Genome-wide DNA methylation analysis in precursor B-cells

Epigenetics

Volumn 9, Issue 12, 2015, Pages 1588-1595

  Almamun, Md ^a   Levinson, Benjamin T ^a   Gater, Susan T ^b   Schnabel, Robert D ^c   Arthur, Gerald L ^a   Wade Davis, J ^c   Taylor, Kristen H ^a  

^a University of Missouri   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

^c UNIVERSITY OF MISSOURI   (United States)

Author keywords

DNA methylation; Enhancer; Next generation sequencing; Precursor B cell; Umbilical cord blood

Indexed keywords

B LYMPHOCYTE RECEPTOR; CD19 ANTIGEN; CD34 ANTIGEN; CD45 ANTIGEN;

ARTICLE; CELL DIFFERENTIATION; CELL MATURATION; CELL SELECTION; CPG ISLAND; DATA PROCESSING; DENSITY GRADIENT CENTRIFUGATION; DIFFERENTIALLY METHYLATED REGION; DNA ISOLATION; DNA METHYLATION; DNA STRUCTURE; GENE EXPRESSION REGULATION; GENE SEQUENCE; GENOME ANALYSIS; GENOMIC INSTABILITY; HEMATOPOIESIS; HUMAN; HUMAN CELL; LEUKOCYTE ACTIVATION; NORMAL HUMAN; PATHOGENESIS; POLYMERASE CHAIN REACTION; PRE B LYMPHOCYTE; SEQUENCE ALIGNMENT; UMBILICAL CORD BLOOD; ACUTE LYMPHOBLASTIC LEUKEMIA; CYTOLOGY; FETUS BLOOD; GENETIC ASSOCIATION; GENETICS; HIGH THROUGHPUT SEQUENCING; LYMPHOCYTE SUBPOPULATION; NEWBORN; PATHOLOGY; PHYSIOLOGY;

CELL DIFFERENTIATION; CPG ISLANDS; DNA METHYLATION; FETAL BLOOD; GENOME-WIDE ASSOCIATION STUDY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INFANT, NEWBORN; LYMPHOCYTE SUBSETS; PRECURSOR CELL LYMPHOBLASTIC LEUKEMIA-LYMPHOMA; PRECURSOR CELLS, B-LYMPHOID;

EID: 84922032618     PISSN: 15592294     EISSN: 15592308     Source Type: Journal    
DOI: 10.4161/15592294.2014.983379     Document Type: Article

References (37)

