(Q34162337)

31 July 2017

title

Negative supercoiling creates single-stranded patches of DNA that are substrates for AID-mediated mutagenesis (English)

1 reference

31 July 2017

6

Antoaneta Belcheva

1 reference

31 July 2017

Jahan-Yar Parsa

1

1 reference

31 July 2017

Shaliny Ramachandran

2

1 reference

31 July 2017

Ahmad Zaheen

3

1 reference

31 July 2017

Rajeev M Nepal

4

1 reference

31 July 2017

Anat Kapelnikov

5

1 reference

31 July 2017

Maribel Berru

7

1 reference

31 July 2017

Diana Ronai

8

1 reference

31 July 2017

Alberto Martin

9

1 reference

31 July 2017

publication date

9 February 2012

1 reference

31 July 2017

1 reference

31 July 2017

volume

8

1 reference

31 July 2017

issue

2

1 reference

31 July 2017

page(s)

e1002518

1 reference

Creative Commons Attribution 4.0 International

31 July 2017

copyright license

start time

9 February 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Sense transcription through the S region is essential for immunoglobulin class switch recombination.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

The RNA exosome targets the AID cytidine deaminase to both strands of transcribed duplex DNA substrates

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Activation-induced cytidine deaminase induces reproducible DNA breaks at many non-Ig Loci in activated B cells

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

RNA polymerase and transcription elongation factor Spt4/5 complex structure

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Uracil residues dependent on the deaminase AID in immunoglobulin gene variable and switch regions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Deep-sequencing identification of the genomic targets of the cytidine deaminase AID and its cofactor RPA in B lymphocytes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Activation-induced cytidine deaminase targets DNA at sites of RNA polymerase II stalling by interaction with Spt5

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

The RNF8/RNF168 ubiquitin ligase cascade facilitates class switch recombination

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

AID-induced decrease in topoisomerase 1 induces DNA structural alteration and DNA cleavage for class switch recombination

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Switch recombination and somatic hypermutation are controlled by the heavy chain 3' enhancer region

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Nano positioning system reveals the course of upstream and nontemplate DNA within the RNA polymerase II elongation complex

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

S region sequence, RNA polymerase II, and histone modifications create chromatin accessibility during class switch recombination

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

The concerted action of Msh2 and UNG stimulates somatic hypermutation at A . T base pairs

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Immunoglobulin switch mu sequence causes RNA polymerase II accumulation and reduces dA hypermutation.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Antisense transcripts of V(D)J rearrangements; artifacts caused by false priming?

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Activities of human exonuclease 1 that promote cleavage of transcribed immunoglobulin switch regions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Transcriptional pausing and stalling causes multiple clustered mutations by human activation-induced deaminase

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Mechanism and regulation of class switch recombination

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Transcription-coupled hypernegative supercoiling of plasmid DNA by T7 RNA polymerase in Escherichia coli topoisomerase I-deficient strains

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Single-stranded DNA structure and positional context of the target cytidine determine the enzymatic efficiency of AID.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Sequence dependence of chromosomal R-loops at the immunoglobulin heavy-chain Smu class switch region

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Activation-induced cytidine deaminase action is strongly stimulated by mutations of the THO complex

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Detection of chromatin-associated single-stranded DNA in regions targeted for somatic hypermutation.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Control of gene conversion and somatic hypermutation by immunoglobulin promoter and enhancer sequences

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

AID mutates a non-immunoglobulin transgene independent of chromosomal position.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

The very 5' end and the constant region of Ig genes are spared from somatic mutation because AID does not access these regions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Inactivation of the SR protein splicing factor ASF/SF2 results in genomic instability

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Mismatch recognition and uracil excision provide complementary paths to both Ig switching and the A/T-focused phase of somatic mutation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Activation-induced cytidine deaminase (AID) can target both DNA strands when the DNA is supercoiled

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Intracellular transcription of G-rich DNAs induces formation of G-loops, novel structures containing G4 DNA

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Nucleic acid structures and enzymes in the immunoglobulin class switch recombination mechanism

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Mutations occur in the Ig Smu region but rarely in Sgamma regions prior to class switch recombination

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

H2AX is required for recombination between immunoglobulin switch regions but not for intra-switch region recombination or somatic hypermutation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Human activation-induced cytidine deaminase causes transcription-dependent, strand-biased C to U deaminations

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

R-loops at immunoglobulin class switch regions in the chromosomes of stimulated B cells

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Activation-induced cytidine deaminase deaminates deoxycytidine on single-stranded DNA but requires the action of RNase

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Somatic hypermutation of the AID transgene in B and non-B cells

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

AID and mismatch repair in antibody diversification

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

AID mutates E. coli suggesting a DNA deamination mechanism for antibody diversification

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Variable deletion and duplication at recombination junction ends: implication for staggered double-strand cleavage in class-switch recombination

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Human genetic defects in class-switch recombination (hyper-IgM syndromes).

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Clonal instability of V region hypermutation in the Ramos Burkitt's lymphoma cell line

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Increased transcription levels induce higher mutation rates in a hypermutating cell line

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Escherichia coli DNA topoisomerase I inhibits R-loop formation by relaxing transcription-induced negative supercoiling.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Transcription generates positively and negatively supercoiled domains in the template.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Supercoiling of the DNA template during transcription

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Transcriptionally driven cruciform formation in vivo

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

Molecular mechanisms of antibody somatic hypermutation.

28 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1002518

Transcription enhances AID-mediated cytidine deamination by exposing single-stranded DNA on the nontemplate strand

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1002518

Genome-wide somatic hypermutation

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1002518

Staggered AID-dependent DNA double strand breaks are the predominant DNA lesions targeted to S mu in Ig class switch recombination

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1002518

Two levels of protection for the B cell genome during somatic hypermutation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1002518

High frequency class switching of an IgM+ B lymphoma clone CH12F3 to IgA+ cells.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1002518

Altered kinetics of nonhomologous end joining and class switch recombination in ligase IV-deficient B cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1002518

AID associates with single-stranded DNA with high affinity and a long complex half-life in a sequence-independent manner.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1002518

Detection and structural analysis of R-loops

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1002518

An evolutionarily conserved target motif for immunoglobulin class-switch recombination

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1002518

AID constrains germinal center size by rendering B cells susceptible to apoptosis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1002518

Effects of Sequence and Structure on the Hypermutability of Immunoglobulin Genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1002518

AID binds to transcription-induced structures in c-MYC that map to regions associated with translocation and hypermutation

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3276561

The influence of transcriptional orientation on endogenous switch region function

28 October 2018

1 reference

12 December 2020

Direct evidence for the effect of transcription on local DNA supercoiling in vivo

1 reference

12 December 2020

Somatic hypermutation of immunoglobulin genes is linked to transcription initiation

1 reference

12 December 2020

Large-scale effects of transcriptional DNA supercoiling in vivo

1 reference

12 December 2020

Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS

1 reference

12 December 2020

10.1371/JOURNAL.PGEN.1002518

Identifiers

DOI

1 reference

31 July 2017

1 reference

31 July 2017

1 reference