Transcription Initiation Mediated by Initiator Binding Protein inSaccharomyces cerevisiae

Ohishi-Shofuda, Tomoko; Suzuki, Yuriko; Yano, Keiji; Sakurai, Hiroshi; Fukasawa, Toshio

doi:10.1006/bbrc.1999.0157

Cited by 3 publications

(3 citation statements)

References 24 publications

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“…According to this definition, metazoan INR should have a dual function as CE and IE. Notably, CE and IE appear to be physically separated in the RPS5 promoter, but probably not in other yeast promoters (46). …”

Section: Resultsmentioning

confidence: 99%

Highly redundant function of multiple AT-rich sequences as core promoter elements in the TATA-less RPS5 promoter of Saccharomyces cerevisiae

Sugihara

Koyamada

Kokubo

2010

Nucleic Acids Research

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In eukaryotes, protein-coding genes are transcribed by RNA polymerase II (pol II) together with general transcription factors (GTFs). TFIID, the largest GTF composed of TATA element-binding protein (TBP) and 14 TBP-associated factors (TAFs), plays a critical role in transcription from TATA-less promoters. In metazoans, several core promoter elements other than the TATA element are thought to be recognition sites for TFIID. However, it is unclear whether functionally homologous elements also exist in TATA-less promoters in Saccharomyces cerevisiae. Here, we identify the cis-elements required to support normal levels of transcription and accurate initiation from sites within the TATA-less and TFIID-dependent RPS5 core promoter. Systematic mutational analyses show that multiple AT-rich sequences are required for these activities and appear to function as recognition sites for TFIID. A single copy of these sequences can support accurate initiation from the endogenous promoter, indicating that they carry highly redundant functions. These results show a novel architecture of yeast TATA-less promoters and support a model in which pol II scans DNA downstream from a recruited site, while searching for appropriate initiation site(s).

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Section: Resultsmentioning

confidence: 99%

Highly redundant function of multiple AT-rich sequences as core promoter elements in the TATA-less RPS5 promoter of Saccharomyces cerevisiae

Sugihara

Koyamada

Kokubo

2010

Nucleic Acids Research

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“…Rather than being a major contributor to core promoter recognition, it may represent a preferred initiation site for the RNA polymerase after it scans downstream from its initial interaction site, which is 20 bp downstream of the TATA box (81), see above. It is noteworthy, however, that one gene in S. cerevisiae, the GAL80 gene, contains a functional Inr sequence, CACT, that exhibits greater similarity to the metazoan Inr consensus and appears to function in a TATA-independent manner (151,152).…”

Section: Evolution Of the Inrmentioning

confidence: 99%

The RNA Polymerase II Core Promoter

Smale

Kadonaga

2003

Annu. Rev. Biochem.

936

882

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The events leading to transcription of eukaryotic protein-coding genes culminate in the positioning of RNA polymerase II at the correct initiation site. The core promoter, which can extend ~35 bp upstream and/or downstream of this site, plays a central role in regulating initiation. Specific DNA elements within the core promoter bind the factors that nucleate the assembly of a functional preinitiation complex and integrate stimulatory and repressive signals from factors bound at distal sites. Although core promoter structure was originally thought to be invariant, a remarkable degree of diversity has become apparent. This article reviews the structural and functional diversity of the RNA polymerase II core promoter.

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“…In metazoans the initiator is defined as a core promoter element distinct from the TATA box that nucleates PIC assembly and is sufficient for accurate transcription (16). Although there is evidence to suggest that some yeast initiators may function in this way (17)(18), most appear to play a more limited role in transcriptional control and influence accuracy but not overall efficiency (2).…”

Section: Eukaryotes Rely On Rna Polymerase II (Rnap Ii)mentioning

confidence: 99%

Quantitative Analysis of in Vivo Initiator Selection by Yeast RNA Polymerase II Supports a Scanning Model

Kuehner

Brow

2006

Journal of Biological Chemistry

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Initiation of transcription by RNA polymerase II (RNAP II) onSaccharomyces cerevisiae messenger RNA (mRNA) genes typically occurs at multiple sites 40 -120 bp downstream of the TATA box. The mechanism that accommodates this extended and variable promoter architecture is unknown, but one model suggests that RNAP II forms an open promoter complex near the TATA box and then scans the template DNA strand for start sites. Unlike most proteincoding genes, small nuclear RNA gene transcription starts predominantly at a single position. We identify a highly efficient initiator element as the primary start site determinant for the yeast U4 small nuclear RNA gene, SNR14. Consistent with the scanning model, transcription of an SNR14 allele with tandemly duplicated start sites initiates primarily from the upstream site, yet the downstream site is recognized with equivalent efficiency by the diminished population of RNAP II molecules that encounter it. A quantitative in vivo assay revealed that SNR14 initiator efficiency is nearly perfect (ϳ90%), which explains the precision of U4 RNA 5 end formation. Initiator efficiency was reduced by cis-acting mutations at ؊8, ؊7, ؊1, and ؉1 and trans-acting substitutions in the TFIIB B-finger. These results expand our understanding of RNAP II initiation preferences and provide new support for the scanning model. Eukaryotes rely on RNA polymerase II (RNAP II)2 to synthesize all messenger RNAs (mRNAs) and most of the small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs) encoded within their nuclear genomes. Efficient and accurate transcription initiation is vital to ensure the proper expression and function of these RNAs. The recruitment of RNAP II to gene promoters is mediated through the assembly of a pre-initiation complex (PIC). RNAP II accessory proteins provide promoter specificity and the structural core for assembly of the PIC. These accessory proteins include the general transcription factors TFIID, TFIIB, TFIIF, TFIIE, and TFIIH (1-3). Some transcription factors engage in sequence-specific contacts with core promoter elements (4); one of the most fundamental interactions for PIC assembly is between the TATA-binding protein subunit of TFIID and the TATA box (5-6). In a stepwise model for PIC assembly, TATA-binding protein binding is followed by the addition of TFIIB, RNAP II-TFIIF, TFIIE, and TFIIH (7).In metazoans, the assembly of a PIC at the TATA box results in start site selection 25-30 bp downstream (4). The architecture of the PIC is such that the transcription start site is placed precisely within the active center of RNAP II (8 -9). In the yeast Saccharomyces cerevisiae, RNAP II initiation typically occurs at multiple sites at variable distances from the TATA box, with most start sites ranging from 40 to 120 bp downstream of the TATA box (10). The initiation mechanism that accommodates this extended and variable promoter architecture is unknown, but it does not appear to be dependent on assembling the yeast PIC in a manner different from that of metazoans. Yeast p...

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Transcription Initiation Mediated by Initiator Binding Protein inSaccharomyces cerevisiae

Cited by 3 publications

References 24 publications

Highly redundant function of multiple AT-rich sequences as core promoter elements in the TATA-less RPS5 promoter of Saccharomyces cerevisiae

Highly redundant function of multiple AT-rich sequences as core promoter elements in the TATA-less RPS5 promoter of Saccharomyces cerevisiae

The RNA Polymerase II Core Promoter

Quantitative Analysis of in Vivo Initiator Selection by Yeast RNA Polymerase II Supports a Scanning Model

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