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Yang T, Mahmood N, Goldberg B, Cevallos J, Hsu P, Kolitz J, Cohen N, Zhang X. Myeloid/lymphoid neoplasm with a novel cryptic RBPMS::FGFR1 rearrangement presenting as de novo acute leukemias. Leuk Lymphoma 2023; 64:2338-2342. [PMID: 37791611 DOI: 10.1080/10428194.2023.2262640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/19/2023] [Indexed: 10/05/2023]
Affiliation(s)
- Tianyu Yang
- Northwell Health, Greenvale, NY, USA
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Greenvale, NY, USA
| | - Nayyara Mahmood
- Northwell Health, Greenvale, NY, USA
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Greenvale, NY, USA
| | - Bradley Goldberg
- Northwell Health, Greenvale, NY, USA
- Zuckerberg Cancer Center, Department of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Greenvale, NY, USA
| | - Johnny Cevallos
- Northwell Health, Greenvale, NY, USA
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Greenvale, NY, USA
| | - Peihong Hsu
- Northwell Health, Greenvale, NY, USA
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Greenvale, NY, USA
| | - Jonathan Kolitz
- Northwell Health, Greenvale, NY, USA
- Zuckerberg Cancer Center, Department of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Greenvale, NY, USA
| | - Ninette Cohen
- Northwell Health, Greenvale, NY, USA
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Greenvale, NY, USA
| | - Xinmin Zhang
- Northwell Health, Greenvale, NY, USA
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Greenvale, NY, USA
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2
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Gadwal A, Purohit P, Khokhar M, Vishnoi JR, Pareek P, Choudhary R, Elhence P, Banerjee M, Sharma P. In silico analysis of differentially expressed-aberrantly methylated genes in breast cancer for prognostic and therapeutic targets. Clin Exp Med 2023; 23:3847-3866. [PMID: 37029310 DOI: 10.1007/s10238-023-01060-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/28/2023] [Indexed: 04/09/2023]
Abstract
Breast cancer (BC) is the leading cause of death among women across the globe. Abnormal gene expression plays a crucial role in tumour progression, carcinogenesis and metastasis of BC. The alteration of gene expression may be through aberrant gene methylation. In the present study, differentially expressed genes which may be regulated by DNA methylation and their pathways associated with BC have been identified. Expression microarray datasets GSE10780, GSE10797, GSE21422, GSE42568, GSE61304, GSE61724 and one DNA methylation profile dataset GSE20713 were downloaded from Gene Expression Omnibus database (GEO). Differentially expressed-aberrantly methylated genes were identified using online Venn diagram tool. Based on fold change expression of differentially expressed-aberrantly methylated genes were chosen through heat map. Protein-protein interaction (PPI) network of the hub genes was constructed by Search Tool for the Retrieval of Interacting Genes (STRING). Gene expression and DNA methylation level of the hub genes were validated through UALCAN. Overall survival analysis of the hub genes was analysed through Kaplan-Meier plotter database for BC. A total of 72 upregulated-hypomethylated genes and 92 downregulated-hypermethylated genes were obtained from GSE10780, GSE10797, GSE21422, GSE42568, GSE61304, GSE61724, and GSE20713 datasets by GEO2R and Venn diagram tool. PPI network of the upregulated-hypomethylated hub genes (MRGBP, MANF, ARF3, HIST1H3D, GSK3B, HJURP, GPSM2, MATN3, KDELR2, CEP55, GSPT1, COL11A1, and COL1A1) and downregulated-hypermethylated hub genes were constructed (APOD, DMD, RBPMS, NR3C2, HOXA9, AMKY2, KCTD9, and EDN1). All the differentially expressed hub genes expression was validated in UALCAN database. 4 in 13 upregulated-hypomethylated and 5 in 8 downregulated-hypermethylated hub genes to be significantly hypomethylated or hypermethylated in BC were confirmed using UALCAN database (p < 0.05). MANF, HIST1H3D, HJURP, GSK3B, GPSM2, MATN3, KDELR2, CEP55, COL1A1, APOD, RBPMS, NR3C2, HOXA9, ANKMY2, and EDN1 were significantly (p < 0.05) associated with poor overall survival (OS). The identified aberrantly methylated-differentially expressed genes and their related pathways and function in BC can serve as novel diagnostic and prognostic biomarkers and therapeutic targets.Please confirm if the author names are presented accurately and in the correct sequence (given name, middle name/initial, family name). Author 4 Given name: [Jeewan Ram] Last name [Vishnoi]. Also, kindly confirm the details in the metadata are correct.It is correct.
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Affiliation(s)
- Ashita Gadwal
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Basni Industrial Area, MIA 2nd Phase, Basni, Jodhpur, Rajasthan, 342005, India
| | - Purvi Purohit
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Basni Industrial Area, MIA 2nd Phase, Basni, Jodhpur, Rajasthan, 342005, India.
