The complexities of eukaryotic transcription initiation: regulation of preinitiation complex assembly

doi:10.1016/0968-0004(91)90164-Q

Trends in Biochemical Sciences

Volume 16, 1991, Pages 402-408

https://doi.org/10.1016/0968-0004(91)90164-Q Get rights and content

Abstract

Individual steps in the assembly of RNA polymerase II and general initiation factors into a preinitiation complex serve as points of control for activators, whose functions require additional cofactors. The full range of induction by activators appears to involve both the reversal of negative constraints and net positive effects on promoter interactions with general factors.

References (39)

PughB.F. et al.
Cell
(1990)
DynlachtB.D. et al.
Cell
(1991)
SimonM.C.
Cell
(1988)
BuratowskiS. et al.
Cell
(1989)
HorikoshiM.
Cell
(1988)
WorkmanJ.L. et al.
Cell
(1988)
LinY-S. et al.
Cell
(1991)
LewinB.
Cell
(1990)
HimmelfarbH.J. et al.
Cell
(1990)
GrunsteinM.
Trends Genet.
(1990)

WorkmanJ.L. et al.

Cell

(1987)

ConawayJ.W. et al.

J. Biol. Chem.

(1991)

SawadogoM. et al.

Annu. Rev. Biochem.

(1990)

SumimotoH.

PtashneM.

Nature

(1988)

MitchellP.J. et al.

Science

(1989)

NakajimaN. et al.

Mol. Cell. Biol.

(1988)

BreathnachR. et al.

Annu. Rev. Biochem.

(1981)

SmaleS.T. et al.

Cited by (423)

