An Autoregulatory Mechanism Imposes Allosteric Control on the V(D)J Recombinase by Histone H3 Methylation

Lü, Chao; Ward, Alyssa; Bettridge, John; Liu, Yun; Desiderio, Stephen

doi:10.1016/j.celrep.2014.12.001

Cited by 40 publications

(63 citation statements)

References 35 publications

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“…Disruption of this autoregulatory region is associated with constitutive increases in RSS binding affinity, catalytic rate, and recombination frequency, thus mimicking the stimulatory effects of H3K4me3 (15). These observations support a model in which RAG activity is suppressed by an autoinhibitory domain whose action is relieved by active chromatin.…”

supporting

confidence: 69%

“…This function is mediated by a noncanonical plant homeodomain (PHD) finger that spans residues 415 through 487 (12,13). Engagement of H3K4me3 by the PHD finger promotes recombination in vivo (7,8) and synthetic peptides bearing the H3K4me3 modification stimulate cleavage of RSS substrates by RAG in vitro (14)(15)(16), consistent with the interpretation that H3K4me3 is an allosteric activator of the V(D)J recombinase.…”

supporting

confidence: 49%

“…This interpretation was reinforced by the identification within RAG-2 of an autoregulatory region, the presence of which was revealed by second site mutations that rescue the activity of RAG-2 lacking a functional PHD finger (15). Disruption of this autoregulatory region is associated with constitutive increases in RSS binding affinity, catalytic rate, and recombination frequency, thus mimicking the stimulatory effects of H3K4me3 (15).…”

mentioning

confidence: 94%

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H3K4me3 induces allosteric conformational changes in the DNA-binding and catalytic regions of the V(D)J recombinase

Bettridge

Pandey

et al. 2017

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

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V(D)J recombination is initiated by the recombination-activating gene (RAG) recombinase, consisting of RAG-1 and RAG-2 subunits. The susceptibility of gene segments to cleavage by RAG is associated with histone modifications characteristic of active chromatin, including trimethylation of histone H3 at lysine 4 (H3K4me3). Binding of H3K4me3 by a plant homeodomain (PHD) in RAG-2 stimulates substrate binding and catalysis, which are functions of RAG-1. This has suggested an allosteric mechanism in which information regarding occupancy of the RAG-2 PHD is transmitted to RAG-1. To determine whether the conformational distribution of RAG is altered by H3K4me3, we mapped changes in solvent accessibility of cysteine thiols by differential isotopic chemical footprinting. Binding of H3K4me3 to the RAG-2 PHD induces conformational changes in RAG-1 within a DNA-binding domain and in the ZnH2 domain, which acts as a scaffold for the catalytic center. Thus, engagement of H3K4me3 by the RAG-2 PHD is associated with dynamic conformational changes in RAG-1, consistent with allosteric control by active chromatin.DNA recombination | genomic plasticity | allosteric control | epigenetic modification | immune development A ll forms of DNA processing-replication, transcription, recombination, and repair-use allosteric regulation, often as a basis for molecular discrimination but also to establish a sequence of interactions or to bias the outcome of a reaction. In many instances the allosteric ligand is a specific DNA structure, as in Cre-mediated recombination, in which the Holliday junction intermediate effects allosteric conformational changes that switch active and inactive Cre monomers (1). In other instances the allosteric ligand is a DNA-bound protein array, as in λ integration, which is driven to completion by a flanking DNA-protein array that biases the conformation of λ-integrase (2).V(D)J recombination, the process by which antigen receptor genes are assembled, is also subject to allosteric control, but in this case the allosteric ligand is a specific chromatin mark rather than a DNA structure. V(D)J recombination is initiated by recombinationactivating gene (RAG)-1 and RAG-2, which together cleave DNA at recombination signal sequences (RSSs) flanking the participating gene segments (3). There are two classes of RSS, termed 12-RSS and 23-RSS, in which heptamer and nonamer elements are separated by spacers of 12 bp or 23 bp; physiological DNA cleavage requires the pairing of a 12-RSS with a 23-RSS (3). V(D)J recombination acts in an ordered, locus-specific fashion during lymphoid development. The accessibility of gene segments to V(D)J recombination is positively correlated with transcription at the unrearranged locus and with histone modifications characteristic of active chromatin, including hypermethylation of histone H3 at lysine 4 (H3K4me3) (4-10).RAG-1 and RAG-2 are 1,040 and 527 aa residues long, respectively. The catalytic core and DNA-binding functions are largely contained within RAG-1 (11). RAG-2, which is also ess...

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supporting

confidence: 69%

supporting

confidence: 49%

mentioning

confidence: 94%

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H3K4me3 induces allosteric conformational changes in the DNA-binding and catalytic regions of the V(D)J recombinase

Bettridge

Pandey

et al. 2017

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

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“…The isotypic region is formed by two H chains with the function of anchoring the Ig to the lymphocyte. This structure represents the generic structure of IgG, IgE, IgA, IgD, or IgM 26,27 . The variable (V) domains of the light chains (V L ) and heavy chains (V H ) of the idiotypic ends can vary widely in amino acid composition, thereby making it possible to sequence thousands of regions encoding Igs from the DNA.…”

Section: Recombination-activating Gene 2 (Rag2) Genementioning

confidence: 99%

“…The variable (V) domains of the light chains (V L ) and heavy chains (V H ) of the idiotypic ends can vary widely in amino acid composition, thereby making it possible to sequence thousands of regions encoding Igs from the DNA. The protein encoded by the Rag2 gene separates, shuffles, and forms new antibodies by recombination 27,28 . The presence of the hyperexpressed Rag2 gene suggests intense antigen-antibody reactions in the cardiac tissue during intestinal IR (IRG).…”

Section: Recombination-activating Gene 2 (Rag2) Genementioning

confidence: 99%

Hyperbaric oxygenation and the genic expression related to oxidative stress in the heart of mice during intestinal ischemia and reperfusion

Neto

Ikejiri²,

Bertoletto³

et al. 2017

Acta Cir. Bras.

