Lorzadeh A, Romero-Wolf M, Goel A, Jadhav U. Epigenetic regulation of intestinal stem cells and disease: a balancing act of DNA and histone methylation. Gastroenterology. 2021;160(7):2267–82.
Article
CAS
PubMed
Google Scholar
Li L, Lorzadeh A, Hirst M. Regulatory variation: an emerging vantage point for cancer biology. Wiley Interdiscip Rev Syst Biol Med. 2014;6(1).
Stricker SH, Köferle A, Beck S. From profiles to function in epigenomics. Nat Rev Genet (Nature Publishing Group). 2016;18:51–66.
Article
CAS
Google Scholar
Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, et al. Integrative analysis of 111 reference human epigenomes. Nature. 2015;518(7539):317–29.
Article
PubMed Central
CAS
Google Scholar
Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, et al. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57–74.
Article
CAS
Google Scholar
Pott S, Lieb JD. What are super-enhancers? Nat Genet. 2014;47:8.
Article
CAS
Google Scholar
Local A, Huang H, Albuquerque CP, Singh N, Lee AY, Wang W, et al. Identification of H3K4me1-associated proteins at mammalian enhancers. Nat Genet. 2018;50:73–82.
Article
CAS
PubMed
Google Scholar
Jaenisch R, Young RA, Kooistra T, Lodato MA, Carey BW, Frampton GM, et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci. 2010;107(50):21931–6.
Article
PubMed
PubMed Central
Google Scholar
Orkin SH, Zon LI. Hematopoiesis: an evolving paradigm for stem cell biology. Cell. 2008;132(4):631–44.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lara-Astiaso D, Weiner A, Lorenzo-Vivas E, Zaretsky I, Jaitin DA, David E, et al. Chromatin state dynamics during blood formation. Science. 2014;345(6199):943–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Corces MR, Buenrostro JD, Wu B, Greenside PG, Chan SM, Koenig JL, et al. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nat Genet. 2016;48(10):1193–203.
Article
CAS
PubMed
PubMed Central
Google Scholar
Buenrostro JD, Corces MR, Lareau CA, Wu B, Schep AN, Aryee MJ, et al. Integrated single-cell analysis maps the continuous regulatory landscape of human hematopoietic differentiation. Cell. 2018;173(6):1535–48.e16.
Article
CAS
PubMed
PubMed Central
Google Scholar
Farlik M, Halbritter F, Müller F, Choudry FA, Ebert P, Klughammer J, et al. DNA Methylation dynamics of human hematopoietic stem cell differentiation. Cell Stem Cell. 2016;19(6):808–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Eaves CJ. Hematopoietic stem cells: concepts, definitions, and the new reality. Blood. 2015;125(17):2605–13.
Article
CAS
PubMed
PubMed Central
Google Scholar
Laurenti E, Göttgens B. From haematopoietic stem cells to complex differentiation landscapes. Nature. 2018;533:418–26.
Article
CAS
Google Scholar
Burda P, Laslo P, Stopka T. The role of PU.1 and GATA-1 transcription factors during normal and leukemogenic hematopoiesis. Leukemia. 2010;24:1249–57.
Article
CAS
PubMed
Google Scholar
Maslova A, Ramirez RN, Ma K, Schmutz H, Wang C, Fox C, et al. Deep learning of immune cell differentiation. Proc Natl Acad Sci U S A. 2020;117(41):25655–66.
Article
CAS
PubMed
PubMed Central
Google Scholar
Notta F, Zandi S, Takayama N, Dobson S, Gan OI, Wilson G, et al. Distinct routes of lineage development reshape the human blood hierarchy across ontogeny. Science. 2016;351(6269).
Knapp DJHF, Hammond CA, Wang F, Aghaeepour N, Miller PH, Beer PA, et al. A topological view of human CD34+ cell state trajectories from integrated single-cell output and proteomic data. Blood. 2019; blood-2018-10-878025.
