Erratum: Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells (Cell (2016) 167(5) (1310–1322.e17)(S0092867416314660)(10.1016/j.cell.2016.10.045);Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells

Cell

Volumn 167, Issue 5, 2016, Pages 1310-1322.e17

  Yu, Vionnie W C ^a,b,c   Yusuf, Rushdia Z ^a,b,c   Oki, Toshihiko ^a,b,c   Wu, Juwell ^d   Saez, Borja ^a,b,c   Wang, Xin ^e   Cook, Colleen ^a,b,c   Baryawno, Ninib ^a,b,c   Ziller, Michael J ^b,c,d   Lee, Eunjung ^e,f   Gu, Hongcang ^d   Meissner, Alexander ^b,c,d   Lin, Charles P ^a,b   Kharchenko, Peter V ^b,e   Scadden, David T ^a,b,c  

^a MASSACHUSETTS GENERAL HOSPITAL   (United States)

^b HARVARD STEM CELL INSTITUTE   (United States)

^c Harvard University   (United States)

^d BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^e HARVARD MEDICAL SCHOOL   (United States)

^f BRIGHAM AND WOMEN S HOSPITAL   (United States)

Author keywords

ATAC seq; clonal tracking; epigenetic memory; hematopoiesis; hematopoietic stem cell; lineage tracing; multi fluorescent mouse model; RNA seq; single cell; transplantation

Indexed keywords

ANIMAL CELL; ARTICLE; CELL CLONE; CELL HETEROGENEITY; CELL PLASTICITY; CELL STRESS; CHROMATIN; CONTROLLED STUDY; DNA METHYLATION; EPIGENETICS; GENETIC TRANSCRIPTION; HEMATOPOIESIS; HEMATOPOIETIC STEM CELL; HOMEOSTASIS; MOUSE; NONHUMAN; PRIORITY JOURNAL; STEM CELL NICHE; TISSUE REPAIR; ANIMAL; CELL LINEAGE; CYTOLOGY; FLUORESCENCE; INFLAMMATION; PATHOLOGY;

ANIMALS; CELL LINEAGE; CLONE CELLS; EPIGENOMICS; FLUORESCENCE; HEMATOPOIESIS; HEMATOPOIETIC STEM CELLS; INFLAMMATION; MICE; TRANSCRIPTION, GENETIC;

EID: 84995806677     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2017.02.010     Document Type: Erratum

References (43)

