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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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Related in: MedlinePlus

Figure 4. AID in the transcription complex. AID, RNA exosome and Spt5 can associate with transcribing RNA polymerase II in two distinct transcription complexes. (A) Following transcription initiation, RNA polymerase II at many transcribed genes enters a phase called “transcription stalling.” The association of RNAP II co-factors NELF and Spt5 and TFIIH leads to the resolution of RNAP II stalling and promotes RNAP II to transition into its transcription elongation phase. AID, by virtue of its association with Spt5, accesses this complex and its associated DNA. Moreover, RNA exosome is recruited to this complex and can associate with AID and Spt5-associated RNAP II to promote DNA deamination during somatic hypermutation in the first 100–200 base pairs downstream of the transcription start site. However, during SHM as well as in CSR, it is possible that the RNAP II is able to overcome the promoter proximal stalling and enter the elongation phase. Here, if it encounters dU residues (incorporated by preceding RNAP II-associated AID complexes), it may stall and recruit RNA exosome and catalyze robust cytidine deamination at DNA regions kilobases downstream from the transcription start sites. (B) If the transcription complex does continue into the elongation phase, it may generate stable DNA secondary structures like R-loops depending upon the physical properties of the transcribed DNA. For example, transcription of switch sequences is proposed to generate stable large R-loop structures due to the presence of G-richness on the template strand. If R-loops or other transcription complex impedance factors are recruited (or preexist), elongating RNAP II molecules that are loaded on the DNA secondary structure containing templates may undergo a second “stalling” event that is analogous to RNAP II pre-termination. In this pre-termination complex RNA exosome actively degrades the nascent transcript to prevent continuity of abortive transcription and aberrant DNA/RNA hybrids that can initiate genomic instability. This RNA exosome-associated RNAP II pretermination complex can potentially associate with AID and provide another hub for AID and its associated co-factors to catalyze DNA deamination. This scenario parallels the transcription stalling associated AID DNA deamination activity observed during class switch recombination.
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Figure 4: Figure 4. AID in the transcription complex. AID, RNA exosome and Spt5 can associate with transcribing RNA polymerase II in two distinct transcription complexes. (A) Following transcription initiation, RNA polymerase II at many transcribed genes enters a phase called “transcription stalling.” The association of RNAP II co-factors NELF and Spt5 and TFIIH leads to the resolution of RNAP II stalling and promotes RNAP II to transition into its transcription elongation phase. AID, by virtue of its association with Spt5, accesses this complex and its associated DNA. Moreover, RNA exosome is recruited to this complex and can associate with AID and Spt5-associated RNAP II to promote DNA deamination during somatic hypermutation in the first 100–200 base pairs downstream of the transcription start site. However, during SHM as well as in CSR, it is possible that the RNAP II is able to overcome the promoter proximal stalling and enter the elongation phase. Here, if it encounters dU residues (incorporated by preceding RNAP II-associated AID complexes), it may stall and recruit RNA exosome and catalyze robust cytidine deamination at DNA regions kilobases downstream from the transcription start sites. (B) If the transcription complex does continue into the elongation phase, it may generate stable DNA secondary structures like R-loops depending upon the physical properties of the transcribed DNA. For example, transcription of switch sequences is proposed to generate stable large R-loop structures due to the presence of G-richness on the template strand. If R-loops or other transcription complex impedance factors are recruited (or preexist), elongating RNAP II molecules that are loaded on the DNA secondary structure containing templates may undergo a second “stalling” event that is analogous to RNAP II pre-termination. In this pre-termination complex RNA exosome actively degrades the nascent transcript to prevent continuity of abortive transcription and aberrant DNA/RNA hybrids that can initiate genomic instability. This RNA exosome-associated RNAP II pretermination complex can potentially associate with AID and provide another hub for AID and its associated co-factors to catalyze DNA deamination. This scenario parallels the transcription stalling associated AID DNA deamination activity observed during class switch recombination.

Mentions: Transcription complexes “stall” at regions proximal to the promoter or during the elongation phase but resolve the paused phase to continue transcribing (Fig. 4A); however, at times due to various factors including environmental stress, DNA sequence context, or other reasons a stalled RNAP II does not continue transcribing further and undergoes premature transcription termination (Fig. 4B). The factors that determine RNAP II elongation competence and prevent premature termination following polII’s stalling are not completely understood. However, efficiency of RNAP II backtracking resolution or its ability to undergo “ RNAP II bubble expansion” are some mechanisms that may allow it to bypass termination and continue on the path of transcription elongation. The mechanism of RNAP II termination at protein coding genes, at non-coding genes, and on sequences undergoing premature termination are very different. In these three scenarios the mechanism of 3′ end processing of the nascent transcript determines whether transcription termination will occur.


