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Research Paper

The landscape of accessible chromatin in quiescent cardiac fibroblasts and cardiac fibroblasts activated after myocardial infarction

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Pages 1020-1039 | Received 19 Mar 2021, Accepted 09 Sep 2021, Published online: 25 Oct 2021

References

  • Fu X, Khalil H, Kanisicak O, et al. Specialized fibroblast differentiated states underlie scar formation in the infarcted mouse heart. J. Clin. Investig. 2018;128(5):2127–2143.
  • Kanisicak O, Khalil H, Ivey MJ, et al. Genetic lineage tracing defines myofibroblast origin and function in the injured heart. Nat. Commun. 2016;7(1):12260.
  • Kaur H, Takefuji M, Ngai CY, et al. Targeted ablation of periostin-expressing activated fibroblasts prevents adverse cardiac remodeling in mice. Circ. Res. 2016;118(12):1906–1917.
  • Pfeffer JM, Pfeffer Ma, Fletcher PJ, et al. Progressive ventricular remodeling in rat with myocardial infarction. Am J Physiol. 1991;260:H1406–1414.
  • Fu X, Liu Q, Li C, et al. Cardiac fibrosis and cardiac fibroblast lineage-tracing: recent advances. Front Physiol. 2020;11:416.
  • Khalil H, Kanisicak O, Prasad V, et al. Fibroblast-specific tgf-β-smad2/3 signaling underlies cardiac fibrosis. J. Clin. Investig. 2017;127(10):3770–3783.
  • Meng Q, Bhandary B, Bhuiyan MS, et al. Myofibroblast-specific tgfbeta receptor ii signaling in the fibrotic response to cardiac myosin binding protein c-induced cardiomyopathy. Circ. Res. 2018;123(12):1285–1297.
  • Dobaczewski M, Bujak M, Li N, et al. Smad3 signaling critically regulates fibroblast phenotype and function in healing myocardial infarction. Circ. Res. 2010;107(3):418–428.
  • Molkentin JD, Bugg D, Ghearing N, et al. Fibroblast-specific genetic manipulation of p38 mitogen-activated protein kinase in vivo reveals its central regulatory role in fibrosis. Circulation. 2017;136(6):549–561.
  • Tsompana M, Buck MJ. Chromatin accessibility: a window into the genome. Epigenetics Chromatin. 2014;7(1):33.
  • Buenrostro JD, Wu B, Litzenburger UM, et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature. 2015;523(7561):486–490.
  • Acharya A, Baek ST, Banfi S, et al. Efficient inducible cre‐mediated recombination in tcf21cell lineages in the heart and kidney. Genesis. 2011;49(11):870–877.
  • Yamamoto M, Shook NA, Kanisicak O, et al. A multifunctional reporter mouse line for cre‐and flp‐dependent lineage analysis. Genesis. 2009;47(2):107–114.
  • Van Berlo JH, Kanisicak O, Maillet M, et al. C-kit+ cells minimally contribute cardiomyocytes to the heart. Nature. 2014;509(7500):337–341.
  • Fu X, Zhao J-X, Zhu M-J, et al. Amp-activated protein kinase α1 but not α2 catalytic subunit potentiates myogenin expression and myogenesis. Mol. Cell. Biol. 2013;33(22):4517–4525.
  • Ming H, Sun J, Pasquariello R, et al. The landscape of accessible chromatin in bovine oocytes and early embryos. Epigenetics. 2021;16(3):300–312.
  • Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for rna-seq data with deseq2. Genome Biol. 2014;15(12):550.
  • Li R, Hu K, Liu H, et al. Onestoprnaseq: a web application for comprehensive and efficient analyses of rna-seq data. Genes (Basel). 2020;11(10):1165.
  • Zhang Y, Liu T, Meyer CA, et al. Model-based analysis of chip-seq (macs). Genome Biol. 2008;9(9):R137.
  • Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–2504.
  • Assenov Y, Ramírez F, Schelhorn SE, et al. Computing topological parameters of biological networks. Bioinformatics. 2008;24(2):282–284.
  • Wiese R, Eiglsperger M, Kaufmann M. Yfiles — visualization and automatic layout of graphs. In: Jünger M, Mutzel P, editors. Graph drawing software. Berlin Heidelberg: Springer Berlin Heidelberg; 2004. p. 173–191.
  • Hood R, Allen C. Cellularity of bovine adipose tissue. J. Lipid Res. 1973;14(6):605–610.
  • Elbarbary RA, Lucas BA, Maquat LE. Retrotransposons as regulators of gene expression. Science. 2016;351(6274):aac7247.
  • Ichiyanagi K. Epigenetic regulation of transcription and possible functions of mammalian short interspersed elements, sines. Genes Genet. Syst. 2013;88(1):19–29.
  • Estécio MR, Gallegos J, Dekmezian M, et al. Sine retrotransposons cause epigenetic reprogramming of adjacent gene promoters. Mol. Cancer Res. 2012;10(10):1332–1342.
  • Chow JC, Ciaudo C, Fazzari MJ, et al. Line-1 activity in facultative heterochromatin formation during x chromosome inactivation. Cell. 2010;141(6):956–969.
  • Sasaki T, Nishihara H, Hirakawa M, et al. Possible involvement of sines in mammalian-specific brain formation. Proc. Natl. Acad. Sci. U. S. A. 2008;105(11):4220–4225.
  • Faulkner GJ, Kimura Y, Daub CO, et al. The regulated retrotransposon transcriptome of mammalian cells. Nat. Genet. 2009;41(5):563–571.
  • Robertson KD. DNA methylation and chromatin - unraveling the tangled web. Oncogene. 2002;21(35):5361–5379.
