title: Genome-wide comparison of PU.1 and Spi-B binding sites in a mouse B lymphoma cell line.
abstract: BACKGROUND
  Spi-B and PU.1 are highly related members of the E26-transformation-specific (ETS) family of transcription factors that have similar, but not identical, roles in B cell development. PU.1 and Spi-B are both expressed in B cells, and have been demonstrated to redundantly activate transcription of genes required for B cell differentiation and function. It was hypothesized that Spi-B and PU.1 occupy a similar set of regions within the genome of a B lymphoma cell line.
  
  
  RESULTS
  To compare binding regions of Spi-B and PU.1, murine WEHI-279 lymphoma cells were infected with retroviral vectors encoding 3XFLAG-tagged PU.1 or Spi-B. Anti-FLAG chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) was performed. Analysis for high-stringency enriched genomic regions demonstrated that PU.1 occupied 4528 regions and Spi-B occupied 3360 regions. The majority of regions occupied by Spi-B were also occupied by PU.1. Regions bound by Spi-B and PU.1 were frequently located immediately upstream of genes associated with immune response and activation of B cells. Motif-finding revealed that both transcription factors were predominantly located at the ETS core domain (GGAA), however, other unique motifs were identified when examining regions associated with only one of the two factors. Motifs associated with unique PU.1 binding included POU2F2, while unique motifs in the Spi-B regions contained a combined ETS-IRF motif.
  
  
  CONCLUSIONS
  Our results suggest that complementary biological functions of PU.1 and Spi-B may be explained by their interaction with a similar set of regions in the genome of B cells. However, sites uniquely occupied by PU.1 or Spi-B provide insight into their unique functions.
authors.affiliation: Department of Microbiology & Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada. lsolomo3@uwo.ca.
authors.forename: Lauren A
authors.initials: LA
authors.lastname: Solomon
authors.affiliation: Department of Microbiology & Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada. sli265@uwo.ca.
authors.forename: Stephen K H
authors.initials: SK
authors.lastname: Li
authors.affiliation: Department of Microbiology & Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada. jpiskorz@uwo.ca.
authors.forename: Jan
authors.initials: J
authors.lastname: Piskorz
authors.affiliation: Department of Microbiology & Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada. lxu48@uwo.ca.
authors.forename: Li S
authors.initials: LS
authors.lastname: Xu
authors.affiliation: Department of Microbiology & Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada. rdekoter@uwo.ca.|Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Canada. rdekoter@uwo.ca.|Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, ON, N6A 5C1, Canada. rdekoter@uwo.ca.
authors.forename: Rodney P
authors.initials: RP
authors.lastname: DeKoter
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001402:B-Lymphocytes / Q000378:metabolism / Q000473:pathology; D001665:Binding Sites / Q000235:genetics; D045744:Cell Line, Tumor; D004268:DNA-Binding Proteins / Q000235:genetics; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D008223:Lymphoma / Q000235:genetics* / Q000473:pathology; D051379:Mice; D011401:Promoter Regions, Genetic; D011518:Proto-Oncogene Proteins / Q000235:genetics* / Q000378:metabolism; D050783:Proto-Oncogene Proteins c-ets / Q000235:genetics* / Q000378:metabolism; D015534:Trans-Activators / Q000235:genetics* / Q000378:metabolism; D000099232:Proto-Oncogene Protein Spi-1
chemical_list: D004268:DNA-Binding Proteins; D011518:Proto-Oncogene Proteins; D050783:Proto-Oncogene Proteins c-ets; D015534:Trans-Activators; D000099232:Proto-Oncogene Protein Spi-1; C514177:Spi-B protein, mouse