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Berardi DE, Bock-Hughes A, Terry AR, Drake LE, Bozek G, Macleod KF. Lipid droplet turnover at the lysosome inhibits growth of hepatocellular carcinoma in a BNIP3-dependent manner. Sci Adv 2022; 8:eabo2510. [PMID: 36223464 PMCID: PMC9555787 DOI: 10.1126/sciadv.abo2510] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 08/23/2022] [Indexed: 05/12/2023]
Abstract
Hepatic steatosis is a major etiological factor in hepatocellular carcinoma (HCC), but factors causing lipid accumulation leading to HCC are not understood. We identify BNIP3 (a mitochondrial cargo receptor) as an HCC suppressor that mitigates against lipid accumulation to attenuate tumor cell growth. Targeted deletion of Bnip3 decreased tumor latency and increased tumor burden in a mouse model of HCC. This was associated with increased lipid in bnip3-/- HCC at early stages of disease, while lipid did not accumulate until later in tumorigenesis in wild-type mice, as Bnip3 expression was attenuated. Low BNIP3 expression in human HCC similarly correlated with increased lipid content and worse prognosis than HCC expressing high BNIP3. BNIP3 suppressed HCC cell growth by promoting lipid droplet turnover at the lysosome in a manner dependent on BNIP3 binding LC3. We have termed this process "mitolipophagy" because it involves the coordinated autophagic degradation of lipid droplets with mitochondria.
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Affiliation(s)
- Damian E. Berardi
- The Ben May Department for Cancer Research, The Gordon Center for Integrative Sciences, W-338, The University of Chicago, 929 E 57th Street, Chicago, IL 60637, USA
| | - Althea Bock-Hughes
- The Ben May Department for Cancer Research, The Gordon Center for Integrative Sciences, W-338, The University of Chicago, 929 E 57th Street, Chicago, IL 60637, USA
- The Committee on Molecular Metabolism and Nutrition, The University of Chicago, 929 E 57th Street, Chicago, IL 60637, USA
| | - Alexander R. Terry
- The Ben May Department for Cancer Research, The Gordon Center for Integrative Sciences, W-338, The University of Chicago, 929 E 57th Street, Chicago, IL 60637, USA
| | - Lauren E. Drake
- The Ben May Department for Cancer Research, The Gordon Center for Integrative Sciences, W-338, The University of Chicago, 929 E 57th Street, Chicago, IL 60637, USA
| | - Grazyna Bozek
- The Ben May Department for Cancer Research, The Gordon Center for Integrative Sciences, W-338, The University of Chicago, 929 E 57th Street, Chicago, IL 60637, USA
| | - Kay F. Macleod
- The Ben May Department for Cancer Research, The Gordon Center for Integrative Sciences, W-338, The University of Chicago, 929 E 57th Street, Chicago, IL 60637, USA
- The Committee on Molecular Metabolism and Nutrition, The University of Chicago, 929 E 57th Street, Chicago, IL 60637, USA
- The Committee on Cancer Biology, The University of Chicago, 929 E 57th Street, Chicago, IL 60637, USA
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2
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Sobreira DR, Joslin AC, Zhang Q, Williamson I, Hansen GT, Farris KM, Sakabe NJ, Sinnott-Armstrong N, Bozek G, Jensen-Cody SO, Flippo KH, Ober C, Bickmore WA, Potthoff M, Chen M, Claussnitzer M, Aneas I, Nóbrega MA. Extensive pleiotropism and allelic heterogeneity mediate metabolic effects of IRX3 and IRX5. Science 2021; 372:1085-1091. [PMID: 34083488 PMCID: PMC8386003 DOI: 10.1126/science.abf1008] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/28/2021] [Indexed: 12/11/2022]
Abstract
Whereas coding variants often have pleiotropic effects across multiple tissues, noncoding variants are thought to mediate their phenotypic effects by specific tissue and temporal regulation of gene expression. Here, we investigated the genetic and functional architecture of a genomic region within the FTO gene that is strongly associated with obesity risk. We show that multiple variants on a common haplotype modify the regulatory properties of several enhancers targeting IRX3 and IRX5 from megabase distances. We demonstrate that these enhancers affect gene expression in multiple tissues, including adipose and brain, and impart regulatory effects during a restricted temporal window. Our data indicate that the genetic architecture of disease-associated loci may involve extensive pleiotropy, allelic heterogeneity, shared allelic effects across tissues, and temporally restricted effects.
