Zinc finger independent genome-wide binding of Sp2 potentiates recruitment of histone-fold protein Nf-y distinguishing it from Sp1 and Sp3

PLoS Genet. 2015 Mar 20;11(3):e1005102. doi: 10.1371/journal.pgen.1005102. eCollection 2015 Mar.

Abstract

Transcription factors are grouped into families based on sequence similarity within functional domains, particularly DNA-binding domains. The Specificity proteins Sp1, Sp2 and Sp3 are paradigmatic of closely related transcription factors. They share amino-terminal glutamine-rich regions and a conserved carboxy-terminal zinc finger domain that can bind to GC rich motifs in vitro. All three Sp proteins are ubiquitously expressed; yet they carry out unique functions in vivo raising the question of how specificity is achieved. Crucially, it is unknown whether they bind to distinct genomic sites and, if so, how binding site selection is accomplished. In this study, we have examined the genomic binding patterns of Sp1, Sp2 and Sp3 in mouse embryonic fibroblasts by ChIP-seq. Sp1 and Sp3 essentially occupy the same promoters and localize to GC boxes. The genomic binding pattern of Sp2 is different; Sp2 primarily localizes at CCAAT motifs. Consistently, re-expression of Sp2 and Sp3 mutants in corresponding knockout MEFs revealed strikingly different modes of genomic binding site selection. Most significantly, while the zinc fingers dictate genomic binding of Sp3, they are completely dispensable for binding of Sp2. Instead, the glutamine-rich amino-terminal region is sufficient for recruitment of Sp2 to its target promoters in vivo. We have identified the trimeric histone-fold CCAAT box binding transcription factor Nf-y as the major partner for Sp2-chromatin interaction. Nf-y is critical for recruitment of Sp2 to co-occupied regulatory elements. Equally, Sp2 potentiates binding of Nf-y to shared sites indicating the existence of an extensive Sp2-Nf-y interaction network. Our results unveil strikingly different recruitment mechanisms of Sp1/Sp2/Sp3 transcription factor members uncovering an unexpected layer of complexity in their binding to chromatin in vivo.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Binding Sites
  • CCAAT-Binding Factor / genetics
  • CCAAT-Binding Factor / metabolism
  • DNA-Binding Proteins / genetics
  • Gene Expression Regulation
  • Genome
  • Histones / genetics
  • Mice
  • Nucleotide Motifs / genetics
  • Promoter Regions, Genetic
  • Protein Interaction Maps / genetics*
  • Regulatory Sequences, Nucleic Acid / genetics
  • Sp1 Transcription Factor / genetics*
  • Sp1 Transcription Factor / metabolism
  • Sp2 Transcription Factor / genetics*
  • Sp2 Transcription Factor / metabolism
  • Sp3 Transcription Factor / genetics*
  • Sp3 Transcription Factor / metabolism
  • Zinc Fingers / genetics*

Substances

  • CCAAT-Binding Factor
  • DNA-Binding Proteins
  • Histones
  • Sp1 Transcription Factor
  • Sp3 protein, mouse
  • Sp2 Transcription Factor
  • Sp3 Transcription Factor

Grant support

This work was supported by a grant of the Deutsche Forschungsgemeinschaft (DFG) to GS (DFG Su 102/8-1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.