Unexplored power of CRISPR-Cas9 in neuroscience, a multi-OMICs review
2024, International Journal of Biological Macromolecules
The neuroscience and neurobiology of gene editing to enhance learning and memory is of paramount interest to the scientific community. The advancements of CRISPR system have created avenues to treat neurological disorders by means of versatile modalities varying from expression to suppression of genes and proteins. Neurodegenerative disorders have also been attributed to non-canonical DNA secondary structures by affecting neuron activity through controlling gene expression, nucleosome shape, transcription, translation, replication, and recombination. Changing DNA regulatory elements which could contribute to the fate and function of neurons are thoroughly discussed in this review. This study presents the ability of CRISPR system to boost learning power and memory, treat or cure genetically-based neurological disorders, and alleviate psychiatric diseases by altering the activity and the irritability of the neurons at the synaptic cleft through DNA manipulation, and also, epigenetic modifications using Cas9. We explore and examine how each different OMIC techniques can come useful when altering DNA sequences. Such insight into the underlying relationship between OMICs and cellular behaviors leads us to better neurological and psychiatric therapeutics by intelligently designing and utilizing the CRISPR/Cas9 technology.
Broad compatibility between yeast UAS elements and core promoters and identification of promoter elements that determine cofactor specificity
2023, Cell Reports
Three classes of yeast protein-coding genes are distinguished by their dependence on the transcription cofactors TFIID, SAGA, and Mediator (MED) Tail, but whether this dependence is determined by the core promoter, upstream activating sequences (UASs), or other gene features is unclear. Also unclear is whether UASs can broadly activate transcription from the different promoter classes. Here, we measure transcription and cofactor specificity for thousands of UAS-core promoter combinations and find that most UASs broadly activate promoters regardless of regulatory class, while few display strong promoter specificity. However, matching UASs and promoters from the same gene class is generally important for optimal expression. We find that sensitivity to rapid depletion of MED Tail or SAGA is dependent on the identity of both UAS and core promoter, while dependence on TFIID localizes to only the promoter. Finally, our results suggest the role of TATA and TATA-like promoter sequences in MED Tail function.
TAF8 regions important for TFIID lobe B assembly or for TAF2 interactions are required for embryonic stem cell survival
2021, Journal of Biological Chemistry
The human general transcription factor TFIID is composed of the TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). In eukaryotic cells, TFIID is thought to nucleate RNA polymerase II (Pol II) preinitiation complex formation on all protein coding gene promoters and thus, be crucial for Pol II transcription. TFIID is composed of three lobes, named A, B, and C. A 5TAF core complex can be assembled in vitro constituting a building block for the further assembly of either lobe A or B in TFIID. Structural studies showed that TAF8 forms a histone fold pair with TAF10 in lobe B and participates in connecting lobe B to lobe C. To better understand the role of TAF8 in TFIID, we have investigated the requirement of the different regions of TAF8 for the in vitro assembly of lobe B and C and the importance of certain TAF8 regions for mouse embryonic stem cell (ESC) viability. We have identified a region of TAF8 distinct from the histone fold domain important for assembling with the 5TAF core complex in lobe B. We also delineated four more regions of TAF8 each individually required for interacting with TAF2 in lobe C. Moreover, CRISPR/Cas9-mediated gene editing indicated that the 5TAF core-interacting TAF8 domain and the proline-rich domain of TAF8 that interacts with TAF2 are both required for mouse embryonic stem cell survival. Thus, our study defines distinct TAF8 regions involved in connecting TFIID lobe B to lobe C that appear crucial for TFIID function and consequent ESC survival.
Effects of essential oil decanal on growth and transcriptome of the postharvest fungal pathogen Penicillium expansum
2018, Postharvest Biology and Technology
Penicillium expansum is a destructive phytopathogen provoking the blue mold decay of pome fruits and producing a polyketide-derived mycotoxin, patulin. In this study, the effects of exogenous essential oil decanal on development and patulin production of P. expansum were determined. Results indicated that 0.12 g L⁻¹ decanal could significantly inhibit the growth of P. expansum in vitro. 0.24 g L⁻¹ decanal showed a good controlling effect against the blue mold rot on apple and pear fruit. Besides, decanal could inhibit patulin production and the expression of genes involved in patulin biosynthesis. Through RNA sequencing approach, 1703, 3247 and 3963 genes were found which have changed abundantly after 6 h, 12 h and 18 h of incubation in decanal treated samples. Differentially expressed genes (DEGs) mainly participated in metabolism and genetic information processing. The expressions of about two-thirds of the DEGs were down-regulated. Among them, DEGs involved in oxidative phosphorylation, transcription, and translation would be partly responsible for growth inhibition of P. expansum. The findings would provide some new insights for exploring the possible antifungal mechanisms of decanal against P. expansum.
Dysregulation of gene expression in the striatum of BACHD rats expressing full-length mutant huntingtin and associated abnormalities on molecular and protein levels
2017, Neuropharmacology
Huntington disease (HD) is an autosomal dominantly inherited neurodegenerative disorder caused by a CAG repeat expansion in the gene coding for the huntingtin protein (HTT). Mutant HTT (mHTT) has been proposed to cause neuronal dysfunction and neuronal loss through multiple mechanisms. Transcriptional changes may be a core pathogenic feature of HD. Utilizing the Affymetrix platform we performed a genome-wide RNA expression analysis in two BACHD transgenic rat lines (TG5 and TG9) at 12 months of age, both of which carry full-length human mHTT but with different expression levels. By defining the threshold of significance at p < 0.01, we found 1608 genes and 871 genes differentially expressed in both TG5 and TG9 rats when compared to the wild type littermates, respectively. We only chose the highly up-/down-regulated genes for further analysis by setting an additional threshold of 1.5 fold change. Comparing gene expression profiles of human HD brains and BACHD rats revealed a high concordance in both functional and IPA (Ingenuity Pathway Analysis) canonical pathways relevant to HD. In addition, we investigated the causes leading to gene expression changes at molecular and protein levels in BACHD rats including the involvement of polyQ-containing transcription factors TATA box-binding protein (TBP), Sp1 and CBP as well as the chromatin structure. We demonstrate that the BACHD rat model recapitulates the gene expression changes of the human disease supporting its role as a preclinical research animal model. We also show for the first time that TFIID complex formation is reduced, while soluble TBP is increased in an HD model. This finding suggests that mHTT is a competitor instead of a recruiter of polyQ-containing transcription factors in the transcription process in HD.
Release of positive transcription elongation factor b (P-TEFb) from 7SK small nuclear ribonucleoprotein (snRNP) activates hexamethylene bisacetamide-inducible protein (HEXIM1) transcription
2014, Journal of Biological Chemistry
Citation Excerpt :
The assembly of the preinitiation complex is necessary before any of these subsequent steps can take place. The minimal preinitiation complex contains RNAPII, the mediator, and general transcription factors such as TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH (2). RNAPII transcribes protein-coding genes in eukaryotes.
By phosphorylating negative elongation factors and the C-terminal domain of RNA polymerase II (RNAPII), positive transcription elongation factor b (P-TEFb), which is composed of CycT1 or CycT2 and CDK9, activates eukaryotic transcription elongation. In growing cells, it is found in active and inactive forms. In the former, free P-TEFb is a potent transcriptional coactivator. In the latter, it is inhibited by HEXIM1 or HEXIM2 in the 7SK small nuclear ribonucleoprotein (snRNP), which contains, additionally, 7SK snRNA, methyl phosphate-capping enzyme (MePCE), and La-related protein 7 (LARP7). This P-TEFb equilibrium determines the state of growth and proliferation of the cell. In this study, the release of P-TEFb from the 7SK snRNP led to increased synthesis of HEXIM1 but not HEXIM2 in HeLa cells, and this occurred only from an unannotated, proximal promoter. ChIP with sequencing revealed P-TEFb-sensitive poised RNA polymerase II at this proximal but not the previously annotated distal HEXIM1 promoter. Its immediate upstream sequences were fused to luciferase reporters and were found to be responsive to many P-TEFb-releasing compounds. The superelongation complex subunits AF4/FMR2 family member 4 (AFF4) and elongation factor RNA polymerase II 2 (ELL2) were recruited to this proximal promoter after P-TEFb release and were required for its transcriptional effects. Thus, P-TEFb regulates its own equilibrium in cells, most likely to maintain optimal cellular homeostasis.

View all citing articles on Scopus

View full text

Trends in Biochemical Sciences

The complexities of eukaryotic transcription initiation: regulation of preinitiation complex assembly

Abstract

Cell

Cell

Cell

Cell

Cell

Cell

Cell

Cell

Cell

Trends Genet.

Cell

J. Biol. Chem.

Annu. Rev. Biochem.

Nature

Science

Mol. Cell. Biol.

Annu. Rev. Biochem.