Advances in RNA polymerase II transcription

doi:10.1016/0955-0674(92)90016-6

Current Opinion in Cell Biology

Volume 4, Issue 3, June 1992, Pages 488-495

https://doi.org/10.1016/0955-0674(92)90016-6 Get rights and content

Abstract

Multiple protein factors are necessary to mediate transcription by RNA polymerase II. Recently, a number of advances have been made in our understanding of how general transcription factors collectively modulate basal transcription in the context of different promoter environments and how this process is activated and repressed by accessory components.

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Formaldehyde-cross-linking underpins many of the most commonly used experimental approaches in the chromatin field, especially in capturing site-specific protein–DNA interactions. Extending such assays to assess the stability and binding kinetics of protein–DNA interactions is more challenging, requiring absolute measurements with a relatively high degree of physical precision. We previously described an experimental framework called the cross-linking kinetics (CLK) assay, which uses time-dependent formaldehyde–cross-linking data to extract kinetic parameters of chromatin binding. Many aspects of formaldehyde behavior in cells are unknown or undocumented, however, and could potentially affect CLK data analyses. Here, we report biochemical results that better define the properties of formaldehyde–cross-linking in budding yeast cells. These results have the potential to inform interpretations of “standard” chromatin assays, including chromatin immunoprecipitation. Moreover, the chemical complexity we uncovered resulted in the development of an improved method for measuring binding kinetics with the CLK approach. Optimum conditions included an increased formaldehyde concentration and more robust glycine-quench conditions. Notably, we observed that formaldehyde–cross-linking rates can vary dramatically for different protein–DNA interactions in vivo. Some interactions were cross-linked much faster than the in vivo macromolecular interactions, making them suitable for kinetic analysis. For other interactions, we found the cross-linking reaction occurred on the same time scale or slower than binding dynamics; for these interactions, it was sometimes possible to compute the in vivo equilibrium-binding constant but not binding on- and off-rates. This improved method yields more accurate in vivo binding kinetics estimates on the minute time scale.
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TFIIA was classified as a general transcription factor when it was first identified. Since then it has been debated to what extent it can actually be regarded as “general”. The most notable feature of TFIIA is the proteolytical cleavage of the TFIIAαβ into a TFIIAα and TFIIAβ moiety which has long remained a mystery. Recent studies have showed that TFIIA is cleaved by Taspase1 which was initially identified as the protease for the proto-oncogene MLL. Cleavage of TFIIA does not appear to serve as a step required for its activation as the uncleaved TFIIA in the Taspase1 knock-outs adequately support bulk transcription. Instead, cleavage of TFIIA seems to affect its turn-over and may be a part of an intricate degradation mechanism that allows fine-tuning of cellular levels of TFIIA. Cleavage might also be responsible for switching transcription program as the uncleaved and cleaved TFIIA might have distinct promoter specificity during development and differentiation. This review will focus on functional characteristics of TFIIA and discuss novel insights in the role of this elusive transcription factor.
III, 1. Aspects of the molecular biology of enteric adenoviruses
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The enteric adenoviruses display a very restricted host range phenotype in tissue culture and, as previously reviewed (Mautner et al., 1995), this is a complex and poorly understood phenomenon. In this chapter we have described some properties of the Ad40 E1A region, which suggest that the basal activity of the E1A promoter, and the activity of the E1A 249R protein are limited in cell lines normally permissive for adenovirus propagation. A fuller understanding of the potential of Ad40 will require the development of gut cell cultures, which more closely mirror the conditions found in the intestine.
The work described in this chapter was carried out while the authors were in the Medical Research Council Virology Unit, Institute of Virology, Glasgow G11 5JR, SCOTLAND.
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Three mutant immunoglobulin heavy chain (IgH) insertion mice were generated in which a targeted nonfunctional IgH passenger transgene was either devoid of promoter (pΔ) or was placed under the transcriptional control of either its own RNA polymerase II–dependent IgH promoter (pII) or a RNA polymerase I–dependent promoter (pI). While the transgene mutation-frequency (0.85%) in memory B cells of pI mice was reduced compared to that in pII mice (1.4%), the distribution and the base exchange pattern of point mutations were comparable. In pΔ mice, the mutation frequency was drastically reduced (0.09%). The mutation frequencies correlated with the levels of transgene-specific pre-mRNA expressed in germinal center B cells isolated from the mutant mice.
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Advances in RNA polymerase II transcription

Abstract

J Biol Chem

Cell

Science

J Biol Chem

J Biol Chem

Mol Cell Biol

Science

Mol Cell Biol

Cell

Initiation of Transcription by RNA Polymerase II: A Multi-step Process

Prog Nucleic Acids Res Mol Biol

The Small Subunit of Transcription Factor IIF Recruits RNA Polymerase II into the Pre-initiation Complex

Structure and Associated DNA-helicase Activity of a General Transcription Initiation Factor that Binds to RNA Polymerase II

Nature

Related RNA Polymerase-binding Regions in Human RAP30/74 and Escherichia coliσ70

Science

Direct and Selective Binding of an Acidic Activation Domain to the TATA-box Factor TFIID

Nature

Reduced Binding of TFIID to Transcriptionally Compromised Mutants of VP16

Nature

Mechanism of Activation of an Acidic Transcriptional Activator in vitro

Cell

Binding of General Transcription Factor TFIIB to an Acidic Activating Region

Nature

Mechanism of RNA Polymerase II-specific Initiation of Transcription in vitro. ATP Requirement and Uncapped Runoff Transcripts

Cell

The Initiator Directs the Assembly of a Transcription Factor IID-dependent Transcription Complex

Transcription from a TATA-less Promoter Requires a Multisubunit TFIID Complex

Genes Dev

Cooperative Interaction of an Initiator-binding Transcription Initiation Factor and the Helix-Loop-Helix Activator USF

Nature

Isolation of a Candidate Repressor/Activator, NF-E1(YY1,d), that Binds to the Immunoglobulin k3′ Enhancer and the Immunoglobulin Heavy-chain mE1 Site

d, A Transcription Factor that Binds to Downstream Elements in Several Polymerase II Promoters, is a Functionally Versatile Zinc Finger Protein

Structural Arrangements of Transcription Control Domains Within the 5′-Untranslated Leader Regions of the HIV-1 and HIV-2 Promoters

Genes Dev

Repression of HIV-1 Transcription by a Cellular Protein

Science

Cloning of a Human Gene Encoding the General Transcription Initiation Factor IIB

Nature

Related RNA Polymerase-binding Regions in Human RAP30/74 and Escherichia coliσ⁷⁰