Chromatin Signatures in Multipotent Human Hematopoietic Stem Cells Indicate the Fate of Bivalent Genes during Differentiation

Cell Stem Cell

Volumn 4, Issue 1, 2009, Pages 80-93

  Cui, Kairong ^a   Zang, Chongzhi ^b   Roh, Tae Young ^a   Schones, Dustin E ^a   Childs, Richard W ^a   Peng, Weiqun ^b   Zhao, Keji ^a  

^a NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

^b GEORGE WASHINGTON UNIVERSITY   (United States)

Author keywords

STEMCELL; SYSBIO

Indexed keywords

HISTONE H2A; HISTONE H3; HISTONE H4; RNA POLYMERASE II;

ARTICLE; CELL DIFFERENTIATION; CHROMATIN; CONTROLLED STUDY; ENHANCER REGION; ERYTHROCYTE; GENE ACTIVATION; GENE EXPRESSION; GENE IDENTIFICATION; GENE SILENCING; HEMATOPOIETIC STEM CELL; HUMAN; HUMAN CELL; MULTIPOTENT STEM CELL; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN METHYLATION; PROTEIN MODIFICATION;

ANTIGENS, CD; ANTIGENS, CD36; BIOLOGICAL MARKERS; CELL DIFFERENTIATION; CELL LINEAGE; CELL MEMBRANE; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; ERYTHROCYTES; GENOME, HUMAN; GLYCOPROTEINS; HEMATOPOIETIC STEM CELLS; HISTONES; HUMANS; METHYLATION; MULTIPOTENT STEM CELLS; PEPTIDES; TRANSCRIPTION FACTORS;

EID: 58049191558     PISSN: 19345909     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.stem.2008.11.011     Document Type: Article

References (46)

