The embryonic transcription factor stage specific activator protein contains a potent bipartite activation domain that interacts with several RNA polymerase II basal transcription factors.

The archaeal basal transcriptional machinery consists of TBP (TATA-binding protein), TFB (transcription factor B; a homologue of eukaryotic TFIIB) and an RNA polymerase that is structurally very similar to eukaryotic RNA polymerase II. This constellation of factors is sufficient to assemble specifically on a TATA box-containing promoter and to initiate transcription at a specific start site. We have used this system to study the functional interaction between basal transcription factors and RNA polymerase, with special emphasis on the post-recruitment function of TFB. A bioinformatics analysis of the B-finger of archaeal TFB and eukaryotic TFIIB reveals that this structure undergoes rapid and apparently systematic evolution in archaeal and eukaryotic evolutionary domains. We provide a detailed analysis of these changes and discuss their possible functional implications.

Download Full-text

Ctk1 promotes dissociation of basal transcription factors from elongating RNA polymerase II

The EMBO Journal ◽

10.1038/emboj.2008.280 ◽

2009 ◽

Vol 28 (3) ◽

pp. 205-212 ◽

Cited By ~ 35

Author(s):

Seong Hoon Ahn ◽

Michael-Christopher Keogh ◽

Stephen Buratowski

Keyword(s):

Transcription Factors ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Basal Transcription ◽

Basal Transcription Factors

Download Full-text

Interaction of the TFIIB zinc ribbon with RNA polymerase II

Biochemical Society Transactions ◽

10.1042/bst0360595 ◽

2008 ◽

Vol 36 (4) ◽

pp. 595-598 ◽

Cited By ~ 6

Author(s):

Laura M. Elsby ◽

Stefan G.E. Roberts

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Structural Models ◽

Initiation Complex ◽

General Transcription Factors ◽

Transcription Factor Iib ◽

General Transcription Factor ◽

Zinc Ribbon

Transcription by RNA polymerase II requires the assembly of the general transcription factors at the promoter to form a pre-initiation complex. The general transcription factor TF (transcription factor) IIB plays a central role in the assembly of the pre-initiation complex, providing a bridge between promoter-bound TFIID and RNA polymerase II/TFIIF. We have characterized a series of TFIIB mutants in their ability to support transcription and recruit RNA polymerase II to the promoter. Our analyses identify several residues within the TFIIB zinc ribbon that are required for RNA polymerase II assembly. Using the structural models of TFIIB, we describe the interface between the TFIIB zinc ribbon region and RNA polymerase II.

Download Full-text

Analysis of transcription factors binding to the human 7SL RNA gene promoter

Biochemistry and Cell Biology ◽

10.1139/o99-051 ◽

1999 ◽

Vol 77 (5) ◽

pp. 431-438 ◽

Cited By ~ 8

Author(s):

Jürgen Müller ◽

Bernd-Joachim Benecke

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Rna Polymerase Iii ◽

Gene Promoter ◽

7Sl Rna ◽

Polymerase Iii ◽

Responsive Element

Transcription of the human 7SL RNA gene by RNA polymerase III depends on the concerted action of transcription factors binding to the gene-internal and gene-external parts of its promoter. Here, we investigated which transcription factors interact with the human 7SL RNA gene promoter and which are required for transcription of the human 7SL RNA gene. A-box/B-box elements were previously identified in 5S RNA, tRNA, and virus associated RNA genes and are recognized by transcription factor IIIC (TFIIIC). The gene-internal promoter region of the human 7SL RNA gene shows only limited similarity to those elements. Nevertheless, competition experiments and the use of highly enriched factor preparations demonstrate that TFIIIC is required for human 7SL transcription. The gene-external part of the promoter includes an authentic cAMP-responsive element previously identified in various RNA polymerase II promoters. Here we demonstrate that members of the activating transcription factor/cyclic AMP-responsive element binding protein (ATF/CREB) transcription factor family bind specifically to this element in vitro. However, the human 7SL RNA gene is not regulated by cAMP in vivo. Furthermore, in vitro transcription of the gene does not depend on ATF/CREB transcription factors. It rather appears that a transcription factor with DNA-binding characteristics like ATF/CREB proteins but otherwise different properties is required for human 7SL RNA transcription.Key words: 7SL RNA, ATF, CRE, TFIIIC, RNA polymerase III.

Download Full-text

Expression analysis of transcription factors in sugarcane during cold stress

Brazilian Journal of Biology ◽

10.1590/1519-6984.242603 ◽

2023 ◽

Vol 83 ◽

Author(s):

S. U. Rehman ◽

K. Muhammad ◽

E. Novaes ◽

Y. Que ◽

A. Din ◽

...