| | - Manoj Khokhar
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Basni Industrial Area, MIA 2nd Phase, Basni, Jodhpur, Rajasthan, 342005, India
| | - Jeewan Ram Vishnoi
- Department of Oncosurgery, All India Institute of Medical Sciences, Jodhpur, Basni Industrial Area, MIA 2nd Phase, Basni, Jodhpur, Rajasthan, 342005, India
| | - Puneet Pareek
- Department of Radiation Oncology, All India Institute of Medical Sciences, Jodhpur, Basni Industrial Area, MIA 2nd Phase, Basni, Jodhpur, Rajasthan, 342005, India
| | - Ramkaran Choudhary
- Department of General Surgery, All India Institute of Medical Sciences, Jodhpur, Basni Industrial Area, MIA 2nd Phase, Basni, Jodhpur, Rajasthan, 342005, India
| | - Poonam Elhence
- Department of Pathology, All India Institute of Medical Sciences, Jodhpur, Basni Industrial Area, MIA 2nd Phase, Basni, Jodhpur, Rajasthan, 342005, India
| | - Mithu Banerjee
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Basni Industrial Area, MIA 2nd Phase, Basni, Jodhpur, Rajasthan, 342005, India
| | - Praveen Sharma
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Basni Industrial Area, MIA 2nd Phase, Basni, Jodhpur, Rajasthan, 342005, India
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3
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Holman AR, Chi NC. Fishing Out the Role of RBPMS2 in Cardiac Splicing. Circ Res 2022; 131:1001-1003. [PMID: 36454855 DOI: 10.1161/circresaha.122.321922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Affiliation(s)
- Alyssa R Holman
- Department of Medicine (A.R.H., N.C.C.).,Biomedical Sciences Graduate Program (A.R.H.), University of California, San Diego, La Jolla, CA
| | - Neil C Chi
- Department of Medicine (A.R.H., N.C.C.).,Institute of Genomic Medicine, School of Medicine (N.C.C.), University of California, San Diego, La Jolla, CA
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4
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Increased Expression of the RBPMS Splice Variants Inhibits Cell Proliferation in Ovarian Cancer Cells. Int J Mol Sci 2022; 23:ijms232314742. [PMID: 36499073 PMCID: PMC9738375 DOI: 10.3390/ijms232314742] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
RNA-Binding Protein with Multiple Splicing (RBPMS) is a member of family proteins that bind to nascent RNA transcripts and regulate their splicing, localization, and stability. Evidence indicates that RBPMS controls the activity of transcription factors associated with cell growth and proliferation, including AP-1 and Smads. Three major RBPMS protein splice variants (RBPMSA, RBPMSB, and RBPMSC) have been described in the literature. We previously reported that reduced RBPMS levels decreased the sensitivity of ovarian cancer cells to cisplatin treatment. However, little is known about the biological role of the RBPMS splice variants in ovarian cancer cells. We performed RT-PCR and Western blots and observed that both RBPMSA and RBPMSC are reduced at the mRNA and protein levels in cisplatin resistant as compared with cisplatin sensitive ovarian cancer cells. The mRNA and protein levels of RBPMSB were not detectable in any of the ovarian cancer cells tested. To better understand the biological role of each RBPMSA and RBPMSC, we transfected these two splice variants in the A2780CP20 and OVCAR3CIS cisplatin resistant ovarian cancer cells and performed cell proliferation, cell migration, and invasion assays. Compared with control clones, a significant reduction in the number of colonies, colony size, cell migration, and invasion was observed with RBPMSA and RBPMSC overexpressed cells. Moreover, A2780CP20-RBPMSA and A2780CP20-RBPMSC clones showed reduced senescence-associated β-galactosidase (β-Gal)-levels when compared with control clones. A2780CP20-RBPMSA clones were more sensitive to cisplatin treatment as compared with A2780CP20-RBPMSC clones. The A2780CP20-RBPMSA and A2780CP20-RBPMSC clones subcutaneously injected into athymic nude mice formed smaller tumors as compared with A2780CP20-EV control group. Additionally, immunohistochemical analysis showed lower proliferation (Ki67) and angiogenesis (CD31) staining in tissue sections of A2780CP20-RBPMSA and A2780CP20-RBPMSC tumors compared with controls. RNAseq studies revealed many common RNA transcripts altered in A2780CP20-RBPMSA and A2780CP20-RBPMSC clones. Unique RNA transcripts deregulated by each RBPMS variant were also observed. Kaplan-Meier (KM) plotter database information identified clinically relevant RBPMSA and RBPMSC downstream effectors. These studies suggest that increased levels of RBPMSA and RBPMSC reduce cell proliferation in ovarian cancer cells. However, only RBPMSA expression levels were associated with the sensitivity of ovarian cancer cells to cisplatin treatment.
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Che Q, Liu M, Zhang D, Lu Y, Xu J, Lu X, Cao X, Liu Y, Dong X, Liu S. Long Noncoding RNA HUPCOS Promotes Follicular Fluid Androgen Excess in PCOS Patients via Aromatase Inhibition. J Clin Endocrinol Metab 2020; 105:5722239. [PMID: 32016412 DOI: 10.1210/clinem/dgaa060] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 02/03/2020] [Indexed: 12/11/2022]
Abstract
CONTEXT Androgen excess is a key feature of polycystic ovary syndrome (PCOS), but the underlying molecular mechanism remains unclear. OBJECTIVE To determine the role and mechanism of novel long noncoding RNA (lncRNA) highly up-regulated in PCOS (HUPCOS) in the androgen excess of PCOS patients. DESIGN The lncRNA expression profile in granulosa cells derived from PCOS and non-PCOS women were analyzed by using microarray assay. Human granulosa cell line KGN was used for mechanism investigation. SETTING This was a university-based study. PATIENTS Thirty-eight PCOS and 38 control patients were recruited: 8 PCOS and 8 control samples used for microarray discovery, the remaining 30 PCOS cases and 30 controls for quantitative RT-PCR validation. MAIN OUTCOME MEASURES The aberrant expression lncRNA profile of PCOS patients was measured using microarray. The relationship of HUPCOS and follicular fluid testosterone was measured. Aromatase expression were analyzed after HUPCOS downregulation. HUPCOS interaction protein was confirmed by RNA pull-down. RESULTS The significantly elevated lncRNA in PCOS granulosa cells was named HUPCOS, which was positively correlated with follicular fluid testosterone of PCOS patients. HUPCOS downregulation increased aromatase expression and promoted conversion of androgen to estrogen. RNA-binding protein with multiple splicing (RBPMS) was the most likely protein that combined with HUPCOS. CONCLUSIONS Our findings suggested that HUPCOS mediated androgen excess in follicular fluid of PCOS patients by suppressing aromatase expression via interaction with RBPMS.