Lorzadeh A, Gutierrez RL, Jackson L, Moksa M, Hirst M. Generation of native chromatin immunoprecipitation sequencing libraries for nucleosome density analysis. J Vis Exp. 2017;2017(130).
Lorzadeh A, Bilenky M, Hammond C, Knapp DJHF, Li L, Miller PH, et al. Nucleosome density ChIP-Seq identifies distinct chromatin modification signatures associated with MNase accessibility. Cell Rep. 2016;17(8):2112–24.
Article
CAS
PubMed
Google Scholar
Stunnenberg HG, Abrignani S, Adams D, de Almeida M, Altucci L, Amin V, et al. The International Human Epigenome Consortium: a blueprint for scientific collaboration and discovery. Cell. 2016;167:1145–9.
Article
CAS
PubMed
Google Scholar
Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, Pelizzola M, et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell. 2010;6(5):479–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wen B, Wu H, Shinkai Y, Irizarry RA, Feinberg AP. Large organized chromatin K9-modifications (LOCKs) distinguish differentiated from embryonic stem cells. Nat Genet. 2009;41(2):246–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ernst J, Kellis M. Chromatin-state discovery and genome annotation with ChromHMM. Nat Protoc. 2017;12:2478–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dong KB, Maksakova IA, Mohn F, Leung D, Appanah R, Lee S, et al. DNA methylation in ES cells requires the lysine methyltransferase G9a but not its catalytic activity. EMBO J. 2008;27(20):2691–701.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lehnertz B, Ueda Y, Derijck AAHA, Braunschweig U, Perez-Burgos L, Kubicek S, et al. Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr Biol. 2003;13(14):1192–200.
Article
CAS
PubMed
Google Scholar
Freitag M, Selker EU. Controlling DNA methylation: many roads to one modification. Curr Opin Genet Dev (Elsevier Ltd). 2005;15:191–9.
Article
CAS
Google Scholar
Barabino A, Plamondon V, Abdouh M, Chatoo W, Flamier A, Hanna R, et al. Loss of Bmi1 causes anomalies in retinal development and degeneration of cone photoreceptors. Development. 2016;143(9):1571–84.
CAS
PubMed
Google Scholar
Abdouh M, Hanna R, El Hajjar J, Flamier A, Bernier G. The polycomb repressive complex 1 protein BMI1 is required for constitutive heterochromatin formation and silencing in mammalian somatic cells. J Biol Chem. 2016;291(1):182–97.
Article
CAS
PubMed
Google Scholar
Park IK, Qian D, Kiel M, Becker MW, Pihalja M, Weissman IL, et al. Bmi-1 is required for maintenance of adult self-renewing haematopoietic stem cells. Nature. 2003;423(6937):302–5.
Article
CAS
PubMed
Google Scholar
Mochizuki-Kashio M, Mishima Y, Miyagi S, Negishi M, Saraya A, Konuma T, et al. Dependency on the polycomb gene Ezh2 distinguishes fetal from adult hematopoietic stem cells. Blood. 2011;118(25):6553–61.
Article
CAS
PubMed
Google Scholar
Breitman TR, Selonick SE, Collins SJ. Induction of differentiation of the human promyelocytic leukemia cell line (HL-60) by retinoic acid. Proc Natl Acad Sci U S A. 1980;77, 2936(5I):–40.
Fiskus W, Wang Y, Sreekumar A, Buckley KM, Shi H, Jillella A, et al. Combined epigenetic therapy with the histone methyltransferase EZH2 inhibitor 3-deazaneplanocin A and the histone deacetylase inhibitor panobinostat against human AML cells. Blood. 2009;114(13):2733–43.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hnisz D, Abraham BJ, Lee TI, Lau A, Saint-André V, Sigova AA, et al. XSuper-enhancers in the control of cell identity and disease. Cell. 2013;155(4):934.
Article
CAS
PubMed
Google Scholar
Álvarez-Errico D, Vento-Tormo R, Sieweke M, Ballestar E. Epigenetic control of myeloid cell differentiation, identity and function. Nat Rev Immunol (Nature Publishing Group). 2015;15:7–17.
