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Zhang X, Qiu X, Zhao W, Song L, Zhang X, Yang L, Tao M. Over-Expression of ARID3B Suppresses Tumor Progression and Predicts Better Prognosis in Patients With Gastric Cancer. Cancer Control 2023; 30:10732748231169403. [PMID: 37071790 PMCID: PMC10126794 DOI: 10.1177/10732748231169403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND ARID3B (AT-rich interaction domain 3B) has been demonstrated to be associated with the progression and patient prognosis of several human tumors. We conducted the present study to investigate the biological behavior and clinical relevance of ARID3B in gastric cancer (GC). METHODS Detection of the expression level in GC tissues and cell lines were performed by Western blot and immunohistochemistry. We also retrospectively analyzed the correlation of ARID3B with clinicopathological characteristics and patient prognosis in gastric cancer. The biological functions of ARID3B in GC cells were further explored by transwell migration assays, wound healing assays and cell proliferation assay. RESULTS The present study suggested that the expression of ARID3B was significantly lower in GC tissues than in adjacent normal tissues. IHC staining in tissues of 406 GC patients from training and validation sets verified that ARID3B over-expression correlated with clinicopathological features, such as degree of differentiation and clinical stage. Meanwhile, ARID3B was proved to be an independent prognostic factor for GC prognosis. Furthermore, over-expression of ARID3B suppressed proliferation in GC cells according CCK8 assay. We found that over-expression of ARID3B inhibited GC cell migration by transwell assay and wound healing assay. Furthermore, EMT markers were detected in ARID3B over-expression GC cells, which showed that ARID3B may inhibit metastasis of GC cells. CONCLUSION Our results firstly revealed that the expression level of ARID3B was closely correlated with clinicopathological features and may serve as an independent prognostic factor for GC patients. More importantly, ARID3B could suppress GC progression, including cell proliferation, migration and metastasis.
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Affiliation(s)
- Xunlei Zhang
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu, China
| | - Xinyue Qiu
- Department of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu, China
| | - Wenjing Zhao
- Cancer Research Center, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu, China
| | - Li Song
- Department of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu, China
| | - Xingsong Zhang
- Department of Pathology, Affiliated Tumor Hospital of Nantong University, Nantong Jiangsu, China
| | - Lei Yang
- Department of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu, China
| | - Min Tao
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of Oncology, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, Jiangsu, China
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Hayakawa K, Li YS, Shinton SA, Bandi SR, Formica AM, Brill-Dashoff J, Hardy RR. Crucial Role of Increased Arid3a at the Pre-B and Immature B Cell Stages for B1a Cell Generation. Front Immunol 2019; 10:457. [PMID: 30930899 PMCID: PMC6428705 DOI: 10.3389/fimmu.2019.00457] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 02/20/2019] [Indexed: 02/03/2023] Open
Abstract
The Lin28b+Let7− axis in fetal/neonatal development plays a role in promoting CD5+ B1a cell generation as a B-1 B cell developmental outcome. Here we identify the Let7 target, Arid3a, as a crucial molecular effector of the B-1 cell developmental program. Arid3a expression is increased at pro-B cell stage and markedly increased at pre-B and immature B cell stages in the fetal/neonatal liver B-1 development relative to that in the Lin28b−Let7+ adult bone marrow (BM) B-2 cell development. Analysis of B-lineage restricted Lin28b transgenic (Tg) mice, Arid3a knockout and Arid3a Tg mice, confirmed that increased Arid3a allows B cell generation without requiring surrogate light chain (SLC) associated pre-BCR stage, and prevents MHC class II cell expression at the pre-B and newly generated immature B cell stages, distinct from pre-BCR dependent B development with MHC class II in adult BM. Moreover, Arid3a plays a crucial role in supporting B1a cell generation. The increased Arid3a leads higher Myc and Bhlhe41, and lower Siglec-G and CD72 at the pre-B and immature B cell stages than normal adult BM, to allow BCR signaling induced B1a cell generation. Arid3a-deficiency selectively blocks the development of B1a cells, while having no detectable effect on CD5− B1b, MZ B, and FO B cell generation resembling B-2 development outcome. Conversely, enforced expression of Arid3a by transgene is sufficient to promote the development of B1a cells from adult BM. Under the environment change between birth to adult, altered BCR repertoire in increased B1a cells occurred generated from adult BM. However, crossed with B1a-restricted VH/D/J IgH knock-in mice allowed to confirm that SLC-unassociated B1a cell increase and CLL/lymphoma generation can occur in aged from Arid3a increased adult BM. These results confirmed that in fetal/neonatal normal mice, increased Arid3a at the pre-B cell and immature B cell stages is crucial for generating B1a cells together with the environment for self-ligand reactive BCR selection, B1a cell maintenance, and potential for development of CLL/Lymphoma in aged mice.