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Affiliation(s)
- Qi Che
- Reproductive Medicine Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Miao Liu
- Reproductive Medicine Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Doudou Zhang
- Reproductive Medicine Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yongning Lu
- Reproductive Medicine Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jun Xu
- Reproductive Medicine Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xinmei Lu
- Reproductive Medicine Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiang Cao
- Reproductive Medicine Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yang Liu
- Reproductive Medicine Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xi Dong
- Reproductive Medicine Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Suying Liu
- Reproductive Medicine Center, Zhongshan Hospital, Fudan University, Shanghai, China
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Akerberg AA, Burns CE, Burns CG. Exploring the Activities of RBPMS Proteins in Myocardial Biology. Pediatr Cardiol 2019; 40:1410-1418. [PMID: 31399780 PMCID: PMC6786954 DOI: 10.1007/s00246-019-02180-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 07/31/2019] [Indexed: 12/22/2022]
Abstract
Numerous RNA-binding proteins (RBPs) are expressed in the heart, and mutations in several RBPs have been implicated in cardiovascular disease through genetic associations, animal modeling, and mechanistic studies. However, the functions of many more cardiac RBPs, and their relevance to disease states, remain to be elucidated. Recently, we have initiated studies to characterize the functions of the RBPs RBPMS and RBPMS2 in regulating myocardial biology in zebrafish and higher vertebrate species. These studies began when we learned, using an unbiased gene discovery approach, that rbpms2a and rbpms2b in zebrafish are robust markers of embryonic myocardium. This observation, which is consistent with published data, suggests that the encoded proteins are likely to be performing critical functions in regulating one or more aspects of cardiomyocyte differentiation, proliferation, survival, and/or contractility. This notion is supported by recent reports demonstrating that zebrafish embryos with disrupted Rbpms2 function exhibit gross signs of cardiac distress. Interestingly, a 20-year-old study determined that myocardial tissue from the frog, chick, and mouse also express high levels of Rbpms and/or Rbpms2, which is suggestive of evolutionary conservation of function. In this review, we will provide a historical account of how RBPMS and RBPMS2 genes were discovered, attempt to clarify some potentially confusing nomenclature, and summarize published observations that inform our ongoing studies.
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Affiliation(s)
- Alexander A Akerberg
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA,Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129,Harvard Medical School, Boston, MA 02115
| | - Caroline E. Burns
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA,Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129,Harvard Medical School, Boston, MA 02115,Harvard Stem Cell Institute, Cambridge, MA 02138,Authors for Correspondence: ()
| | - C. Geoffrey Burns
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA,Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129,Harvard Medical School, Boston, MA 02115,Authors for Correspondence: ()
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7
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Nakagaki-Silva EE, Gooding C, Llorian M, Jacob AG, Richards F, Buckroyd A, Sinha S, Smith CW. Identification of RBPMS as a mammalian smooth muscle master splicing regulator via proximity of its gene with super-enhancers. eLife 2019; 8:46327. [PMID: 31283468 PMCID: PMC6613909 DOI: 10.7554/elife.46327] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/12/2019] [Indexed: 01/08/2023] Open
Abstract
Alternative splicing (AS) programs are primarily controlled by regulatory RNA-binding proteins (RBPs). It has been proposed that a small number of master splicing regulators might control cell-specific splicing networks and that these RBPs could be identified by proximity of their genes to transcriptional super-enhancers. Using this approach we identified RBPMS as a critical splicing regulator in differentiated vascular smooth muscle cells (SMCs). RBPMS is highly down-regulated during phenotypic switching of SMCs from a contractile to a motile and proliferative phenotype and is responsible for 20% of the AS changes during this transition. RBPMS directly regulates AS of numerous components of the actin cytoskeleton and focal adhesion machineries whose activity is critical for SMC function in both phenotypes. RBPMS also regulates splicing of other splicing, post-transcriptional and transcription regulators including the key SMC transcription factor Myocardin, thereby matching many of the criteria of a master regulator of AS in SMCs.