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Hyperbaric oxygenation and the genic expression related to oxidative stress in the heart of mice during intestinal ischemia and reperfusion 1 3-Experimental SurgeryActa Cir Bras. 2017;32(11):913-923 AbstractPurpose: To investigate the effects of hyperbaric oxygenation (HBO) on intestinal ischemia and reperfusion (IR) injury, we evaluated the expression of 84 genes related to oxidative stress and the antioxidant response in mouse hearts. Methods: Four groups were subjected to 60 minutes of intestinal ischemia followed by 60 minutes of reperfusion: IRG, ischemia and reperfusion group without HBO; HBO-IG, which received HBO during ischemia; HBO-RG, which received HBO during reperfusion; and HBO-IRG, which received HBO during ischemia and reperfusion. The control group (CG) underwent anesthesia and laparotomy and was observed for 120 minutes. The (RT-qPCR) method was applied. Genes with expression levels three times below or above the threshold cycle were considered significantly hypoexpressed or hyperexpressed, respectively (Student's t-test p<0.05).Results: Eight genes (9.52%) were hyperexpressed in the IRG. When the HBO groups were compared to the IRG, we found a decrease in the expression of eight genes in the HBO-IG, five genes in the HBO-RG, and seven genes in the HBO-IRG. Conclusion:The reduction in the expression of genes related to oxidative stress and antioxidant defense following HBO in mouse hearts resulting from intestinal IR injury was more favorable during the ischemic period than during the reperfusion period. Thirty male isogenic mice (C57BL/6) from the Center for the Development of Experimental Models in Medicine and Biology (CEDEME -UNIFESP) were housed under controlled temperature and light conditions with a 12:12 hour light: dark cycle and free access to water and pelleted rations for up to 6 hours before the surgical procedures. Anesthetic and surgical proceduresThe mice were anesthetized intramuscularly with 44 mg.kg -1 of ketamine hydrochloride solution (Ketamina AgenerUnião Química, São Paulo), 2.5 mg.kg -1 of xylazine hydrochloride (Calmium -União Química, São Paulo), and 0.75 mg.kg -1 of acepromazine (Acepran -Rhobifarma, Hortolândia-SP). The control group (CG) was anesthetized, subjected to laparotomy without occlusion of the superior mesenteric vessels, and observed for 120 minutes. The IR group (IRG) was subjected to 60 minutes of superior mesenteric artery occlusion, followed by 60 minutes of reperfusion. Three groups received HBO as follows: during ischemia (HBO-IG), during reperfusion (HBO-RG), and during ischemia and during reperfusion (HBO-IRG). Material collection procedureSamples were taken from the small intestine and the heart. The fragments of the hearts and the intestinal segments were washed with saline solution, wrapped in labeled aluminum foil, immersed in liquid nitrogen (-196°C), and sent to the Laboratory ■ IntroductionIschemia-reperfusion (IR) injuries with cellular alterations and humoral disorders lead to an imbalance in homeostasis 1 . These injuries occur as a resu...

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The Circadian Gene Clock Regulates Bone Formation Via PDIA3

Yuan

Hua

Yang

et al. 2016

Journal of Bone and Mineral Research

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The expression patterns of clock-controlled genes (ccgs) are regulated by circadian rhythm, which is a major regulatory and physiological mechanism tied to the solar day. Disruptions in circadian rhythm contribute to the development of cardiovascular diseases, cancer, metabolic syndromes, and aging. It has been reported that bone remodeling is also regulated by circadian rhythm. However, the molecular mechanism by which the circadian gene Clock regulates bone remodeling has yet to be elucidated. Here, we show that Clock mutant mice exhibit a significant reduction in bone density as well as increased apoptosis. Protein disulfide isomerase family A member 3 (PDIA3) is a 1,25-dihydroxy-vitamin D3 [1α,25(OH)2D3] receptor that can regulate bone formation and apoptosis. Using luciferase and ChIP assays, we confirmed that Pdia3 is a ccg. Clock activates Pdia3 transcription by binding the E-box promoter, and transcription is decreased in Clock mutant mice. Forced expression of Pdia3 or of Clock completely rescues the osteogenic disorders found in the mutant background and inhibits apoptosis in vivo and in vitro. Furthermore, ablation of PDIA3 via RNA interference completely blocks the compensatory effect of forced expression of Clock in osteoblasts. Our results demonstrate that the core circadian gene Clock regulates bone formation via transcriptional control of 1,2,5(OH)2D3 receptor PDIA3. © 2016 American Society for Bone and Mineral Research.

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An Autoregulatory Mechanism Imposes Allosteric Control on the V(D)J Recombinase by Histone H3 Methylation

Cited by 40 publications

References 35 publications

H3K4me3 induces allosteric conformational changes in the DNA-binding and catalytic regions of the V(D)J recombinase

H3K4me3 induces allosteric conformational changes in the DNA-binding and catalytic regions of the V(D)J recombinase

Hyperbaric oxygenation and the genic expression related to oxidative stress in the heart of mice during intestinal ischemia and reperfusion

The Circadian Gene Clock Regulates Bone Formation Via PDIA3

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