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Affiliation(s)
- Débora R Sobreira
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
| | - Amelia C Joslin
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Qi Zhang
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Iain Williamson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Grace T Hansen
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Kathryn M Farris
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Noboru J Sakabe
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Nasa Sinnott-Armstrong
- Department of Genetics, Stanford University, Stanford 94305 CA, USA
- Metabolism Program and Cardiovascular Disease Initiative, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Grazyna Bozek
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Sharon O Jensen-Cody
- Department of Pharmacology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Kyle H Flippo
- Department of Pharmacology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Matthew Potthoff
- Department of Pharmacology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Mengjie Chen
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Melina Claussnitzer
- Metabolism Program and Cardiovascular Disease Initiative, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02131, USA
| | - Ivy Aneas
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
| | - Marcelo A Nóbrega
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
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3
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Springer MZ, Poole LP, Drake LE, Bock-Hughes A, Boland ML, Smith AG, Hart J, Chourasia AH, Liu I, Bozek G, Macleod KF. BNIP3-dependent mitophagy promotes cytosolic localization of LC3B and metabolic homeostasis in the liver. Autophagy 2021; 17:3530-3546. [PMID: 33459136 DOI: 10.1080/15548627.2021.1877469] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mitophagy formed the basis of the original description of autophagy by Christian de Duve when he demonstrated that GCG (glucagon) induced macroautophagic/autophagic turnover of mitochondria in the liver. However, the molecular basis of liver-specific activation of mitophagy by GCG, or its significance for metabolic stress responses in the liver is not understood. Here we show that BNIP3 is required for GCG-induced mitophagy in the liver through interaction with processed LC3B; an interaction that is also necessary to localize LC3B out of the nucleus to cytosolic mitophagosomes in response to nutrient deprivation. Loss of BNIP3-dependent mitophagy caused excess mitochondria to accumulate in the liver, disrupting metabolic zonation within the liver parenchyma, with expansion of zone 1 metabolism at the expense of zone 3 metabolism. These results identify BNIP3 as a regulator of metabolic homeostasis in the liver through its effect on mitophagy and mitochondrial mass distribution.
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Affiliation(s)
- Maya Z Springer
- The Ben May Department for Cancer Research, The Gordon Center for Integrative Sciences, W-338 the University of Chicago, Chicago, IL, USA.,The Committee on Cancer Biology, The University of Chicago, Chicago, IL, USA
| | - Logan P Poole
- The Ben May Department for Cancer Research, The Gordon Center for Integrative Sciences, W-338 the University of Chicago, Chicago, IL, USA.,The Committee on Cancer Biology, The University of Chicago, Chicago, IL, USA
| | - Lauren E Drake
- The Ben May Department for Cancer Research, The Gordon Center for Integrative Sciences, W-338 the University of Chicago, Chicago, IL, USA
| | - Althea Bock-Hughes
- The Ben May Department for Cancer Research, The Gordon Center for Integrative Sciences, W-338 the University of Chicago, Chicago, IL, USA.,The University of Chicago, Chicago, IL, USA
| | - Michelle L Boland
- The Ben May Department for Cancer Research, The Gordon Center for Integrative Sciences, W-338 the University of Chicago, Chicago, IL, USA.,The University of Chicago, Chicago, IL, USA
| | - Alexandra G Smith
- The Ben May Department for Cancer Research, The Gordon Center for Integrative Sciences, W-338 the University of Chicago, Chicago, IL, USA.,The Committee on Cancer Biology, The University of Chicago, Chicago, IL, USA
| | - John Hart
- Department of Pathology, University of Chicago, Chicago, USA
| | - Aparajita H Chourasia
- The Ben May Department for Cancer Research, The Gordon Center for Integrative Sciences, W-338 the University of Chicago, Chicago, IL, USA.,The Committee on Cancer Biology, The University of Chicago, Chicago, IL, USA
| | - Ivan Liu
- The Ben May Department for Cancer Research, The Gordon Center for Integrative Sciences, W-338 the University of Chicago, Chicago, IL, USA
| | - Grazyna Bozek
- The Ben May Department for Cancer Research, The Gordon Center for Integrative Sciences, W-338 the University of Chicago, Chicago, IL, USA
| | - Kay F Macleod
- The Ben May Department for Cancer Research, The Gordon Center for Integrative Sciences, W-338 the University of Chicago, Chicago, IL, USA.,The Committee on Cancer Biology, The University of Chicago, Chicago, IL, USA.,The University of Chicago, Chicago, IL, USA
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4
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Montefiori LE, Sobreira DR, Sakabe NJ, Aneas I, Joslin AC, Hansen GT, Bozek G, Moskowitz IP, McNally EM, Nóbrega MA. A promoter interaction map for cardiovascular disease genetics. eLife 2018; 7:e35788. [PMID: 29988018 PMCID: PMC6053306 DOI: 10.7554/elife.35788] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 06/21/2018] [Indexed: 12/17/2022] Open
Abstract
Over 500 genetic loci have been associated with risk of cardiovascular diseases (CVDs); however, most loci are located in gene-distal non-coding regions and their target genes are not known. Here, we generated high-resolution promoter capture Hi-C (PCHi-C) maps in human induced pluripotent stem cells (iPSCs) and iPSC-derived cardiomyocytes (CMs) to provide a resource for identifying and prioritizing the functional targets of CVD associations. We validate these maps by demonstrating that promoters preferentially contact distal sequences enriched for tissue-specific transcription factor motifs and are enriched for chromatin marks that correlate with dynamic changes in gene expression. Using the CM PCHi-C map, we linked 1999 CVD-associated SNPs to 347 target genes. Remarkably, more than 90% of SNP-target gene interactions did not involve the nearest gene, while 40% of SNPs interacted with at least two genes, demonstrating the importance of considering long-range chromatin interactions when interpreting functional targets of disease loci.