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Affiliation(s)
- Kyoko Hayakawa
- Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Yue-Sheng Li
- Fox Chase Cancer Center, Philadelphia, PA, United States
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3
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Pratama E, Tian X, Lestari W, Iseki S, Ichwan SJA, Ikeda MA. Critical role of ARID3B in the expression of pro-apoptotic p53-target genes and apoptosis. Biochem Biophys Res Commun 2015; 468:248-54. [PMID: 26519881 DOI: 10.1016/j.bbrc.2015.10.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 10/23/2015] [Indexed: 01/17/2023]
Abstract
ARID3A and ARID3B are transcriptional targets of p53. Recently, it has been reported that ARID3A plays a critical role in the transcriptional activation of pro-arrest p21 in response to DNA damage. However, the role of ARID3B in the p53 regulatory pathway remains poorly understood. Here we show that ARID3A and ARID3B specifically bind to putative ARID3-binding sites in p53 target genes in vitro and in vivo. ARID3B and, to a lesser extent, ARID3A silencing blocked transcriptional activation of pro-apoptotic p53 target genes, such as PUMA, PIG3, and p53. Furthermore, ectopic ARID3B, to a lesser extent, ARID3A expression activated the pro-apoptotic gene expression, and only ARID3B induced apoptosis. Finally, ARID3B but not ARID3A silencing blocked apoptosis induction following DNA damage. These results indicated that, although ARID3B and ARID3A share overlapping functions, ARID3B play a key role in the expression of pro-apoptotic p53-target genes and apoptosis.
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Affiliation(s)
- Endrawan Pratama
- Department of Molecular Craniofacial Embryology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Xiaohui Tian
- Department of Oral Implantology and Regenerative Dental Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Widya Lestari
- Faculty of Dentistry, International Islamic University Malaysia, Kuantan, Malaysia
| | - Sachiko Iseki
- Department of Molecular Craniofacial Embryology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Masa-Aki Ikeda
- Department of Molecular Craniofacial Embryology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.
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Song M, Kim H, Kim WK, Hong SP, Lee C, Kim H. High expression of AT-rich interactive domain 3A (ARID3A) is associated with good prognosis in colorectal carcinoma. Ann Surg Oncol 2013; 21 Suppl 4:S481-9. [PMID: 24366420 DOI: 10.1245/s10434-013-3435-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Indexed: 12/20/2022]
Abstract
BACKGROUND AT-rich interactive domain 3A (ARID3A) is a member of the ARID family of DNA-binding proteins. Previous reports have shown that ARID3A controls cell growth in a p53-dependent manner. Recently, it has been reported that expression of the ARID3A protein was markedly increased in colon cancer tissue compared with matched normal colonic mucosa. However, little is currently known about the role of ARID3A in colorectal cancer (CRC). The aim of this study was to investigate the clinical significance of ARID3A expression in CRC. METHODS We examined ARID3A expression in 690 CRC patients using tissue microarray and immunohistochemistry. Kaplan-Meier analysis and Cox proportional hazard models were used to estimate the impact of ARID3A expression on overall survival. RESULTS Of the 690 cases, 195 tumors were strongly positive for ARID3A, 187 were weakly positive, and 308 were negative. ARID3A expression in CRC was significantly correlated with age, degree of differentiation, depth of invasion, lymph node metastasis, distant metastasis, tumor-node-metastasis stage, status of microsatellite instability, and carcinoembryonic antigen levels. The overall survival of CRC patients with strong ARID3A expression was significantly longer than that of patients with weak or negative ARID3A expression. We also performed an additional survival analysis on 388 colon cancer patients and 302 rectal cancer patients. In doing so, a favorable prognostic effect of ARID3A expression was revealed only in the colon cancer group (p = 0.002), not in rectal cancer. Moreover, we showed that the effect of ARID3A on the survival was correlated with p53 status. Using multivariate analysis, we found that strong expression of ARID3A was an independent predictor for better prognosis in CRC. CONCLUSIONS Our data suggested that strong expression of ARID3A may predict a good prognosis in patients with CRC.
