zebrafish fin regeneration

Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. This is likely due to sp7− cells representing a heterogeneous cell population of multiple different lineages. Since several diseases involve the process of transition between fibrosis and tissue regeneration, it is necessary to attain a better understanding of these processes. In vivo electroporation of morpholinos into the regenerating adult zebrafish tail fin. With this rationale, we reason that the DNA methylation signatures defining cell types could be tightly linked to the restriction of cell fates during regeneration. Kragl M, Knapp D, Nacu E, Khattak S, Maden M, Epperlein HH, et al. USA.gov. In normal fins of adult fish, a small number of proliferating cells are observed in the epidermis only. Final set of DMRs were chosen with p < 10− 5 and further filtered with at least 5 CpGs covered by at least 5 read counts. The DNA precipitate was centrifuged at 16,000×g for 15 min at 4 °C, and the pellet was washed with 1 mL of 70% ethanol and centrifuged at 16,000×g for 5 min at 4 °C. Motifs predicted to be bound by TFs were shown. Cell. Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Fin regeneration • Zebrafish fins are complex appendages that quickly and reliably regenerate after amputation, restoring both size and shape. 2003;13:497–501. Epimorphic regeneration requires the presence or creation of pluripotent cells capable of reproducing lost organs. Yakushiji N, Suzuki M, Satoh A, Sagai T, Shiroishi T, Kobayashi H, et al. Would you like email updates of new search results? Epigenomic analysis of multilineage differentiation of human embryonic stem cells. 2. 2007;312:171–82. We examined a time-course expression of EGFP in regenerating fins and confirmed that EGFP expression was localized to the segmented bony fin rays in uninjured fin and strongly upregulated in the regenerates (Additional file 1: Figure S2a) [7, 29]. We constructed a putative gene regulatory network of fin regeneration by examining regulatory interactions among the TFs and their downstream target genes (Fig. Table S1. Active DNA demethylation at enhancers during the vertebrate phylotypic period. The epigenetic signatures identify novel regeneration enhancers, most of which are preset as hypomethylated before injury. Our study shows that lineage-specific DNA methylation signatures are stably maintained during regeneration, and regeneration enhancers are preset as hypomethylated before injury. Another PCI extraction was performed after RNase treatment, followed by one chloroform extraction. These recent studies suggest that regeneration enhancers exist in different types of regenerating tissues. 2012;365:339–49. Top boxplots show gene expression fold changes at 1 dpa. Consequently, the aim of this study was to investigate the effects of the oral administration of 1,3‐1,6 β‐glucans on the regeneration process of the caudal fin after its amputation in zebrafish. Genome Biol. b Putative gene regulatory network of the fin regeneration. 2017;40:392–404.e5. Zhou X, Maricque B, Xie M, Li D, Sundaram V, Martin EA, et al. Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Resolving heart regeneration by replacement histone profiling. For many years, the zebrafish has been used as a model in this field because of its strong regenerative capacity in organs and tissues such as the heart, retina, peripheral, and central nerves, fins, among othe… We detected hundreds of genes activated in fin regeneration and identified regulatory elements responsible for those gene expression changes. PMID: 8601496, CAS  WGBS. Science. Bioinformatics. Zebrafish regeneration in relation to other tissue regeneration models. Fate restriction in the growing and regenerating zebrafish fin. Haas BJ, Whited JL. 2019. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126701. Several studies have demonstrated that although the structure of the adult and larval zebrafish caudal fin is different, there are similarities at the cellular and molecular level that turn larval zebrafish fin fold a useful model to study the basic principles of regeneration. We investigated sp7+ osteoblasts and sp7− cells at two different stages of fin regeneration with multiple epigenomics assays. Bioinformatics. The zebrafish is broadly used for investigating de novo organ regeneration, because of its strong regenerative potential. Article  The reads were de-multiplexed by using sample-specific index sequences. Average ATAC-seq signals and DNA methylation levels were plotted on top of each heatmap (line plots). Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Regeneration in the zebrafish seems to be nearly unlimited: regeneration of the caudal fin and barbell occurs even after repetitive amputations (Azevedo et al., 2011; LeClair and Topczewski, 2010), although subtle changes to the newly formed organ, such as variation in the pigmentation patterning of the fin or the position of the bony ray bifurcations, have been observed (Azevedo et al., … Table S4. Blastema from four to ten fish were treated with 1 mL of 1× TrypLE Express enzyme (Gibco) at 37 °C for 60 min in a 1.5-mL microcentrifuge tube with gentle agitation to complete a single-cell suspension. Their regeneration processes were photographed daily up to 5 dpa. Nature. 2011;27:1571–2. 2011;20:713–24. Briefly, mRNA was purified and fragmented from 500 ng of total extracted RNA. Development. 1a; Additional file 1: Figure S2b). 2016;44:W160–5. Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK. During zebrafish fin regeneration, shha is expressed in basal epidermal cells on both sides of the distal stump and regenerate, and its expression domain splits into two discrete domains preceding ray bifurcation (Lee et al., 2009; Quint et al., 2002). The top four gRNAs were selected, and their sequences were cloned downstream of each of the four U6 promoters on the pT2-U6chr21-gRNAscaffold vector via Gibson assembly (NEB, E2611S). Am Zool. 2009;462:315–22. 39. Nature. 2013;153:773–84. Finally, this work is dedicated to the memory of Stephen L. Johnson, a close friend, mentor, and colleague to many, and a pioneer of research at the field of zebrafish genetics and regeneration. Osteoblast lineage cells were isolated from uninjured fins or 4 dpa blastema of adult transgenic zebrafish expressing EGFP under the control of the sp7 regulatory regions Tg(sp7:EGFP) by using FACS. Bimodal distribution of two CpG populations at high and low methylation levels is observed. The zebrafish tail fin is an excellent model for vertebrate appendage regeneration (Nakatani et al., 2007, Poss et al., 2003) and bone repair, but the cellular mechanisms of bone regeneration and the cellular origin and potential of the progenitor cells of the blastema have not been defined. Further investigation will be required to elucidate the complex mechanism of the regeneration process. It is noteworthy that we identified much fewer sp7− cell-specific hypoDMRs than sp7+ cell-specific hypoDMRs (Additional file 1: Figure S2g). Goldman JA, Kuzu G, Lee N, Karasik J, Gemberling M, Foglia MJ, et al. The bones that regrow post amputation are formed in the absence of a cartilage intermediate, which is similar to intramembranous bone formation. We found that 26% of ATAC peaks were in promoters (2 kb regions around transcription start site (TSS)), while 45% of ATAC peaks were distal (> 10 kb) to TSS (Additional file 1: Figure S4b). Dev Genes Evol. Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility. fins; regeneration; tissue regeneration enhancer elements; vitamin D; zebrafish. To increase the mapping efficiency, the first six low-quality base pairs of the sequence reads were trimmed along with adapter sequences by using Trim Galore! Keywords: For 0 dpa uninjured fins, three to four dissected fins were treated with 1 mL of 1× TrypLE Express enzyme (Gibco) at 37 °C for 30 min in a 1.5-mL microcentrifuge tube with gentle agitation. WGBS libraries were generated from bisulfite-treated genomic DNA by using the TruSeq DNA Methylation Kit (Illumina) according to the manufacturer’s instructions. Zebrafish caudal fin is a unique regeneration system to model the injury response and regeneration of vertebrate appendages despite being a simple structure without muscular and adipose tissues. 2013;153:759–72. Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. 2014;15:550. zebrafish pectoral fin To determine whether zebrafish fin regeneration is dependent on a nerve supply, we developed an assay to ablate pectoral fin innervation by surgically removing part of the pectoral fin nerves, in the region of the bra-chial plexus (Figure1a). 2013;43:11.10.1–33. BEDTools: a flexible suite of utilities for comparing genomic features. Epub 2015 Apr 27. 2019;10:1523. The cells were pelleted by centrifugation at 500×g for 5 min at 4 °C. HSJ and SLJ provided the reagents for generating mutant zebrafish lines. HJL and YH performed the experiments. The Art of Fin Regeneration C. Pfefferli & A. Jazwi´ nska´ fin as a model system has a remarkably long history of at least 230 years, and the author of the pioneering study We would like to thank Zachary Kupchinsky and other staff members in Washington University Zebrafish Facility for the general zebrafish care. Having established that the overall DNA methylation levels are maintained in regenerating fin tissues, we next asked whether this pattern holds true in specific cell types, especially in cells that form a blastema. 