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Quantitative profiling of BATF family proteins/JUNB/IRF hetero-trimers using Spec-seq
BACKGROUND: BATF family transcription factors (BATF, BATF2 and BATF3) form hetero-trimers with JUNB and either IRF4 or IRF8 to regulate cell fate in T cells and dendritic cells in vivo. While each combination of the hetero-trimer has a distinct role, some degree of cross-compensation was observed. T...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5869772/ https://www.ncbi.nlm.nih.gov/pubmed/29587652 http://dx.doi.org/10.1186/s12867-018-0106-7 |
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author | Chang, Yiming K. Zuo, Zheng Stormo, Gary D. |
author_facet | Chang, Yiming K. Zuo, Zheng Stormo, Gary D. |
author_sort | Chang, Yiming K. |
collection | PubMed |
description | BACKGROUND: BATF family transcription factors (BATF, BATF2 and BATF3) form hetero-trimers with JUNB and either IRF4 or IRF8 to regulate cell fate in T cells and dendritic cells in vivo. While each combination of the hetero-trimer has a distinct role, some degree of cross-compensation was observed. The basis for the differential actions of IRF4 and IRF8 with BATF factors and JUNB is still unknown. We propose that the differences in function between these hetero-trimers may be caused by differences in their DNA binding preferences. While all three BATF family transcription factors have similar binding preferences when binding as a hetero-dimer with JUNB, the cooperative binding of IRF4 or IRF8 to the hetero-dimer/DNA complex could change the preferences. We used Spec-seq, which allows for the efficient and accurate determination of relative affinity to a large collection of sequences in parallel, to find differences between cooperative DNA binding of IRF4, IRF8 and BATF family members. RESULTS: We found that without IRF binding, all three hetero-dimer pairs exhibit nearly the same binding preferences to both expected wildtype binding sites TRE (TGA(C/G)TCA) and CRE (TGACGTCA). IRF4 and IRF8 show the very similar DNA binding preferences when binding with any of the three hetero-dimers. No major change of binding preferences was found in the half-sites between different hetero-trimers. IRF proteins bind with substantially lower affinity with either a single nucleotide spacer between IRF and BATF binding site or with an alternative mode of binding in the opposite orientation. In addition, the preference to CRE binding site was reduced with either IRF binding in all BATF–JUNB combinations. CONCLUSIONS: The specificities of BATF, BATF2 and BATF3 are all very similar as are their interactions with IRF4 and IRF8. IRF proteins binding adjacent to BATF sites increases affinity substantially compared to sequences with spacings between the sites, indicating cooperative binding through protein–protein interactions. The preference for the type of BATF binding site, TRE or CRE, is also altered when IRF proteins bind. These in vitro preferences aid in the understanding of in vivo binding activities. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12867-018-0106-7) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5869772 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-58697722018-03-29 Quantitative profiling of BATF family proteins/JUNB/IRF hetero-trimers using Spec-seq Chang, Yiming K. Zuo, Zheng Stormo, Gary D. BMC Mol Biol Research Article BACKGROUND: BATF family transcription factors (BATF, BATF2 and BATF3) form hetero-trimers with JUNB and either IRF4 or IRF8 to regulate cell fate in T cells and dendritic cells in vivo. While each combination of the hetero-trimer has a distinct role, some degree of cross-compensation was observed. The basis for the differential actions of IRF4 and IRF8 with BATF factors and JUNB is still unknown. We propose that the differences in function between these hetero-trimers may be caused by differences in their DNA binding preferences. While all three BATF family transcription factors have similar binding preferences when binding as a hetero-dimer with JUNB, the cooperative binding of IRF4 or IRF8 to the hetero-dimer/DNA complex could change the preferences. We used Spec-seq, which allows for the efficient and accurate determination of relative affinity to a large collection of sequences in parallel, to find differences between cooperative DNA binding of IRF4, IRF8 and BATF family members. RESULTS: We found that without IRF binding, all three hetero-dimer pairs exhibit nearly the same binding preferences to both expected wildtype binding sites TRE (TGA(C/G)TCA) and CRE (TGACGTCA). IRF4 and IRF8 show the very similar DNA binding preferences when binding with any of the three hetero-dimers. No major change of binding preferences was found in the half-sites between different hetero-trimers. IRF proteins bind with substantially lower affinity with either a single nucleotide spacer between IRF and BATF binding site or with an alternative mode of binding in the opposite orientation. In addition, the preference to CRE binding site was reduced with either IRF binding in all BATF–JUNB combinations. CONCLUSIONS: The specificities of BATF, BATF2 and BATF3 are all very similar as are their interactions with IRF4 and IRF8. IRF proteins binding adjacent to BATF sites increases affinity substantially compared to sequences with spacings between the sites, indicating cooperative binding through protein–protein interactions. The preference for the type of BATF binding site, TRE or CRE, is also altered when IRF proteins bind. These in vitro preferences aid in the understanding of in vivo binding activities. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12867-018-0106-7) contains supplementary material, which is available to authorized users. BioMed Central 2018-03-27 /pmc/articles/PMC5869772/ /pubmed/29587652 http://dx.doi.org/10.1186/s12867-018-0106-7 Text en © The Author(s) 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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 Chang, Yiming K. Zuo, Zheng Stormo, Gary D. Quantitative profiling of BATF family proteins/JUNB/IRF hetero-trimers using Spec-seq |
title | Quantitative profiling of BATF family proteins/JUNB/IRF hetero-trimers using Spec-seq |
title_full | Quantitative profiling of BATF family proteins/JUNB/IRF hetero-trimers using Spec-seq |
title_fullStr | Quantitative profiling of BATF family proteins/JUNB/IRF hetero-trimers using Spec-seq |
title_full_unstemmed | Quantitative profiling of BATF family proteins/JUNB/IRF hetero-trimers using Spec-seq |
title_short | Quantitative profiling of BATF family proteins/JUNB/IRF hetero-trimers using Spec-seq |
title_sort | quantitative profiling of batf family proteins/junb/irf hetero-trimers using spec-seq |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5869772/ https://www.ncbi.nlm.nih.gov/pubmed/29587652 http://dx.doi.org/10.1186/s12867-018-0106-7 |
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