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Research Paper

A temporal transcriptome and methylome in human embryonic stem cell-derived cardiomyocytes identifies novel regulators of early cardiac development

ORCID Icon, ORCID Icon, ORCID Icon, , , & show all
Pages 1013-1026 | Received 04 Jul 2018, Accepted 09 Sep 2018, Published online: 19 Oct 2018

References

  • Luna-Zurita L, Stirnimann CU, Glatt S, et al. Complex interdependence regulates heterotypic transcription factor distribution and coordinates cardiogenesis. Cell. 2016;164:999–1014.
  • Ang Y-S, Rivas RN, Ribeiro AJS, et al. Disease model of GATA4 mutation reveals transcription factor cooperativity in human cardiogenesis. Cell. 2016;167:1734–1749.e22.
  • Paige SL, Thomas S, Stoick-Cooper CL, et al. A temporal chromatin signature in human embryonic stem cells identifies regulators of cardiac development. Cell. 2012;151:221–232.
  • Lan F, Lee AS, Liang P, et al. Abnormal calcium handling properties underlie familial hypertrophic cardiomyopathy pathology in patient-specific induced pluripotent stem cells. Cell Stem Cell. 2013;12:101–113.
  • Wamstad JA, Alexander JM, Truty RM, et al. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell. 2012;151:206–220.
  • Nakano H, Minami I, Braas D, et al. Glucose inhibits cardiac muscle maturation through nucleotide biosynthesis. Elife. 2017;6:025003.
  • Zhu H, Scharnhorst KS, Stieg AZ, et al. Two dimensional electrophysiological characterization of human pluripotent stem cell-derived cardiomyocyte system. Sci Rep. 2017;7:43210.
  • Minami I, Yamada K, Otsuji TG, et al. A small molecule that promotes cardiac differentiation of human pluripotent stem cells under defined, cytokine- and xeno-free conditions. Cell Rep. 2012;2:1448–1460.
  • Liu Q, Jiang C, Xu J, et al. Genome-wide temporal profiling of transcriptome and open chromatin of early cardiomyocyte differentiation derived from hiPSCs and hESCs. Circ Res. 2017;121:376–391.
  • Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4:44–57.
  • Nichols J, Zevnik B, Anastassiadis K, et al. Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4. Cell. 1998;95:379–391.
  • Kubalak SW, Miller-Hance WC, O’Brien TX, et al. Chamber specification of atrial myosin light chain-2 expression precedes septation during murine cardiogenesis. J Biol Chem. 1994;269:16961–16970.
  • Krämer A, Green J, Pollard J, et al. Causal analysis approaches in ingenuity pathway analysis. Bioinformatics. 2014;30:523–530.
  • Vaquerizas JM, Kummerfeld SK, Teichmann SA, et al. A census of human transcription factors: function, expression and evolution. Nat Rev Genet. 2009;10:252–263.
  • Deng C, Li Y, Zhou L, et al. HoxBlinc RNA recruits Set1/MLL complexes to activate hox gene expression patterns and mesoderm lineage development. Cell Rep. 2016;14:103–114.
  • Arndt A-K, Schafer S, Drenckhahn J-D, et al. Fine mapping of the 1p36 deletion syndrome identifies mutation of PRDM16 as a cause of cardiomyopathy. Am J Hum Genet. 2013;93:67–77.
  • Zaveri HP, Beck TF, Hernández-García A, et al. Identification of critical regions and candidate genes for cardiovascular malformations and cardiomyopathy associated with deletions of chromosome 1p36. PLoS One. 2014;9:e85600.
  • Rossi G, Antonini S, Bonfanti C, et al. Nfix regulates temporal progression of muscle regeneration through modulation of myostatin expression. Cell Rep. 2016;14:2238–2249.
  • Taglietti V, Maroli G, Cermenati S, et al. Nfix induces a switch in Sox6 transcriptional activity to regulate MyHC-I Expression in fetal muscle. Cell Rep. 2016;17:2354–2366.
  • Han P, Li W, Lin C-H, et al. A long noncoding RNA protects the heart from pathological hypertrophy. Nature. 2014;514:102–106.