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Affiliation(s)
| | - Clare Gooding
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Miriam Llorian
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.,Francis Crick Institute, London, United Kingdom
| | - Aishwarya G Jacob
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.,Anne McLaren Laboratory, Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Frederick Richards
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Adrian Buckroyd
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Sanjay Sinha
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.,Anne McLaren Laboratory, Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
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8
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Torre M, Jessop N, Hornick JL, Alexandrescu S. Expanding the spectrum of pediatric NTRK-rearranged fibroblastic tumors to the central nervous system: A case report with RBPMS-NTRK3 fusion. Neuropathology 2018; 38:624-630. [PMID: 30187580 DOI: 10.1111/neup.12513] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/05/2018] [Accepted: 08/05/2018] [Indexed: 01/20/2023]
Abstract
We report a case of a 20-month-old male presenting with seizures who was found to have a hyperintense lesion on T2-weighted images of magnetic resonance imaging in the left medial temporal lobe that was initially clinically and radiologically thought to be either low-grade glioma or focal cortical dysplasia. Histologic, immunohistochemical and molecular evaluation (array comparative genomic hybridization, Archer fusion panel) of the resection specimen demonstrated a highly infiltrative fibroblastic spindle cell neoplasm with mild nuclear atypia and an RBPMS-NTRK3 fusion. NTRK-fused mesenchymal tumors are known to involve extracranial sites but, to our knowledge, have not been described within the central nervous system. Accurate and timely diagnosis of this entity has important prognostic and therapeutic implications, as NTRK-fused tumors may recur locally and may respond to selective kinase inhibitor therapies.
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Affiliation(s)
- Matthew Torre
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Nicholas Jessop
- Massachusetts General Hospital Center for Integrated Diagnostics and Harvard Medical School, Boston, Massachusetts, USA
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Sanda Alexandrescu
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
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9
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Ye L, Gu L, Caprioli J, Piri N. RNA-binding protein Rbpms is represented in human retinas by isoforms A and C and its transcriptional regulation involves Sp1-binding site. Mol Genet Genomics 2018; 293:819-830. [PMID: 29423656 PMCID: PMC6033630 DOI: 10.1007/s00438-018-1423-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/03/2018] [Indexed: 11/26/2022]
Abstract
Rbpms (RNA-binding protein with multiple splicing) is a member of the RRM (RNA Recognition Motif) family of RNA-binding proteins, which is expressed as multiple alternatively spliced transcripts encoding different protein isoforms. We have shown earlier that Rbpms expression in the retina is restricted to retinal ganglion cells (RGCs), and have characterized this gene as a marker for RGCs. The aim of this study was to identify isoforms representing Rbpms in human retinas and to analyze its transcriptional regulation. We found that Rbpms is expressed as transcription variants 1 and 3 encoding isoforms A and C, respectively. These isoforms are encoded by the same first 6 exons but have different C-terminal ends encoded by exon 8 in variant 1 and exon 7 in variant 3. Computational analysis of the Rbpms 5' untranslated and flanking regions reveals the presence of three CpG islands and four predicted promoter regions (PPRs). The effect of PPR 1 (- 1672/- 1420) and PPR2 (- 330/- 79) on transcriptional activation was minimal, whereas PPR 3 (- 73/+ 177) and PPR4 (+ 274/+ 524) induced the expression by ~ 7 and ninefold compared to control, respectively. The maximum activity, a 30-fold increase above the control level, was obtained from the construct containing both PPRs 3 and 4. Site-directed mutagenesis of several cis-elements within PPR3 and PPR4 including five for Sp1, one for AP1, and two for NF-kB showed that mutation of the first three and especially the first GC box resulted in a threefold downregulation of gene expression. AP1, NF-kB, and two downstream Sp1 sites had no significant effect on expression level. The possible involvement of the GC box 1 at position - 54 in transcriptional regulation of Rbpms was corroborated by EMSA, which showed formation of a DNA-protein complex in the presence of the oligonucleotide corresponding to this Sp1-binding site.
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Affiliation(s)
- Linda Ye
- Jules Stein Eye Institute, UCLA School of Medicine, 100 Stein Plaza, Los Angeles, CA, 90095, USA
| | - Lei Gu
- Jules Stein Eye Institute, UCLA School of Medicine, 100 Stein Plaza, Los Angeles, CA, 90095, USA
| | - Joseph Caprioli
- Jules Stein Eye Institute, UCLA School of Medicine, 100 Stein Plaza, Los Angeles, CA, 90095, USA
- Brain Research Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Natik Piri
- Jules Stein Eye Institute, UCLA School of Medicine, 100 Stein Plaza, Los Angeles, CA, 90095, USA.
- Brain Research Institute, University of California Los Angeles, Los Angeles, CA, USA.
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10
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Soufari H, Mackereth CD. Conserved binding of GCAC motifs by MEC-8, couch potato, and the RBPMS protein family. RNA (NEW YORK, N.Y.) 2017; 23:308-316. [PMID: 28003515 PMCID: PMC5311487 DOI: 10.1261/rna.059733.116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/19/2016] [Indexed: 05/16/2023]
Abstract
Precise regulation of mRNA processing, translation, localization, and stability relies on specific interactions with RNA-binding proteins whose biological function and target preference are dictated by their preferred RNA motifs. The RBPMS family of RNA-binding proteins is defined by a conserved RNA recognition motif (RRM) domain found in metazoan RBPMS/Hermes and RBPMS2, Drosophila couch potato, and MEC-8 from Caenorhabditis elegans In order to determine the parameters of RNA sequence recognition by the RBPMS family, we have first used the N-terminal domain from MEC-8 in binding assays and have demonstrated a preference for two GCAC motifs optimally separated by >6 nucleotides (nt). We have also determined the crystal structure of the dimeric N-terminal RRM domain from MEC-8 in the unbound form, and in complex with an oligonucleotide harboring two copies of the optimal GCAC motif. The atomic details reveal the molecular network that provides specificity to all four bases in the motif, including multiple hydrogen bonds to the initial guanine. Further studies with human RBPMS, as well as Drosophila couch potato, confirm a general preference for this double GCAC motif by other members of the protein family and the presence of this motif in known targets.
