The basal initiation machinery: beyond the general transcription factors.

doi:10.1016/J.CEB.2009.03.006

Home
/
Papers
/
The basal initiation machinery: beyond the general transcription factors.

Journal Article•DOI•

The basal initiation machinery: beyond the general transcription factors.

Timothy W. Sikorski¹, Stephen Buratowski¹•Institutions (1)

Harvard University¹

01 Jun 2009-Current Opinion in Cell Biology (NIH Public Access)-Vol. 21, Iss: 3, pp 344-351

TL;DR: A simple model in which basal transcription factors sequentially assembled with RNA Polymerase II to generate a preinitiation complex (PIC) indicates that PIC composition is not universal, but promoter-dependent.

read less

About: This article is published in Current Opinion in Cell Biology.The article was published on 2009-06-01 and is currently open access. It has received 193 citations till now. The article focuses on the topics: General transcription factor & Transcription factor II F.

...read moreread less

Citations

PDF

Open Access

More filters

Journal Article•DOI•

Transcriptional Regulation and Its Misregulation in Disease

[...]

Tong Ihn Lee¹, Richard A. Young¹•Institutions (1)

Massachusetts Institute of Technology¹

14 Mar 2013-Cell

TL;DR: Recent advances in understanding of transcriptional regulation are reviewed and how these have provided new insights into transcriptional misregulation in disease are discussed.

...read moreread less

1,180 citations

Cites background from "The basal initiation machinery: bey..."

...These coactivators include the Mediator complex, P300 and general transcription factors (Juven-Gershon and Kadonaga, 2010; Malik and Roeder, 2010; Sikorski and Buratowski, 2009; Taatjes, 2010)....
[...]
...These coactivators include the Mediator complex, P300, and general transcription factors, among others (Juven-Gershon and Kadonaga, 2010; Malik and Roeder, 2010; Sikorski and Buratowski, 2009; Taatjes, 2010)....
[...]

Journal Article•DOI•

ATP-dependent chromatin remodeling: genetics, genomics and mechanisms

[...]

Diana C. Hargreaves¹, Gerald R. Crabtree²•Institutions (2)

Stanford University¹, Howard Hughes Medical Institute²

01 Mar 2011-Cell Research

TL;DR: The mechanistic bases underlying the genetic requirements for BAF and other chromatin remodelers in development and cancer are relatively unexplored and will be a focus of this review.

...read moreread less

Abstract: Macromolecular assemblies that regulate chromatin structure using the energy of ATP hydrolysis have critical roles in development, cancer, and stem cell biology. The ATPases of this family are encoded by 27 human genes and are usually associated with several other proteins that are stable, non-exchangeable subunits. One fundamental mechanism used by these complexes is thought to be the movement or exchange of nucleosomes to regulate transcription. However, recent genetic studies indicate that chromatin remodelers may also be involved in regulating other aspects of chromatin structure during many cellular processes. The SWI/SNF family in particular appears to have undergone a substantial change in subunit composition and mechanism coincident with the evolutionary advent of multicellularity and the appearance of linking histones. The differential usage of this greater diversity of mammalian BAF subunits is essential for the development of specific cell fates, including the progression from pluripotency to multipotency to committed neurons. Recent human genetic screens have revealed that BRG1, ARID1A, BAF155, and hSNF5 are frequently mutated in tumors, indicating that BAF complexes also play a critical role in the initiation or progression of cancer. The mechanistic bases underlying the genetic requirements for BAF and other chromatin remodelers in development and cancer are relatively unexplored and will be a focus of this review.

...read moreread less

809 citations

Journal Article•DOI•

Mechanisms and Consequences of Alternative Polyadenylation

[...]

Dafne Campigli Di Giammartino¹, Kensei Nishida¹, James L. Manley¹•Institutions (1)

Columbia University¹

16 Sep 2011-Molecular Cell

TL;DR: What is known about the mechanisms governing both global and gene-specific APA and the functional consequences of alternative polyadenylation are reviewed.

...read moreread less

635 citations

Cites background from "The basal initiation machinery: bey..."

...An interesting analogy is with TATA-less promoters, which use the same set of core transcription factors but involving different interactions with promoter sequences (Juven-Gershon et al., 2008; Sikorski and Buratowski, 2009)....
[...]
...promoters, which use the same set of core transcription factors but involving different interactions with promoter sequences (Juven-Gershon et al., 2008; Sikorski and Buratowski, 2009)....
[...]

Journal Article•DOI•

The RNA polymerase II CTD coordinates transcription and RNA processing

[...]

Jing-Ping Hsin¹, James L. Manley¹•Institutions (1)

Columbia University¹

01 Oct 2012-Genes & Development

TL;DR: Findings regarding modification and function of the C-terminal domain are reviewed, highlighting the important role this unique domain plays in coordinating gene activity.

