Translation Initiator of Short 5′ UTR (TISU) is a unique regulatory element of both transcription and translation initiation. It is present in a sizable number of genes with basic cellular functions and a very short untranslated region (5′ UTR). Here, we investigated translation initiation from short 5′ UTR mRNAs with AUG in various contexts. Reducing 5′ UTR length to the minimal functional size increases leaky scanning from weak and strong initiators but hardly affects translation initiation and ribosomal binding directed by TISU. Ribosome interaction with TISU mRNA is cap dependent and involves AUG downstream nucleotides that compensate for the absent 5′ UTR contacts. Interestingly, eIF1 inhibits cap-proximal AUG selection within weak or strong contexts but not within TISU. Furthermore, TISU-directed translation is unaffected by inhibition of the RNA helicase eIF4A. Thus, TISU directs efficient cap-dependent translation initiation without scanning, a mechanism that would be advantageous when intracellular levels of eIF1 and eIF4A fluctuate.

Transcription is controlled by cis regulatory elements, which if localized downstream to the transcriptional start site (TSS), in the 5′UTR, could influence translation as well. However presently there is little evidence for such composite regulatory elements. We have identified by computational analysis an abundant element located downstream to the TSS up to position +30, which controls both transcription and translation. This element has an invariable ATG sequence, which serves as the translation initiation codon in 64% of the genes bearing it. In these genes the initiating AUG is preceded by an extremely short 5′UTR. We show that translation in vitro and in vivo is initiated exclusively from the AUG of this motif, and that the AUG flanking sequences create a strong translation initiation context. This motif is distinguished from the well-known Kozak in its unique ability to direct efficient and accurate translation initiation from mRNAs with a very short 5′UTR. We therefore named it TISU for Translation Initiator of Short 5′UTR. Interestingly, this translation initiation element is also an essential transcription regulatory element of Yin Yang 1. Our characterization of a common transcription and translation element points to a link between mammalian transcription and translation initiation.

Background: Diversity in rates of gene expression is essential for basic cell functions and is controlled by a variety of intricate mechanisms. Revealing general mechanisms that control gene expression is important for understanding normal and pathological cell functions and for improving the design of expression systems. Here we analyzed the relationship between general features of genes and their contribution to expression levels.

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 TAF4b⅐TAF12 DNA binding and show that this complex binds DNA with high affinity. The DNA length required for optimal binding is ϳ70 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.Two types of DNA elements regulate transcription of protein-encoding genes in eukaryotes. Enhancer elements, which may be localized proximally or distally relative to the transcription initiation site, are the binding sites for gene-specific transcription factors. A core promoter, situated close to the transcription start site (TSS), 2 serves as the site on which RNA polymerase II and the general transcription factors bind and assemble into a pre-initiation complex (1, 2). Enhancer-bound transcription factors activate transcription by modulating chromatin structure or by recruiting the transcription machinery to the core promoter.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). Within TFIID TBP is responsible for recognition and binding of TATA-containing promoters. The TAFs are also important for core promoter recognition, and they bind primarily to non-TATA-box elements, interacting with sequences upstream and downstream to the TATA box (5-13). In addition certain TAF subcomplexes have been reported to specifically bind different core promoter elements. The TAF1⅐TAF2 complex binds to the Initiator element (14) and Drosophila TAF6 and TAF9 crosslinked to the downstream promoter element in the context of TFIID (15), and, as a reconstituted complex, these were shown to associate with a downstream promoter element-containing promoter (16).A feature common to 9 of the 14 TAFs is the histone-fold domain (HFD) (17)(18)(19)(20). The presence of histone-fold TAFs within TFIID led to the proposal that there is a nucleosomallike interaction between HFD TAFs and DNA (21). Recently we reported that the H4-H3-like TAF6...