DMSO in PBST), the embryos were stained with mouse anti-GFP (Invitrogen, Carlsbad, CA, USA) and rabbit anti-phosphohistone H3 antibody (Santa Cruz) primary antibody at 4°C overnight. Alexa Fluor 488-conjugated anti-mouse (Invitrogen) and Alexa Fluor 594-conjugated anti-rabbit (Invitrogen) were used as secondary antibodies. Images were taken using Olympus FV 1000 confocal microscopy equipped with the FV10-ASW version 3 software.
Terminal transferase UTP nick end labeling (TUNEL) was performed using the In Situ Cell Death Detection Kit, TMR red (Roche), according to the manufacturer’s recommendations.
Genomic DNA and RNA isolation
Tg (cmyb:EGFP) embryos at one-cell stage were injected with dnmt1 ATG morpholino. Cells positive for cmyb-EGFP were sorted and collected from homogenized embryos at 3 dpf. Genomic DNA (gDNA) and total mRNA were extracted using the TRIzol reagent (Life Technologies) according to the manufacturer’s instructions.
Quantitative real-time PCR
Reverse transcription was carried out using the super script first-strand synthesis system (Life Technologies) according to the manufacturer’s instructions. Real-time quantitative PCR (Applied Biosystems, Foster City, CA, USA) was used for relative quantification of
cebpa gene expression. The expression level of
cebpa was normalized to the expression of housekeeping gene
GAPDH. The primers used for real-time quantitative PCR were listed in Additional file
2.
Bisulfite sequencing PCR (BSP) assay
The DNA methylation assay was performed using the EZ DNA Methylation Kit (Zymo Research, Irvine, CA, USA) according to the manufacturer’s recommendations. The treatment of DNA with bisulfite results in the selective conversion of unmethylated cytosine to uracil, whereas methylated cytosine remains unchanged. Methprimer (
http://www.urogene.org/methprimer/) was used to predict the CpG islands. The following primers were used for bisulfite-specific polymerase chain reaction of the regulation regions of the
cebpa gene: BSP1 Fw: 5′-GTTTTATAGAAGTTTGTTAGAGGGG-3′ and Rv: 5′-AACAAACCCAACCCTTCTTTATTAT-3′; BSP2 Fw: 5′-TTTTTTTTAGATGGTTTGTTTTAGG-3′ and Rv: 5′-ATAAATTCACCCAAAAATTCAAAAC-3′; BSP3 Fw: 5′-TTTGATAATTAGTATGAATTGTTTTGTTTT-3′ and RV: 5′-AACTTTAACCATATTATCCAAAATCACAT-3′; BSP4 Fw: 5′-ATATTTTTTGTGTAGATTTAAAATGGTGTT-3′ and Rv: 5′-TACTCCATATAACACATTTAATCCAACTAA-3′. PCR products were subcloned into pMD18-T Vector (Takara, Kyoto, Japan), and transformed bacteria were cultured overnight. Clones (eight to ten) of each BSP were sequenced for confirmation.
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Competing interests
The authors declare that they have no competing interests.
Authors’ contributions
XL performed the experiments and analyzed the data. XJ, YX, HY, KM, YC, and YJ assisted with the experiments. MD, WP, SC, ZC, HdT, LZ, YZ, JZ, and JZ designed the research plan. JZ and JZ wrote the paper. All authors read and approved the final manuscript.