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Affiliation(s)
| | - Debora R Sobreira
- Department of Human GeneticsThe University of ChicagoChicagoUnited States
| | - Noboru J Sakabe
- Department of Human GeneticsThe University of ChicagoChicagoUnited States
| | - Ivy Aneas
- Department of Human GeneticsThe University of ChicagoChicagoUnited States
| | - Amelia C Joslin
- Department of Human GeneticsThe University of ChicagoChicagoUnited States
| | - Grace T Hansen
- Department of Human GeneticsThe University of ChicagoChicagoUnited States
| | - Grazyna Bozek
- Department of Human GeneticsThe University of ChicagoChicagoUnited States
| | - Ivan P Moskowitz
- Department of Human GeneticsThe University of ChicagoChicagoUnited States
- Department of Pediatrics and PathologyThe University of ChicagoChicagoUnited States
| | - Elizabeth M McNally
- Center for Genetic MedicineNorthwestern University Feinberg School of MedicineChicagoUnited States
| | - Marcelo A Nóbrega
- Department of Human GeneticsThe University of ChicagoChicagoUnited States
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5
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Ratnam S, Bozek G, Martin T, Gallagher SJ, Payne CJ, Storb U. Ssm1b expression and function in germ cells of adult mice and in early embryos. Mol Reprod Dev 2017; 84:596-613. [PMID: 28464323 DOI: 10.1002/mrd.22826] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 04/13/2017] [Indexed: 12/17/2022]
Abstract
Ssm1b (Strain-specific modifier of DNA methylation 1b) is a Krüppel-associated box (KRAB) zinc finger gene that promotes CpG methylation in the mouse transgene HRD (Heavy chain enhancer, rearrangement by deletion). We report here that Ssm1b expression and concomitant HRD methylation are also present in the male and female germ cells of adult mice. Ssm1b is expressed in both diploid (2N) and haploid (1N) oocytes, as well as in 1N spermatids and spermatozoa, but not in 2N spermatogonia. Interestingly, Ssm1b mRNA is not detected in any other adult mouse organ examined, although Ssm1-family mRNAs are highly expressed in the heart. Reflecting strain specificity, Ssm1b expression and HRD methylation are not observed in early-stage C3H/HeJ mouse embryos; however, an Ssm1b-like gene that closely resembles an Ssm1b-like gene previously found in wild-derived mice is expressed in cultured embryonic stem cells derived from C3H/HeJ embryos, suggesting that culture conditions affect its expression. Collectively, this work demonstrates that HRD methylation by Ssm1b is more temporally restricted during spermatogenesis compared to oogenesis, and is altered when embryonic stem cells are cultured from C3H/HeJ inner cell mass cells.
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Affiliation(s)
- Sarayu Ratnam
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois
| | - Grazyna Bozek
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois
| | - Terence Martin
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois
| | - Shannon J Gallagher
- Human Molecular Genetics Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Christopher J Payne
- Human Molecular Genetics Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois.,Departments of Pediatrics and Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Ursula Storb
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois
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6
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Ratnam S, Engler P, Bozek G, Mao L, Podlutsky A, Austad S, Martin T, Storb U. Identification of Ssm1b, a novel modifier of DNA methylation, and its expression during mouse embryogenesis. Development 2014; 141:2024-34. [PMID: 24803651 DOI: 10.1242/dev.105726] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The strain-specific modifier Ssm1 is responsible for the strain-dependent methylation of particular E. coli gpt-containing transgenic sequences. Here, we identify Ssm1 as the KRAB-zinc finger (ZF) gene 2610305D13Rik located on distal chromosome 4. Ssm1b is a member of a gene family with an unusual array of three ZFs. Ssm1 family members in C57BL/6 (B6) and DBA/2 (D2) mice have various amino acid changes in their ZF domain and in the linker between the KRAB and ZF domains. Ssm1b is expressed up to E8.5; its target transgene gains partial methylation by this stage as well. At E9.5, Ssm1b mRNA is no longer expressed but by then its target has become completely methylated. By contrast, in D2 embryos the transgene is essentially unmethylated. Methylation during B6 embryonic development depends on Dnmt3b but not Mecp2. In differentiating B6 embryonic stem cells methylation spreads from gpt to a co-integrated neo gene that has a similarly high CpG content as gpt, but neo alone is not methylated. In adult B6 mice, Ssm1b is expressed in ovaries, but in other organs only other members of the Ssm1 family are expressed. Interestingly, the transgene becomes methylated when crossed into some, but not other, wild mice that were kept outbred in the laboratory. Thus, polymorphisms for the methylation patterns seen among laboratory inbred strains are also found in a free-living population. This may imply that mice that do not have the Ssm1b gene may use another member of the Ssm1 family to control the potentially harmful expression of certain endogenous or exogenous genes.
