The activation-induced cytidine deaminase (AID) efficiently targets DNA in nucleosomes but only during transcription

Poirier, Michael G.; Allen, Michael J.; North, Justin A.; Lal, Ratnesh; Widom, Jonathan; Storb, Ursula

doi:10.1083/jcb1853oia5

Cited by 16 publications

(27 citation statements)

References 23 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Thus, the meaning of RNAPII accumulation across S regions may be distinct from its promoter-proximal pausing. Previous studies showed that, in the absence of transcription, nucleosomes prevented AIDmediated cytidine deamination (65), whereas with transcription, AID readily gained access to DNA in nucleosomes on both strands (65). Therefore, we propose that RNAPII pausing at S regions probably facilitates the repositioning of repressive nucleosomes to create a permissive chromatin architecture that allows AID to access target DNA sequences.…”

Section: Discussionmentioning

confidence: 88%

Target DNA Sequence Directly Regulates the Frequency of Activation-Induced Deaminase-Dependent Mutations

Chen

Viboolsittiseri

O’Connor

et al. 2012

The Journal of Immunology

View full text Add to dashboard Cite

Activation-induced deaminase (AID) catalyses class switch recombination (CSR) and somatic hypermutation (SHM) in B lymphocytes to enhance Ab diversity. CSR involves breaking and rejoining highly repetitive switch (S) regions in the IgH (Igh) locus. S regions appear to be preferential targets of AID. To determine whether S region sequence per se, independent of Igh cis regulatory elements, can influence AID targeting efficiency and mutation frequency, we established a knock-in mouse model by inserting a core Sγ1 region into the first intron of proto-oncogene Bcl6, which is a non-Ig target of SHM. We found that the mutation frequency of the inserted Sγ1 region was dramatically higher than that of the adjacent Bcl6 endogenous sequence. Mechanistically, S region-enhanced SHM was associated with increased recruitment of AID and RNA polymerase II, together with Spt5, albeit to a lesser extent. Our studies demonstrate that target DNA sequences influence mutation frequency via regulating AID recruitment. We propose that the nucleotide sequence preference may serve as an additional layer of AID regulation by restricting its mutagenic activity to specific sequences despite the observation that AID has the potential to access the genome widely.

show abstract

Section: Discussionmentioning

confidence: 88%

Target DNA Sequence Directly Regulates the Frequency of Activation-Induced Deaminase-Dependent Mutations

Chen

Viboolsittiseri

O’Connor

et al. 2012

The Journal of Immunology

View full text Add to dashboard Cite

show abstract

“…Therefore, the in vitro assay for DNA deamination by AID should be reexamined using mammalian Pol II and its cofactors on chromatin templates; previous studies have used naked DNA and T7 polymerase (9,35). It would also be important to examine how FACT and nucleosomes with H3K4me3 are influencing the DNA deamination reaction, and whether AID or uracil DNA glycosylase is preferentially recruited to chromatin with H3K4me3.…”

Section: Discussionmentioning

confidence: 99%

Histone3 lysine4 trimethylation regulated by the facilitates chromatin transcription complex is critical for DNA cleavage in class switch recombination

