DNA methylation status of DNAJA4 is essential for human erythropoiesis

References

• Stephenson JR , AxelradAA , McleodDL , ShreeveMM. Induction of colonies of hemoglobin-synthesizing cells by erythropoietin in vitro. Proc. Natl Acad. Sci. USA68(7), 1542–1546 (1971).
   PubMed Web of Science ®Google Scholar
• Hu J , LiuJ , XueFet al. Isolation and functional characterization of human erythroblasts at distinct stages: implications for understanding of normal and disordered erythropoiesis in vivo. Blood121(16), 3246–3253 (2013).
   PubMed Web of Science ®Google Scholar
• Hattangadi SM , WongP , ZhangL , FlygareJ , LodishHF. From stem cell to red cell: regulation of erythropoiesis at multiple levels by multiple proteins, RNAs, and chromatin modifications. Blood118(24), 6258–6268 (2011).
   PubMed Web of Science ®Google Scholar
• Sankaran VG , GallagherPG. Applications of high-throughput DNA sequencing to benign hematology. Blood122(22), 3575–3582 (2013).
   PubMed Web of Science ®Google Scholar
• Cancer Genome Atlas Research Network , LeyTJ , MillerCet al.Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N. Engl. J. Med.368(22), 2059–2074 (2013).
   PubMed Web of Science ®Google Scholar
• Busque L , PatelJP , FigueroaMEet al. Recurrent somatic TET2 mutations in normal elderly individuals with clonal hematopoiesis. Nat. Genet.44(11), 1179–1181 (2012).
   PubMed Web of Science ®Google Scholar
• Shlush LI , ZandiS , MitchellAet al. Identification of pre-leukaemic haematopoietic stem cells in acute leukaemia. Nature506(7488), 328–333 (2014).
   PubMed Web of Science ®Google Scholar
• Schulz VP , YanH , Lezon-GeydaKet al. A unique epigenomic landscape defines human erythropoiesis. Cell Rep.28(11), 2996–3009 e2997 (2019).
   PubMed Web of Science ®Google Scholar
• Bartholdy B , LajugieJ , YanZet al. Mechanisms of establishment and functional significance of DNA demethylation during erythroid differentiation. Blood Adv.2(15), 1833–1852 (2018).
   PubMed Web of Science ®Google Scholar
• Haladyna JN , YamauchiT , NeffT , BerntKM. Epigenetic modifiers in normal and malignant hematopoiesis. Epigenomics7(2), 301–320 (2015).
   PubMed Web of Science ®Google Scholar
• Sall C , FogtHjorth C. In vitro drug–drug interactions of decitabine and tetrahydrouridine involving drug transporters and drug metabolising enzymes. Xenobiotica52(1), 1–15 (2022).
   PubMed Web of Science ®Google Scholar
• Craig EA , HuangP , AronR , AndrewA. The diverse roles of J-proteins, the obligate Hsp70 co-chaperone. Rev. Physiol. Biochem. Pharmacol.156, 1–21 (2006).
   PubMed Web of Science ®Google Scholar
• Tummala H , WalneAJ , WilliamsMet al. DNAJC21 mutations link a cancer-prone bone marrow failure syndrome to corruption in 60S ribosome subunit maturation. Am. J. Hum. Genet.99(1), 115–124 (2016).
   PubMed Web of Science ®Google Scholar
• Wang D , ZengT , LinZet al. Long non-coding RNA SNHG5 regulates chemotherapy resistance through the miR-32/DNAJB9 axis in acute myeloid leukemia. Biomed. Pharmacother.123, 109802 (2020).
   PubMed Web of Science ®Google Scholar
• Kadakia R , ZhengY , ZhangZ , ZhangW , JosefsonJL , HouL. Association of cord blood methylation with neonatal leptin: an epigenome wide association study. PLOS ONE14(12), e0226555 (2019).
   PubMed Web of Science ®Google Scholar
• Mahoney SE , YaoZ , KeyesCC , TapscottSJ , DiedeSJ. Genome-wide DNA methylation studies suggest distinct DNA methylation patterns in pediatric embryonal and alveolar rhabdomyosarcomas. Epigenetics7(4), 400–408 (2012).