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Affiliation(s)
- Meiying Song
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
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5
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The herpes simplex virus immediate-early ubiquitin ligase ICP0 induces degradation of the ICP0 repressor protein E2FBP1. J Virol 2011; 85:3356-66. [PMID: 21248039 DOI: 10.1128/jvi.02105-10] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
E2FBP1/hDRIL1, a DNA-binding A/T-rich interaction domain (ARID) family transcription factor, is expressed ubiquitously in human tissues and plays an essential role in maintaining the proliferation potential of passage-limited human fibroblasts by dissociating promyelocytic leukemia nuclear bodies (PML-NBs). This effect on PML-NBs is similar to that of viral immediate-early gene products, such as infected cellular protein 0 (ICP0) from human herpes simplex virus 1 (HSV-1), which also disrupts PML-NBs to override the intrinsic cellular defense. Here we report that E2FBP1 inhibits accumulation of ICP0 RNA and, at the same time, is degraded via ICP0's herpes ubiquitin ligase 2 (HUL-2) activity upon HSV-1 infection. These reciprocal regulatory roles of ICP0 and E2FBP1 are linked in an ARID-dependent fashion. Our results suggest that E2FBP1 functions as an intrinsic cellular defense factor in spite of its PML-NB dissociation function.
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Prieur A, Nacerddine K, van Lohuizen M, Peeper DS. SUMOylation of DRIL1 directs its transcriptional activity towards leukocyte lineage-specific genes. PLoS One 2009; 4:e5542. [PMID: 19436740 PMCID: PMC2677661 DOI: 10.1371/journal.pone.0005542] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2009] [Accepted: 04/18/2009] [Indexed: 11/18/2022] Open
Abstract
DRIL1 is an ARID family transcription factor that can immortalize primary mouse fibroblasts, bypass RASV12-induced cellular senescence and collaborate with RASV12 or MYC in mediating oncogenic transformation. It also activates immunoglobulin heavy chain transcription and engages in heterodimer formation with E2F to stimulate E2F-dependent transcription. Little, however, is known about the regulation of DRIL1 activity. Recently, DRIL1 was found to interact with the SUMO-conjugating enzyme Ubc9, but the functional relevance of this association has not been assessed. Here, we show that DRIL1 is sumoylated both in vitro and in vivo at lysine 398. Moreover, we provide evidence that PIASy functions as a specific SUMO E3-ligase for DRIL1 and promotes its sumoylation both in vitro and in vivo. Furthermore, consistent with the subnuclear localization of PIASy in the Matrix-Associated Region (MAR), SUMO-modified DRIL1 species are found exclusively in the MAR fraction. This post-translational modification interferes neither with the subcellular localization nor the DNA-binding activity of the protein. In contrast, DRIL1 sumoylation impairs its interaction with E2F1 in vitro and modifies its transcriptional activity in vivo, driving transcription of subset of genes regulating leukocyte fate. Taken together, these results identify sumoylation as a novel post-translational modification of DRIL1 that represents an important mechanism for targeting and modulating DRIL1 transcriptional activity.