1. Ansel K.M., Djuretic I., Tanasa B., and Rao A. Regulation of Th2 differentiation and Il4 locus accessibility. Annu. Rev. Immunol. 24 (2006) 607-656
2. Azuara V., Perry P., Sauer S., Spivakov M., Jorgensen H.F., John R.M., Gouti M., Casanova M., Warnes G., Merkenschlager M., and Fisher A.G. Chromatin signatures of pluripotent cell lines. Nat. Cell Biol. 8 (2006) 532-538
3. Barski A., Cuddapah S., Cui K., Roh T.Y., Schones D.E., Wang Z., Wei G., Chepelev I., and Zhao K. High-resolution profiling of histone methylations in the human genome. Cell 129 (2007) 823-837
4. Bernstein B.E., Kamal M., Lindblad-Toh K., Bekiranov S., Bailey D.K., Huebert D.J., McMahon S., Karlsson E.K., Kulbokas III E.J., Gingeras T.R., et al. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120 (2005) 169-181
5. Bernstein B.E., Mikkelsen T.S., Xie X., Kamal M., Huebert D.J., Cuff J., Fry B., Meissner A., Wernig M., Plath K., et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125 (2006) 315-326
6. Bitan M., Shapira M.Y., Resnick I.B., Zilberman I., Miron S., Samuel S., Ackerstein A., Elad S., Israel S., Amar A., et al. Successful transplantation of haploidentically mismatched peripheral blood stem cells using CD133+-purified stem cells. Exp. Hematol. 33 (2005) 713-718
7. 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
8. Chambeyron S., and Bickmore W.A. Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. Genes Dev. 18 (2004) 1119-1130
9. de Laat W., Klous P., Kooren J., Noordermeer D., Palstra R.J., Simonis M., Splinter E., and Grosveld F. Three-dimensional organization of gene expression in erythroid cells. Curr. Top. Dev. Biol. 82 (2008) 117-139
10. Donze D., Townes T.M., and Bieker J.J. Role of erythroid Kruppel-like factor in human gamma- to beta-globin gene switching. J. Biol. Chem. 270 (1995) 1955-1959
11. Ford A.M., Bennett C.A., Healy L.E., Towatari M., Greaves M.F., and Enver T. Regulation of the myeloperoxidase enhancer binding proteins Pu1, C-EBP alpha, -beta, and -delta during granulocyte-lineage specification. Proc. Natl. Acad. Sci. USA 93 (1996) 10838-10843
12. Giarratana M.C., Kobari L., Lapillonne H., Chalmers D., Kiger L., Cynober T., Marden M.C., Wajcman H., and Douay L. Ex vivo generation of fully mature human red blood cells from hematopoietic stem cells. Nat. Biotechnol. 23 (2005) 69-74
13. Grosveld F., van Assendelft G.B., Greaves D.R., and Kollias G. Position-independent, high-level expression of the human beta-globin gene in transgenic mice. Cell 51 (1987) 975-985
14. Guenther M.G., Levine S.S., Boyer L.A., Jaenisch R., and Young R.A. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130 (2007) 77-88
15. Heintzman N.D., Stuart R.K., Hon G., Fu Y., Ching C.W., Hawkins R.D., Barrera L.O., Van Calcar S., Qu C., Ching K.A., et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet. 39 (2007) 311-318
16. Hu M., Krause D., Greaves M., Sharkis S., Dexter M., Heyworth C., and Enver T. Multilineage gene expression precedes commitment in the hemopoietic system. Genes Dev. 11 (1997) 774-785
17. Ivanova N.B., Dimos J.T., Schaniel C., Hackney J.A., Moore K.A., and Lemischka I.R. A stem cell molecular signature. Science 298 (2002) 601-604
18. Krumlauf R. Hox genes in vertebrate development. Cell 78 (1994) 191-201
19. Lepikhov K., and Walter J. Differential dynamics of histone H3 methylation at positions K4 and K9 in the mouse zygote. BMC Dev. Biol. 4 (2004) 12 10.1186/1471-213X-4-12
20. Litt M.D., Simpson M., Gaszner M., Allis C.D., and Felsenfeld G. Correlation between histone lysine methylation and developmental changes at the chicken beta-globin locus. Science 293 (2001) 2453-2455
21. Meissner A., Mikkelsen T.S., Gu H., Wernig M., Hanna J., Sivachenko A., Zhang X., Bernstein B.E., Nusbaum C., Jaffe D.B., et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454 (2008) 766-770
22. Migliaccio G., Di Pietro R., di Giacomo V., Di Baldassarre A., Migliaccio A.R., Maccioni L., Galanello R., and Papayannopoulou T. In vitro mass production of human erythroid cells from the blood of normal donors and of thalassemic patients. Blood Cells Mol. Dis. 28 (2002) 169-180
23. Mikkelsen T.S., Ku M., Jaffe D.B., Issac B., Lieberman E., Giannoukos G., Alvarez P., Brockman W., Kim T.K., Koche R.P., et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448 (2007) 553-560