   PubMed Web of Science ®Google Scholar
• Roifman M , ChoufaniS , TurinskyALet al. Genome-wide placental DNA methylation analysis of severely growth-discordant monochorionic twins reveals novel epigenetic targets for intrauterine growth restriction. Clin. Epigenetics8, 70 (2016).
   PubMed Web of Science ®Google Scholar
• Qu X , ZhangS , WangSet al. TET2 deficiency leads to stem cell factor-dependent clonal expansion of dysfunctional erythroid progenitors. Blood132(22), 2406–2417 (2018).
   PubMed Web of Science ®Google Scholar
• Xu J , ShaoZ , GlassKet al. Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. Dev. Cell23(4), 796–811 (2012).
   PubMed Web of Science ®Google Scholar
• Pellagatti A , CazzolaM , GiagounidisAet al. Deregulated gene expression pathways in myelodysplastic syndrome hematopoietic stem cells. Leukemia24(4), 756–764 (2010).
   PubMed Web of Science ®Google Scholar
• Raghavachari N , XuX , MunsonPJ , GladwinMT. Characterization of whole blood gene expression profiles as a sequel to globin mRNA reduction in patients with sickle cell disease. PLOS ONE4(8), e6484 (2009).
   PubMed Web of Science ®Google Scholar
• Nanou A , ToumpekiC , FanisPet al. Sex-specific transcriptional profiles identified in beta-thalassemia patients. Haematologica106(4), 1207–1211 (2021).
   PubMed Web of Science ®Google Scholar
• Gao J , AksoyBA , DogrusozUet al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci. Signal.6(269), pl1 (2013).
   PubMed Web of Science ®Google Scholar
• Love MI , HuberW , AndersS. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol.15(12), 550 (2014).
   PubMed Web of Science ®Google Scholar
• Tsherniak A , VazquezF , MontgomeryPGet al. Defining a cancer dependency map. Cell170(3), 564–576 e516 (2017).
   PubMed Web of Science ®Google Scholar
• Kim D , PerteaG , TrapnellC , PimentelH , KelleyR , SalzbergSL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol.14(4), R36 (2013).
   PubMed Web of Science ®Google Scholar
• Trapnell C , RobertsA , GoffLet al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc.7(3), 562–578 (2012).
   PubMed Web of Science ®Google Scholar
• Krueger F , AndrewsSR. Bismark: a flexible aligner and methylation caller for bisulfite-seq applications. Bioinformatics27(11), 1571–1572 (2011).
   PubMed Web of Science ®Google Scholar
• Akalin A , KormakssonM , LiSet al. methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol.13(10), R87 (2012).
   PubMed Web of Science ®Google Scholar
• Langmead B , SalzbergSL. Fast gapped-read alignment with Bowtie 2. Nat. Methods9(4), 357–359 (2012).
   PubMed Web of Science ®Google Scholar
• Ramirez F , DundarF , DiehlS , GruningBA , MankeT. deepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res.42(Web Server issue), W187–W191 (2014).
   PubMed Web of Science ®Google Scholar
• Langfelder P , HorvathS. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics9, 559 (2008).
   PubMed Web of Science ®Google Scholar
• Tang Z , KangB , LiC , ChenT , ZhangZ. GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis. Nucleic Acids Res.47(W1), W556–W560 (2019).
   PubMed Web of Science ®Google Scholar
• Perkins A . Erythroid Kruppel like factor: from fishing expedition to gourmet meal. Int. J. Biochem. Cell Biol.31(10), 1175–1192 (1999).
   PubMed Web of Science ®Google Scholar
• Tallack MR , WhitingtonT , YuenWSet al. A global role for KLF1 in erythropoiesis revealed by ChIP-seq in primary erythroid cells. Genome Res.20(8), 1052–1063 (2010).
   PubMed Web of Science ®Google Scholar
• Blank U , KarlssonS. The role of Smad signaling in hematopoiesis and translational hematology. Leukemia25(9), 1379–1388 (2011).
   PubMed Web of Science ®Google Scholar
• Challen GA , BolesNC , ChambersSM , GoodellMA. Distinct hematopoietic stem cell subtypes are differentially regulated by TGF-beta1. Cell Stem Cell6(3), 265–278 (2010).