1. Aiuti, A., Biasco, L., Scaramuzza, S., Ferrua, F., Cicalese, M.P., Baricordi, C., Dionisio, F., Calabria, A., Giannelli, S., Castiello, M.C., et al. Lentiviral hematopoietic stem cell gene therapy in patients with Wiskott-Aldrich syndrome. Science, 341, 2013, 1233151.
2. Anders, S., Huber, W., Differential expression analysis for sequence count data. Genome Biol., 11, 2010, R106.
3. Biasco, L., Pellin, D., Scala, S., Dionisio, F., Basso-Ricci, L., Leonardelli, L., Scaramuzza, S., Baricordi, C., Ferrua, F., Cicalese, M.P., et al. In vivo tracking of human hematopoiesis reveals patterns of clonal dynamics during early and steady-state reconstitution phases. Cell Stem Cell 19 (2016), 107–119.
4. Bock, C., Beerman, I., Lien, W.H., Smith, Z.D., Gu, H., Boyle, P., Gnirke, A., Fuchs, E., Rossi, D.J., Meissner, A., DNA methylation dynamics during in vivo differentiation of blood and skin stem cells. Mol. Cell 47 (2012), 633–647.
5. Busch, K., Klapproth, K., Barile, M., Flossdorf, M., Holland-Letz, T., Schlenner, S.M., Reth, M., Höfer, T., Rodewald, H.R., Fundamental properties of unperturbed haematopoiesis from stem cells in vivo. Nature 518 (2015), 542–546.
6. Chambers, S.M., Boles, N.C., Lin, K.Y., Tierney, M.P., Bowman, T.V., Bradfute, S.B., Chen, A.J., Merchant, A.A., Sirin, O., Weksberg, D.C., et al. Hematopoietic fingerprints: an expression database of stem cells and their progeny. Cell Stem Cell 1 (2007), 578–591.
7. Ding, L., Ley, T.J., Larson, D.E., Miller, C.A., Koboldt, D.C., Welch, J.S., Ritchey, J.K., Young, M.A., Lamprecht, T., McLellan, M.D., et al. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature 481 (2012), 506–510.
8. Dykstra, B., Kent, D., Bowie, M., McCaffrey, L., Hamilton, M., Lyons, K., Lee, S.J., Brinkman, R., Eaves, C., Long-term propagation of distinct hematopoietic differentiation programs in vivo. Cell Stem Cell 1 (2007), 218–229.
9. Dykstra, B., Olthof, S., Schreuder, J., Ritsema, M., de Haan, G., Clonal analysis reveals multiple functional defects of aged murine hematopoietic stem cells. J. Exp. Med. 208 (2011), 2691–2703.
10. Essers, M.A., Offner, S., Blanco-Bose, W.E., Waibler, Z., Kalinke, U., Duchosal, M.A., Trumpp, A., IFNalpha activates dormant haematopoietic stem cells in vivo. Nature 458 (2009), 904–908.
11. Fan, J., Salathia, N., Liu, R., Kaeser, G.E., Yung, Y.C., Herman, J.L., Kaper, F., Fan, J.B., Zhang, K., Chun, J., Kharchenko, P.V., Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis. Nat. Methods 13 (2016), 241–244.
12. Forsberg, E.C., Passegué, E., Prohaska, S.S., Wagers, A.J., Koeva, M., Stuart, J.M., Weissman, I.L., Molecular signatures of quiescent, mobilized and leukemia-initiating hematopoietic stem cells. PLoS ONE, 5, 2010, e8785.
13. Gerrits, A., Dykstra, B., Kalmykowa, O.J., Klauke, K., Verovskaya, E., Broekhuis, M.J., de Haan, G., Bystrykh, L.V., Cellular barcoding tool for clonal analysis in the hematopoietic system. Blood 115 (2010), 2610–2618.
14. Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y.C., Laslo, P., Cheng, J.X., Murre, C., Singh, H., Glass, C.K., Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38 (2010), 576–589.
15. Jordan, C.T., Lemischka, I.R., Clonal and systemic analysis of long-term hematopoiesis in the mouse. Genes Dev. 4 (1990), 220–232.
16. Kharchenko, P.V., Tolstorukov, M.Y., Park, P.J., Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat. Biotechnol. 26 (2008), 1351–1359.
17. Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., Salzberg, S.L., TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol., 14, 2013, R36.
18. Kittler, R., Pelletier, L., Heninger, A.K., Slabicki, M., Theis, M., Miroslaw, L., Poser, I., Lawo, S., Grabner, H., Kozak, K., et al. Genome-scale RNAi profiling of cell division in human tissue culture cells. Nat. Cell Biol. 9 (2007), 1401–1412.
19. Kühn, R., Schwenk, F., Aguet, M., Rajewsky, K., Inducible gene targeting in mice. Science 269 (1995), 1427–1429.
20. Langmead, B., Salzberg, S.L., Fast gapped-read alignment with Bowtie 2. Nat. Methods 9 (2012), 357–359.
21. Lara-Astiaso, D., Weiner, A., Lorenzo-Vivas, E., Zaretsky, I., Jaitin, D.A., David, E., Keren-Shaul, H., Mildner, A., Winter, D., Jung, S., et al. Immunogenetics. Chromatin state dynamics during blood formation. Science 345 (2014), 943–949.
22. Lemischka, I.R., Retroviral lineage studies: some principals and applications. Curr. Opin. Genet. Dev. 3 (1993), 115–118.
23. Lemischka, I.R., Raulet, D.H., Mulligan, R.C., Developmental potential and dynamic behavior of hematopoietic stem cells. Cell 45 (1986), 917–927.