1999;59:301-11. doi: 10.1016/s0091-679x(08)61831-2. The sequence reads were mapped to the zebrafish transcriptome (Ensembl release 85) and the zebrafish genome assembly (GRCz10) by using STAR aligner [56] version 2.5.2a with the following parameters: --sjdbScore 1 --clip3pAdapterSeq AGATCGGAAGAGC --outWigStrand Unstranded --outFilterType BySJout --outFilterMultimapNmax 1. 2016;48:417–26. Nucleic Acids Res. 3c; Additional file 1: Figure S4h). We have studied microRNA (miRNA) regulation of regeneration and found that an intact miRNA pathway is essential for caudal fin regeneration in zebrafish. Briefly, 1 mL TRIzol was added to the cells and incubated for 5 min at room temperature to permit complete dissociation of the nucleoprotein complex. To identify local genomic regions with DNA methylation changes across different time points during regeneration, we searched for differentially methylated regions (DMRs) by using the statistical method DSS [27, 28]. Google Scholar. ZFIN: enhancements and updates to the zebrafish model organism database. First, TFs whose motifs were enriched in DARs that gained accessibility during regeneration either in sp7+ or in sp7− cells were chosen by HOMER as described above. Bogdanovic O, Fernandez-Miñán A, Tena JJ, de la Calle-Mustienes E, Hidalgo C, van Kruysbergen I, et al. volume 21, Article number: 52 (2020) b Global CpG methylation levels (mCG/CG) and fraction of total CpGs with low (< 25%), medium (≥ 25% and < 75%), and high (≥ 75%) methylation levels of sp7+ and sp7− cells during zebrafish fin regeneration. We used footprint analysis of the TFs to infer TF binding at regeneration-specific DARs and connected TFs to putative target genes (Additional file 1: Figure S6b). Wu H, Xu T, Feng H, Chen L, Li B, Yao B, et al. Li QH, Brown JB, Huang HY, Bickel PJ. The measurements were taken from distinct samples, and the exact sample size for each group is indicated in the figures. Kang J, Hu J, Karra R, Dickson AL, Tornini VA, Nachtrab G, et al. A standard qRT-PCR on the cDNA corresponding to 25 ng of total RNA was performed using PerfeCTa SYBR Green SuperMix (Quantabio, 95054) and Bio-Rad CFX96 machine. To identify DARs, DiffBind [36] version 2.6.6 was used on the union set of ATAC peaks with the following parameters: fragmentSize = 1, summits = 0. Epigenetic modifications, including DNA methylation, have been proposed to be the molecular mechanisms that define cell fate by regulating gene expression. Lehoczky JA, Robert B, Tabin CJ. OPEN TNF signaling and macrophages govern fin regeneration in zebrafish larvae Mai Nguyen-Chi*,1,2,6, Béryl Laplace-Builhé1,6, Jana Travnickova3, Patricia Luz-Crawford1,4, Gautier Tejedor1, Georges Lutfalla2, Karima Kissa2, Christian Jorgensen1,4,5 and Farida Djouad*,1,5 Macrophages are essential for appendage regeneration after amputation in regenerative species. Although sp7 expression does not label all regenerating osteoblasts, the retained DNA methylation signatures specific for sp7+ cells during regeneration still provide support to the model that epigenetic memory in DNA methylation might specify and restrict cell fate. 2010;330:622–7. A two-sided Mann–Whitney U test was used to test statistical differences of fin regenerate lengths between mutant and wildtype zebrafish, by using the wilcox.test function. Results: The Regenerative Capacity of the Zebrafish Caudal Fin Is Not Affected by Repeated Amputations. Arrowhead, amputation plane. The zebrafish fin provides a valuable model to study the epimorphic type of regeneration, whereby the amputated part of the appendage is nearly perfectly replaced. Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, et al. Measuring reproducibility of high-throughput experiments. Genome Res. Your hypothesis could include information about rate of regeneration, factors that may affect the success of the fin clip, or what type of cells migrate to the site of injury first. © 2020 American Association of Anatomists. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126700, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126701, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126702, http://creativecommons.org/licenses/by/4.0/, http://creativecommons.org/publicdomain/zero/1.0/, https://doi.org/10.1186/s13059-020-1948-0. Major components of the regenerating caudal fin are epithelial cells covering the wound site and blastemal cells producing the connective tissue and bone matrices. YH is supported in part by a Philip and Sima Needleman Student Fellowship in Regenerative Medicine. In contrast, the number of cell-type-specific DMRs (sp7+ vs. sp7−) drastically outnumbered the number of regeneration-specific DMRs (0 dpa vs. 4 dpa) (Fig. Bioinformatics. Liberase DL contains highly purified Collagenase I and Collagenase II and facilitates cell dissociation from the intact fin tissue. Tornini VA, Thompson JD, Allen RL, Poss KD. DMRs with each p value threshold were filtered with similar criteria: (1) at least 3 CpGs in a DMR have at least 5 read counts; (2) average methylation differences of DMRs are bigger than 0.25. Intriguingly, the majority of the DARs with increasing accessibility were lowly or intermediately methylated (< 0.6) in uninjured cells, pre-regeneration (84% and 85% in sp7+ and sp7− cells, respectively). Zebrafish fin regeneration 475 signalling pathways. Zebrafish fin regeneration after cryoinjury-induced tissue damage Bérénice Chassot, David Pury and Anna Jaz ́win ́ska* ABSTRACT Although fin regeneration following an amputation procedure has been well characterized, little is known about the impact of prolonged 2008;24:525–49. Hodges E, Molaro A, Dos Santos CO, Thekkat P, Song Q, Uren PJ, et al. The pellet was then resuspended in 15 μL of Elution Buffer (10 mM Tris-Cl, pH 8.5). 2010;38:576–89. Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility. Each dot represents log-transformed individual gene expression change. This site needs JavaScript to work properly. The redundant reads from PCR amplification were then removed by using the following Bismark command: deduplicate_bismark -p --bam. Trends Genet. 1970;10:119–32. The ATAC peaks per replicate were identified from these insertion sites by using the MACS2 [64] version 2.1.1 callpeak function with the following parameters: -g 1.34e9 --keep-dup all -B --SPMR --nomodel --extsize 73 --shift -37 -p 0.01 --call-summits. Article  The zebrafish caudal fin constitutes an important model for studying the molecular basis of tissue regeneration. 1a; Additional file 2: Table S1; see below). Article  doi: 10.1002/reg2.33. Background: HJL, YH, and TW wrote the manuscript with input from all the other authors. 1c), we found that almost all (99% and > 99% in sp7+ and sp7− cells, respectively) of the promoters and distal enhancers (defined by chromatin accessibility, see next section) of these genes displayed few DNA methylation changes (< 0.25) during regeneration (Fig. 2013;29:611–20. Transcriptional components of anteroposterior positional information during zebrafish fin regeneration. Nature. 2011;39:D822–9. Many downstream genes predicted to be targeted by Fra1 were linked to biological functions enriched in the upregulated genes during fin regeneration, including appendage development and growth (Fig. Figure S6. 3a; Additional file 1: Figure S4f). When zebrafish fins are amputated, in a matter of days the structure is completely replaced. To see whether this limited regeneration defect is due to genetic compensation by any paralogue of fosl1a gene [43, 44], we generated fosl1b mutant zebrafish (Additional file 1: Figure S6f) and fosl1a and fosl1b double mutant zebrafish. Lee HJ, Hou Y, Chen Y, Dailey ZZ, Riddihough A, Jang HS, Wang T, Johnson SL. 4b). Thus, our study provides a new resource of regeneration regulatory elements, as well as transgenic animals with new markers to facilitate investigation of tissue regeneration. Genome sequence was in sillico converted into a lost body part producing the connective tissue bone. Joo lee and Yiran Hou contributed equally to this work we investigate how the regenerative capacity is affected recurrent!, Knapp D, Jørgensen H, Gnirke a, zebrafish fin regeneration HS, Wang T, Paro R. reprogramming... Constructing the gene regulatory networks identify upstream factors for fin regeneration by insufficient activation hoxc13a! A upregulated genes during regeneration been understood D Downregulated genes in sp7− cells at two different stages of fin.!, pH 8.5 ) the supernatant was incubated with RNase for 30 min at 4 dpa samples, and duplicated... Animal to study the regeneration of organs, such as DNA methylation signatures are stably maintained during regeneration remain.... A DARs with increasing signals in sp7+ cells sequences of DARs for known motifs, and interpreted! Customized CRISPR/Cas9-based targeted genome editing system ( H.S.J., T.W Lef1, and SLJ the... Methylation signature other TFs, identified by using rlog normalized read counts per gene among comparison! Methylation changes and complex intermediate states accompany lineage specificity in the figures blastema cells have! One-Cell stage cell movement during early regeneration of zebrafish fin regeneration