   PubMed Web of Science ®Google Scholar
• Yu Y , MoY , EbenezerDet al. High resolution methylome analysis reveals widespread functional hypomethylation during adult human erythropoiesis. J. Biol. Chem.288(13), 8805–8814 (2013).
   PubMed Web of Science ®Google Scholar
• An X , SchulzVP , LiJet al. Global transcriptome analyses of human and murine terminal erythroid differentiation. Blood123(22), 3466–3477 (2014).
   PubMed Web of Science ®Google Scholar
• Grosso R , FaderCM , ColomboMI. Autophagy: a necessary event during erythropoiesis. Blood Rev.31(5), 300–305 (2017).
   PubMed Web of Science ®Google Scholar
• Liu Q , LuoL , RenCet al. The opposing roles of the mTOR signaling pathway in different phases of human umbilical cord blood-derived CD34+ cell erythropoiesis. Stem Cells38(11), 1492–1505 (2020).
   PubMed Web of Science ®Google Scholar
• Lahiri A , HedlM , AbrahamC. MTMR3 risk allele enhances innate receptor-induced signaling and cytokines by decreasing autophagy and increasing caspase-1 activation. Proc Natl Acad. Sci. USA112(33), 10461–10466 (2015).
   PubMed Web of Science ®Google Scholar
• Larabi A , BarnichN , NguyenHTT. New insights into the interplay between autophagy, gut microbiota and inflammatory responses in IBD. Autophagy16(1), 38–51 (2020).
   PubMed Web of Science ®Google Scholar
• Mengus C , NeutznerM , BentoAet al. VCP/p97 cofactor UBXN1/SAKS1 regulates mitophagy by modulating MFN2 removal from mitochondria. Autophagy18(1), 171–190 (2022).
   PubMed Web of Science ®Google Scholar
• Papadopoulos C , KirchnerP , BugMet al. VCP/p97 cooperates with YOD1, UBXD1 and PLAA to drive clearance of ruptured lysosomes by autophagy. EMBO J.36(2), 135–150 (2017).
   PubMed Web of Science ®Google Scholar
• Balwani M , SardhE , VenturaPet al. Phase 3 trial of RNAi therapeutic givosiran for acute intermittent porphyria. N. Engl. J. Med.382(24), 2289–2301 (2020).
   PubMed Web of Science ®Google Scholar
• Zhang Y , XiaoH , XiongQ , WuC , LiP. Two novel hydroxymethylbilane synthase splicing mutations predispose to acute intermittent porphyria. Int. J. Mol. Sci.22(20), 11008 (2021).
   PubMed Web of Science ®Google Scholar
• Hohfeld J . Regulation of the heat shock conjugate Hsc70 in the mammalian cell: the characterization of the anti-apoptotic protein BAG-1 provides novel insights. Biol. Chem.379(3), 269–274 (1998).
   PubMed Web of Science ®Google Scholar
• Takayama S , XieZ , ReedJC. An evolutionarily conserved family of Hsp70/Hsc70 molecular chaperone regulators. J. Biol. Chem.274(2), 781–786 (1999).
   PubMed Web of Science ®Google Scholar
• Alholle A , BriniAT , GharaneiSet al. Functional epigenetic approach identifies frequently methylated genes in Ewing sarcoma. Epigenetics8(11), 1198–1204 (2013).
   PubMed Web of Science ®Google Scholar
• Mathangasinghe Y , FauvetB , JaneSM , GoloubinoffP , NillegodaNB. The Hsp70 chaperone system: distinct roles in erythrocyte formation and maintenance. Haematologica106(6), 1519–1534 (2021).
   PubMed Web of Science ®Google Scholar
• Duan Y , WangH , Mitchell-SilbaughKet al. Heat shock protein 60 regulates yolk sac erythropoiesis in mice. Cell Death Dis.10(10), 766 (2019).
   PubMedGoogle Scholar
• Ghosh A , GareeG , SweenyEA , NakamuraY , StuehrDJ. Hsp90 chaperones hemoglobin maturation in erythroid and nonerythroid cells. Proc. Natl Acad. Sci. USA115(6), E1117–E1126 (2018).
   PubMed Web of Science ®Google Scholar
• Rees DC , WilliamsTN , GladwinMT. Sickle-cell disease. Lancet376(9757), 2018–2031 (2010).
