ATAC-seq on biobanked specimens defines a unique chromatin accessibility structure in naïve SLE B cells

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Scharer, Christopher D ^a   Blalock, Emily L ^a   Barwick, Benjamin G ^a   Haines, Robert R ^a   Wei, Chungwen ^a   Sanz, Ignacio ^a   Boss, Jeremy M ^a  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CRYOPROTECTIVE AGENT; DIMETHYL SULFOXIDE; TRANSPOSASE;

B LYMPHOCYTE; BIOASSAY; BLOOD BANK; CHEMISTRY; CHROMATIN; CHROMOSOMAL MAPPING; CRYOPRESERVATION; CYTOLOGY; DNA SEQUENCE; DRUG EFFECTS; GENE LOCUS; GENETIC EPIGENESIS; GENETICS; GENOTYPE; HUMAN; IMMUNOLOGY; METABOLISM; PATHOLOGY; PROCEDURES; SYSTEMIC LUPUS ERYTHEMATOSUS; TRANSPOSON;

B-LYMPHOCYTES; BIOLOGICAL ASSAY; BLOOD BANKS; CHROMATIN; CHROMOSOME MAPPING; CRYOPRESERVATION; CRYOPROTECTIVE AGENTS; DIMETHYL SULFOXIDE; DNA TRANSPOSABLE ELEMENTS; EPIGENESIS, GENETIC; GENETIC LOCI; GENOTYPE; HUMANS; LUPUS ERYTHEMATOSUS, SYSTEMIC; SEQUENCE ANALYSIS, DNA; TRANSPOSASES;

EID: 84973325068     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep27030     Document Type: Article

References (39)