  • Wang L, Ma X, Xu X, et al. Systematic identification and characterization of cardiac long intergenic noncoding RNAs in zebrafish. Sci Rep. 2017;7:1250.
  • Pang L, Hu J, Zhang G, et al. Dysregulated long intergenic non-coding RNA modules contribute to heart failure. Oncotarget. 2016;7:59676–59690.
  • Kioka N, Ueda K, Amachi T. Vinexin, CAP/ponsin, ArgBP2: a novel adaptor protein family regulating cytoskeletal organization and signal transduction. Cell Struct Funct. 2002;27:1–7.
  • Roignot J, Soubeyran P. ArgBP2 and the SoHo family of adapter proteins in oncogenic diseases. Cell Adh Migr. 2009;3:167–170.
  • Anekal PV, Yong J, Manser E. Arg kinase-binding protein 2 (ArgBP2) interaction with α-actinin and actin stress fibers inhibits cell migration. J Biol Chem. 2015;290:2112–2125.
  • Geng J, Picker J, Zheng Z, et al. Chromosome microarray testing for patients with congenital heart defects reveals novel disease causing loci and high diagnostic yield. BMC Genomics. 2014;15:1127.
  • Zhang Q, Gao X, Li C, et al. Impaired dendritic development and memory in Sorbs2 knock-out mice. J Neurosci. 2016;36:2247–2260.
  • Lange M, Kaynak B, Forster UB, et al. Regulation of muscle development by DPF3, a novel histone acetylation and methylation reader of the BAF chromatin remodeling complex. Genes Dev. 2008;22:2370–2384.
  • Zeng L, Zhang Q, Li S, et al. Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b. Nature. 2010;466:258–262.
  • Cui H, Schlesinger J, Schoenhals S, et al. Phosphorylation of the chromatin remodeling factor DPF3a induces cardiac hypertrophy through releasing HEY repressors from DNA. Nucleic Acids Res. 2016;44:2538–2553.
  • Li Y, Du X, Li F, et al. A novel zinc-finger protein ZNF436 suppresses transcriptional activities of AP-1 and SRE. Mol Biol Rep. 2006;33:287–294.
  • Mehta G, Kumarasamy S, Wu J, et al. MITF interacts with the SWI/SNF subunit, BRG1, to promote GATA4 expression in cardiac hypertrophy. J Mol Cell Cardiol. 2015;88:101–110.
  • Tshori S, Gilon D, Beeri R, et al. Transcription factor MITF regulates cardiac growth and hypertrophy. J Clin Invest. 2006;116:2673–2681.
  • Steimle JD, Moskowitz IP. TBX5: a key regulator of heart development. Curr Top Dev Biol. 2017;122:195–221.
  • Potthoff MJ, Olson EN. MEF2: a central regulator of diverse developmental programs. Development. 2007;134:4131–4140.
  • Du KL, Ip HS, Li J, et al. Myocardin is a critical serum response factor cofactor in the transcriptional program regulating smooth muscle cell differentiation. Mol Cell Biol. 2003;23:2425–2437.
  • Okano M, Bell DW, Haber DA, et al. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell. 1999;99:247–257.
  • Arshi A, Nakashima Y, Nakano H, et al. Rigid microenvironments promote cardiac differentiation of mouse and human embryonic stem cells. Sci Technol Adv Mater. 2013;14:025003.
  • Lam L, Chin L, Halder RC, et al. Epigenetic changes in T-cell and monocyte signatures and production of neurotoxic cytokines in ALS patients. FASEB J. 2016;30:3461–3473.
  • Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25:1105–1111.
  • Anders S, Pyl PT, Huber W. HTSeq–a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31:166–169.
  • Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
  • Cabili MN, Trapnell C, Goff L, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011;25:1915–1927.
  • Guo W, Fiziev P, Yan W, et al. BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. BMC Genomics. 2013;14:774.
  • Guo W, Zhu P, Pellegrini M, et al. CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data. Bioinformatics. 2018;34:381–387.
  • Heinz S, Benner C, Spann N, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38:576–589.

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