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Affiliation(s)
- Sarayu Ratnam
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
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7
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Ratnam S, Bozek G, Nicolae D, Storb U. The pattern of somatic hypermutation of Ig genes is altered when p53 is inactivated. Mol Immunol 2010; 47:2611-8. [PMID: 20691478 DOI: 10.1016/j.molimm.2010.05.291] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 05/24/2010] [Accepted: 05/27/2010] [Indexed: 10/19/2022]
Abstract
Mice with a deletion of the p53 gene have normal antibody titers against sheep red blood cells and normal switching to all Ig isotypes. In older mice (11 and 16 weeks old) the somatic hypermutation (SHM) frequencies are progressively reduced. In young mice (8 weeks old) with p53 deletion, the SHM frequencies are normal. However, the mutation pattern is changed in all p53-/- mice: mutations at A are increased. Surprisingly, deletion of the Ung2 gene in addition to the deletion of p53 corrected the A mutation frequencies to those of control mice. Known interactions of p53 protein with several proteins involved in error-prone BER during SHM may explain these findings. There is no indication that the absence of p53 affects the function of AID. Inactivation of p21 does not alter SHM, supporting the idea that the p53 protein is involved in SHM by its direct association with the SHM process. There is no significant change of mutations at T. Thus, the hypermutability at A is strand-biased (transcription? replication?). The translesion polymerase pol eta has so far been found to be the sole mutator at A and T in mice. However, the pattern in p53-/- mice is compatible with the possible inhibition by p53 of another translesion polymerase, pol iota, which in the absence of p53 may be recruited to error-prone repair of abasic sites in SHM.
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Affiliation(s)
- Sarayu Ratnam
- Department of Molecular Genetics and Cell Biology, University of Chicago, 920 East 58th Street, Chicago, IL 60637, United States
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8
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Shen HM, Bozek G, Pinkert CA, McBride K, Wang L, Kenter A, Storb U. Expression of AID transgene is regulated in activated B cells but not in resting B cells and kidney. Mol Immunol 2007; 45:1883-92. [PMID: 18067961 DOI: 10.1016/j.molimm.2007.10.041] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2007] [Accepted: 10/26/2007] [Indexed: 12/18/2022]
Abstract
Activation-induced DNA cytidine deaminase (AID) is required for somatic hypermutation (SHM) and efficient class switch recombination (CSR) of immunoglobulin (Ig) genes. We created AID-transgenic mice that express AID ubiquitously under the control of a beta-actin promoter. When crossed with AID-/- mice, the AID-transgenic,AID-/- mice carried out SHM and CSR, showing that the AID transgenes were functional. However, the frequencies of SHM in V- and switch-regions, and CSR were reduced compared to those in a wild type AID background. Several criteria suggested that the inefficiency of SHM was due to reduced AID activity, rather than lack of recruiting error-prone DNA repair. High levels of AID mRNA were produced in resting B cells and kidney, cells that do not express AID in wild type mice. Compared with these cells, activated B cells expressed about an order of magnitude less AID mRNA suggesting that there may be a post-transcriptional mechanism that regulates AID mRNA levels in professional AID producers but not other cells. The AID protein expressed in resting B cells and kidney was phosphorylated at serine-38. Despite this modification, known to enhance AID activity, resting B cells did not undergo SHM. Apparently, the large amounts of AID in resting B cells are not targeted to Ig genes in vivo, in contrast to findings in vitro.
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Affiliation(s)
- Hong Ming Shen
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
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9
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Affiliation(s)
- Ursula Storb
- Department of Molecular Genetics and Cell Biology, University of Chicago, USA
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10
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Abstract
Somatic hypermutation (SHM) and class switch recombination (CSR) are initiated by activation-induced cytosine deaminase (AID). The uracil, and potentially neighboring bases, are processed by error-prone base excision repair and mismatch repair. Deficiencies in Ung, Msh2, or Msh6 affect SHM and CSR. To determine whether Msh2/Msh6 complexes which recognize single-base mismatches and loops were the only mismatch-recognition complexes required for SHM and CSR, we analyzed these processes in Msh6(-/-)Ung(-/-) mice. SHM and CSR were affected in the same degree and fashion as in Msh2(-/-)Ung(-/-) mice; mutations were mostly C,G transitions and CSR was greatly reduced, making Msh2/Msh3 contributions unlikely. Inactivating Ung alone reduced mutations from A and T, suggesting that, depending on the DNA sequence, varying proportions of A,T mutations arise by error-prone long-patch base excision repair. Further, in Msh6(-/-)Ung(-/-) mice the 5' end and the 3' region of Ig genes was spared from mutations as in wild-type mice, confirming that AID does not act in these regions. Finally, because in the absence of both Ung and Msh6, transition mutations from C and G likely are "footprints" of AID, the data show that the activity of AID is restricted drastically in vivo compared with AID in cell-free assays.