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

Rna Polymerase ◽

Cold Stress ◽

Rna Polymerase Ii ◽

Rna Polymerase Iii ◽

Regulatory Region ◽

Transcription Factor Activity ◽

Factor Activity ◽

Upregulated Genes

Abstract Transcription factors (TF) are a wide class of genes in plants, and these can regulate the expression of other genes in response to various environmental stresses (biotic and abiotic). In the current study, transcription factor activity in sugarcane was examined during cold stress. Initially, RNA transcript reads of two sugarcane cultivars (ROC22 and GT08-1108) under cold stress were downloaded from SRA NCBI database. The reads were aligned into a reference genome and the differential expression analyses were performed with the R/Bioconductor edgeR package. Based on our analyses in the ROC22 cultivar, 963 TF genes were significantly upregulated under cold stress among a total of 5649 upregulated genes, while 293 TF genes were downregulated among a total of 3,289 downregulated genes. In the GT08-1108 cultivar, 974 TF genes were identified among 5,649 upregulated genes and 283 TF genes were found among 3,289 downregulated genes. Most transcription factors were annotated with GO categories related to protein binding, transcription factor binding, DNA-sequence-specific binding, transcription factor complex, transcription factor activity in RNA polymerase II, the activity of nucleic acid binding transcription factor, transcription corepressor activity, sequence-specific regulatory region, the activity of transcription factor of RNA polymerase II, transcription factor cofactor activity, transcription factor activity from plastid promoter, transcription factor activity from RNA polymerase I promoter, polymerase II and RNA polymerase III. The findings of above results will help to identify differentially expressed transcription factors during cold stress. It also provides a comprehensive analysis of the regulation of the transcription activity of many genes. Therefore, this study provides the molecular basis for improving cold tolerance in sugarcane and other economically important grasses.

Download Full-text

An RNA Polymerase II Complex Containing All Essential Initiation Factors Binds to the Activation Domain of PAR Leucine Zipper Transcription Factor Thyroid Embryonic Factor

Molecular and Cellular Biology ◽

10.1128/mcb.19.2.1242 ◽

1999 ◽

Vol 19 (2) ◽

pp. 1242-1250 ◽

Cited By ~ 11

Author(s):

Vincent Ossipow ◽

Philippe Fonjallaz ◽

Ueli Schibler

Keyword(s):

Transcription Factor ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Transcription Initiation ◽

Leucine Zipper ◽

Transactivation Domain ◽

Activation Domain ◽

Basic Leucine Zipper ◽

Embryonic Factor

ABSTRACT Transcription initiation of protein-encoding genes involves the assembly of RNA polymerase II and a number of general transcription factors at the promoter. A mammalian RNA polymerase II complex containing all of the components required for promoter-specific transcription initiation can be isolated by immunopurification with a monoclonal antibody directed against the cyclin-dependent kinase CDK7, a subunit of the general transcription factor TFIIH. In vitro transcription by this immunopurified RNA polymerase II complex is effectively stimulated by thyroid embryonic factor (TEF), a basic leucine zipper transcription factor. Thus, the RNA polymerase II complex must also contain components required for activated transcription that interact with the transactivation domain of TEF. This conjecture was verified by affinity selection experiments in which the TEF transcription activation domain was used as a bait. Indeed, an RNA polymerase II complex containing all of the accessory proteins required for transcription initiation can be enriched by its affinity to recombinant proteins containing the TEF transactivation domain. These results are compatible with a mechanism by which TEF can recruit an RNA polymerase II holoenzyme to the promoter in a single step.

Download Full-text

Recruitment of the protein phosphatase-1 catalytic subunit to promoters by the dual-function transcription factor RFX1

10.1101/493429 ◽

2018 ◽

Author(s):

Yoav Lubelsky ◽

Yosef Shaul

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Protein Phosphatase ◽

Target Genes ◽

Dna Binding Proteins ◽

Protein Phosphatase 1 ◽

Dual Function ◽

Repression Domain

SummeryRFX proteins are a family of conserved DNA binding proteins involved in various, essential cellular and developmental processes. RFX1 is a ubiquitously expressed, dual-activity transcription factor capable of both activation and repression of target genes.The exact mechanism by which RFX1 regulates its target is not known yet. In this work, we show that the C-terminal repression domain of RFX1 interacts with the Serine/Threonine protein phosphatase PP1c, and that interaction with RFX1 can target PP1c to specific sites in the genome. Given that PP1c was shown to de-phosphorylate several transcription factors, as well as the regulatory C-terminal domain of RNA Polymerase II the recruitment of PP1c to promoters may be a mechanism by which RFX1 regulates the target genes.

Download Full-text