Cargando…
Genome-wide comparison of PU.1 and Spi-B binding sites in a mouse B lymphoma cell line
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 transcrip...
Autores principales: | , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2015
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4334403/ https://www.ncbi.nlm.nih.gov/pubmed/25765478 http://dx.doi.org/10.1186/s12864-015-1303-0 |
_version_ | 1782358181599510528 |
---|---|
author | Solomon, Lauren A Li, Stephen KH Piskorz, Jan Xu, Li S DeKoter, Rodney P |
author_facet | Solomon, Lauren A Li, Stephen KH Piskorz, Jan Xu, Li S DeKoter, Rodney P |
author_sort | Solomon, Lauren A |
collection | PubMed |
description | 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1303-0) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4334403 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-43344032015-02-20 Genome-wide comparison of PU.1 and Spi-B binding sites in a mouse B lymphoma cell line Solomon, Lauren A Li, Stephen KH Piskorz, Jan Xu, Li S DeKoter, Rodney P BMC Genomics Research Article 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1303-0) contains supplementary material, which is available to authorized users. BioMed Central 2015-02-14 /pmc/articles/PMC4334403/ /pubmed/25765478 http://dx.doi.org/10.1186/s12864-015-1303-0 Text en © Solomon et al.; licensee BioMed Central. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Solomon, Lauren A Li, Stephen KH Piskorz, Jan Xu, Li S DeKoter, Rodney P Genome-wide comparison of PU.1 and Spi-B binding sites in a mouse B lymphoma cell line |
title | Genome-wide comparison of PU.1 and Spi-B binding sites in a mouse B lymphoma cell line |
title_full | Genome-wide comparison of PU.1 and Spi-B binding sites in a mouse B lymphoma cell line |
title_fullStr | Genome-wide comparison of PU.1 and Spi-B binding sites in a mouse B lymphoma cell line |
title_full_unstemmed | Genome-wide comparison of PU.1 and Spi-B binding sites in a mouse B lymphoma cell line |
title_short | Genome-wide comparison of PU.1 and Spi-B binding sites in a mouse B lymphoma cell line |
title_sort | genome-wide comparison of pu.1 and spi-b binding sites in a mouse b lymphoma cell line |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4334403/ https://www.ncbi.nlm.nih.gov/pubmed/25765478 http://dx.doi.org/10.1186/s12864-015-1303-0 |
work_keys_str_mv | AT solomonlaurena genomewidecomparisonofpu1andspibbindingsitesinamouseblymphomacellline AT listephenkh genomewidecomparisonofpu1andspibbindingsitesinamouseblymphomacellline AT piskorzjan genomewidecomparisonofpu1andspibbindingsitesinamouseblymphomacellline AT xulis genomewidecomparisonofpu1andspibbindingsitesinamouseblymphomacellline AT dekoterrodneyp genomewidecomparisonofpu1andspibbindingsitesinamouseblymphomacellline |