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Affiliation(s)
- Heddy Soufari
- University of Bordeaux, Institut Européen de Chimie et Biologie, F-33607 Pessac, France
- Inserm U1212, CNRS UMR 5320, ARNA Laboratory, F-33076 Bordeaux, France
| | - Cameron D Mackereth
- University of Bordeaux, Institut Européen de Chimie et Biologie, F-33607 Pessac, France
- Inserm U1212, CNRS UMR 5320, ARNA Laboratory, F-33076 Bordeaux, France
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11
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van Rooij FJ, Qayyum R, Smith AV, Zhou Y, Trompet S, Tanaka T, Keller MF, Chang LC, Schmidt H, Yang ML, Chen MH, Hayes J, Johnson AD, Yanek LR, Mueller C, Lange L, Floyd JS, Ghanbari M, Zonderman AB, Jukema JW, Hofman A, van Duijn CM, Desch KC, Saba Y, Ozel AB, Snively BM, Wu JY, Schmidt R, Fornage M, Klein RJ, Fox CS, Matsuda K, Kamatani N, Wild PS, Stott DJ, Ford I, Slagboom PE, Yang J, Chu AY, Lambert AJ, Uitterlinden AG, Franco OH, Hofer E, Ginsburg D, Hu B, Keating B, Schick UM, Brody JA, Li JZ, Chen Z, Zeller T, Guralnik JM, Chasman DI, Peters LL, Kubo M, Becker DM, Li J, Eiriksdottir G, Rotter JI, Levy D, Grossmann V, Patel KV, Chen CH, Ridker PM, Tang H, Launer LJ, Rice KM, Li-Gao R, Ferrucci L, Evans MK, Choudhuri A, Trompouki E, Abraham BJ, Yang S, Takahashi A, Kamatani Y, Kooperberg C, Harris TB, Jee SH, Coresh J, Tsai FJ, Longo DL, Chen YT, Felix JF, Yang Q, Psaty BM, Boerwinkle E, Becker LC, Mook-Kanamori DO, Wilson JG, Gudnason V, O'Donnell CJ, Dehghan A, Cupples LA, Nalls MA, Morris AP, Okada Y, Reiner AP, Zon LI, Ganesh SK, Ganesh SK. Genome-wide Trans-ethnic Meta-analysis Identifies Seven Genetic Loci Influencing Erythrocyte Traits and a Role for RBPMS in Erythropoiesis. Am J Hum Genet 2017; 100:51-63. [PMID: 28017375 DOI: 10.1016/j.ajhg.2016.11.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 11/16/2016] [Indexed: 11/26/2022] Open
Abstract
Genome-wide association studies (GWASs) have identified loci for erythrocyte traits in primarily European ancestry populations. We conducted GWAS meta-analyses of six erythrocyte traits in 71,638 individuals from European, East Asian, and African ancestries using a Bayesian approach to account for heterogeneity in allelic effects and variation in the structure of linkage disequilibrium between ethnicities. We identified seven loci for erythrocyte traits including a locus (RBPMS/GTF2E2) associated with mean corpuscular hemoglobin and mean corpuscular volume. Statistical fine-mapping at this locus pointed to RBPMS at this locus and excluded nearby GTF2E2. Using zebrafish morpholino to evaluate loss of function, we observed a strong in vivo erythropoietic effect for RBPMS but not for GTF2E2, supporting the statistical fine-mapping at this locus and demonstrating that RBPMS is a regulator of erythropoiesis. Our findings show the utility of trans-ethnic GWASs for discovery and characterization of genetic loci influencing hematologic traits.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Santhi K Ganesh
- Division of Cardiovascular Medicine, Department of Internal Medicine, Department of Human Genetics, University of Michigan, 1500 E. Medical Center Drive, Ann Arbor, MI 48109, USA.
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Shanmugaapriya S, van Caam A, de Kroon L, Vitters EL, Walgreen B, van Beuningen H, Davidson EB, van der Kraan PM. Expression of TGF-β Signaling Regulator RBPMS (RNA-Binding Protein With Multiple Splicing) Is Regulated by IL-1β and TGF-β Superfamily Members, and Decreased in Aged and Osteoarthritic Cartilage. Cartilage 2016; 7:333-45. [PMID: 27688842 PMCID: PMC5029562 DOI: 10.1177/1947603515623991] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVE RNA-binding protein with multiple splicing (RBPMS) has been shown to physically interact with Smads and enhance transforming growth factor-β (TGF-β)-mediated Smad2/3 transcriptional activity in mammalian cells. Objective of this study was to examine whether expression of RBPMS is regulated by interleukin-1β (IL)-1β and TGF-β superfamily growth factors and whether expression of RBPMS is altered during aging and experimental osteoarthritis. METHODS Expression of RBPMS protein was investigated in chondrocyte cell lines of murine (H4) and human (G6) origin using Western blot analysis. Regulation of RBPMS expression in H4 chondrocytes at mRNA level was done by reverse transcriptase-quantitative polymerase chain reaction. Furthermore, characterization of Smad signaling pathways regulating RBPMS expression was performed by blocking studies using small molecule inhibitors or by transfection studies with adenoviral vector constructs (constitutive-active ALK1 and constitutive-active ALK5). Expression of RBPMS in cartilage of different age groups of C57BL/6N mice (6 months and 20 months) and in a surgically induced osteoarthritis (OA) mouse model was analyzed using immunohistochemistry. RESULTS RBPMS was shown to be expressed in chondrocytes and cartilage of murine, human, and bovine origin. TGF-β inhibited RBPMS expression while BMP2 and IL-1β increased its expression. TGF-β-induced inhibition was blocked by ALK5 inhibitor. Overexpression of ca-ALK1 stimulated RBPMS expression. Moreover, RBPMS expression was found to be reduced with ageing and in OA pathogenesis. CONCLUSIONS Expression of RBPMS in chondrocytes is regulated by TGF-β superfamily members and IL-1β, indicating a counter-regulatory mechanism. Expression of RBPMS, in cartilage and its reduction during ageing and OA might suggest its potential role in the maintenance of normal articular cartilage.
