Genome-wide comparison of PU.1 and Spi-B binding sites in a mouse B lymphoma cell line

BMC Genomics
Lauren A SolomonRodney P DeKoter

Abstract

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. 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 ...Continue Reading

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Citations

Jan 8, 2017·The Journal of Immunology : Official Journal of the American Association of Immunologists·Carolina R BatistaRodney P DeKoter
Jun 7, 2019·Epigenetics : Official Journal of the DNA Methylation Society·Wenbin LiuYixian Zheng
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Nov 3, 2017·The Journal of Immunology : Official Journal of the American Association of Immunologists·Pingzhang WangDalong Ma
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Mar 7, 2021·International Journal of Molecular Sciences·Viktoria FuhrHilka Rauert-Wunderlich
May 29, 2018·Journal of Chemical Theory and Computation·Cheng Tan, Shoji Takada

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Datasets Mentioned

BETA
GSE31039
GSE37074

Methods Mentioned

BETA
immunoprecipitation
ChIP-seq
ChIP
footprinting
PCR
Assay

Software Mentioned

BETA
minus
JASPAR
Map Bowtie
Heatmapper
regulatory Element Annotation System ( CEAS )
DiffBind
DeepTools
profiler
MFOLD

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