Targeting Of Somatic Hypermutation By immunoglobulin Enhancer And Enhancer-Like Sequences

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

Oliveira

Janković

et al. 2014

Activation-induced cytidine deaminase (AID) initiates class switch recombination (CSR) and somatic hypermutation (SHM) by deaminating cytosine residues in immunoglobulin genes (Igh, Igκ, and Igλ). At a lower frequency, AID also causes collateral DNA damage at non-Ig loci, including genes that are rearranged or mutated in Bcell lymphoma. Precisely how AID is recruited to these off-target sites is not entirely understood. To gain further insight into how AID selects its targets, we compared AID-mediated translocations in two different cell types, B cells and mouse embryonic fibroblasts (MEFs). AID targets a distinct set of hotspots in the two cell types. In both cases, hotspots are concentrated in highly transcribed but stalled genes. However, transcription alone is insufficient to recruit AID activity. Comparison of genes similarly transcribed in B cells and MEFs but targeted in only one of the two cell types reveals a common set of epigenetic features associated with AID recruitment in both cells. AID target genes are enriched in chromatin modifications associated with active enhancers (such as H3K27Ac) and marks of active transcription (such as H3K36me3) in both fibroblasts and B cells, indicating that these features are universal mediators of AID recruitment.chromosome translocation | mouse embryonic fibroblast | active enhancer | transcription elongation | lymphoma

Section: Discussionmentioning

confidence: 82%

mentioning

confidence: 71%

Epigenetic targeting of activation-induced cytidine deaminase

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

Oliveira

Janković

et al. 2014

“…First, Ig enhancers are required for hypermutation and recombination of both variable (V) domains and switch (S) DNA repeats that precede antibody gene constant (C) regions (Buerstedde et al, 2014). Second, transcription of S repeats leads to substantial RNA PolII pausing (Rajagopal et al, 2009; Wang et al, 2009), and Spt5, a PolII pausing factor, enables hypermutation and recombination by associating with AID (Pavri et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

B Cell Super-Enhancers and Regulatory Clusters Recruit AID Tumorigenic Activity

Qian

Dose

et al. 2014

Cell

243

258

SUMMARY The antibody gene mutator activation-induced cytidine deaminase (AID) promiscuously damages oncogenes, leading to chromosomal translocations and tumorigenesis. Why nonimmunoglobulin loci are susceptible to AID activity is unknown. Here, we study AID-mediated lesions in the context of nuclear architecture and the B cell regulome. We show that AID targets are not randomly distributed across the genome but are predominantly grouped within super-enhancers and regulatory clusters. Unexpectedly, in these domains, AID deaminates active promoters and eRNA+ enhancers interconnected in some instances over megabases of linear chromatin. Using genome editing, we demonstrate that 3D-linked targets cooperate to recruit AID-mediated breaks. Furthermore, a comparison of hypermutation in mouse B cells, AID-induced kataegis in human lymphomas, and translocations in MEFs reveals that AID damages different genes in different cell types. Yet, in all cases, the targets are predominantly associated with topological complex, highly transcribed super-enhancers, demonstrating that these compartments are key mediators of AID recruitment.

“…Transcription-associated proteins and RNA processing factors also participate in the AID mutational process and, in some cases, physically interact with AID (14)(15)(16)(17). In addition, other transacting proteins (18,19), including chaperones (20), chromatin modifiers and remodelers (21)(22)(23), cell cycle regulators (24), developmental factors (25), and cisacting sequences (26,27), appear to affect mutations. However, all of these factors also have pleiotropic effects on non-Ig genes in B cells, so they do not appear to be solely responsible for the targeting of AID-induced mutations to the Ig V. Because many nonIg genes are also highly transcribed in activated B cells and AID appears to occupy many sites in such cells (28,29) and can also cause mutations in non-B cells, it is important to understand why the very high rate of mutation in the SHM is not seen in other highly expressed genes in B cells.…”

mentioning

confidence: 99%

Overlapping hotspots in CDRs are critical sites for V region diversification

Wei

Chahwan

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

et al. 2015

Activation-induced deaminase (AID) mediates the somatic hypermutation (SHM) of Ig variable (V) regions that is required for the affinity maturation of the antibody response. An intensive analysis of a published database of somatic hypermutations that arose in the IGHV3-23*01 human V region expressed in vivo by human memory B cells revealed that the focus of mutations in complementary determining region (CDR)1 and CDR2 coincided with a combination of overlapping AGCT hotspots, the absence of AID cold spots, and an abundance of polymerase eta hotspots. If the overlapping hotspots in the CDR1 or CDR2 did not undergo mutation, the frequency of mutations throughout the V region was reduced. To model this result, we examined the mutation of the human IGHV3-23*01 biochemically and in the endogenous heavy chain locus of Ramos B cells. Deep sequencing revealed that IGHV3-23*01 in Ramos cells accumulates AID-induced mutations primarily in the AGCT in CDR2, which was also the most frequent site of mutation in vivo. Replacing the overlapping hotspots in CDR1 and CDR2 with neutral or cold motifs resulted in a reduction in mutations within the modified motifs and, to some degree, throughout the V region. In addition, some of the overlapping hotspots in the CDRs were at sites in which replacement mutations could change the structure of the CDR loops. Our analysis suggests that the local sequence environment of the V region, and especially of the CDR1 and CDR2, is highly evolved to recruit mutations to key residues in the CDRs of the IgV region.A fter an encounter with antigen and subsequent migration into the germinal centers of the secondary lymphoid organs, B cells undergo a regulated cascade of mutational events that occur at a very high frequency and are largely restricted to the variable (V) and switch (S) regions of the Ig heavy chain locus and the V region of the light chain locus. These mutagenic events are responsible for the somatic hypermutation (SHM) of the V regions and the class switch recombination of the constant (C) regions that are required for protective antibodies (1, 2). Both SHM and class switch recombination are initiated by activationinduced deaminase (AID) that preferentially deaminates the dC residues in WRC (W = A/T, R = A/G) hotspot motifs at frequencies 2-10-fold higher than SYC (S = G/C; Y = C/T) cold spots (3-7). During V region SHM, the resulting dU:G mismatch can then be replicated during S-phase to produce transition mutations, be processed by uracil-DNA glycosylase 2 and apurinic/ apyrimidinic endonucleases through the base excision repair pathway to produce both transitions and transversions (8-10), or be recognized by MutS homolog (MSH)2/MSH6 of the mismatch repair (MMR) complex that recruits the low-fidelity polymerase eta (Polη) to generate additional mutations at neighboring A:T residues (11).The specificity of AID targeting to the Ig gene has been under intense investigation. Studies have shown that AID deamination and mutagenesis targets single-stranded DNA substrates generated during ...