...read moreread less

Abstract: The C-terminal domain (CTD) of the RNA polymerase II largest subunit consists of multiple heptad repeats (consensus Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7), varying in number from 26 in yeast to 52 in vertebrates. The CTD functions to help couple transcription and processing of the nascent RNA and also plays roles in transcription elongation and termination. The CTD is subject to extensive post-translational modification, most notably phosphorylation, during the transcription cycle, which modulates its activities in the above processes. Therefore, understanding the nature of CTD modifications, including how they function and how they are regulated, is essential to understanding the mechanisms that control gene expression. While the significance of phosphorylation of Ser2 and Ser5 residues has been studied and appreciated for some time, several additional modifications have more recently been added to the CTD repertoire, and insight into their function has begun to emerge. Here, we review findings regarding modification and function of the CTD, highlighting the important role this unique domain plays in coordinating gene activity.

...read moreread less

564 citations

Journal Article•DOI•

An Oct4-Centered Protein Interaction Network in Embryonic Stem Cells

[...]

Debbie L. C. van den Berg¹, Tim Snoek¹, Nicholas P. Mullin², Adam Yates², Karel Bezstarosti¹, Jeroen Demmers¹, Ian Chambers², Raymond A. Poot¹ - Show less +4 more•Institutions (2)

Erasmus University Rotterdam¹, University of Edinburgh²

02 Apr 2010-Cell Stem Cell

TL;DR: An improved affinity protocol is used to purify Oct4-interacting proteins from mouse embryonic stem cells to bring greater definition to the circuitry controlling pluripotent cell identity and finds that Esrrb associated with the basal transcription machinery and also detect interactions between transcription factors and components of the TGF-β, Notch, and Wnt signaling pathways.

...read moreread less

554 citations

Cites background from "The basal initiation machinery: bey..."

...Intriguingly, Esrrb also interacts with the Mediator complex, RNA polymerase II subunits (RNApol2), and TBP plus Tafs (TFIID complex; Figure 2E; Tables S5 and S9), which are all components of the basal transcription machinery (Sikorski and Buratowski, 2009)....
[...]

1
2
3
4
…
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39

Collapse

References

PDF

Open Access

More filters

Patent•DOI•

Dissecting the regulatory circuitry of a eukaryotic genome

[...]

Frank C.P. Holstege¹, Richard A. Young¹•Institutions (1)

Massachusetts Institute of Technology¹

27 May 2003-Cell

TL;DR: The results reveal an unanticipated level of regulation which is superimposed on that due to gene-specific transcription factors, a novel mechanism for coordinate regulation of specific sets of genes when cells encounter limiting nutrients, and evidence that the ultimate targets of signal transduction pathways can be identified within the initiation apparatus.

...read moreread less

1,963 citations

Journal Article•DOI•

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

[...]

Leighton J. Core¹, Joshua J. Waterfall¹, John T. Lis¹•Institutions (1)

Cornell University¹

19 Dec 2008-Science

TL;DR: Global run-on sequencing, GRO-seq, shows that peaks of promoter-proximal polymerase reside on ∼30% of human genes, transcription extends beyond pre-messenger RNA 3′ cleavage, and antisense transcription is prevalent.

...read moreread less

Abstract: RNA polymerases are highly regulated molecular machines. We present a method (global run-on sequencing, GRO-seq) that maps the position, amount, and orientation of transcriptionally engaged RNA polymerases genome-wide. In this method, nuclear run-on RNA molecules are subjected to large-scale parallel sequencing and mapped to the genome. We show that peaks of promoter-proximal polymerase reside on ∼30% of human genes, transcription extends beyond pre-messenger RNA 3′ cleavage, and antisense transcription is prevalent. Additionally, most promoters have an engaged polymerase upstream and in an orientation opposite to the annotated gene. This divergent polymerase is associated with active genes but does not elongate effectively beyond the promoter. These results imply that the interplay between polymerases and regulators over broad promoter regions dictates the orientation and efficiency of productive transcription.

...read moreread less

1,945 citations

Journal Article•DOI•

A Multiprotein Mediator of Transcriptional Activation and Its Interaction with the C-Terminal Repeat Domain of RNA Polymerase II

[...]

Young Joon Kim¹, Stefan Björklund¹, Yang Li¹, Michael H. Sayre¹, Roger D. Kornberg¹ - Show less +1 more•Institutions (1)

Stanford University¹

20 May 1994-Cell

TL;DR: A mediator was isolated from yeast that enabled a response to the activator proteins GAL4-VP16 and GCN4 in a transcription system reconstituted with essentially homogeneous basal factors and RNA polymerase II and conferred 8-fold greater activity in basal transcription and 12-fold more efficiency of phosphorylation by the TFIIH-associated C-terminal repeat domain (CTD) kinase, indicative of mediator-CTD interaction.

...read moreread less

1,077 citations

"The basal initiation machinery: bey..." refers background in this paper

...Irrespective of how it is recruited, how does Mediator promote basal transcription? One mechanism may involve stimulating phosphorylation of the RNApII largest subunit C-terminal domain (CTD) by TFIIH kinase [42]....
[...]

Journal Article•DOI•

A high-resolution map of active promoters in the human genome

[...]