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Affiliation(s)
- Alexandre Prieur
- Department of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Karim Nacerddine
- Department of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Maarten van Lohuizen
- Department of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daniel S. Peeper
- Department of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- * E-mail:
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7
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Lin L, Zhou Z, Zheng L, Alber S, Watkins S, Ray P, Kaminski N, Zhang Y, Morse D. Cross talk between Id1 and its interactive protein Dril1 mediate fibroblast responses to transforming growth factor-beta in pulmonary fibrosis. THE AMERICAN JOURNAL OF PATHOLOGY 2008; 173:337-46. [PMID: 18583319 DOI: 10.2353/ajpath.2008.070915] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The presence of activated fibroblasts or myofibroblasts represents a hallmark of progressive lung fibrosis. Because the transcriptional response of fibroblasts to transforming growth factor-beta(1) (TGF-beta(1)) is a determinant of disease progression, we investigated the role of the transcriptional regulator inhibitor of differentiation-1 (Id1) in the setting of lung fibrosis. Mice lacking the gene for Id1 had increased susceptibility to bleomycin-induced lung fibrosis, and fibroblasts lacking Id1 exhibited enhanced responses to TGF-beta(1). Because the effect of Id1 on fibrosis could not be explained by known mechanisms, we performed protein interaction screening and identified a novel binding partner for Id1, known as dead ringer-like-1 (Dril1). Dril1 shares structural similarities with Id1 and was recently implicated in TGF-beta(1) signaling during embryogenesis. To date, little is known about the function of Dril1 in humans. Although it has not been previously implicated in fibrotic disease, we found that Dril1 was highly expressed in lungs from patients with idiopathic pulmonary fibrosis and was regulated by TGF-beta(1) in human fibroblasts. Dril1 enhanced activation of TGF-beta(1) target genes, whereas Id1 decreased expression of these same molecules. Id1 inhibited DNA binding by Dril1, and the two proteins co-localized in vitro and in vivo, providing a potential mechanism for suppression of fibrosis by Id1 through inhibition of the profibrotic function of Dril1.
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Affiliation(s)
- Ling Lin
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15217, USA
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8
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Zibara K, Garin G, McGregor JL. Identification, structural, and functional characterization of a new early gene (6A3-5, 7 kb): implication in the proliferation and differentiation of smooth muscle cells. J Biomed Biotechnol 2005; 2005:254-70. [PMID: 16192684 PMCID: PMC1224700 DOI: 10.1155/jbb.2005.254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Arterial smooth muscle cells (SMCs) play a major role in atherosclerosis and restenosis. Differential display was used to compare transcription profiles of synthetic SMCs to proliferating rat cultured SMC line. An isolated cDNA band (6A3-5) was shown by northern (7 kb) to be upregulated in the proliferating cell line. A rat tissue northern showed differential expression of this gene in different tissues. Using 5' RACE and screening of a rat brain library, part of the cDNA was cloned and sequenced (5.4 kb). Sequence searches showed important similarities with a new family of transcription factors, bearing ARID motifs. A polyclonal antibody was raised and showed a protein band of 175 kd, which is localized intracellularly. We also showed that 6A3-5 is upregulated in dedifferentiated SMC (P9) in comparison to contractile SMC ex vivo (P0). This work describes cloning, structural, and functional characterization of a new early gene involved in SMC phenotype modulation.
