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Transcriptional stalling in B-lymphocytes: a mechanism for antibody diversification and maintenance of genomic integrity.

Sun J, Rothschild G, Pefanis E, Basu U - Transcription (2013)

Bottom Line: B cells utilize three DNA alteration strategies-V(D)J recombination, somatic hypermutation (SHM) and class switch recombination (CSR)-to somatically mutate their genome, thereby expressing a plethora of antibodies tailor-made against the innumerable antigens they encounter while in circulation.Of these three events, the single-strand DNA cytidine deaminase, Activation Induced cytidine Deaminase (AID), is responsible for SHM and CSR.Recent advances, discussed in this review article, point toward various components of RNA polymerase II "stalling" machinery as regulators of AID activity during antibody diversification and maintenance of B cell genome integrity.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology and Immunology; College of Physicians and Surgeons; Columbia University; New York, NY USA.

ABSTRACT
B cells utilize three DNA alteration strategies-V(D)J recombination, somatic hypermutation (SHM) and class switch recombination (CSR)-to somatically mutate their genome, thereby expressing a plethora of antibodies tailor-made against the innumerable antigens they encounter while in circulation. Of these three events, the single-strand DNA cytidine deaminase, Activation Induced cytidine Deaminase (AID), is responsible for SHM and CSR. Recent advances, discussed in this review article, point toward various components of RNA polymerase II "stalling" machinery as regulators of AID activity during antibody diversification and maintenance of B cell genome integrity.

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Figure 3. Subcellular control of AID activity by various post-transcriptional regulatory pathways. AID mRNA is recognized by two miRNAs (miR-155, miR-181) that bind to its 3′UTR to regulate AID mRNA translational efficiency and prevent AID hyperactivity caused by its overexpression.55-58 One proposed mode of cytoplasmic AID protein regulation is the chaperone complex HSP9059 and EF1a,60 controlling AID’s ability to translocate into the nucleus of B cells. AID uses its nuclear localization signal (NLS) to translocate into the nucleus where its steady-state nuclear protein levels are further controlled by another chaperone, REGγ 61. AID translocated in the nucleus can have multiple fates that include its ubiquitination62,63 and its phosphorylation at various serine, threonine, or tyrosine residues (see (B) for details of known phosphorylation sites64-68). Phosphorylated AID forms a complex with its cofactors 14–3-369 and RPA17,70 and PTPBP271 and binds to the stalled RNA polymerase II complex (marked by RNAP II stalling marker Spt5)40 at AID target sequences, where it interacts with the DNA/RNA hybrid and the 3′-5′ RNA exonuclease, RNA exosome.48 It is postulated that the macromolecular complex RNA exosome provides AID the ability to deaminate both strands of its DNA substrate by processing the RNA present in the RNA/DNA hybrid associated with the transcription complex. The DNA DSBs in the immunoglobulin switch regions are intermediates that ultimately are utilized by the cellular DNA DSB response factors to complete CSR. (B) Schematic representation of AID phosphorylation sites along with AID’s cytidine deaminase domain, nuclear localization signal (NLS), APOBEC-like region, and nuclear export signal (NES) motif. (C) A detailed chart of various regulatory elements of AID that are known to directly control its activity. The protein factors and AID modifications are schematized in (A). The mRNA stability of AID is regulated by various miRNAs, as indicated in (C).55-58
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Figure 3: Figure 3. Subcellular control of AID activity by various post-transcriptional regulatory pathways. AID mRNA is recognized by two miRNAs (miR-155, miR-181) that bind to its 3′UTR to regulate AID mRNA translational efficiency and prevent AID hyperactivity caused by its overexpression.55-58 One proposed mode of cytoplasmic AID protein regulation is the chaperone complex HSP9059 and EF1a,60 controlling AID’s ability to translocate into the nucleus of B cells. AID uses its nuclear localization signal (NLS) to translocate into the nucleus where its steady-state nuclear protein levels are further controlled by another chaperone, REGγ 61. AID translocated in the nucleus can have multiple fates that include its ubiquitination62,63 and its phosphorylation at various serine, threonine, or tyrosine residues (see (B) for details of known phosphorylation sites64-68). Phosphorylated AID forms a complex with its cofactors 14–3-369 and RPA17,70 and PTPBP271 and binds to the stalled RNA polymerase II complex (marked by RNAP II stalling marker Spt5)40 at AID target sequences, where it interacts with the DNA/RNA hybrid and the 3′-5′ RNA exonuclease, RNA exosome.48 It is postulated that the macromolecular complex RNA exosome provides AID the ability to deaminate both strands of its DNA substrate by processing the RNA present in the RNA/DNA hybrid associated with the transcription complex. The DNA DSBs in the immunoglobulin switch regions are intermediates that ultimately are utilized by the cellular DNA DSB response factors to complete CSR. (B) Schematic representation of AID phosphorylation sites along with AID’s cytidine deaminase domain, nuclear localization signal (NLS), APOBEC-like region, and nuclear export signal (NES) motif. (C) A detailed chart of various regulatory elements of AID that are known to directly control its activity. The protein factors and AID modifications are schematized in (A). The mRNA stability of AID is regulated by various miRNAs, as indicated in (C).55-58