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Affiliation(s)
- S. Shanmugaapriya
- Department of Biomedical Science, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - A. van Caam
- Experimental Rheumatology, Department of Rheumatology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - L. de Kroon
- Experimental Rheumatology, Department of Rheumatology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Elly L. Vitters
- Experimental Rheumatology, Department of Rheumatology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - B Walgreen
- Experimental Rheumatology, Department of Rheumatology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - H. van Beuningen
- Experimental Rheumatology, Department of Rheumatology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - E. Blaney Davidson
- Experimental Rheumatology, Department of Rheumatology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Peter M. van der Kraan
- Experimental Rheumatology, Department of Rheumatology, Radboud University Medical Center, Nijmegen, the Netherlands,Peter M. van der Kraan, Radboud University Medical Center, 272, PO Box 9101, 6500 HB Nijmegen, the Netherlands.
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13
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Wang Y, Wang W, Liu J, Huang X, Liu R, Xia H, Brecha NC, Pu M, Gao J. Protective Effect of ALA in Crushed Optic Nerve Cat Retinal Ganglion Cells Using a New Marker RBPMS. PLoS One 2016; 11:e0160309. [PMID: 27504635 PMCID: PMC4978478 DOI: 10.1371/journal.pone.0160309] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 07/14/2016] [Indexed: 01/20/2023] Open
Abstract
In this study we first sought to determine whether RNA-binding protein with multiple splicing (RBPMS) can serve as a specific marker for cat retina ganglion cells (RGCs) using retrograde labeling and immunohistochemistry staining. RBPM was then used as an RGC marker to study RGC survival after optic nerve crush (ONC) and alpha-lipoic acid (ALA) treatment in cats. ALA treatment yielded a peak density of RBPMS-alpha cells within the peak isodensity zone (>60/mm2) which did not differ from ONC retinas. The area within the zone was significantly enlarged (control: 2.3%, ONC: 0.06%, ONC+ALA: 0.1%). As for the 10-21/mm2 zone, ALA treatment resulted in a significant increase in area (control: 34.5%, ONC: 12.1%, ONC+ALA: 35.9%). ALA can alleviate crush-induced RGC injury.
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Affiliation(s)
- Yanling Wang
- Department of Anatomy, School of Basic Medical Sciences, Peking University, Beijing, China
- Key Laboratory on Machine Perception (Ministry of Education), Peking University, Beijing, China
- Key Laboratory for Visual Impairment and Restoration (Ministry of Education), Peking University, Beijing, China
| | - Wenyao Wang
- Department of Anatomy, School of Basic Medical Sciences, Peking University, Beijing, China
- Key Laboratory on Machine Perception (Ministry of Education), Peking University, Beijing, China
- Key Laboratory for Visual Impairment and Restoration (Ministry of Education), Peking University, Beijing, China
| | - Jessica Liu
- Department of Neurobiology and Molecular, Cellular and Integrative Physiology, UCLA, Los Angeles, California, United States of America
- Jules Stein Eye Institute, UCLA, Los Angeles, California, United States of America
- UCLA College of Life Sciences, University of California, Los Angeles, CA, United States of America
| | - Xin Huang
- Department of Anatomy, School of Basic Medical Sciences, Peking University, Beijing, China
- Key Laboratory on Machine Perception (Ministry of Education), Peking University, Beijing, China
- Key Laboratory for Visual Impairment and Restoration (Ministry of Education), Peking University, Beijing, China
| | - Ruixing Liu
- Department of Anatomy, School of Basic Medical Sciences, Peking University, Beijing, China
- Key Laboratory on Machine Perception (Ministry of Education), Peking University, Beijing, China
- Key Laboratory for Visual Impairment and Restoration (Ministry of Education), Peking University, Beijing, China
| | - Huika Xia
- Department of Anatomy, School of Basic Medical Sciences, Peking University, Beijing, China
- Key Laboratory on Machine Perception (Ministry of Education), Peking University, Beijing, China
- Key Laboratory for Visual Impairment and Restoration (Ministry of Education), Peking University, Beijing, China
| | - Nicholas C. Brecha
- Department of Neurobiology and Molecular, Cellular and Integrative Physiology, UCLA, Los Angeles, California, United States of America
- Jules Stein Eye Institute, UCLA, Los Angeles, California, United States of America
- UCLA College of Life Sciences, University of California, Los Angeles, CA, United States of America
| | - Mingliang Pu
- Department of Anatomy, School of Basic Medical Sciences, Peking University, Beijing, China
- Key Laboratory on Machine Perception (Ministry of Education), Peking University, Beijing, China
- Key Laboratory for Visual Impairment and Restoration (Ministry of Education), Peking University, Beijing, China
| | - Jie Gao
- Department of Anatomy, School of Basic Medical Sciences, Peking University, Beijing, China
- Key Laboratory on Machine Perception (Ministry of Education), Peking University, Beijing, China
- Key Laboratory for Visual Impairment and Restoration (Ministry of Education), Peking University, Beijing, China
- * E-mail:
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Kelley M, Yochem J, Krieg M, Calixto A, Heiman MG, Kuzmanov A, Meli V, Chalfie M, Goodman MB, Shaham S, Frand A, Fay DS. FBN-1, a fibrillin-related protein, is required for resistance of the epidermis to mechanical deformation during C. elegans embryogenesis. eLife 2015; 4. [PMID: 25798732 PMCID: PMC4395870 DOI: 10.7554/elife.06565] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/20/2015] [Indexed: 12/19/2022] Open