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Affiliation(s)
- Kazem Zibara
- INSERM XR331, Faculty of Medicine RTH Laënnec, 69372 Lyon, France
- *Kazem Zibara:
| | - Gwenaële Garin
- Genomics and Atherothrombosis Laboratory, Thrombosis Research Institute, London
SW3 6LR, UK
| | - John L. McGregor
- Center for Cardiovascular Biology and Medicine, King's College, University of London,
London WC2R 2LS, UK
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9
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Nixon JC, Rajaiya J, Webb CF. Mutations in the DNA-binding domain of the transcription factor Bright act as dominant negative proteins and interfere with immunoglobulin transactivation. J Biol Chem 2004; 279:52465-72. [PMID: 15456761 DOI: 10.1074/jbc.m403028200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Bright, for B cell regulator of immunoglobulin heavy chain transcription, binds A+T-rich sequences in the intronic enhancer regions of the murine heavy chain locus and 5'-flanking sequences of some variable heavy chain promoters. Most resting B cells do not express Bright; however, it is induced after stimulation with antigen or polyclonal mitogens. Bright activation results in up-regulation of mu transcription; however, it is not clear whether Bright function is critical for normal B cell development. To begin to address Bright function during B cell development, seven mutated forms of Bright were produced. Five of the seven mutants revealed little or no DNA binding activity. Furthermore, because Bright binds DNA as a dimer, two of the mutants formed complexes with wild type Bright and acted in a dominant negative fashion. Dominant negative Bright prevented the up-regulation of mu transcription in transfected Chinese hamster ovary cells transfected with wild type Bright. These data identify regions within Bright that are required for the DNA binding activity of Bright and for its function as a transcription factor.
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Affiliation(s)
- Jamee C Nixon
- Oklahoma Medical Research Foundation, 825 N. E. 13 Street, Oklahoma City, Oklahoma 73104, USA
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Fukuyo Y, Mogi K, Tsunematsu Y, Nakajima T. E2FBP1/hDril1 modulates cell growth through downregulation of promyelocytic leukemia bodies. Cell Death Differ 2004; 11:747-59. [PMID: 15017387 DOI: 10.1038/sj.cdd.4401412] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Promyelocytic leukemia nuclear bodies (PML-NBs) comprise multiple regulatory factors and play crucial roles in the maintenance of cellular integrity, while unregulated activation of PML-NBs induces death and premature senescence. Hence, the function of PML-NBs must be directed properly; however, the mechanism that regulates PML-NBs remains unclear. In this paper, we show that PML-NBs are disintegrated by an AT-rich interaction domain family protein E2FBP1/hDril1 through specific desumoylation of promyelocytic leukemia protein (PML) in vivo and in vitro. RNA interference-mediated downregulation of E2FBP1/hDril1 results in hyperplasis of PML-NBs and consequent commitment to PML-dependent premature senescence. Thus, the function of E2FBP1/hDril1 is required for maintenance of survival potential of the cells. Our data suggest a novel mechanism to govern cellular integrity through the modulation of nuclear depots.
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Affiliation(s)
- Y Fukuyo
- Department of Molecular Cellular Oncology and Microbiology, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
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11
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Nixon JC, Rajaiya JB, Ayers N, Evetts S, Webb CF. The transcription factor, Bright, is not expressed in all human B lymphocyte subpopulations. Cell Immunol 2004; 228:42-53. [PMID: 15203319 DOI: 10.1016/j.cellimm.2004.03.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2003] [Accepted: 03/21/2004] [Indexed: 01/23/2023]
Abstract
Bright is an ARID family transcription factor that increases immunoglobulin heavy chain transcription. In the mouse, Bright expression is tightly regulated and B cell-restricted and the Bright protein associates with Bruton's tyrosine kinase (Btk), the defective enzyme in X-linked immunodeficiency. Human X-linked agammaglobulinemia results from defects in Btk and leads to early blocks in B lymphocyte development. Because so little is known about human Bright, we sought to determine where human Bright is expressed in normal B cell differentiation and whether it also forms complexes with Btk. Although human and mouse Bright exhibited similar expression patterns in normal B cells, many human transformed B cell lines did not express Bright protein. However, the human protein bound prototypic Bright DNA-binding motifs and, like mouse Bright, was capable of associating with Btk. These data suggest potentially important similarities exist in Bright expression and activity in human and mouse B lymphocytes.