Stanlie

Aida

Muramatsu

et al. 2010

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

100

143

View full text Add to dashboard Cite

Ig class switch recombination (CSR) requires expression of activation-induced cytidine deaminase (AID) and transcription through target switch (S) regions. Here we show that knockdown of the histone chaperone facilitates chromatin transcription (FACT) completely inhibited S region cleavage and CSR in IgA-switch-inducible CH12F3-2A B cells. FACT knockdown did not reduce AID or S region transcripts but did decrease histone3 lysine4 trimethylation (H3K4me3) at both the Sμ and Sα regions. Because knockdown of FACT or H3K4 methyltransferase cofactors inhibited DNA cleavage in H3K4me3-depleted S regions, H3K4me3 may serve as a mark for recruiting CSR recombinase. These findings revealed an unexpected evolutionary conservation between CSR and meiotic recombination.A ntigen stimulation of B lymphocytes induces the expression of activation-induced cytidine deaminase (AID), which is responsible for generation of antibody memory (1, 2). Somatic hypermutation and class switch recombination (CSR) are two genetic events that engrave antibody memory into the Ig heavychain (H) locus of the B cell genome. CSR takes place between two switch (S) regions, located upstream of the individual H constant regions (C H ) and converts the isotype from IgM to another class by bringing the specific C H region close to the H variable region (V H ) exons and looping out the intervening DNA segment (3).Gene-targeting experiments in the IgH locus have shown that active transcription through the S regions is an essential requirement of CSR (4, 5). This transcription initiates from the I promoter, located upstream of each S region, and proceeds through the I exon, the intronic S region, the C H exons, and the C H introns. The mature transcripts, designated as germline transcripts (GLTs), are generated by splicing out the S region and C H intronic sequences (3). However, it is not well understood whether the transcription itself, the transcription products, or both are important for CSR. The original chromatin-opening hypothesis suggested that transcription of the S region causes its chromatin structure to be relatively open, which increases its accessibility to a putative recombinase (6, 7). In fact, the migration of the transcription machinery accumulates positive and negative supercoil in its front and rear, respectively.During this process, R-loop formation was detected in the DNA from switching B cells by the bisulfite sensitivity assay (8). The R-loop formation was considered to support the DNA deamination hypothesis proposed for the function of AID, as the single-strand DNA can serve as an efficient substrate of cytidine deamination by AID, as demonstrated in vitro (9). This hypothesis postulates that dU generated by AID deamination is recognized as a dU/dG mismatch and excised by uracil DNA glycosylase (10). The abasic sites thus formed is then cleaved by apyrimidinic/apurinic endonuclease. It has been also proposed that dU/dG mismatches are recognized and cleaved by mismatch repair proteins such as Msh2 and Msh6.On the other hand, AID was...

show abstract

“…28,29 Recently, it was shown that in vitro nucleosomes prevent AID access, unless the immunoglobulin segment is being transcribed. 30 Transcription is required for SHM in vivo, presumably in part to loosen the contact of nucleosomes with the DNA. 31 During transcription, the single-stranded DNA (ssDNA) is prone to AID-mediated C to U conversion, producing U:G mismatches in the DNA.…”

Section: Discussionmentioning

confidence: 99%

Targets of somatic hypermutation within immunoglobulin light chain genes in zebrafish

Marianes

Zimmerman

2010

Immunology

View full text Add to dashboard Cite

Summary In mammals, somatic hypermutation (SHM) of immunoglobulin (Ig) genes is critical for the generation of high‐affinity antibodies and effective immune responses. Knowledge of sequence‐specific biases in the targeting of somatic mutations can be useful for studies aimed at understanding antibody repertoires produced in response to infections, B‐cell neoplasms, or autoimmune disease. To evaluate potential nucleotide targets of somatic mutation in zebrafish (Danio rerio), an enriched IgL cDNA library was constructed and > 250 randomly selected clones were sequenced and analysed. In total, 55 unique VJ‐C sequences were identified encoding a total of 125 mutations. Mutations were most prevalent in VL with a bias towards single base transitions and increased mutation in the complementarity‐determining regions (CDRs). Overall, mutations were overrepresented at WRCH/DGYW motifs suggestive of activation‐induced cytidine deaminase (AID) targeting which is common in mice and humans. In contrast to mammalian models, N and P addition was not observed and mutations at AID hotspots were largely restricted to palindromic WRCH/DGYW motifs. Mutability indexes for di‐ and trinucleotide combinations confirmed C/G targets within WRCH/DGYW motifs to be statistically significant mutational hotspots and showed trinucleotides ATC and ATG to be mutation coldspots. Additive mutations in VJ‐C sequences revealed patterns of clonal expansion consistent with affinity maturation responses seen in higher vertebrates. Taken together, the data reveal specific nucleotide targets of SHM in zebrafish and suggest that AID and affinity maturation contribute to antibody diversification in this emerging immunological model.

show abstract

The activation-induced cytidine deaminase (AID) efficiently targets DNA in nucleosomes but only during transcription

Cited by 16 publications

References 23 publications

Target DNA Sequence Directly Regulates the Frequency of Activation-Induced Deaminase-Dependent Mutations

Target DNA Sequence Directly Regulates the Frequency of Activation-Induced Deaminase-Dependent Mutations

Histone3 lysine4 trimethylation regulated by the facilitates chromatin transcription complex is critical for DNA cleavage in class switch recombination

Targets of somatic hypermutation within immunoglobulin light chain genes in zebrafish

Contact Info

Product

Resources

About