Abstract
During development, biomechanical forces contour the body and provide shape to internal organs. Using genetic and molecular approaches in combination with a FRET-based tension sensor, we characterized a pulling force exerted by the elongating pharynx (foregut) on the anterior epidermis during C. elegans embryogenesis. Resistance of the epidermis to this force and to actomyosin-based circumferential constricting forces is mediated by FBN-1, a ZP domain protein related to vertebrate fibrillins. fbn-1 was required specifically within the epidermis and FBN-1 was expressed in epidermal cells and secreted to the apical surface as a putative component of the embryonic sheath. Tiling array studies indicated that fbn-1 mRNA processing requires the conserved alternative splicing factor MEC-8/RBPMS. The conserved SYM-3/FAM102A and SYM-4/WDR44 proteins, which are linked to protein trafficking, function as additional components of this network. Our studies demonstrate the importance of the apical extracellular matrix in preventing mechanical deformation of the epidermis during development. DOI:http://dx.doi.org/10.7554/eLife.06565.001 For an animal embryo to develop, its cells must organize themselves into tissues and organs. For example, skin and the lining of internal organs—such as the lungs and gut—are made from cells called epithelial cells, which are tightly linked to form flat sheets. In a microscopic worm called Caenorhabditis elegans, the outermost layer of epithelial cells (called the epidermis) forms over the surface of the embryo early on in embryonic development. Shortly afterwards, the embryonic epidermis experiences powerful contractions along the surface of the embryo. The force generated by these contractions converts the embryo from an oval shape to a roughly cylindrical form. These contractions also squeeze the internal tissues and organs, which correspondingly elongate along with the epidermis. It has been known for decades that such ‘mechanical’ forces are important for the normal development of embryos. However, it remains poorly understood how these forces generate tissues and organs of the proper shape—partly because it is difficult to measure forces in living embryos. It is also not clear how the mechanical properties of specific tissues are controlled. Now, Kelley, Yochem, Krieg et al. have analyzed the development of C. elegans' embryos and discovered a novel mechanical interplay between the feeding organ (called the pharynx) and the worm's epidermis. The experiments involved studying several mutant worms that perturb epidermal contractions and disrupt the attachment of the pharynx to the epidermis. These studies suggested that the pharynx exerts a strong inward pulling force on the epidermis during development. Using recently developed methods, Kelley, Yochem, Krieg et al. then measured mechanical forces within intact worm embryos and demonstrated that greater forces were experienced in cells that were being pulled by the pharynx. Kelley, Yochem, Krieg et al. further analyzed how the epidermis normally resists this pulling force from the pharynx and implicated a protein called FBN-1. This worm protein is structurally related to a human protein that is affected in people with a disorder called Marfan Syndrome. Worm embryos without the FBN-1 protein become severely deformed because they are unable to withstand mechanical forces at the epidermis. FBN-1 is normally synthesized and then transported to the outside of the worm embryo by epidermal cells, where it is thought to assemble into a meshwork of long fibers. This provides a strong scaffold that attaches to the epidermis to prevent the epidermis from undergoing excessive deformation while it experiences mechanical forces. The work of Kelley, Yochem, Krieg et al. provides an opportunity to understand how FBN-1 and other fiber-forming proteins are produced and transported to the cell surface. Moreover, these findings may have implications for human diseases and birth defects that result from an inability of tissues to respond appropriately to mechanical forces. DOI:http://dx.doi.org/10.7554/eLife.06565.002
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Affiliation(s)
- Melissa Kelley
- Department of Molecular Biology, University of Wyoming, Laramie, United States
| | - John Yochem
- Department of Molecular Biology, University of Wyoming, Laramie, United States
| | - Michael Krieg
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States
| | - Andrea Calixto
- Department of Biological Sciences, Columbia University, New York, United States
| | - Maxwell G Heiman
- Department of Genetics, Harvard Medical School, Boston Children's Hospital, Boston, United States
| | - Aleksandra Kuzmanov
- Department of Molecular Biology, University of Wyoming, Laramie, United States
| | - Vijaykumar Meli
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, United States
| | - Martin Chalfie
- Department of Biological Sciences, Columbia University, New York, United States
| | - Miriam B Goodman
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States
| | - Shai Shaham
- Laboratory of Developmental Genetics, The Rockefeller University, New York, United States
| | - Alison Frand
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, United States
| | - David S Fay
- Department of Molecular Biology, University of Wyoming, Laramie, United States
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15