Article
CAS
Google Scholar
Deaton AM, Webb S, Kerr ARW, Illingworth RS, Guy J, Andrews R, et al. Cell type-specific DNA methylation at intragenic CpG islands in the immune system. Genome Res. 2011;21(7):1074–86.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stewart MH, Albert M, Sroczynska P, Cruickshank VA, Guo Y, Rossi DJ, et al. The histone demethylase Jarid1b is required for hematopoietic stem cell self-renewal in mice. Blood. 2015;125(13):2075–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bröske AM, Vockentanz L, Kharazi S, Huska MR, Mancini E, Scheller M, et al. DNA methylation protects hematopoietic stem cell multipotency from myeloerythroid restriction. Nat Genet. 2009;41(11):1207–15.
Article
PubMed
CAS
Google Scholar
Bock C, Beerman I, Lien WH, Smith ZD, Gu H, Boyle P, et al. DNA methylation dynamics during in vivo differentiation of blood and skin stem cells. Mol Cell. 2012;47(4):633–47.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hodges E, Molaro A, Dos Santos CO, Thekkat P, Song Q, Uren PJ, et al. Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol Cell. 2011;44(1):17–28.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xie H, Xu J, Hsu JH, Nguyen M, Fujiwara Y, Peng C, et al. Polycomb repressive complex 2 regulates normal hematopoietic stem cell function in a developmental-stage-specific manner. Cell Stem Cell. 2014;14(1):68–80.
Article
CAS
PubMed
Google Scholar
Yu W, Zhang F, Wang S, Fu Y, Chen J, Liang X, et al. Depletion of polycomb repressive complex 2 core component EED impairs fetal hematopoiesis. Cell Death Dis. 2017;8:e2774.
Article
CAS
Google Scholar
Petruk S, Mariani SA, De Dominici M, Porazzi P, Minieri V, Cai J, et al. Structure of nascent chromatin is essential for hematopoietic lineage specification. Cell Rep. 2017;19(2):295–306.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kamminga LM, Bystrykh LV, De Boer A, Houwer S, Douma J, Weersing E, et al. The Polycomb group gene Ezh2 prevents hematopoietic stem cell exhaustion. Blood. 2006;107(5):2170–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xu J, Shao Z, Li D, Xie H, Kim W, Huang J, et al. Developmental control of polycomb subunit composition by GATA factors mediates a switch to non-canonical functions. Mol Cell. 2015;57(2):304–16.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ernst T, Chase AJ, Score J, Hidalgo-Curtis CE, Bryant C, Jones AV, et al. Inactivating mutations of the histone methyltransferase gene EZH2 in myeloid disorders. Nat Genet. 2010;42(8):722–6.
Article
CAS
PubMed
Google Scholar
Ganji G, Gilbert SA, Diaz E, Chen SB, Pappalardi MB, Jiang Y, et al. Mutation of A677 in histone methyltransferase EZH2 in human B-cell lymphoma promotes hypertrimethylation of histone H3 on lysine 27 (H3K27). Proc Natl Acad Sci. 2012;109(8):2989–94.
Article
PubMed
PubMed Central
Google Scholar
Zhu J, Adli M, Zou JY, Verstappen G, Coyne M, Zhang X, et al. Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell. 2013;152(3):642–54.
Article
CAS
PubMed
PubMed Central
Google Scholar
Waddington CH. Genetic assimilation of the bithorax phenotype. Evolution (N Y). 2006.
Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell. 2006;125(2):315–26.