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Affiliation(s)
- Jamee C Nixon
- Department of Microbiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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12
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Amore G, Yavrouian RG, Peterson KJ, Ransick A, McClay DR, Davidson EH. Spdeadringer, a sea urchin embryo gene required separately in skeletogenic and oral ectoderm gene regulatory networks. Dev Biol 2003; 261:55-81. [PMID: 12941621 DOI: 10.1016/s0012-1606(03)00278-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Spdeadringer (Spdri) gene encodes an ARID-class transcription factor not previously known in sea urchin embryos. We show that Spdri is a key player in two separate developmental gene regulatory networks (GRNs). Spdri is expressed in a biphasic manner, first, after 12 h and until ingression in the skeletogenic descendants of the large micromeres; second, after about 20 h in the oral ectoderm, where its transcripts remain present at 30-50 mRNA molecules/cell far into development. In both territories, the periods of Spdri expression follow prior territorial specification events. The functional significance of each phase of expression was assessed by determining the effect of an alphaSpdri morpholino antisense oligonucleotide (MASO) on expression of 17 different mesodermal genes, 8 different oral ectoderm genes, and 18 other genes expressed specifically during endomesoderm specification. These effects were measured by quantitative PCR, supplemented by whole-mount in situ hybridization and morphological observations. Spdri is shown to act in the micromere descendants in the pathways that result in the expression of batteries of terminal skeletogenic genes. But, in the oral ectoderm, the same gene participates in the central GRN controlling oral ectoderm identity. Spdri is linked in the oral ectoderm GRN with several other genes encoding transcriptional regulators that are expressed specifically in various regions of the oral ectoderm. If its expression is blocked by treatment with alphaSpdri MASO, oral-specific features disappear and expression of the aboral ectoderm marker spec1 encompasses the whole of the ectoderm. In addition to disappearance of the oral ectoderm, morphological consequences of alphaSpdri MASO treatment include failure of spiculogenesis and of correct primary mesenchyme cell (pmc) patterning in the postgastrular embryo, and also failure of gastrulation. To further analyze these phenotypes, chimeric embryos were constructed consisting of two labeled micromeres combined with micromereless 4th cleavage host embryos; either the micromeres or the hosts contained alphaSpdri MASO. These experiments showed that, while Spdri expression is required autonomously for expression of skeletogenic genes prior to ingression, complete skeletogenesis also requires the expression of oral ectoderm patterning information. Presentation of this information on the oral side of the blastocoel in turn depends on Spdri expression in the oral ectoderm. Failure of gastrulation is not due to indirect interference with endomesodermal specification per se, since all endomesodermal genes tested function normally in alphaSpdri MASO embryos. Part of its cause is interference by alphaSpdri MASO with a late signaling function on the part of the micromere descendants that is needed to complete clearance of the Soxb1 repressor of gastrulation from the prospective endoderm, but in addition there is a nonautonomous oral ectoderm effect.
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Affiliation(s)
- Gabriele Amore
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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13
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Abstract
The Caenorhabditis elegans hermaphrodite nervous system is composed of 302 neurons that fall into at least 118 diverse classes. Here we describe cfi-1, a gene that contributes to the development of neuronal diversity. cfi-1 promotes appropriate differentiation of the URA sensory neurons and inhibits URA from expressing the male-specific CEM neuronal fate. The UNC-86 POU homeodomain protein is present in CEM and URA neurons, and can promote expression of CEM-specific genes in both CEM and URA, but CFI-1 inhibits expression of these genes in the URA cells. cfi-1 also promotes appropriate differentiation and glutamate receptor expression in the AVD and PVC interneurons. cfi-1 encodes a conserved neuron- and muscle-restricted DNA-binding protein containing an A/T rich interaction domain (ARID). ARID proteins regulate early patterning and muscle fate in Drosophila, but they have not previously been implicated in the control of neuronal subtype identity.
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Affiliation(s)
- Shai Shaham
- Department of Anatomy and Department of Biochemistry and Biophysics, The University of California, San Francisco, San Francisco, California 94143, USA.