24. Livet, J., Weissman, T.A., Kang, H., Draft, R.W., Lu, J., Bennis, R.A., Sanes, J.R., Lichtman, J.W., Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature 450 (2007), 56–62.
25. Lu, R., Neff, N.F., Quake, S.R., Weissman, I.L., Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding. Nat. Biotechnol. 29 (2011), 928–933.
26. Lu, F., Liu, Y., Jiang, L., Yamaguchi, S., Zhang, Y., Role of Tet proteins in enhancer activity and telomere elongation. Genes Dev. 28 (2014), 2103–2119.
27. Mazurier, F., Gan, O.I., McKenzie, J.L., Doedens, M., Dick, J.E., Lentivector-mediated clonal tracking reveals intrinsic heterogeneity in the human hematopoietic stem cell compartment and culture-induced stem cell impairment. Blood 103 (2004), 545–552.
28. Morita, Y., Ema, H., Nakauchi, H., Heterogeneity and hierarchy within the most primitive hematopoietic stem cell compartment. J. Exp. Med. 207 (2010), 1173–1182.
29. Muller-Sieburg, C.E., Cho, R.H., Karlsson, L., Huang, J.F., Sieburg, H.B., Myeloid-biased hematopoietic stem cells have extensive self-renewal capacity but generate diminished lymphoid progeny with impaired IL-7 responsiveness. Blood 103 (2004), 4111–4118.
30. Notta, F., Mullighan, C.G., Wang, J.C., Poeppl, A., Doulatov, S., Phillips, L.A., Ma, J., Minden, M.D., Downing, J.R., Dick, J.E., Evolution of human BCR-ABL1 lymphoblastic leukaemia-initiating cells. Nature 469 (2011), 362–367.
31. Oki, T., Nishimura, K., Kitaura, J., Togami, K., Maehara, A., Izawa, K., Sakaue-Sawano, A., Niida, A., Miyano, S., Aburatani, H., et al. A novel cell-cycle-indicator, mVenus-p27K-, identifies quiescent cells and visualizes G0-G1 transition. Sci. Rep., 4, 2014, 4012.
32. Picelli, S., Björklund, A.K., Faridani, O.R., Sagasser, S., Winberg, G., Sandberg, R., Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat. Methods 10 (2013), 1096–1098.
33. Shi, P.A., Hematti, P., von Kalle, C., Dunbar, C.E., Genetic marking as an approach to studying in vivo hematopoiesis: progress in the non-human primate model. Oncogene 21 (2002), 3274–3283.
34. Snippert, H.J., van der Flier, L.G., Sato, T., van Es, J.H., van den Born, M., Kroon-Veenboer, C., Barker, N., Klein, A.M., van Rheenen, J., Simons, B.D., Clevers, H., Intestinal crypt homeostasis results from neutral competition between symmetrically dividing Lgr5 stem cells. Cell 143 (2010), 134–144.
35. Snodgrass, R., Keller, G., Clonal fluctuation within the haematopoietic system of mice reconstituted with retrovirus-infected stem cells. EMBO J. 6 (1987), 3955–3960.
36. Sun, D., Luo, M., Jeong, M., Rodriguez, B., Xia, Z., Hannah, R., Wang, H., Le, T., Faull, K.F., Chen, R., et al. Epigenomic profiling of young and aged HSCs reveals concerted changes during aging that reinforce self-renewal. Cell Stem Cell 14 (2014), 673–688.
37. Sun, J., Ramos, A., Chapman, B., Johnnidis, J.B., Le, L., Ho, Y.J., Klein, A., Hofmann, O., Camargo, F.D., Clonal dynamics of native haematopoiesis. Nature 514 (2014), 322–327.
38. Tsang, J.C., Yu, Y., Burke, S., Buettner, F., Wang, C., Kolodziejczyk, A.A., Teichmann, S.A., Lu, L., Liu, P., Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells. Genome Biol., 16, 2015, 178.
39. Venezia, T.A., Merchant, A.A., Ramos, C.A., Whitehouse, N.L., Young, A.S., Shaw, C.A., Goodell, M.A., Molecular signatures of proliferation and quiescence in hematopoietic stem cells. PLoS Biol., 2, 2004, e301.
40. Verovskaya, E., Broekhuis, M.J., Zwart, E., Weersing, E., Ritsema, M., Bosman, L.J., van Poele, T., de Haan, G., Bystrykh, L.V., Asymmetry in skeletal distribution of mouse hematopoietic stem cell clones and their equilibration by mobilizing cytokines. J. Exp. Med. 211 (2014), 487–497.
41. Wilson, N.K., Kent, D.G., Buettner, F., Shehata, M., Macaulay, I.C., Calero-Nieto, F.J., Sánchez Castillo, M., Oedekoven, C.A., Diamanti, E., Schulte, R., et al. Combined single-cell functional and gene expression analysis resolves heterogeneity within stem cell populations. Cell Stem Cell 16 (2015), 712–724.
42. Wu, Y., Zhou, H., Fan, X., Zhang, Y., Zhang, M., Wang, Y., Xie, Z., Bai, M., Yin, Q., Liang, D., et al. Correction of a genetic disease by CRISPR-Cas9-mediated gene editing in mouse spermatogonial stem cells. Cell Res. 25 (2015), 67–79.
43. Xi, R., Lee, S., Xia, Y., Kim, T.M., Park, P.J., Copy number analysis of whole-genome data using BIC-seq2 and its application to detection of cancer susceptibility variants. Nucleic Acids Res. 44 (2016), 6274–6286.