Article
CAS
PubMed
Google Scholar
Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature. 2007;448(7153):553–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Goldrath AW, Bhattacharya D, Weissman IL, Mathis D, Benoist C, Luckey CJ. Memory T and memory B cells share a transcriptional program of self-renewal with long-term hematopoietic stem cells. Proc Natl Acad Sci. 2006;103(9):3304–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Swift J, Spinler KR, Discher DE, Mohandas N, Chasis JA, Shin J-W. Lamins regulate cell trafficking and lineage maturation of adult human hematopoietic cells. Proc Natl Acad Sci. 2013;110(47):18892–7.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sabari BR, Dall’Agnese A, Boija A, Klein IA, Coffey EL, Shrinivas K, et al. Coactivator condensation at super-enhancers links phase separation and gene control. Science. 2018;361(6400):eaar3958.
Article
PubMed
PubMed Central
CAS
Google Scholar
Butterfield YS, Kreitzman M, Thiessen N, Corbett RD, Li Y, Pang J, et al. JAGuaR: Junction Alignments to Genome for RNA-Seq Reads. Desvaux M. PLoS One. 2014;9(7):e102398.
Tarasov A, Vilella AJ, Cuppen E, Nijman IJ, Prins P. Sambamba: fast processing of NGS alignment formats. Bioinformatics. 2015;31(12):2032–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mingay M, Chaturvedi A, Bilenky M, Cao Q, Jackson L, Hui T, et al. Vitamin C-induced epigenomic remodelling in IDH1 mutant acute myeloid leukaemia. Leukemia. 2018;32(1):11–20.
Article
CAS
PubMed
Google Scholar
Gascard P, Bilenky M, Sigaroudinia M, Zhao J, Li L, Carles A, et al. Epigenetic and transcriptional determinants of the human breast. Nat Commun. 2015;6:6351.
Article
CAS
PubMed
Google Scholar
Tripathi S, Pohl MO, Zhou Y, Rodriguez-Frandsen A, Wang G, Stein DA, et al. Meta- and orthogonal integration of influenza “oMICs” data defines a role for UBR4 in virus budding. Cell Host Microbe. 2015;18(6):723–35.
Article
CAS
PubMed
PubMed Central
Google Scholar
Team RDC, R Development Core Team R. R: a language and environment for statistical computing. R Found Stat Comput. 2016.
Kimura H, Hayashi-Takanaka Y, Goto Y, Takizawa N, Nozaki N. The organization of histone H3 modifications as revealed by a panel of specific monoclonal antibodies. Cell Struct Funct. 2008;33(1):61–73.
Article
CAS
PubMed
Google Scholar
Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26(5):589–95.
Article
PubMed
PubMed Central
CAS
Google Scholar
Feng J, Liu T, Qin B, Zhang Y, Liu XS. Identifying ChIP-seq enrichment using MACS. Nat Protoc. 2012;7(9):1728–40.
Article
CAS
PubMed
Google Scholar
Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38(4):576–89.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 2016;44(W1):W160–5.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ernst J, Kellis M. ChromHMM: automating chromatin-state discovery and characterization. Nat Methods. 2012;9:215–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Löffler-Wirth H, Kalcher M, Binder H. OposSOM: R-package for high-dimensional portraying of genome-wide expression landscapes on bioconductor. Bioinformatics. 2015;31(19):3225–7.
Article
PubMed
CAS
Google Scholar
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841–2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Madani Tonekaboni SA, Mazrooei P, Kofia V, Haibe-Kains B, Lupien M. Identifying clusters of cis-regulatory elements underpinning TAD structures and lineage-specific regulatory networks. Genome Res. 2019;29(10):1733–43.
Article
PubMed
PubMed Central
CAS
Google Scholar
Grant CE, Bailey TL, Noble WS. FIMO: scanning for occurrences of a given motif. Bioinformatics. 2011;27(7):1017–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hui T, Cao Q, Wegrzyn-Woltosz J, O’Neill K, Hammond CA, Knapp DJHF, et al. High-Resolution single-cell DNA methylation measurements reveal epigenetically distinct hematopoietic stem cell subpopulations. Stem Cell Rep. 2018;11(2):578–92.
Article
CAS
Google Scholar
Le Meur N, Hahne F, Ellis B, FHB E. FlowCore: data structures package for flow cytometry data: Bioconductor Project; 2007.
Google Scholar