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Affiliation(s)
- Hong Ming Shen
- Department of Molecular Genetic and Cell Biology, University of Chicago, Chicago, IL 60637, USA
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11
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Volgina VV, Sun T, Bozek G, Martin TE, Storb U. Scarcity of lambda 1 B cells in mice with a single point mutation in C lambda 1 is due to a low BCR signal caused by misfolded lambda 1 light chain. Mol Immunol 2006; 44:1417-28. [PMID: 16860389 DOI: 10.1016/j.molimm.2006.04.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2006] [Revised: 04/17/2006] [Accepted: 04/25/2006] [Indexed: 01/04/2023]
Abstract
The presence of valine-154 instead of glycine in the constant region of lambda1 causes a severe lambda1 B cell defect in SJL and lambda1-valine knock-in mice with a compensatory increase in lambda2,3 B cells. The defect is due to low signaling by the lambda1-valine BCR. lambda1-Valine B cells deficient in the SHP-1 phosphatase survive better than lambda2,3 B cells in these mice, or lambda1 B cells in lambda1 wildtype mice. Low signaling is apparently due to misfolding of the lambda1-valine light chain as demonstrated by the absence of a regular beta-sheet structure determined by circular dichroism, the sedimentation of the light chain in solution, and the association of valine-valine constant regions in a yeast two-hybrid assay. lambda1-Valine B cells that survive apparently have a higher BCR signal, presumably because of their specific lambda1-heavy chain combination or having encountered a high-affiniy antigen. lambda1-Valine mice have increased B1 cells which were shown by others to have a higher signaling potential. Valine mice crossed with non-conventional gamma2b transgenic mice, in which B cell development is accelerated and in which B1 cells and high signaling cells are greatly reduced, have essentially no, lambda2,3 B cells, but increased numbers of lambda1-valine B cells. This supports the conclusion that the major defect in lambda1-valine mice is the inability of valine-preB cells to produce a threshold signal for B cell development. The reduction of lambda2,3 B cells in valine mice with a gamma2b transgene shows that the majority of their compensatory increase is almost entirely of the B1 cell type.
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Affiliation(s)
- Veronica V Volgina
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
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12
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Longerich S, Tanaka A, Bozek G, Nicolae D, Storb U. The very 5' end and the constant region of Ig genes are spared from somatic mutation because AID does not access these regions. ACTA ACUST UNITED AC 2006; 202:1443-54. [PMID: 16301749 PMCID: PMC2212980 DOI: 10.1084/jem.20051604] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Somatic hypermutation (SHM) is restricted to VDJ regions and their adjacent flanks in immunoglobulin (Ig) genes, whereas constant regions are spared. Mutations occur after about 100 nucleotides downstream of the promoter and extend to 1–2 kb. We have asked why the very 5′ and most of the 3′ region of Ig genes are unmutated. Does the activation-induced cytosine deaminase (AID) that initiates SHM not gain access to these regions, or does AID gain access, but the resulting uracils are repaired error-free because error-prone repair does not gain access? The distribution of mutations was compared between uracil DNA glycosylase (Ung)-deficient and wild-type mice in endogenous Ig genes and in an Ig transgene. If AID gains access to the 5′ and 3′ regions that are unmutated in wild-type mice, one would expect an “AID footprint,” namely transition mutations from C and G in Ung-deficient mice in the regions normally devoid of SHM. We find that the distribution of total mutations and transitions from C and G is indistinguishable in wild-type and Ung-deficient mice. Thus, AID does not gain access to the 5′ and constant regions of Ig genes. The implications for the role of transcription and Ung in SHM are discussed.
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13
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Storb U, Peters A, Kim N, Shen HM, Bozek G, Michael N, Hackett J, Klotz E, Reynolds JD, Loeb LA, Martin TE. Molecular aspects of somatic hypermutation of immunoglobulin genes. Cold Spring Harb Symp Quant Biol 2001; 64:227-34. [PMID: 11232290 DOI: 10.1101/sqb.1999.64.227] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- U Storb
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637, USA
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14
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Hicks GG, Singh N, Nashabi A, Mai S, Bozek G, Klewes L, Arapovic D, White EK, Koury MJ, Oltz EM, Van Kaer L, Ruley HE. Fus deficiency in mice results in defective B-lymphocyte development and activation, high levels of chromosomal instability and perinatal death. Nat Genet 2000; 24:175-9. [PMID: 10655065 DOI: 10.1038/72842] [Citation(s) in RCA: 216] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The gene FUS (also known as TLS (for translocated in liposarcoma) and hnRNP P2) is translocated with the gene encoding the transcription factor ERG-1 in human myeloid leukaemias. Although the functions of wild-type FUS are unknown, the protein contains an RNA-recognition motif and is a component of nuclear riboprotein complexes. FUS resembles a transcription factor in that it binds DNA, contributes a transcriptional activation domain to the FUS-ERG oncoprotein and interacts with several transcription factors in vitro. To better understand FUS function in vivo, we examined the consequences of disrupting Fus in mice. Our results indicate that Fus is essential for viability of neonatal animals, influences lymphocyte development in a non-cell-intrinsic manner, has an intrinsic role in the proliferative responses of B cells to specific mitogenic stimuli and is required for the maintenance of genomic stability. The involvement of a nuclear riboprotein in these processes in vivo indicates that Fus is important in genome maintenance.