24. Mohn F., Weber M., Rebhan M., Roloff T.C., Richter J., Stadler M.B., Bibel M., and Schubeler D. Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Mol. Cell 30 (2008) 755-766
25. Morrison S.J., Uchida N., and Weissman I.L. The biology of hematopoietic stem cells. Annu. Rev. Cell Dev. Biol. 11 (1995) 35-71
26. Ng H.H., Robert F., Young R.A., and Struhl K. Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol. Cell 11 (2003) 709-719
27. Orford K., Kharchenko P., Lai W., Dao M.C., Worhunsky D.J., Ferro A., Janzen V., Park P.J., and Scadden D.T. Differential H3K4 methylation identifies developmentally poised hematopoietic genes. Dev. Cell 14 (2008) 798-809
28. Pan G., Tian S., Nie J., Yang C., Ruotti V., Wei H., Jonsdottir G.A., Stewart R., and Thomson J.A. Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells. Cell Stem Cell 1 (2007) 299-312
29. Ramalho-Santos M., Yoon S., Matsuzaki Y., Mulligan R.C., and Melton D.A. "Stemness": transcriptional profiling of embryonic and adult stem cells. Science 298 (2002) 597-600
30. Ramos C.A., Bowman T.A., Boles N.C., Merchant A.A., Zheng Y., Parra I., Fuqua S.A., Shaw C.A., and Goodell M.A. Evidence for diversity in transcriptional profiles of single hematopoietic stem cells. PLoS Genet. 2 (2006) e159 10.1371/journal.pgen.0020159
31. Roh T.Y., Cuddapah S., and Zhao K. Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Genes Dev. 19 (2005) 542-552
32. Roh T.Y., Cuddapah S., Cui K., and Zhao K. The genomic landscape of histone modifications in human T cells. Proc. Natl. Acad. Sci. USA 103 (2006) 15782-15787
33. Roh T.Y., Wei G., Farrell C.M., and Zhao K. Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns. Genome Res. 17 (2007) 74-81
34. Santos F., Peters A.H., Otte A.P., Reik W., and Dean W. Dynamic chromatin modifications characterise the first cell cycle in mouse embryos. Dev. Biol. 280 (2005) 225-236
35. Sanyal M., Tung J.W., Karsunky H., Zeng H., Selleri L., Weissman I.L., Herzenberg L.A., and Cleary M.L. B-cell development fails in the absence of the Pbx1 proto-oncogene. Blood 109 (2007) 4191-4199
36. Surani M.A., Hayashi K., and Hajkova P. Genetic and epigenetic regulators of pluripotency. Cell 128 (2007) 747-762
37. Szilvassy S.J. The biology of hematopoietic stem cells. Arch. Med. Res. 34 (2003) 446-460
38. Takahashi S., Onodera K., Motohashi H., Suwabe N., Hayashi N., Yanai N., Nabesima Y., and Yamamoto M. Arrest in primitive erythroid cell development caused by promoter-specific disruption of the GATA-1 gene. J. Biol. Chem. 272 (1997) 12611-12615
39. Ting C.N., Olson M.C., Barton K.P., and Leiden J.M. Transcription factor GATA-3 is required for development of the T-cell lineage. Nature 384 (1996) 474-478
40. Venezia T.A., Merchant A.A., Ramos C.A., Whitehouse N.L., Young A.S., Shaw C.A., and Goodell M.A. Molecular signatures of proliferation and quiescence in hematopoietic stem cells. PLoS Biol. 2 (2004) e301 10.1371/journal.pbio.0020301
41. Wang Z., Zang C., Rosenfeld J.A., Schones D.E., Barski A., Cuddapah S., Cui K., Roh T.Y., Peng W., Zhang M.Q., and Zhao K. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat. Genet. 40 (2008) 897-903
42. Warren L., Bryder D., Weissman I.L., and Quake S.R. Transcription factor profiling in individual hematopoietic progenitors by digital RT-PCR. Proc. Natl. Acad. Sci. USA 103 (2006) 17807-17812
43. Weber M., Hellmann I., Stadler M.B., Ramos L., Paabo S., Rebhan M., and Schubeler D. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet. 39 (2007) 457-466
44. Wong S., Zhi N., Filippone C., Keyvanfar K., Kajigaya S., Brown K.E., and Young N.S. Ex vivo-generated CD36+ erythroid progenitors are highly permissive to human parvovirus B19 replication. J. Virol. 82 (2008) 2470-2476
45. Yin A.H., Miraglia S., Zanjani E.D., Almeida-Porada G., Ogawa M., Leary A.G., Olweus J., Kearney J., and Buck D.W. AC133, a novel marker for human hematopoietic stem and progenitor cells. Blood 90 (1997) 5002-5012
46. Zhao X.D., Han X., Chew J.L., Liu J., Chiu K.P., Choo A., Orlov Y.L., Sung W.K., Shahab A., Kuznetsov V.A., et al. Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell 1 (2007) 286-298