The DNA replication fork can pass RNA polymerase without displacing the nascent transcript

Liu, Bin; Wong, Mei Lie; Tinker, Rachel L.; Geiduschek, E. Peter; Alberts, Bruce

doi:10.1038/366033a0

Cited by 104 publications

(62 citation statements)

References 40 publications

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“…The replication apparatus from T4 phage can bypass E. coli RNAP in head-on and codirectional orientations after pausing times of Ϸ1.7 sec and Ͻ1 sec, respectively (33,34). DNA polymerase from 29 can bypass B. subtilis RNAP during head-on encounters.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide coorientation of replication and transcription reduces adverse effects on replication in Bacillus subtilis

Wang

Berkmen

Grossman

2007

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

104

119

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In many bacteria, there is a strong bias for genes to be encoded on the leading strand of DNA, resulting in coorientation of replication and transcription. In Bacillus subtilis, transcription of the majority of genes (75%) is cooriented with replication. By using genomewide profiling of replication with DNA microarrays, we found that this coorientation bias reduces adverse effects of transcription on replication. We found that in wild-type cells, transcription did not appear to affect the rate of replication elongation. However, in mutants with reversed transcription bias for an extended region of the chromosome, replication elongation was slower. This reduced replication rate depended on transcription and was limited to the region in which the directions of replication and transcription are opposed. These results support the hypothesis that the strong bias to coorient transcription and replication is due to selective pressure for processive, efficient, and accurate replication.DNA microarrays ͉ elongation of replication ͉ genomic organization ͉ genomic stability ͉ origin of replication M any aspects of the organization of bacterial genomes are conserved and important for cell survival. DNA rearrangements, including large chromosomal inversions, can lead to inviability, decreased fitness, and impaired development (1-4). It has been proposed that genomic organization affects replication, transcription, and segregation of genomes (5).One benefit of proper genomic organization may be the reduction of potential conflicts between replication and transcription (5-7). The same DNA template is used by RNA polymerase (RNAP) for transcription and by the replisome (DNA polymerase and associated proteins) for replication. Transcription complexes that are stalled, initiating, or terminating can slow or block replication (8, 9). RNAP and the replisome can collide when moving toward each other (head-on), or when the replisome, which moves faster than RNAP, catches up with RNAP moving in the same direction (codirectional). Head-on and codirectional collisions can occur when genes are on the lagging and leading strands, respectively.The consequences of head-on and codirectional collisions are different. In Escherichia coli, high levels of transcription can effectively slow or block progression of replication forks if transcription and replication are head-on, but not if they are codirectional (10). In French's landmark study, an inducible plasmid-derived origin of replication was positioned on either side of an rRNA operon, one of the most highly transcribed operons. Replication fork progression, monitored by EM, was much slower when running against, rather than with, the direction of transcription. Plasmid DNA replication in E. coli can also be hindered by head-on transcription from a strong inducible promoter, probably because of collisions between the replisome and RNAP (ref.

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Section: Discussionmentioning

confidence: 99%

Genome-wide coorientation of replication and transcription reduces adverse effects on replication in Bacillus subtilis

Wang

Berkmen

Grossman

2007

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

104

119

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“…DNA sequences that have the potential to form secondary structures (Bedinger et al, 1989) or tracts of purines or pyrimidines in the DNA (Rao, 1994), have been shown to act as pausing sites during replication. Progression of the replication fork is also hampered during co-directional collisions with a transcription complex (French, 1992;Liu et al, 1993;Liu and Alberts, 1995;Elías-Arnanz and Salas, 1997). Under specific unfavourable growth conditions, i.e.…”

Section: Introductionmentioning

confidence: 99%

DNA polymerase template switching at specific sites on the φ29 genome causes the in vivo accumulation of subgenomic φ29 DNA molecules

