Basic Mechanisms of Transcript Elongation and Its Regulation

Uptain, Susan M.; Kane, Caroline M.; Chamberlin, Michael J.

doi:10.1146/annurev.biochem.66.1.117

Cited by 421 publications

(345 citation statements)

References 403 publications

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“…This assumption can be motivated by noting that translocation is not the rate-limiting step in transcription elongation (42). In E. coli, elongation proceeds at Ϸ10-35 nt͞s at saturating (millimolar) NTP concentrations (43) while the prefactor in the Arrhenius rate of unfolding of short RNA duplexes is Ϸ30 s Ϫ1 . The latter follows from the estimated half-life of a GC-rich 10-bp RNA duplex of 100 years (44)!…”

Section: Kinetic Modeling Of Transcriptional Pausingmentioning

confidence: 99%

Thermodynamic and kinetic modeling of transcriptional pausing

Tadigotla

Maoiléidigh

Sengupta

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

106

185

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We present a statistical mechanics approach for the prediction of backtracked pauses in bacterial transcription elongation derived from structural models of the transcription elongation complex (EC). Our algorithm is based on the thermodynamic stability of the EC along the DNA template calculated from the sequence-dependent free energy of DNA–DNA, DNA–RNA, and RNA–RNA base pairing associated with ( i ) the translocational and size fluctuations of the transcription bubble; ( ii ) changes in the associated DNA–RNA hybrid; and ( iii ) changes in the cotranscriptional RNA secondary structure upstream of the RNA exit channel. The calculations involve no adjustable parameters except for a cutoff used to discriminate paused from nonpaused complexes. When applied to 100 experimental pauses in transcription elongation by Escherichia coli RNA polymerase on 10 DNA templates, the approach produces statistically significant results. We also present a kinetic model for the rate of recovery of backtracked paused complexes. A crucial ingredient of our model is the incorporation of kinetic barriers to backtracking resulting from steric clashes of EC with the cotranscriptionally generated RNA secondary structure, an aspect not included explicitly in previous attempts at modeling the transcription elongation process.

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Section: Kinetic Modeling Of Transcriptional Pausingmentioning

confidence: 99%

Thermodynamic and kinetic modeling of transcriptional pausing

Tadigotla

Maoiléidigh

Sengupta

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

106

185

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“…For RNA polymerase II, a fraction of ternary complexes cease elongation within the transcription unit in a regulated fashion (1). In vivo, it is experimentally difficult to determine if these complexes have paused or have arrested.…”

Section: Discussionmentioning

confidence: 99%

Intrinsic Transcript Cleavage in Yeast RNA Polymerase II Elongation Complexes

Weilbaecher

Awrey

Edwards

et al. 2003

Journal of Biological Chemistry

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Transcript elongation can be interrupted by a variety of obstacles, including certain DNA sequences, DNAbinding proteins, chromatin, and DNA lesions. Bypass of many of these impediments is facilitated by elongation factor TFIIS through a mechanism that involves cleavage of the nascent transcript by the RNA polymerase II/TFIIS elongation complex. Highly purified yeast RNA polymerase II is able to perform transcript hydrolysis in the absence of TFIIS. The "intrinsic" cleavage activity is greatly stimulated at mildly basic pH and requires divalent cations. Both arrested and stalled complexes can carry out the intrinsic cleavage reaction, although not all stalled complexes are equally efficient at this reaction. Arrested complexes in which the nascent transcript was cleaved in the absence of TFIIS were reactivated to readthrough blocks to elongation. Thus, cleavage of the nascent transcript is sufficient for reactivating some arrested complexes. Small RNA products released following transcript cleavage in stalled ternary complexes differ depending upon whether the cleavage has been induced by TFIIS or has occurred in mildly alkaline conditions. In contrast, both intrinsic and TFIIS-induced small RNA cleavage products are very similar when produced from an arrested ternary complex. Although ␣-amanitin interferes with the transcript cleavage stimulated by TFIIS, it has little effect on the intrinsic cleavage reaction. A mutant RNA polymerase previously shown to be refractory to TFIIS-induced transcript cleavage is essentially identical to the wild type polymerase in all tested aspects of intrinsic cleavage.Gene expression can be controlled by regulating any step of the transcription cycle: promoter binding, initiation, promoter escape, elongation, or termination. After transcript synthesis begins, the ability to suppress or complete the synthesis of an RNA transcript is vital to the cell, and a substantial and growing number of genes have been reported to be regulated during transcript elongation (1).The ternary elongation complex consists of the RNA polymerase, the template DNA, and the nascent RNA transcript. Surratt et al. (2) discovered that bacterial RNA polymerase ternary complexes have a mechanism for transcript shortening, endonucleolytic cleavage near the 3Ј-end of the transcript. After transcript cleavage, the 3Ј-fragment is released while the 5Ј-fragment is retained in an active ternary complex. A single cleavage event can liberate from 1 to 17 nt 1 of RNA bearing a 5Ј-monophosphate (3-6). Remarkably, transcription accurately resumes from the site of transcript cleavage to re-synthesize the excised RNA.Transcript cleavage activity is conserved in many DNA-dependent RNA polymerases, including bacterial RNA polymerases, vaccinia virus RNA polymerase (7), RNA polymerase I (8, 9), RNA polymerase II (10 -14), and RNA polymerase III (15). Accessory factors that stimulate transcript cleavage in ternary complexes have been identified in both prokaryotes (GreA and GreB) and eukaryotes (reviewed in Refs. 3,9,[16][17]...

