DNA binding site selection by RNA polymerase II TAFs: a TAFII250-TAFII150 complex recognizes the Initiator

Chalkley, Gillian E.; Verrijzer, C. Peter

doi:10.1093/emboj/18.17.4835

Cited by 218 publications

(185 citation statements)

References 69 publications

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“…TAF1 gene sequence NM_004606 was used for alignment of the data. (11) identified in this study and those reported previously probands (1)(2)(3)(4)(5)(6)(7)(8)(9)(10). TAF1 variants in probands (1-6) were previously reported by O'Rawe et al [4].…”

Section: Competing Interestssupporting

confidence: 83%

“…Transcription factor II D (TFIID) is one of several general transcription factors that make up the RNA polymerase II pre-initiation complex. A minimal pre-initiation complex includes RNA polymerase II and six general transcription factors: TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH [1,2]. Moreover, TFIID is composed of the TATA box-binding protein (TBP) and several TBP-associated factors (TAFs) which are required for transcription from TATA-containing and TATA-less promoters.…”

Section: Introductionmentioning

confidence: 99%

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A novel variant in TAF1 affects gene expression and is associated with X-linked TAF1 intellectual disability syndrome

et al. 2018

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We investigated the genome of a 5-year old male who presented with global developmental delay (motor, cognitive, and speech), hypotonia, possibly ataxia, and cerebellar hypoplasia of unknown origin. Whole genome sequencing and mRNA-sequencing were performed on a family containing an affected proband, his unaffected parents and maternal grandfather. To explore the molecular and functional consequences of the variant, we performed cell proliferation assays, qRT-PCR array, immunoblotting, calcium imaging, and neurite outgrowth experiments in SH-SY5Y neuroblastoma cells to compare the properties of the wild type TAF1, deletion of TAF1, and TAF1 variant p.Ser1600Gly samples. The whole genome data identified several gene variants. However, the genome sequence data failed to implicate a candidate gene as many of the variants were of unknown significance. By combining genome sequence data with transcriptomic data, a probable candidate variant, p.Ser1600Gly, emerged in TAF1. Moreover, the RNA-seq data revealed a 90:10 extremely skewed X-chromosome inactivation in the mother. Our results show that neuronal ion channel genes were differentially expressed between TAF1 deletion and TAF1 variant p.Ser1600Gly cells, when compared to their respective controls, and that the TAF1 variant may impair neuronal differentiation and cell proliferation. Taken together, our data suggests that this novel variant in TAF1 plays a key role in the development of a recently described X-linked syndrome, TAF1 intellectual disability syndrome, and further extends our knowledge of a potential link between TAF1 deficiency and defects in neuronal cell function.

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Section: Competing Interestssupporting

confidence: 83%

Section: Introductionmentioning

confidence: 99%

A novel variant in TAF1 affects gene expression and is associated with X-linked TAF1 intellectual disability syndrome

et al. 2018

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“…First, there is considerable evidence that TFIID binds to the Inr in a sequence-specific manner (e.g., see Kaufmann and Smale 1994;Martinez et al 1994;Purnell et al 1994;Burke and Kadonaga 1996;Oelgeschläger et al 1996). More specifically, it appears that TAF II 150 and TAF II 250 (i.e., TAF2 and TAF1; Tora 2002) are the key subunits of TFIID that interact with the Inr (Verrijzer et al 1994(Verrijzer et al , 1995Kaufmann et al 1998;Chalkley and Verrijzer 1999). Aside from TFIID binding to the Inr, it has also been observed that purified RNA polymerase II (or RNA polymerase II along with TBP, TFIIB, TFIIF) is able to recognize the Inr and to mediate transcription in an Inr-dependent manner in the absence of TAFs (Carcamo et al 1991;Weis and Reinberg 1997).…”

Section: The Initiator (Inr)mentioning

confidence: 99%

The RNA polymerase II core promoter: a key component in the regulation of gene expression

Butler¹,

Kadonaga²

2002

Genes Dev.

538

433

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“…TFIID, a protein complex composed of the TBP (TATA-box binding protein) and TBP-associated factors (TAFs), is the first protein complex that recognizes the core promoter: TBP binds the TATA-box motif, TAF1 and TAF2 bind the Inr motif and TAF6 and TAF9 bind the DPE and MTE motifs. 23,25,[28][29][30][31] Several tissue-specific variants of TAFs have been discovered: TAF4 variants are important for ovarian development and spermatogenesis in mice, while Drosophila and human TAF5 and TAF7 paralogs are implicated in male gametogenesis, thus providing the TFIID with unique functions in a tissue-specific transcription environment. [32][33][34][35][36][37] Following the binding of TFIID, TFIIA binds and stabilizes the association of TFIID with the TATA-box.…”

Section: Introductionmentioning

confidence: 99%

TRF2: TRansForming the view of general transcription factors

et al. 2015

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These authors contributed equally to this work.Keywords: core promoter elements/motifs, DPE, embryonic development, histone gene cluster, RNAP II transcription, ribosomal protein genes, spermiogenesis, TBP-related factors, TRF2, TCT Transcriptional regulation is pivotal for development and differentiation of organisms. Transcription of eukaryotic protein-coding genes by RNA polymerase II (RNAP II) initiates at the core promoter. Core promoters, which encompass the transcription start site, may contain functional core promoter elements, such as the TATA box, initiator, TCT and downstream core promoter element. TRF2 (TATA-box-binding protein-related factor 2) does not bind TATA box-containing promoters. Rather, it is recruited to core promoters via sequences other than the TATA box. We review the recent findings implicating TRF2 as a basal transcription factor in the regulation of diverse biological processes and specialized transcriptional programs.

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DNA binding site selection by RNA polymerase II TAFs: a TAFII250-TAFII150 complex recognizes the Initiator

Cited by 218 publications

References 69 publications

A novel variant in TAF1 affects gene expression and is associated with X-linked TAF1 intellectual disability syndrome

A novel variant in TAF1 affects gene expression and is associated with X-linked TAF1 intellectual disability syndrome

The RNA polymerase II core promoter: a key component in the regulation of gene expression

TRF2: TRansForming the view of general transcription factors

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