   PubMed Web of Science ®Google Scholar
• Ades L , ItzyksonR , FenauxP. Myelodysplastic syndromes. Lancet383(9936), 2239–2252 (2014).
   PubMed Web of Science ®Google Scholar
• Colah R , GorakshakarA , NadkarniA. Global burden, distribution and prevention of beta-thalassemias and hemoglobin E disorders. Expert Rev. Hematol.3(1), 103–117 (2010).
   PubMed Web of Science ®Google Scholar
• Lowenberg B , DowningJR , BurnettA. Acute myeloid leukemia. N. Engl. J. Med.341(14), 1051–1062 (1999).
   PubMed Web of Science ®Google Scholar
• Estey E , DohnerH. Acute myeloid leukaemia. Lancet368(9550), 1894–1907 (2006).
   PubMed Web of Science ®Google Scholar
• Dohner H , WeisdorfDJ , BloomfieldCD. Acute myeloid leukemia. N. Engl. J. Med.373(12), 1136–1152 (2015).
   PubMed Web of Science ®Google Scholar
• Bennett JM , CatovskyD , DanielMTet al. Proposals for the classification of chronic (mature) B and T lymphoid leukaemias. French–American–British (FAB) Cooperative Group. J. Clin. Pathol.42(6), 567–584 (1989).
   PubMed Web of Science ®Google Scholar
• Kirtonia A , PandyaG , SethiG , PandeyAK , DasBC , GargM. A comprehensive review of genetic alterations and molecular targeted therapies for the implementation of personalized medicine in acute myeloid leukemia. J. Mol. Med.98(8), 1069–1091 (2020).
   PubMed Web of Science ®Google Scholar
• Lee HJ , HoreTA , ReikW. Reprogramming the methylome: erasing memory and creating diversity. Cell Stem Cell14(6), 710–719 (2014).
   PubMed Web of Science ®Google Scholar
• Saitou M , KagiwadaS , KurimotoK. Epigenetic reprogramming in mouse pre-implantation development and primordial germ cells. Development139(1), 15–31 (2012).
   PubMed Web of Science ®Google Scholar
• Bird A . DNA methylation patterns and epigenetic memory. Genes Dev.16(1), 6–21 (2002).
   PubMed Web of Science ®Google Scholar
• Hackett JA , SuraniMA. Beyond DNA: programming and inheritance of parental methylomes. Cell153(4), 737–739 (2013).
   PubMed Web of Science ®Google Scholar
• Arlet JB , RibeilJA , GuillemFet al. HSP70 sequestration by free alpha-globin promotes ineffective erythropoiesis in beta-thalassaemia. Nature514(7521), 242–246 (2014).
   PubMed Web of Science ®Google Scholar
• Frisan E , VandekerckhoveJ , DeThonel Aet al. Defective nuclear localization of Hsp70 is associated with dyserythropoiesis and GATA-1 cleavage in myelodysplastic syndromes. Blood119(6), 1532–1542 (2012).
   PubMed Web of Science ®Google Scholar
• Ribeil JA , ZermatiY , VandekerckhoveJet al. Hsp70 regulates erythropoiesis by preventing caspase-3-mediated cleavage of GATA-1. Nature445(7123), 102–105 (2007).
   PubMed Web of Science ®Google Scholar
• Sun YZ , RenY , ZhangYJet al. DNAJA4 deficiency enhances NF-kappa B-related growth arrest induced by hyperthermia in human keratinocytes. J. Dermatol. Sci.91(3), 256–267 (2018).
   PubMed Web of Science ®Google Scholar
• Wei ZD , SunYZ , TuCXet al. DNAJA4 deficiency augments hyperthermia-induced clusterin and ERK activation: two critical protective factors of human keratinocytes from hyperthermia-induced injury. J. Eur. Acad. Dermatol. Venereol.34(10), 2308–2317 (2020).
   PubMed Web of Science ®Google Scholar
• He L , KennedyAS , HouckSet al. DNAJB12 and Hsp70 triage arrested intermediates of N1303K-CFTR for endoplasmic reticulum-associated autophagy. Mol. Biol. Cell32(7), 538–553 (2021).
   PubMed Web of Science ®Google Scholar