Mentions: Before the advent of genome sequencing technology, it was assumed that AID only mutates the variable region genes and switch sequences of the immunoglobulin loci. This assumption existed due to the argument that AID-generated mutations are deleterious to the genomic integrity of cells and thus there should be a factor that only promotes AID mutations in the Ig locus. However, recent studies utilizing genome sequencing technologies have generated a detailed map of AID target sequences genome wide and these studies have also correlated AID association with levels of mutagenesis at transcribed genes in the IgH locus as well as at other genes.25,36 Chromatin immunoprecipitation studies of AID and components of transcribing RNAP II in B cells indicate that RNAP II, in addition to generating secondary DNA structures for AID, may directly contribute toward AID recruitment. Many protein factors and AID modification events have been postulated to generate secondary DNA structures and/or target AID to regions of the B cell genome. A summary of these AID regulatory events is schematically represented in Figure 3a and 3b and described in Figure 3C. Detailed descriptions of direct AID regulatory events have already been extensively discussed previously.37,38 In the following sections we discuss AID’s interaction with various states of RNAP II with which AID may bind and how these AID/ RNAP II complexes determine somatic mutagenesis in the B cell genome.


Transcriptional stalling in B-lymphocytes: a mechanism for antibody diversification and maintenance of genomic integrity.

Sun J, Rothschild G, Pefanis E, Basu U - Transcription (2013)