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Affiliation(s)
- G G Hicks
- Manitoba Institute of Cell Biology and the University of Manitoba, Winnipeg, Canada.
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Shen X, Bozek G, Pinkert CA, Storb U. The C(H)1 and transmembrane domains of mu in the context of a gamma2b transgene do not suffice to promote B cell maturation. Int Immunol 1999; 11:1663-71. [PMID: 10508184 DOI: 10.1093/intimm/11.10.1663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mice carrying a gamma2b transgene have been shown previously to be deficient in B cell development. In particular, a developmental block exists at the pre-B cell stage. The few B cells that develop all express endogenous micro heavy chains. The phenotype suggests that gamma2b exerts a strong feedback inhibition on endogenous Ig gene rearrangement, but, unlike micro, cannot support further B cell development. In this study we have created hybrid transgenes between gamma2b and micro. Transgenic mice with a C(H)1 domain of micro, or both a C(H)1 and transmembrane/cytoplasmic domain of micro replacing the respective domains of a gamma2b transgene, have the same B cell defect as gamma2b transgenic mice. Interestingly, the severity of the defect is correlated with the level of expression of the transgene, suggesting that the degree of feedback inhibition of Ig gene rearrangement depends on the level and timing of Ig production. Crossing the gamma2b/micro transgenes into a Bcl-x(L) transgenic line allows immature gamma2b B cells to survive, but not to develop to maturity. Therefore, the missing function of micro is not simply an anti-apoptotic effect.
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Affiliation(s)
- X Shen
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
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Kim N, Bozek G, Lo JC, Storb U. Different mismatch repair deficiencies all have the same effects on somatic hypermutation: intact primary mechanism accompanied by secondary modifications. J Exp Med 1999; 190:21-30. [PMID: 10429667 PMCID: PMC2195558 DOI: 10.1084/jem.190.1.21] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/1999] [Accepted: 05/06/1999] [Indexed: 02/02/2023] Open
Abstract
Somatic hypermutation of Ig genes is probably dependent on transcription of the target gene via a mutator factor associated with the RNA polymerase (Storb, U., E.L. Klotz, J. Hackett, Jr., K. Kage, G. Bozek, and T.E. Martin. 1998. J. Exp. Med. 188:689-698). It is also probable that some form of DNA repair is involved in the mutation process. It was shown that the nucleotide excision repair proteins were not required, nor were mismatch repair (MMR) proteins. However, certain changes in mutation patterns and frequency of point mutations were observed in Msh2 (MutS homologue) and Pms2 (MutL homologue) MMR-deficient mice (for review see Kim, N., and U. Storb. 1998. J. Exp. Med. 187:1729-1733). These data were obtained from endogenous immunoglobulin (Ig) genes and were presumably influenced by selection of B cells whose Ig genes had undergone certain mutations. In this study, we have analyzed somatic hypermutation in two MutL types of MMR deficiencies, Pms2 and Mlh1. The mutation target was a nonselectable Ig-kappa gene with an artificial insert in the V region. We found that both Pms2- and Mlh1-deficient mice can somatically hypermutate the Ig test gene at approximately twofold reduced frequencies. Furthermore, highly mutated sequences are almost absent. Together with the finding of genome instability in the germinal center B cells, these observations support the conclusion, previously reached for Msh2 mice, that MMR-deficient B cells undergoing somatic hypermutation have a short life span. Pms2- and Mlh-1-deficient mice also resemble Msh2-deficient mice with respect to preferential targeting of G and C nucleotides. Thus, it appears that the different MMR proteins do not have unique functions with respect to somatic hypermutation. Several intrinsic characteristics of somatic hypermutation remain unaltered in the MMR-deficient mice: a preference for targeting A over T, a strand bias, mutational hot spots, and hypermutability of the artificial insert are all seen in the unselectable Ig gene. This implies that the MMR proteins are not required for and most likely are not involved in the primary step of introducing the mutations. Instead, they are recruited to repair certain somatic point mutations, presumably soon after these are created.