1. Hystad ME, Myklebust JH, Bø TH, Sivertsen EA, Rian E, Forfang L, Munthe E, Rosenwald A, Chiorazzi M, Jonassen I, et al. Characterization of early stages of human B cell development by gene expression profiling. J Immunol 2007; 179(6): 3662-71; PMID:17785802; http://dx.doi.org/ 10.4049/jimmunol.179.6.3662.
2. van Zelm MC, van der Burg M, de Ridder D, Barendregt BH, de Haas EF, Reinders MJ, Lankester AC, Révész T, Staal FJ, van Dongen JJ. Ig gene rearrangement steps are initiated in early human precursor B cell subsets and correlate with specific transcription factor expression. J Immunol 2005; 175(9):5912-22; PMID:16237084; http://dx. doi.org/10.4049/jimmunol.175.9.5912.
3. Pérez-Vera P, Reyes-León A, Fuentes-Pananá EM. Signaling proteins and transcription factors in normal and malignant early B cell development. Bone Marrow Res 2011; 2011:502751; http://dx.doi.org/10.1155/2011/ 502751.
4. Matthias P, Rolink AG. Transcriptional networks in developing and mature B cells. Nat Rev Immunol 2005; 5(6):497-508; PMID:15928681; http://dx.doi. org/10.1038/nri1633.
5. Harmston N, Lenhard B. Chromatin and epigenetic features of long-range gene regulation. Nucleic Acids Res 2013; 41(15):7185-99; PMID:23766291; http:// dx.doi.org/10.1093/nar/gkt499.
6. Razin A, Riggs AD. DNA methylation and gene function. Science 1980; 210(4470):604-610; PMID:6254144; http://dx.doi.org/10.1126/science. 6254144.
7. Berger LS. The complex language of chromatin regulation during transcription. Nature 2007; 447:407-412; PMID:17522673; http://dx.doi.org/10.1038/nature 05915.
8. Newell-Price J, Clark AJL, King P. DNA Methylation and Silencing of Gene Expression. Trends Endocrinol Metab 2000; 11(4):142-148; PMID:10754536; http:// dx.doi.org/10.1016/S1043-2760(00)00248-4.
9. Bird A. The Essentials of DNA Methylation. Cell 1992; 70:5-8; PMID:1377983; http://dx.doi.org/ 10.1016/0092-8674(92)90526-I.
10. Ohgane J, Yagi S, Shiota K. Epigenetics: the DNA methylation profile of tissue-dependent and differentially methylated regions in cells. Placenta 2008; 29 Suppl A:S29-35; PMID:18031808; http://dx.doi.org/ 10.1016/j.placenta.2007.09.011.
11. Song F, Smith JF, Kimura MT, Morrow AD, Matsuyama T, Nagase H, Held WA. Association of tissuespecific differentially methylated regions (TDMs) with differential gene expression. Proc Natl Acad Sci U S A 2005; 102(9):3336-41; PMID:15728362; http://dx. doi.org/10.1073/pnas.0408436102.
12. Bröske AM, Vockentanz L, Kharazi S, Huska MR, Mancini E, Scheller M, Kuhl C, Enns A, Prinz M, Jaenisch R, et al. DNA methylation protects hematopoietic stem cell multipotency from myeloerythroid restriction. Nat Genet 2009; 41(11):1207-15; PMID:19801979; http://dx.doi.org/10.1038/ng.463.
13. Hodges E, Molaro A, Dos Santos CO, Thekkat P, Song Q, Uren PJ, Park J, Butler J, Rafii S, McCombie WR, 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; PMID:21924933; http://dx.doi. org/10.1016/j.molcel.2011.08.026.
14. Zhang B, Zhou Y, Lin N, Lowdon RF, Hong C, Nagarajan RP, et al. Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm. Genome Res 2013; 23(9):1522-40; PMID:23804400; http://dx.doi. org/10.1101/gr.156539.113.
15. Aran D, Sabato S, Hellman A. DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes. Genome Biol 2013; 14(3):R21; PMID:23497655; http://dx.doi.org/10.1186/gb-2013- 14-3-r21.
16. Rauch T, Pfeifer GP. Methylated-CpG island recovery assay: a new technique for the rapid detection of methylated- CpG islands in cancer. Lab Invest 2005; 85 (9):1172-8; PMID:16025148; http://dx.doi.org/ 10.1038/labinvest.3700311.
17. Caldwell CW, Poje E, Helikson MA. B-cell precursors in normal pediatric bone marrow. Am J Clin Pathol 1991; 95(6):816-823; PMID:2042591.
18. Almamun M, Schnabel JL, Gater ST, Ning J, Taylor KH. Isolation of precursor B-cell subsets from umbilical cord blood. J Vis Exp 2013; 74; http://dx.doi.org/ 10.3791/50402.
19. Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 2012; 13:484-492; PMID:22641018; http://dx.doi.org/ 10.1038/nrg3230.
20. Ji H, Ehrlich LI, Seita J, Murakami P, Doi A, Lindau P, Lee H, Aryee MJ, Irizarry RA, Kim K, et al. Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature 2010; 467 (7313):338-42; PMID:20720541; http://dx.doi.org/ 10.1038/nature09367.
21. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. Circos: An information aesthetic for comparative genomics. Genome Res 2009; 19:1639-1645; PMID:19541911; http://dx. doi.org/10.1101/gr.092759.109.
22. Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nature Protoc 2009; 4 (1):44-57; http://dx.doi.org/10.1038/nprot.2008.211.
23. Bulger M, Groudine M. Functional and mechanistic diversity of distal transcription enhancers. Cell 2011; 144(3):327-39; PMID:21295696; http://dx.doi.org/ 10.1016/j.cell.2011.01.024.
24. Xu J, Shao Z, Glass K, Bauer DE, Pinello L, Van Handel B, Hou S, Stamatoyannopoulos JA, Mikkola HK, Yuan GC, et al. Combinatorial assembly of developmental stage specific enhancers control gene expression programs during human erythropoiesis. Dev Cell 2012; 23:796-811; PMID:23041383; http://dx.doi. org/10.1016/j.devcel.2012.09.003.
25. Bogdanovic O, Fernandez-Miñán A, Tena JJ, de la Calle-Mustienes E, Hidalgo C, van Kruysbergen I, van Heeringen SJ, Veenstra GJ, Gómez-Skarmeta JL. Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis. Genome Res 2012; 22(10):2043-53; PMID:22593555; http://dx.doi. org/10.1101/gr.134833.111.
26. Hogart A, Lichtenberg J, Ajay SS, Anderson S. NIH Intramural Sequencing Center, Margulies EH, Bodine DM. Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites. Genome Res 2012; 22(8):1407-18; PMID:22684279; http://dx.doi.org/10.1101/gr.132878.111.
27. Lee ST, Xiao Y, Muench MO, Xiao J, Fomin ME, Wiencke JK, Zheng S, Dou X, de Smith A, Chokkalingam A, et al. A global DNA methylation and gene expression analysis of early human B-cell development reveals a demethylation signature and transcription factor network. Nucleic Acids Res 2012; 40(22):11339- 51; PMID:23074194; http://dx.doi.org/10.1093/nar/ gks957.
28. Shore A, Karamitri A, Kemp P, Speakman JR, Lomax MA. Role of Ucp1 enhancer methylation and chromatin remodelling in the control of Ucp1 expression in murine adipose tissue. Diabetologia 2010; 53(6):1164- 73; PMID:20238096; http://dx.doi.org/10.1007/ s00125-010-1701-4.
29. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 2011; 17:10-12; http://dx.doi.org/10.14806/ej.17. 1.200.
30. Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods 2012; 9:357-359; PMID:22388286; http://dx.doi.org/10.1038/nmeth. 1923.
31. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics 2009; 25:2078-9; PMID:19505943; http://dx.doi.org/10.1093/bioinformatics/ btp352.
32. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008; 9(9):R137; http://dx.doi.org/ 10.1186/gb-2008-9-9-r137.
33. Quinlan A, Hall I. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010; 26(6): 841-842; PMID:20110278; http://dx. doi.org/10.1093/bioinformatics/btq033.
34. Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 2010; 38 (4):576-589; PMID:20513432; http://dx.doi.org/ 10.1016/j.molcel.2010.05.004.
35. Chavez L, Jozefczuk J, Grimm C, Dietrich J, Timmermann B, Lehrach H, Herwig R, Adjaye J. Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage. Genome Res. 2010; 20(10):1441-50; PMID:20802089; http://dx.doi.org/ 10.1101/gr.110114.110.
36. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, et al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol 2008; 26:779-85; PMID:18612301; http://dx.doi.org/10.1038/nbt1414.
37. Bourgon R, Gentleman R, Huber W. Independent filtering increases detection power for high-throughput experiments. Proc Natl Acad Sci U S A 2010; 107:9546-51; PMID:20460310; http://dx.doi.org/ 10.1073/pnas.0914005107.