  • Martinowich K, Hattori D, Wu H, et al. DNA methylation-related chromatin remodeling in activity-dependent bdnf gene regulation. Science. 2003;302(5646):890–893.
  • Yin Y, Morgunova E, Jolma A, et al. Impact of cytosine methylation on DNA binding specificities of human transcription factors. Science. 2017;356(6337):eaaj2239.
  • Zhu H, Wang G, Qian J. Transcription factors as readers and effectors of DNA methylation. Nat. Rev. Genet. 2016;17(9):551–565.
  • Bulger M, Groudine M. Functional and mechanistic diversity of distal transcription enhancers. Cell. 2011;144(3):327–339.
  • Golan-Lagziel T, Lewis YE, Shkedi O, et al. Analysis of rat cardiac myocytes and fibroblasts identifies combinatorial enhancer organization and transcription factor families. J Mol Cell Cardiol. 2018;116:91–105.
  • Grossman SR, Engreitz J, Ray JP, et al. Positional specificity of different transcription factor classes within enhancers. Proc. Natl. Acad. Sci. U. S. A. 2018;115(30):E7222–e7230.
  • Albrecht-Schgoer K, Schgoer W, Holfeld J, et al. The angiogenic factor secretoneurin induces coronary angiogenesis in a model of myocardial infarction by stimulation of vascular endothelial growth factor signaling in endothelial cells. Circulation. 2012;126(21):2491–2501.
  • Fuda NJ, Ardehali MB, Lis JT. Defining mechanisms that regulate rna polymerase ii transcription in vivo. Nature. 2009;461(7261):186–192.
  • Boettiger AN, Levine M. Synchronous and stochastic patterns of gene activation in the Drosophila Embryo. Science. 2009;325(5939):471–473.
  • Guhaniyogi J, Brewer G. Regulation of mrna stability in mammalian cells. Gene. 2001;265(1–2):11–23.
  • Hao S, Baltimore D. The stability of mrna influences the temporal order of the induction of genes encoding inflammatory molecules. Nat. Immunol. 2009;10(3):281–288.
  • Acharya A, Baek ST, Huang G, et al. The bhlh transcription factor tcf21 is required for lineage-specific emt of cardiac fibroblast progenitors. Development. 2012;139(12):2139–2149.
  • Billings SE, Pierzchalski K, Butler Tjaden NE, et al. The retinaldehyde reductase dhrs3 is essential for preventing the formation of excess retinoic acid during embryonic development. FASEB J. 2013;27(12):4877–4889.
  • Sazonova O, Zhao Y, Nürnberg S, et al. Characterization of tcf21 downstream target regions identifies a transcriptional network linking multiple independent coronary artery disease loci. PLoS Genet. 2015;11(5):e1005202.
  • Huang GN, Thatcher JE, McAnally J, et al. C/ebp transcription factors mediate epicardial activation during heart development and injury. Science. 2012;338(6114):1599–1603.
  • Braitsch CM, Combs MD, Quaggin SE, et al. Pod1/tcf21 is regulated by retinoic acid signaling and inhibits differentiation of epicardium-derived cells into smooth muscle in the developing heart. Dev. Biol. 2012;368(2):345–357.
  • Baek ST, Tallquist MD. Nf1 limits epicardial derivative expansion by regulating epithelial to mesenchymal transition and proliferation. Development. 2012;139(11):2040–2049.
  • Eferl R, Wagner EF. Ap-1: a double-edged sword in tumorigenesis. Nat. Rev. Cancer. 2003;3(11):859–868.
  • Shaulian E, Karin M. Ap-1 in cell proliferation and survival. Oncogene. 2001;20(19):2390–2400.
  • Avouac J, Palumbo K, Tomcik M, et al. Inhibition of activator protein 1 signaling abrogates transforming growth factor β-mediated activation of fibroblasts and prevents experimental fibrosis. Arthritis Rheum. 2012;64(5):1642–1652.
  • Seidenberg J, Stellato M, Hukara A, et al. The ap-1 transcription factor fosl-2 regulates autophagy in cardiac fibroblasts during myocardial fibrogenesis. Int. J. Mol. Sci. 2021;22(4):1861.
  • Jonsson MKB, Hartman RJG, Ackers-Johnson M, et al. A transcriptomic and epigenomic comparison of fetal and adult human cardiac fibroblasts reveals novel key transcription factors in adult cardiac fibroblasts. JACC. 2016;1:590–602.
  • Xiao Y, Hill MC, Zhang M, et al. Hippo signaling plays an essential role in cell state transitions during cardiac fibroblast development. Dev. Cell. 2018;45(2):153–169.e156.
  • Xiao Y, Hill MC, Li L, et al. Hippo pathway deletion in adult resting cardiac fibroblasts initiates a cell state transition with spontaneous and self-sustaining fibrosis. Genes Dev. 2019;33(21–22):1491–1505.
  • Kim W, Barron DA, San Martin R, et al. Runx1 is essential for mesenchymal stem cell proliferation and myofibroblast differentiation. Proc. Natl. Acad. Sci. U. S. A. 2014;111(46):16389–16394.
  • Koth J, Wang X, Killen AC, et al. Runx1 promotes scar deposition and inhibits myocardial proliferation and survival during zebrafish heart regeneration. Development. 2020;147(8). DOI:10.1242/dev.186569
  • Kimura A, Inose H, Yano F, et al. Runx1 and runx2 cooperate during sternal morphogenesis. Development. 2010;137(7):1159–1167.