Murthy

Meijer

Blanco

et al. 1998

Molecular Microbiology

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SummaryThe accumulation of subgenomic phage 29 DNA molecules with specific sizes was observed after prolonged infection times with delayed lysis phage mutants. Whereas the majority of the molecules had a size of 4 kb, additional DNA species were observed with sizes of 8.2, 6.5, 2.3, 2 and 1 kb. Most of the molecules were shown to originate from the right end of the linear Bacillus subtilis phage 29 genome. The nature of the 4, 2.3, 2 and 1 kb molecules was studied. The 2 kb molecules were shown to be single-stranded self-complementary strands forming hairpin structures. The other molecules consisted of palindromic linear double-stranded DNA molecules. Most probably, the subgenomic DNA molecules were formed when the moving phage replication fork from the right origin encountered a block that induces the DNA polymerase to switch template. Once formed, the subgenomic molecules are then amplified in vivo. Determination of the centres of symmetry of the 4 and 1 kb molecules revealed that both contained the almost 16 bp perfect dyad symmetry element (DSE): 5Ј-TGTTtCAC-GTGg-AACA-3Ј being a likely candidate for a protein binding site. Database analysis showed that this sequence occurs four times in the 29 genome. In addition, the almost identical sequence 5Ј-TgGTTTCAC-GTGGAAt-CA-3Ј was found once. These five DSEs are all located in the right half of the 29 genome, and the same sequences are also present in the linear DNA of related B. subtilis phages. Most interestingly, this sequence is also found in the spoOJ gene of the B. subtilis chromosome. Recently, it has been shown that the SpoOJ protein is associated in vivo with the same DSE. As the same subgenomic 29 DNA molecules accumulate after infection of B. subtilis spoOJ deletion strains, it is likely that, in addition to and/or independently of SpoOJ, other protein(s) bind to DSE.

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“…Therefore we propose that after stalling at the lesion, the hybrid transiently dissociates to allow the DNA to move past the transcript during scrunching. This concept is adapted from the model of Liu et al (1993), who showed that an elongating E. coli transcription complex can continue transcription and generate a full-length RNA transcript after being bypassed by a DNA replication complex using the same template strand. The hybrid dissociation step is likely to require opening of the 'clamp' that closes on the hybrid in the elongation complex (Gnatt et al, 2001).…”

Section: Mechanistic Considerationsmentioning

confidence: 99%

“…The proposed tethering protein is not shown. After incorporating U opposite the cyclo-dA lesion and stalling (A), the CM partially opens, allowing dissociation of the hybrid, but with retention of the nascent RNA (see Liu et al, 1993;B). Downstream DNA is pulled into the polymerase past the RNA transcript and extruded upstream by a scrunching mechanism (C).…”

Section: Speculations On the Role Of Csbmentioning

confidence: 99%

Transcriptional bypass of bulky DNA lesions causes new mutant RNA transcripts in human cells

Marietta

Brooks

2007

EMBO Reports

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Here, we characterize the mutant transcripts resulting from bypass of an 8,5 0 -cyclo-2 0 -deoxyadenosine (cyclo-dA) or cyclobutane pyrimidine dimer (CPD) by human RNA polymerase II (Pol II) in vivo. With the cyclo-dA lesion, we observed two new types of mutant transcripts. In the first type, the polymerase inserted uridine opposite the lesion and then misincorporated adenosine opposite the template deoxyadenosine downstream (5 0 ) of the lesion. The second type contained deletions of 7, 13 or 21 nucleotides (nt) after uridine incorporation opposite the lesion. The frequency of the different types of transcript from the cyclo-dA lesion in mutant human cell lines suggests that the Cockayne syndrome B protein affects the probability of deletion transcript formation. With the CPD-containing construct, we also detected rare transcripts containing 12 nt deletions. These results indicate that RNA pol II in living human cells can bypass helixdistorting DNA lesions that are substrates for nucleotide excision repair, resulting in transcriptional mutagenesis.

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The DNA replication fork can pass RNA polymerase without displacing the nascent transcript

Cited by 104 publications

References 40 publications

Genome-wide coorientation of replication and transcription reduces adverse effects on replication in Bacillus subtilis

Genome-wide coorientation of replication and transcription reduces adverse effects on replication in Bacillus subtilis

DNA polymerase template switching at specific sites on the φ29 genome causes the in vivo accumulation of subgenomic φ29 DNA molecules

Transcriptional bypass of bulky DNA lesions causes new mutant RNA transcripts in human cells

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