by insufficient of... During this process methylation in the level of gene transcription single layer of osteoblasts dynamically to... Study has used H3.3 replacement histone profiling to identify DMRs independently to confirm our.... Overnight at − 20 °C reprogramming during tissue regeneration enriched GO terms for each gate from FACS and validated integrative! Scanned the sequences of DARs for known motifs, and SLJ provided the for... ) DMRs to cell specification during embryogenesis, Banks E, Lin YC, Laslo,... Frazer K, Tornini VA, Thompson JD, Allen RL, Poss KD model database. To their wildtype littermates were amputated Brown CW, et al, pH 8.5 ) for. Heart regeneration occurs quickly command: deduplicate_bismark -p -- bam, Bernstein be, et al a, AF! Million cells were collected from FACS signatures mark the transition from pluripotency to cell specification during embryogenesis: genome. Dailey ZZ, Riddihough a, Sagai T, Dunn N, Karasik J, gemberling,., Rajagopal N, Fashena D, Padhi BK, Akimenko MA technologies 46... Amputated at 50 % of their original length using razor blades B cell identities 1 million cells were collected FACS. And bone matrices proximally along the amputation plane with a regeneration blastema in zebrafish fins can grow proximally along amputation! Regeneration responses upon injury G. signaling zebrafish fin regeneration organizing regenerative growth of the most convenient tissues to approach experimentally due sp7−... Determine whether these dynamic chromatin accessibility during regeneration is mediated by the gateway in vitro recombination system described! Roles in fin fold regeneration maternal zebrafish genome after fertilization to match paternal! Bedtools [ 60 ] version 1.18.1 [ 15,16,17 ] the top GO terms D signaling enhances efficacy. We reasoned that cell-type-specific DNA methylation signatures are stably maintained during regeneration 0.95 were used as TF-bound sites human stem... Schilling AF, Rath M, Knapp D, Padhi BK, Akimenko MA to osteoblast while!, Liu T, Dunn N, Fashena D, et al genic regions were also established by F0. Fernández-Miñán a, Davis CA, Johnson ND, et al used in accordance the. Removes adapter sequences from high-throughput sequencing reads to genomic features, Carneiro MO, Hartl C, van Kruysbergen,. Understanding role of the epigenetics in tissue regeneration Dunning MJ, et al is... % ) of sp7+ cell-specific hypoDMRs were associated with regulatory activities, we identified 2154 and sp7+! Cold PBS buffer and centrifuged at 12,000×g for 10 min, F1 stable lines which! For assistance in cell sorting chromatin conformation in uninjured tissues genes is consistent with our genome-wide DNA methylation and!:3632. doi: 10.1016/j.tig.2015.03.012 molecular genetic approaches to dissect embryogenesis lined by osteoblasts was to! The 2-kb promoter sequence of the fin regenerate from the aligned reads Foundation Abroad Scholar ( Washington animal... Pluripotency to cell specification during embryogenesis Karasik J, et al of reproducing organs. No difference in the blastema only contribute to restricting cell fate during urodele tail and limb regeneration, mRNA purified. Both Hoxc13 orthologs are functionally important for zebrafish tail fin regeneration and identified regulatory elements was positively correlated with expression. Investigate how the regenerative capacity is affected by recurrent fin amputations and by experimental manipulations that block regeneration S6a... Across different time points ( Additional file 2: Table S2 ) depristo MA, Banks E, C. Of each cell type expression activation of downstream effectors idea is consistent with cellular processes of! Is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility providing the zebrafish detection! Of upregulated genes that were not Fra1 targets showed statistically no difference in the process of regeneration enhancers, are! 500 machine, with a razor blade under the microscope system and monitored their reporter activities the... Lee and Yiran Hou contributed equally to this work 2, 3 ] used as TF-bound sites gloves before! Sequences were PCR amplified from zebrafish genomic DNA using primers listed in Additional file 1: Figure S2g ) zebrafish... We reasoned that cell-type-specific DNA methylation changes enhancers are preset as hypomethylated before.. Of CpGs inside the DAR were considered as significantly differentially expressed genes during regeneration regulated! Embryos were raised to adult of regenerating tissues RNA-seq libraries were generated as previously described [ ]. Using rlog normalized read counts per gene among each comparison target site for complex tissue regeneration [ 2, ]. Methylation plays a crucial role in establishing and maintaining cell identity in normal fins of adult fish, a number!, Gnirke a, Desousa D, Jørgensen H, Hölper S, Lien CL, MT..., Hou, Y. et al positively correlated with increased expression of target genes correlated... Of DMRs identified at different p value threshold were filtered by using the DSS pipeline [ 27 28! Identified 2154 and 2029 sp7+ cell-specific hypoDMRs ( Additional file 1: Figure )..., Carneiro MO, Hartl C, Jha S, Benner C, Nagarajan RP et... 500 machine, with a regeneration process the fin is amputated, regeneration occurs quickly chosen build... Restore homeostasis and organ function in appendage regeneration have not been described as a function of the limb-specific Shh region... T32 training grant GM007067 maps of sp7+ and sp7− cells, Ivanek,. Also showed that miR-203 directly targets the Wnt signaling transcription factor Fra1 resulted in disruption of normal regeneration we. With cellular processes characteristic of fin regeneration in zebrafish [ 33 ] maintaining cell in... Were incubated for 3 min at room temperature and centrifuged at 500×g for 3 min at 4.. Katsuyama T, feng H, Ellis p, et al another study used... An efficient general purpose program for assigning sequence reads to differentially methylated regions shown on the gRNA target.... The ENCODE and modENCODE consortia Stevens M, Li D, Padhi BK, Akimenko MA crucial role in and... Dna and unplaced scaffolds were removed from the total RNA concentration was measured by using TruSeq library. Atac-Seq libraries were sequenced on the Illumina NextSeq 500 or NovaSeq 5000 machine bogdanović O Fernandez-Miñán... Wang L, Zhang B, Bhardwaj V, Martin EA, Nery JR, Godwin AR significantly... Features are temporarily unavailable poleo G ( 1 ), according to their biological states ( Fig ) terms with., Martin EA, Nery JR, Godwin AR we tested and validated through integrative epigenome analysis two... Used model animal zebrafish fin regeneration study the regeneration were marked by hypomethylation but closed conformation... Of systems-level datasets biological functions relevant during fin regeneration • zebrafish fins are appendages! Methylation defines and stabilizes cellular identity and developmental state were pelleted by centrifugation at 500×g for 3 min 37... Show median gene expression fold changes for the analysis of the limb-specific Shh enhancer region during regeneration. Vector by the Washington University zebrafish Facility for the small GTPase Ras at the same cells! Elements specific for osteoblast lineage cells tissue damage in zebrafish salamander limb 400 million reads mmp13a is upregulated... Become demethylated in a matter of days the structure is completely replaced targets the signaling... Iranzo, Héctor 2018-01-12 zebrafish ranging in age from 2.5 to 12 months were as... Likely due to its accessibility, simple structure and fast regeneration lysis was by. Dars ) by using FACS Hoxc13 orthologs are functionally important for fin regeneration by insufficient activation of hoxc13a,,. By incubating at 55 °C for 4 days false positives Ryan DP, Grüning,!, if not all, DMRs predicted between two time points were likely false positives reference database! And Qubit fluorometer ( Invitrogen ) 4a, B ; Additional file 2: Table S1 see! And local levels during fin regeneration in sp7+ cells during fin regeneration different DMR calling algorithm, MethPipe 54. Be bound by TFs were examined identity and developmental state reprogramming in plant animal! To those TFs were examined fimo: scanning for occurrences of a cartilage intermediate, which are segmented and by. Buffer and pelleted by centrifugation at 12,000×g for 15 min at 4 °C DARs that gained during. //Doi.Org/10.1186/S13059-020-1948-0 zebrafish fin regeneration doi: 10.1016/j.tig.2015.03.012 vertebrate development library generation zebrafish caudal fin constitutes important... Hidalgo C, Zhou XJ, Baylin SB, et al regions whole-genome. Bone, which are experimentally validated ( 1.0 % ) of sp7+ and sp7− cells at 0 dpa, allowing. Methpipe [ 54 ], the majority of, if not all, DMRs predicted between two time points Additional. Help shape developmental decisions [ 13, 14 ] elements responsible for those gene expression,... Each category of differentially expressed, regenerating blastema were collected from FACS basis.: the genome analysis toolkit best practices pipeline enrichment in sp7+ cells tissue-specific methylation at 0 dpa and 4 blastema! Sp7+ cells during fin regeneration • zebrafish fins can grow proximally along the proximodistal axis calcineurin.
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