TAF4/4b·TAF12 Displays a Unique Mode of DNA Binding and Is Required for Core Promoter Function of a Subset of Genes

Irwin Davidson,Rofa Elfakess,Sandra Moshonov,Kfir Gazit,Michal Sharon,Rivka Dikstein,Gabrielle Mengus

doi:10.1074/jbc.m109.011486

Abstract

The major core promoter-binding factor in polymerase II transcription machinery is TFIID, a complex consisting of TBP, the TATA box-binding protein, and 13 to 14 TBP-associated factors (TAFs). Previously we found that the histone H2A-like TAF paralogs TAF4 and TAF4b possess DNA-binding activity. Whether TAF4/TAF4b DNA binding directs TFIID to a specific core promoter element or facilitates TFIID binding to established core promoter elements is not known. Here we analyzed the mode of TAF4b.TAF12 DNA binding and show that this complex binds DNA with high affinity. The DNA length required for optimal binding is approximately 70 bp. Although the complex displays a weak sequence preference, the nucleotide composition is less important than the length of the DNA for high affinity binding. Comparative expression profiling of wild-type and a DNA-binding mutant of TAF4 revealed common core promoter features in the down-regulated genes that include a TATA-box and an Initiator. Further examination of the PEL98 gene from this group showed diminished Initiator activity and TFIID occupancy in TAF4 DNA-binding mutant cells. These findings suggest that DNA binding by TAF4/4b-TAF12 facilitates the association of TFIID with the core promoter of a subset of genes.

Highlights

The major core promoter-binding factor within the general transcription apparatus is TFIID, a large complex composed of the TATA-binding protein (TBP) and about 14 TBP-associated factors (TAFs)
The homology of TAF4/TAF4b1⁄7TAF12 to histones H2A-H2B [19], and the observation that the optimal length for DNA binding is 70 bp, which is half the length of nucleosomal DNA (146 bp) are consistent with the notion that the TFIID interaction with DNA through the TAFs resembles in some way a nucleosome [20]
Another feature of the TAF4b1⁄7TAF12 complex is that it can form a stable complex with DNA at a high DNA:protein ratio suggesting that it requires several contacts with the DNA

Summary

Introduction

The major core promoter-binding factor within the general transcription apparatus is TFIID, a large complex composed of the TATA-binding protein (TBP) and about 14 TBP-associated factors (TAFs) (for recent reviews see Refs. 3, 4). In this subset of genes, TAF4 can facilitate the binding of TFIID to the core promoter by providing additional contacts with DNA.

Results

Conclusion