Figure 3. Subcellular control of AID activity by various post-transcriptional regulatory pathways. AID mRNA is recognized by two miRNAs (miR-155, miR-181) that bind to its 3′UTR to regulate AID mRNA translational efficiency and prevent AID hyperactivity caused by its overexpression.55-58 One proposed mode of cytoplasmic AID protein regulation is the chaperone complex HSP9059 and EF1a,60 controlling AID’s ability to translocate into the nucleus of B cells. AID uses its nuclear localization signal (NLS) to translocate into the nucleus where its steady-state nuclear protein levels are further controlled by another chaperone, REGγ 61. AID translocated in the nucleus can have multiple fates that include its ubiquitination62,63 and its phosphorylation at various serine, threonine, or tyrosine residues (see (B) for details of known phosphorylation sites64-68). Phosphorylated AID forms a complex with its cofactors 14–3-369 and RPA17,70 and PTPBP271 and binds to the stalled RNA polymerase II complex (marked by RNAP II stalling marker Spt5)40 at AID target sequences, where it interacts with the DNA/RNA hybrid and the 3′-5′ RNA exonuclease, RNA exosome.48 It is postulated that the macromolecular complex RNA exosome provides AID the ability to deaminate both strands of its DNA substrate by processing the RNA present in the RNA/DNA hybrid associated with the transcription complex. The DNA DSBs in the immunoglobulin switch regions are intermediates that ultimately are utilized by the cellular DNA DSB response factors to complete CSR. (B) Schematic representation of AID phosphorylation sites along with AID’s cytidine deaminase domain, nuclear localization signal (NLS), APOBEC-like region, and nuclear export signal (NES) motif. (C) A detailed chart of various regulatory elements of AID that are known to directly control its activity. The protein factors and AID modifications are schematized in (A). The mRNA stability of AID is regulated by various miRNAs, as indicated in (C).55-58
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Figure 3: Figure 3. Subcellular control of AID activity by various post-transcriptional regulatory pathways. AID mRNA is recognized by two miRNAs (miR-155, miR-181) that bind to its 3′UTR to regulate AID mRNA translational efficiency and prevent AID hyperactivity caused by its overexpression.55-58 One proposed mode of cytoplasmic AID protein regulation is the chaperone complex HSP9059 and EF1a,60 controlling AID’s ability to translocate into the nucleus of B cells. AID uses its nuclear localization signal (NLS) to translocate into the nucleus where its steady-state nuclear protein levels are further controlled by another chaperone, REGγ 61. AID translocated in the nucleus can have multiple fates that include its ubiquitination62,63 and its phosphorylation at various serine, threonine, or tyrosine residues (see (B) for details of known phosphorylation sites64-68). Phosphorylated AID forms a complex with its cofactors 14–3-369 and RPA17,70 and PTPBP271 and binds to the stalled RNA polymerase II complex (marked by RNAP II stalling marker Spt5)40 at AID target sequences, where it interacts with the DNA/RNA hybrid and the 3′-5′ RNA exonuclease, RNA exosome.48 It is postulated that the macromolecular complex RNA exosome provides AID the ability to deaminate both strands of its DNA substrate by processing the RNA present in the RNA/DNA hybrid associated with the transcription complex. The DNA DSBs in the immunoglobulin switch regions are intermediates that ultimately are utilized by the cellular DNA DSB response factors to complete CSR. (B) Schematic representation of AID phosphorylation sites along with AID’s cytidine deaminase domain, nuclear localization signal (NLS), APOBEC-like region, and nuclear export signal (NES) motif. (C) A detailed chart of various regulatory elements of AID that are known to directly control its activity. The protein factors and AID modifications are schematized in (A). The mRNA stability of AID is regulated by various miRNAs, as indicated in (C).55-58
Mentions: Before the advent of genome sequencing technology, it was assumed that AID only mutates the variable region genes and switch sequences of the immunoglobulin loci. This assumption existed due to the argument that AID-generated mutations are deleterious to the genomic integrity of cells and thus there should be a factor that only promotes AID mutations in the Ig locus. However, recent studies utilizing genome sequencing technologies have generated a detailed map of AID target sequences genome wide and these studies have also correlated AID association with levels of mutagenesis at transcribed genes in the IgH locus as well as at other genes.25,36 Chromatin immunoprecipitation studies of AID and components of transcribing RNAP II in B cells indicate that RNAP II, in addition to generating secondary DNA structures for AID, may directly contribute toward AID recruitment. Many protein factors and AID modification events have been postulated to generate secondary DNA structures and/or target AID to regions of the B cell genome. A summary of these AID regulatory events is schematically represented in Figure 3a and 3b and described in Figure 3C. Detailed descriptions of direct AID regulatory events have already been extensively discussed previously.37,38 In the following sections we discuss AID’s interaction with various states of RNAP II with which AID may bind and how these AID/ RNAP II complexes determine somatic mutagenesis in the B cell genome.

Bottom Line: B cells utilize three DNA alteration strategies-V(D)J recombination, somatic hypermutation (SHM) and class switch recombination (CSR)-to somatically mutate their genome, thereby expressing a plethora of antibodies tailor-made against the innumerable antigens they encounter while in circulation.Of these three events, the single-strand DNA cytidine deaminase, Activation Induced cytidine Deaminase (AID), is responsible for SHM and CSR.Recent advances, discussed in this review article, point toward various components of RNA polymerase II "stalling" machinery as regulators of AID activity during antibody diversification and maintenance of B cell genome integrity.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology and Immunology; College of Physicians and Surgeons; Columbia University; New York, NY USA.

ABSTRACT
B cells utilize three DNA alteration strategies-V(D)J recombination, somatic hypermutation (SHM) and class switch recombination (CSR)-to somatically mutate their genome, thereby expressing a plethora of antibodies tailor-made against the innumerable antigens they encounter while in circulation. Of these three events, the single-strand DNA cytidine deaminase, Activation Induced cytidine Deaminase (AID), is responsible for SHM and CSR. Recent advances, discussed in this review article, point toward various components of RNA polymerase II "stalling" machinery as regulators of AID activity during antibody diversification and maintenance of B cell genome integrity.

Show MeSH