1. Yong, W. H., Dry, S. M. & Shabihkhani, M. A practical approach to clinical and research biobanking. Methods Mol Biol 1180, 137-162, doi: 10.1007/978-1-4939-1050-2-8 (2014).
2. Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 10, 1213-1218, doi: 10.1038/nmeth.2688 (2013).
3. Landt, S. G. et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome research 22, 1813-1831, doi: 10.1101/gr.136184.111 (2012).
4. Davie, K. et al. Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling. PLoS genetics 11, e1004994, doi: 10.1371/journal.pgen.1004994 (2015).
5. Majumder, P., Gomez, J. A., Chadwick, B. P. & Boss, J. M. The insulator factor CTCF controls MHC class II gene expression and is required for the formation of long-distance chromatin interactions. J Exp Med 205, 785-798 (2008).
6. Scharer, C. D. et al. Genome-wide CIITA-binding profile identifies sequence preferences that dictate function versus recruitment. Nucleic Acids Res 43, 3128-3142, doi: 10.1093/nar/gkv182 (2015).
7. Whyte, W. A. et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153, 307-319, doi: 10.1016/j.cell.2013.03.035 (2013).
8. Wang, J. et al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome research 22, 1798-1812, doi: 10.1101/gr.139105.112 (2012).
9. Gaffney, D. J. et al. Controls of nucleosome positioning in the human genome. PLoS genetics 8, e1003036, doi: 10.1371/journal. pgen.1003036 (2012).
10. Wei, C. et al. A new population of cells lacking expression of CD27 represents a notable component of the B cell memory compartment in systemic lupus erythematosus. J Immunol 178, 6624-6633 (2007).
11. Tipton, C. M. et al. Diversity, cellular origin and autoreactivity of antibody-secreting cell population expansions in acute systemic lupus erythematosus. Nat Immunol 16, 755-765, doi: 10.1038/ni.3175 (2015).
12. Dorner, T., Jacobi, A. M., Lee, J. & Lipsky, P. E. Abnormalities of B cell subsets in patients with systemic lupus erythematosus. J Immunol Methods 363, 187-197, doi: 10.1016/j.jim.2010.06.009 (2011).
13. Cappione, A., 3rd et al. Germinal center exclusion of autoreactive B cells is defective in human systemic lupus erythematosus. J Clin Invest 115, 3205-3216, doi: 10.1172/JCI24179 (2005).
14. Javierre, B. M. et al. Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus. Genome Res 20, 170-179, doi: 10.1101/gr.100289.109 (2010).
15. Absher, D. M. et al. Genome-wide DNA methylation analysis of systemic lupus erythematosus reveals persistent hypomethylation of interferon genes and compositional changes to CD4+ T-cell populations. PLoS genetics 9, e1003678, doi: 10.1371/journal. pgen.1003678 (2013).
16. Cambier, J. C. Autoimmunity risk alleles: hotspots in B cell regulatory signaling pathways. J Clin Invest 123, 1928-1931, doi: 10.1172/JCI69289 (2013).
17. Vaughn, S. E., Kottyan, L. C., Munroe, M. E. & Harley, J. B. Genetic susceptibility to lupus: the biological basis of genetic risk found in B cell signaling pathways. J Leukoc Biol 92, 577-591, doi: 10.1189/jlb.0212095 (2012).
18. Farh, K. K. et al. Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature 518, 337-343, doi: 10.1038/nature13835 (2015).
19. Chung, S. A. et al. Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production. PLoS genetics 7, e1001323, doi: 10.1371/journal.pgen.1001323 (2011).
20. Kariuki, S. N. et al. Cutting edge: autoimmune disease risk variant of STAT4 confers increased sensitivity to IFN-alpha in lupus patients in vivo. J Immunol 182, 34-38 (2009).
21. Roszer, T. et al. Autoimmune kidney disease and impaired engulfment of apoptotic cells in mice with macrophage peroxisome proliferator-activated receptor gamma or retinoid X receptor alpha deficiency. J Immunol 186, 621-631, doi: 10.4049/jimmunol.1002230 (2011).
22. Murphy, T. L., Tussiwand, R. & Murphy, K. M. Specificity through cooperation: BATF-IRF interactions control immune-regulatory networks. Nat Rev Immunol 13, 499-509, doi: 10.1038/nri3470 (2013).
23. Ise, W. et al. The transcription factor BATF controls the global regulators of class-switch recombination in both B cells and T cells. Nat Immunol 12, 536-543, doi: 10.1038/ni.2037 (2011).
24. Betz, B. C. et al. Batf coordinates multiple aspects of B and T cell function required for normal antibody responses. J Exp Med 207, 933-942, doi: 10.1084/jem.20091548 (2010).
25. Dozmorov, M. G., Wren, J. D. & Alarcon-Riquelme, M. E. Epigenomic elements enriched in the promoters of autoimmunity susceptibility genes. Epigenetics 9, 276-285, doi: 10.4161/epi.27021 (2014).
26. Hochberg, M. C. Updating the American College of Rheumatology revised criteria for the classification of systemic lupus erythematosus. Arthritis Rheum 40, 1725, doi: 10.1002/1529-0131(199709)40:9〈1725::AID-ART29〉3.0.CO;2-Y (1997).
27. Lara-Astiaso, D. et al. Immunogenetics. Chromatin state dynamics during blood formation. Science 345, 943-949, doi: 10.1126/science.1256271 (2014).
28. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25, doi: 10.1186/gb-2009-10-3-r25 (2009).
29. Heinz, S. et al. Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol Cell 38, 576-589, doi: 10.1016/j.molcel.2010.05.004 (2010).
30. Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics (Oxford, England) 26, 139-140, doi: 10.1093/bioinformatics/btp616 (2010).
31. Huang da, W., Sherman, B. T. & Lempicki, R. A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37, 1-13, doi: 10.1093/nar/gkn923 (2009).
32. Huang da, W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4, 44-57, doi: 10.1038/nprot.2008.211 (2009).
33. Lawrence, M. et al. Software for Computing and Annotating Genomic Ranges. PLoS Comput Biol 9, doi: 10.1371/journal. pcbi.1003118 (2013).
34. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics (Oxford, England) 25, 2078-2079, doi: 10.1093/bioinformatics/btp352 (2009).
35. Li, H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics (Oxford, England) 27, 2987-2993, doi: 10.1093/bioinformatics/btr509 (2011).
36. Gerstein, M. B. et al. Architecture of the human regulatory network derived from ENCODE data. Nature 489, 91-100, doi: 10.1038/nature11245 (2012).
37. Wang, J. et al. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res 41, D171-176, doi: 10.1093/nar/gks1221 (2013).
38. Grant, C. E., Bailey, T. L. & Noble, W. S. FIMO: scanning for occurrences of a given motif. Bioinformatics (Oxford, England) 27, 1017-1018, doi: 10.1093/bioinformatics/btr064 (2011).
39. Sandelin, A., Alkema, W., Engstrom, P., Wasserman, W. W. & Lenhard, B. JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res 32, D91-94, doi: 10.1093/nar/gkh012 (2004).