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Affiliation(s)
- N Kim
- Department of Biochemistry and Molecular Biology, University of Chicago, Illinois 60637, USA
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17
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Sun T, Ezekiel UR, Erskine L, Agulo R, Bozek G, Roth D, Storb U. Signal joint formation is inhibited in murine scid preB cells and fibroblasts in substrates with homopolymeric coding ends. Mol Immunol 1999; 36:551-8. [PMID: 10475610 DOI: 10.1016/s0161-5890(99)00053-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
During B and T lymphocyte development, immunoglobulin and T cell receptor genes are assembled from the germline V, (D) and J gene segments (Lewis, S.M., 1994. The mechanism of V(D)J joining: lessons from molecular, immunological and comparative analyses. Adv. Immunol. 56, 27-150). These DNA rearrangements, responsible for immune system diversity, are mediated by a site specific recombination machinery via recognition signal sequences (RSSs) composed of conserved heptamers and nonamers separated by spacers of 12 or 23 nucleotides (Lewis, S.M., 1994. The mechanism of V(D)J joining: lessons from molecular, immunological and comparative analyses. Adv. Immunol. 56, 27-150). Recombination occurs only between a RSS with a 12mer spacer and a RSS with a 23mer spacer (Lewis, S.M., 1994. The mechanism of V(D)J joining: lessons from molecular, immunological and comparative analyses. Adv. Immunol. 56, 27-150). RAG1 and RAG2 proteins cleave precisely at the RSS-coding sequence border leading to flush signal ends and coding ends with a hairpin structure (Eastman, M., Leu, T., Schatz, D., 1996. Initiation of V(D)J recombination in vitro obeying the 12/23 rule. Nature 380, 85-88; Roth, D.B., Menetski, J.P., Nakajima, P.B., Bosma, M.J., Gellert, M., 1992. V(D)J recombination: broken DNA molecules with covalently sealed (hairpin) coding ends in scid mouse thymocytes. Cell 983-991: Roth, D.B., Zhu, C., Gellert. M., 1993. Characterization of broken DNA molecules associated with V(D)J recombination. Proc. Natl. Acad. Sci. USA 90, 10,788-10,792; van Gent, D., McBlane, J.. Sadofsky, M., Hesse, J., Gellert, M., 1995. Initiation of V(D)J recombination in a cell-free system. Cell 81, 925-934). Signal ends join, forming a signal joint. The hairpin coding ends are opened by a yet unknown endonuclease, and are further processed to form the coding joint (Lewis, S.M., 1994. The mechanism of V(D)J joining: lessons from molecular, immunological and comparative analyses. Ad. Immunol. 56, 27-150.) The murine scid mutation has been shown to affect coding joints, but much less signal joint formation. In this study we demonstrate that the murine scid mutation inhibits correct signal joint formation when both coding ends contain homopolymeric sequences. We suggest that this finding may be due to the function of the SCID protein as an assembly component in V(D)J recombination.
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Affiliation(s)
- T Sun
- Department of Molecular Genetics and Cell Biology, University of Chicago, IL 60637, USA
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Chen G, Cizeau J, Vande Velde C, Park JH, Bozek G, Bolton J, Shi L, Dubik D, Greenberg A. Nix and Nip3 form a subfamily of pro-apoptotic mitochondrial proteins. J Biol Chem 1999; 274:7-10. [PMID: 9867803 DOI: 10.1074/jbc.274.1.7] [Citation(s) in RCA: 224] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We have identified Nix, a homolog of the E1B 19K/Bcl-2 binding and pro-apoptotic protein Nip3. Human and murine Nix have a 56 and 53% amino acid identity to human and murine Nip3, respectively. The carboxyl terminus of Nix, including a transmembrane domain, is highly homologous to Nip3 but it bears a longer and distinct asparagine/proline-rich N terminus. Human Nip3 maps to chromosome 14q11.2-q12, whereas Nix/BNip3L was found on 8q21. Nix encodes a 23. 8-kDa protein but it is expressed as a 48-kDa protein, suggesting that it homodimerizes similarly to Nip3. Following transfection, Nix protein undergoes progressive proteolysis to an 11-kDa C-terminal fragment, which is blocked by the proteasome inhibitor lactacystin. Nix colocalizes with the mitochondrial matrix protein HSP60, and removal of the putative transmembrane domain (TM) results in general cytoplasmic and nuclear expression. When transiently expressed, Nix and Nip3 but not TM deletion mutants rapidly activate apoptosis. Nix can overcome the suppressers Bcl-2 and Bcl-XL, although high levels of Bcl-XL expression will inhibit apoptosis. We propose that Nix and Nip3 form a new subfamily of pro-apoptotic mitochondrial proteins.
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Affiliation(s)
- G Chen
- Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, Manitoba R3E 0V9, Canada
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Engler P, Doglio LT, Bozek G, Storb U. A cis-acting element that directs the activity of the murine methylation modifier locus Ssm1. Proc Natl Acad Sci U S A 1998; 95:10763-8. [PMID: 9724778 PMCID: PMC27969 DOI: 10.1073/pnas.95.18.10763] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Silencing of chromosomal domains has been described in diverse systems such as position effect variegation in insects, silencing near yeast telomeres, and mammalian X chromosome inactivation. In mammals, silencing is associated with methylation at CpG dinucleotides, but little is known about how methylation patterns are established or altered during development. We previously described a strain-specific modifier locus, Ssm1, that controls the methylation of a complex transgene. In this study we address the questions of the nature of Ssm1's targets and whether its effect extends into adjacent sequences. By examining the inheritance of methylation patterns in a series of mice harboring deletion derivatives of the original transgene, we have identified a discrete segment, derived from the gpt gene of Escherichia coli, that is a major determinant for Ssm1-mediated methylation. Methylation analysis of sequences adjacent to a transgenic target indicates that the influence of this modifier extends into the surrounding chromosome in a strain-dependent fashion. Implications for the mechanism of Ssm1 action are discussed.