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“…For example, the immunopurified TATA-box binding protein associated factor (TAFIID) contains the cleavage polyadenylation-specific factor (CPSF) (Dantonel et al, 1997) required for the formation of the 3Ј end of the mRNA (Keller and Minvielle-Sebastia, 1997). After transcription has initiated, CPSF dissociates from TAFIID and associates with the elongating RNA polymerase II (Dantonel et al, 1997), which has a C-terminal region, required for efficient mRNA processing (McCracken et al, 1997), that is highly phosphorylated during the early elongation phase (Uptain et al, 1997).…”

Section: Coordinate Activity-induced Transcription Initiation and Termentioning

confidence: 99%

“…Detection of inducible intranuclear foci thus provides a powerful tool to assess exon and intron sequences that are transcribed rapidly in response to MECS. Absence of intranuclear signal with probes beyond intron 5 thus indicates that activityinduced Homer 1 transcripts stop prematurely (Uptain et al, 1997) within intron 5, possibly facilitated by alternative poly(A) site selection (Edwalds-Gilbert et al, 1997).…”

Section: Homer Ieg Transcripts Terminate Within Intronmentioning

confidence: 99%

Synaptic Activity-Induced Conversion of Intronic to Exonic Sequence in Homer 1 Immediate Early Gene Expression

et al. 2002

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Three Homer genes regulate the activity of metabotropic glutamate receptors mGluR1a and mGluR5 and their coupling to releasable intracellular Ca2+pools and ion channels. Only the Homer 1 gene evolved bimodal expression of constitutive (Homer 1b and c) and immediate early gene (IEG) products (Homer 1a and Ania 3). The IEG forms compete functionally with the constitutive Homer proteins. The complex expression of the Homer 1 gene, unique for IEGs, focused our attention on the gene organization. In contrast to most IEGs, which have genes that are <5 kb, the Homer 1 gene was found to span ∼100 kb. The constitutive Homer 1b/c forms are encoded by exons 1–10, whereas the IEG forms are encoded by exons 1–5 and parts of intron 5. RNase protection demonstrated a >10-fold activity-dependent increase in mRNA levels exclusively for the IEG forms. Moreover, fluorescentin situhybridization documented that new primary Homer 1 transcripts are induced in neuronal nuclei within a few minutes after seizure, typical of IEGs, and that Homer 1b-specific exons are excluded from the activity-induced transcripts. Thus, at the resting state of the neurons, the entire gene is constitutively transcribed at low levels to yield Homer 1b/c transcripts. Neuronal activity sharply increases the rate of transcription initiation, with most transcripts now ending within the central intron. These coordinate transcriptional events rapidly convert a constitutive gene to an IEG and regulate the expression of functionally different Homer 1 proteins.

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Basic Mechanisms of Transcript Elongation and Its Regulation

Cited by 421 publications

References 403 publications

Thermodynamic and kinetic modeling of transcriptional pausing

Thermodynamic and kinetic modeling of transcriptional pausing

Intrinsic Transcript Cleavage in Yeast RNA Polymerase II Elongation Complexes

Synaptic Activity-Induced Conversion of Intronic to Exonic Sequence in Homer 1 Immediate Early Gene Expression

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