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14
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Iwahara J, Iwahara M, Daughdrill GW, Ford J, Clubb RT. The structure of the Dead ringer-DNA complex reveals how AT-rich interaction domains (ARIDs) recognize DNA. EMBO J 2002; 21:1197-209. [PMID: 11867548 PMCID: PMC125891 DOI: 10.1093/emboj/21.5.1197] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The AT-rich interaction domain (ARID) is a DNA-binding module found in many eukaryotic transcription factors. Using NMR spectroscopy, we have determined the first ever three-dimensional structure of an ARID--DNA complex (mol. wt 25.7 kDa) formed by Dead ringer from Drosophila melanogaster. ARIDs recognize DNA through a novel mechanism involving major groove immobilization of a large loop that connects the helices of a non-canonical helix-turn-helix motif, and through a concomitant structural rearrangement that produces stabilizing contacts from a beta-hairpin. Dead ringer's preference for AT-rich DNA originates from three positions within the ARID fold that form energetically significant contacts to an adenine-thymine base step. Amino acids that dictate binding specificity are not highly conserved, suggesting that ARIDs will bind to a range of nucleotide sequences. Extended ARIDs, found in several sequence-specific transcription factors, are distinguished by the presence of a C-terminal helix that may increase their intrinsic affinity for DNA. The prevalence of serine amino acids at all specificity determining positions suggests that ARIDs within SWI/SNF-related complexes will interact with DNA non-sequence specifically.
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Affiliation(s)
- Junji Iwahara
- Department of Chemistry and Biochemistry, UCLA-DOE Laboratory of Structural Biology and Molecular Medicine and the Molecular Biology Institute, University of California, Los Angeles, 405 Hilgard Avenue, Los Angeles, CA 90095-1570, USA
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15
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Abstract
Bright, or B cell regulator of immunoglobulin heavy chain transcription, is a B lymphocyte-specific protein first discovered for its ability to increase immunoglobulin transcription three- to sevenfold in antigen-activated B cells. It interacts with DNA through an ARID, or A/T-rich interaction domain, and is the only member of a previously undescribed family of DNA-binding proteins for which target genes have been identified. The mechanism(s) by which Bright facilitates transcription are unknown. Several proteins that associate with Bright may shed light upon its function. These include the nuclear matrix proteins sp100 and LYSp100B, and suggest that Bright may affect chromatin configuration and nuclear sublocalization. Furthermore, Bruton's tyrosine kinase is required for Bright binding activity, suggesting links between Bright, cell signaling cascades, and X-linked immunodeficiency disease.
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Affiliation(s)
- C F Webb
- Immunobiology and Cancer Program, Oklahoma Medical Research Foundation, Oklahoma City 73104, USA.
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Peeper DS, Shvarts A, Brummelkamp T, Douma S, Koh EY, Daley GQ, Bernards R. A functional screen identifies hDRIL1 as an oncogene that rescues RAS-induced senescence. Nat Cell Biol 2002; 4:148-53. [PMID: 11812999 DOI: 10.1038/ncb742] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Primary fibroblasts respond to activated H-RAS(V12) by undergoing premature arrest, which resembles replicative senescence. This irreversible 'fail-safe mechanism' requires p19(ARF), p53 and the Retinoblastoma (Rb) family: upon their disruption, RAS(V12)-expressing cells fail to undergo senescence and continue to proliferate. Similarly, co-expression of oncogenes such as c-MYC or E1A rescues RAS(V12)-induced senescence. To identify novel genes that allow escape from RAS(V12)-induced senescence, we designed an unbiased, retroviral complementary DNA library screen. We report on the identification of DRIL1, the human orthologue of the mouse Bright and Drosophila dead ringer transcriptional regulators. DRIL1 renders primary murine fibroblasts unresponsive to RAS(V12)-induced anti-proliferative signalling by p19(ARF)/p53/p21(CIP1), as well as by p16(INK4a). In this way, DRIL1 not only rescues RAS(V12)-induced senescence but also causes these fibroblasts to become highly oncogenic. Furthermore, DRIL1 immortalizes mouse fibroblasts, in the presence of high levels of p16(INK4a). Immortalization by DRIL1, whose product binds the pRB-controlled transcription factor E2F1 (ref. 8), is correlated with induction of E2F1 activity. Correspondingly, DRIL1 induces the E2F1 target Cyclin E1, overexpression of which is sufficient to trigger escape from senescence. Thus, DRIL1 disrupts cellular protection against RAS(V12)-induced proliferation downstream of the p19(ARF)/p53 pathway.