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Affiliation(s)
- P Engler
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA.
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Storb U, Klotz EL, Hackett J, Kage K, Bozek G, Martin TE. A hypermutable insert in an immunoglobulin transgene contains hotspots of somatic mutation and sequences predicting highly stable structures in the RNA transcript. J Exp Med 1998; 188:689-98. [PMID: 9705951 PMCID: PMC2213363 DOI: 10.1084/jem.188.4.689] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/1998] [Revised: 06/10/1998] [Indexed: 11/23/2022] Open
Abstract
Immunoglobulin (Ig) genes expressed in mature B lymphocytes can undergo somatic hypermutation upon cell interaction with antigen and T cells. The mutation mechanism had previously been shown to depend upon transcription initiation, suggesting that a mutator factor was loaded on an RNA polymerase initiating at the promoter and causing mutations during elongation (Peters, A., and U. Storb. 1996. Immunity. 4:57-65). To further elucidate this process we have created an artificial substrate consisting of alternating EcoRV and PvuII restriction enzyme sites (EPS) located within the variable (V) region of an Ig transgene. This substrate can easily be assayed for the presence of mutations in DNA from transgenic lymphocytes by amplifying the EPS insert and determining by restriction enzyme digestion whether any of the restriction sites have been altered. Surprisingly, the EPS insert was mutated many times more frequently than the flanking Ig sequences. In addition there were striking differences in mutability of the different nucleotides within the restriction sites. The data favor a model of somatic hypermutation where the fine specificity of the mutations is determined by nucleotide sequence preferences of a mutator factor, and where the general site of mutagenesis is determined by the pausing of the RNA polymerase due to secondary structures within the nascent RNA.
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Affiliation(s)
- U Storb
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637, USA.
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Ezekiel UR, Sun T, Bozek G, Storb U. The composition of coding joints formed in V(D)J recombination is strongly affected by the nucleotide sequence of the coding ends and their relationship to the recombination signal sequences. Mol Cell Biol 1997; 17:4191-7. [PMID: 9199354 PMCID: PMC232272 DOI: 10.1128/mcb.17.7.4191] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
V(D)J recombination proceeds in two stages. Precise cleavage at the border of the conserved recombination signal sequences (RSSs) and the coding ends results in flush double-stranded signal ends and coding ends terminating in hairpins. In the second stage, the signal and coding ends are processed into signal and coding joints. Coding ends containing certain nucleotide homopolymers affect the efficiency of V(D)J recombination. In this study, we have tested the effect of small changes in coding-end nucleotide composition on the frequency of coding- and signal joint formation. Furthermore, we have determined the sequences of coding joints resulting from recombination of coding ends with different compositions. We found that the presence of two T nucleotides 5' of both RSSs, but not a single T, reduces the frequency of signal joint formation, i.e., interferes with the cleavage stage of V(D)J recombination. However, coding-joint processing is sensitive even to a single T. Both the sequence of the coding ends and the particular RSS (12-mer or 23-mer) with which the coding end is associated affect the final composition of the coding joints. Thus, the presence of P nucleotides, the conservation of one undeleted coding end, the formation of joints without any deletions, and the template-dependent insertion of nucleotides are strongly influenced by the coding-end nucleotide composition and/or RSS association. The implications of these results with respect to the processing of coding ends are discussed.
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Affiliation(s)
- U R Ezekiel
- Department of Molecular Genetics and Cell Biology, University of Chicago, Illinois 60637, USA
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Doglio L, Kim JY, Bozek G, Storb U. Expression of lambda and kappa genes can occur in all B cells and is initiated around the same pre-B-cell developmental stage. Dev Immunol 1994; 4:13-26. [PMID: 7620323 PMCID: PMC2275945 DOI: 10.1155/1994/87352] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Transgenic mice that carry a lambda 2 transgene under the control of the V lambda 2 promoter and the E lambda 2-4 enhancer (lambda 2E lambda mice) are described. A high proportion of B cells in the spleen and the bone marrow express the lambda transgene on the cell membrane. lambda 2 protein is synthesized by all lambda 2E lambda-derived spleen B-cell hybridomas that have retained the transgene, suggesting that all B cells have the ability to express lambda genes. Feedback inhibition of endogenous kappa-gene rearrangement is significant, but not complete. The results are similar to those with transgenic mice expressing the same lambda 2 transgene under the control of the heavy-chain enhancer (lambda 2EH mice). Although the lambda 2EH transgene is expressed before the lambda 2E lambda transgene, feedback inhibition seems to occur at about the same stage of B-cell development, regardless of the timing of expression of the lambda transgenes. Apparently, feedback is not necessarily coincident with the assembly of a heavy-chain/light-chain complex in pre-B cells. Expression of lambda in the normal fetal liver coincides with the expression of kappa; thus, it appears that lambda-gene transcription is not delayed. The differential rearrangement of kappa and lambda genes is discussed in the light of these findings.
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Affiliation(s)
- L Doglio
- Department of Molecular Genetics and Cell Biology, University of Chicago, Illinois 60637, USA
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