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 4. AID in the transcription complex. AID, RNA exosome and Spt5 can associate with transcribing RNA polymerase II in two distinct transcription complexes. (A) Following transcription initiation, RNA polymerase II at many transcribed genes enters a phase called “transcription stalling.” The association of RNAP II co-factors NELF and Spt5 and TFIIH leads to the resolution of RNAP II stalling and promotes RNAP II to transition into its transcription elongation phase. AID, by virtue of its association with Spt5, accesses this complex and its associated DNA. Moreover, RNA exosome is recruited to this complex and can associate with AID and Spt5-associated RNAP II to promote DNA deamination during somatic hypermutation in the first 100–200 base pairs downstream of the transcription start site. However, during SHM as well as in CSR, it is possible that the RNAP II is able to overcome the promoter proximal stalling and enter the elongation phase. Here, if it encounters dU residues (incorporated by preceding RNAP II-associated AID complexes), it may stall and recruit RNA exosome and catalyze robust cytidine deamination at DNA regions kilobases downstream from the transcription start sites. (B) If the transcription complex does continue into the elongation phase, it may generate stable DNA secondary structures like R-loops depending upon the physical properties of the transcribed DNA. For example, transcription of switch sequences is proposed to generate stable large R-loop structures due to the presence of G-richness on the template strand. If R-loops or other transcription complex impedance factors are recruited (or preexist), elongating RNAP II molecules that are loaded on the DNA secondary structure containing templates may undergo a second “stalling” event that is analogous to RNAP II pre-termination. In this pre-termination complex RNA exosome actively degrades the nascent transcript to prevent continuity of abortive transcription and aberrant DNA/RNA hybrids that can initiate genomic instability. This RNA exosome-associated RNAP II pretermination complex can potentially associate with AID and provide another hub for AID and its associated co-factors to catalyze DNA deamination. This scenario parallels the transcription stalling associated AID DNA deamination activity observed during class switch recombination.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
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Figure 4: Figure 4. AID in the transcription complex. AID, RNA exosome and Spt5 can associate with transcribing RNA polymerase II in two distinct transcription complexes. (A) Following transcription initiation, RNA polymerase II at many transcribed genes enters a phase called “transcription stalling.” The association of RNAP II co-factors NELF and Spt5 and TFIIH leads to the resolution of RNAP II stalling and promotes RNAP II to transition into its transcription elongation phase. AID, by virtue of its association with Spt5, accesses this complex and its associated DNA. Moreover, RNA exosome is recruited to this complex and can associate with AID and Spt5-associated RNAP II to promote DNA deamination during somatic hypermutation in the first 100–200 base pairs downstream of the transcription start site. However, during SHM as well as in CSR, it is possible that the RNAP II is able to overcome the promoter proximal stalling and enter the elongation phase. Here, if it encounters dU residues (incorporated by preceding RNAP II-associated AID complexes), it may stall and recruit RNA exosome and catalyze robust cytidine deamination at DNA regions kilobases downstream from the transcription start sites. (B) If the transcription complex does continue into the elongation phase, it may generate stable DNA secondary structures like R-loops depending upon the physical properties of the transcribed DNA. For example, transcription of switch sequences is proposed to generate stable large R-loop structures due to the presence of G-richness on the template strand. If R-loops or other transcription complex impedance factors are recruited (or preexist), elongating RNAP II molecules that are loaded on the DNA secondary structure containing templates may undergo a second “stalling” event that is analogous to RNAP II pre-termination. In this pre-termination complex RNA exosome actively degrades the nascent transcript to prevent continuity of abortive transcription and aberrant DNA/RNA hybrids that can initiate genomic instability. This RNA exosome-associated RNAP II pretermination complex can potentially associate with AID and provide another hub for AID and its associated co-factors to catalyze DNA deamination. This scenario parallels the transcription stalling associated AID DNA deamination activity observed during class switch recombination.
Mentions: Transcription complexes “stall” at regions proximal to the promoter or during the elongation phase but resolve the paused phase to continue transcribing (Fig. 4A); however, at times due to various factors including environmental stress, DNA sequence context, or other reasons a stalled RNAP II does not continue transcribing further and undergoes premature transcription termination (Fig. 4B). The factors that determine RNAP II elongation competence and prevent premature termination following polII’s stalling are not completely understood. However, efficiency of RNAP II backtracking resolution or its ability to undergo “ RNAP II bubble expansion” are some mechanisms that may allow it to bypass termination and continue on the path of transcription elongation. The mechanism of RNAP II termination at protein coding genes, at non-coding genes, and on sequences undergoing premature termination are very different. In these three scenarios the mechanism of 3′ end processing of the nascent transcript determines whether transcription termination will occur.

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
Related in: MedlinePlus