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Affiliation(s)
- Daniel S Peeper
- Division of Molecular Carcinogenesis and Center for Biomedical Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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Hoffman HM, Bastian JF, Bird LM. Humoral immunodeficiency with facial dysmorphology and limb anomalies: a new syndrome. Clin Dysmorphol 2001; 10:1-8. [PMID: 11152140 DOI: 10.1097/00019605-200101000-00001] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We report a 6 year old girl with an isolated humoral immune deficiency and a unique combination of dysmorphic features. Physical findings include microcephaly, micrognathia, sickle shaped eyebrows, hypoplastic alae nasi, thenar hypoplasia, partial 4-5 syndactyly of toes, recessed great toes, anterior anus, and hypoplastic labia minora. Radiographic findings include triphalangeal thumbs and hypoplastic first metatarsals. She has postnatal growth retardation and her development is substantially slower than her twin's. Her clinical course has been complicated by recurrent sinopulmonary infections and pneumococcal bacteraemia. Laboratory evaluation revealed hypogammaglobulinaemia, absent B cells, and a 46,XX karyotype. A review of the literature and the London Dysmorphology Database did not produce any recognizable syndromes that match her constellation of findings. She may represent a unique syndrome of unknown etiology.
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Affiliation(s)
- H M Hoffman
- Division of Rheumatology, Allergy and Immunology, University of California at San Diego, 92093-0635, USA.
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Abstract
Members of the recently discovered ARID (AT-rich interaction domain) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure.
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Affiliation(s)
- R D Kortschak
- Centre for Molecular Genetics of Development and Dept of Genetics, University of Adelaide, Adelaide, SA 5005, Australia
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Dallas PB, Pacchione S, Wilsker D, Bowrin V, Kobayashi R, Moran E. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. Mol Cell Biol 2000; 20:3137-46. [PMID: 10757798 PMCID: PMC85608 DOI: 10.1128/mcb.20.9.3137-3146.2000] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2000] [Accepted: 02/03/2000] [Indexed: 01/19/2023] Open
Abstract
p270 is an integral member of human SWI-SNF complexes, first identified through its shared antigenic specificity with p300 and CREB binding protein. The deduced amino acid sequence of p270 reported here indicates that it is a member of an evolutionarily conserved family of proteins distinguished by the presence of a DNA binding motif termed ARID (AT-rich interactive domain). The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions.
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Affiliation(s)
- P B Dallas
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140, USA
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Shandala T, Kortschak RD, Gregory S, Saint R. The Drosophila dead ringer gene is required for early embryonic patterning through regulation of argos and buttonhead expression. Development 1999; 126:4341-9. [PMID: 10477301 DOI: 10.1242/dev.126.19.4341] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The dead ringer (dri) gene of Drosophila melanogaster is a member of the recently discovered ARID-box family of eukaryotic genes that encode proteins with a conserved DNA binding domain. dri itself is highly conserved, with specific orthologs in the human, mouse, zebrafish and C. elegans genomes. We have generated dri mutant alleles to show that dri is essential for anterior-posterior patterning and for muscle development in the embryo. Consistent with the mutant phenotype and the sequence-specific DNA-binding properties of its product, dri was found to be essential for the normal early embryonic expression pattern of several key regulatory genes. In dri mutant embryos, expression of argos in the terminal domains was severely reduced, accounting for the dri mutant head phenotype. Conversely, buttonhead expression was found to be deregulated in the trunk region, accounting for the appearance of ectopic cephalic furrows. Curiously, dri was found also to be required for maintenance of expression of the ventrolateral region of even-skipped stripe four. This study establishes dri as an essential co-factor in the regulated expression of specific patterning genes during early embryogenesis.
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Affiliation(s)
- T Shandala
- Department of Genetics, The University of Adelaide, Adelaide SA 5005, Australia
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