Tae Hoon Kim¹, Leah O. Barrera¹, Ming Zheng², Chunxu Qu¹, Michael A. Singer, Todd Richmond, Ying Nian Wu², Roland Green, Bing Ren¹, Bing Ren³ - Show less +6 more•Institutions (3)

Ludwig Institute for Cancer Research¹, University of California, Los Angeles², University of California, San Diego³

11 Aug 2005-Nature

TL;DR: A genome-wide map of active promoters in human fibroblast cells, determined by experimentally locating the sites of PIC binding throughout the human genome is described, providing a global view of the functional relationships among transcriptional machinery, chromatin structure and gene expression in human cells.

...read moreread less

Abstract: In eukaryotic cells, transcription of every protein-coding gene begins with the assembly of an RNA polymerase II preinitiation complex (PIC) on the promoter. The promoters, in conjunction with enhancers, silencers and insulators, define the combinatorial codes that specify gene expression patterns. Our ability to analyse the control logic encoded in the human genome is currently limited by a lack of accurate information regarding the promoters for most genes. Here we describe a genome-wide map of active promoters in human fibroblast cells, determined by experimentally locating the sites of PIC binding throughout the human genome. This map defines 10,567 active promoters corresponding to 6,763 known genes and at least 1,196 un-annotated transcriptional units. Features of the map suggest extensive use of multiple promoters by the human genes and widespread clustering of active promoters in the genome. In addition, examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. These results provide a global view of the functional relationships among transcriptional machinery, chromatin structure and gene expression in human cells.

...read moreread less

969 citations

"The basal initiation machinery: bey..." refers background in this paper

...As expected, basal factors are greatly enriched at active promoters [24 ,25], although the correlation is not perfect [6]....
[...]
...Surprisingly, TAF1 promoter occupancy and gene expression levels correlate at only 75% of genes [6], casting doubt upon the simple assumption that TFIID binding necessarily leads to transcription....
[...]

Journal Article•DOI•

The general transcription machinery and general cofactors.

[...]

Mary C. Thomas¹, Cheng Ming Chiang¹•Institutions (1)

Case Western Reserve University¹

01 May 2006-Critical Reviews in Biochemistry and Molecular Biology

TL;DR: These cofactors are capable of repressing basal transcription when activators are absent and stimulating transcription in the presence of activators, with emphasis on the events occurring after the chromatin has been remodeled but prior to the formation of the first phosphodiester bond.

...read moreread less

Abstract: In eukaryotes, the core promoter serves as a platform for the assembly of transcription preinitiation complex (PIC) that includes TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, and RNA polymerase II (pol II), which function collectively to specify the transcription start site. PIC formation usually begins with TFIID binding to the TATA box, initiator, and/or downstream promoter element (DPE) found in most core promoters, followed by the entry of other general transcription factors (GTFs) and pol II through either a sequential assembly or a preassembled pol II holoenzyme pathway. Formation of this promoter-bound complex is sufficient for a basal level of transcription. However, for activator-dependent (or regulated) transcription, general cofactors are often required to transmit regulatory signals between gene-specific activators and the general transcription machinery. Three classes of general cofactors, including TBP-associated factors (TAFs), Mediator, and upstream stimulatory activity (USA)-derived positive cofactors (PC1/PARP-1, PC2, PC3/DNA topoisomerase I, and PC4) and negative cofactor 1 (NC1/HMGB1), normally function independently or in combination to fine-tune the promoter activity in a gene-specific or cell-type-specific manner. In addition, other cofactors, such as TAF1, BTAF1, and negative cofactor 2 (NC2), can also modulate TBP or TFIID binding to the core promoter. In general, these cofactors are capable of repressing basal transcription when activators are absent and stimulating transcription in the presence of activators. Here we review the roles of these cofactors and GTFs, as well as TBP-related factors (TRFs), TAF-containing complexes (TFTC, SAGA, SLIK/SALSA, STAGA, and PRC1) and TAF variants, in pol II-mediated transcription, with emphasis on the events occurring after the chromatin has been remodeled but prior to the formation of the first phosphodiester bond.

...read moreread less

928 citations

"The basal initiation machinery: bey..." refers background in this paper

...Esnault C, Ghavi-Helm Y, Brun S, Soutourina J, Van Berkum N, Boschiero C, Holstege F, Werner M: Mediator-dependent recruitment of TFIIH modules in preinitiation complex....
[...]
...A different point mutation of Med11 decreased the occupancy of the TFIIK submodule of TFIIH at some but not all active promoters, suggesting that Mediator’s role in PIC recruitment could be promoter dependent as well [45 ]....
[...]
...At some promoters Mediator can recruit TFIIH and TFIIE independently of RNApII [45]....
[...]
...Giglia-Mari G, Coin F, Ranish JA, Hoogstraten D, Theil A, Wijgers N, Jaspers NG, Raams A, Argentini M, van der Spek PJ et al.: A new, tenth subunit of TFIIH is responsible for the DNA repair syndrome trichothiodystrophy group A. Nat Genet 2004, 36:714-719....
[...]
...(1) TBP assembling onto promoter regions via TFIID leads to recruitment of the other basal initiation factors, as outlined in the stepwise assembly pathway [1]....
[...]