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Rodriguez AR, de Sevilla Müller LP, Brecha NC. The RNA binding protein RBPMS is a selective marker of ganglion cells in the mammalian retina. J Comp Neurol 2014; 522:1411-43. [PMID: 24318667 DOI: 10.1002/cne.23521] [Citation(s) in RCA: 324] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 11/27/2013] [Accepted: 12/03/2013] [Indexed: 12/12/2022]
Abstract
There are few neurochemical markers that reliably identify retinal ganglion cells (RGCs), which are a heterogeneous population of cells that integrate and transmit the visual signal from the retina to the central visual nuclei. We have developed and characterized a new set of affinity-purified guinea pig and rabbit antibodies against RNA-binding protein with multiple splicing (RBPMS). On western blots these antibodies recognize a single band at 〜24 kDa, corresponding to RBPMS, and they strongly label RGC and displaced RGC (dRGC) somata in mouse, rat, guinea pig, rabbit, and monkey retina. RBPMS-immunoreactive cells and RGCs identified by other techniques have a similar range of somal diameters and areas. The density of RBPMS cells in mouse and rat retina is comparable to earlier semiquantitative estimates of RGCs. RBPMS is mainly expressed in medium and large DAPI-, DRAQ5-, NeuroTrace- and NeuN-stained cells in the ganglion cell layer (GCL), and RBPMS is not expressed in syntaxin (HPC-1)-immunoreactive cells in the inner nuclear layer (INL) and GCL, consistent with their identity as RGCs, and not displaced amacrine cells. In mouse and rat retina, most RBPMS cells are lost following optic nerve crush or transection at 3 weeks, and all Brn3a-, SMI-32-, and melanopsin-immunoreactive RGCs also express RBPMS immunoreactivity. RBPMS immunoreactivity is localized to cyan fluorescent protein (CFP)-fluorescent RGCs in the B6.Cg-Tg(Thy1-CFP)23Jrs/J mouse line. These findings show that antibodies against RBPMS are robust reagents that exclusively identify RGCs and dRGCs in multiple mammalian species, and they will be especially useful for quantification of RGCs.
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Affiliation(s)
- Allen R Rodriguez
- Department of Neurobiology, David Geffen School of Medicine at Los Angeles, University of California at Los Angeles, Los Angeles, California, 90095-1763
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16
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Fu J, Cheng L, Wang Y, Yuan P, Xu X, Ding L, Zhang H, Jiang K, Song H, Chen Z, Ye Q. The RNA-binding protein RBPMS1 represses AP-1 signaling and regulates breast cancer cell proliferation and migration. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1-13. [PMID: 25281386 DOI: 10.1016/j.bbamcr.2014.09.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 09/14/2014] [Accepted: 09/23/2014] [Indexed: 12/01/2022]
Abstract
The activator protein-1 (AP-1) transcription factor complex plays a crucial role in tumor growth and progression. However, how AP-1 transcriptional activity is repressed is not fully understood. Here, we show that RNA-binding protein with multiple splicing 1 (RBPMS1) physically and functionally interacts with AP-1 in vitro and in vivo. The RNA-recognition motif (RRM) and C-terminus of the RBPMS1 isoforms RBPMS1A and RBPMS1C, but not RBPMS1B, interacted with cFos, a member of the AP-1 family that dimerizes with cJun to stimulate AP-1 transcriptional activity. RBPMS1 did not associate with Jun proteins. RBPMS1A and RBPMS1C bound to the basic leucine zipper (bZIP) domain of cFos that mediates dimerization of AP-1 proteins. In addition, RBPMS1A-C interacted with the transcription factor Smad3, which was shown to interact with cJun and increase AP-1 transcriptional activity. RBPMS1 inhibited c-Fos or Smad3-mediated AP-1 transactivation and the expression of AP-1 target genes known to be the key regulators of cancer growth and progression, including vascular endothelial growth factor (VEGF) and cyclin D1. Mechanistically, RBPMS1 blocks the formation of the cFos/cJun or Smad3/cJun complex as well as the recruitment of cFos or Smad3 to the promoters of AP-1 target genes. In cultured cells and a mouse xenograft model, RBPMS1 inhibited the growth and migration of breast cancer cells through c-Fos or Smad3. These data suggest that RBPMS1 is a critical repressor of AP-1 signaling and RBPMS1 activation may be a useful strategy for cancer treatment.
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Affiliation(s)
- Jie Fu
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing, China; Department of Pharmacology and Toxicology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Long Cheng
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing, China
| | - Yu Wang
- School of Life Sciences, Shandong University, Shandong, China
| | - Ping Yuan
- Fujian Center for Disease Control and Prevention, Fujian, China
| | - Xiaojie Xu
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing, China
| | - Lihua Ding
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing, China
| | - Hao Zhang
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing, China
| | - Kai Jiang
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing, China
| | - Haifeng Song
- Department of Pharmacology and Toxicology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Zhongwu Chen
- Department of Interventional Radiology, The Affiliated First Hospital, Fujian Medical University, Fujian, China.
| | - Qinong Ye
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing, China.
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Farazi TA, Leonhardt CS, Mukherjee N, Mihailovic A, Li S, Max KE, Meyer C, Yamaji M, Cekan P, Jacobs NC, Gerstberger S, Bognanni C, Larsson E, Ohler U, Tuschl T. Identification of the RNA recognition element of the RBPMS family of RNA-binding proteins and their transcriptome-wide mRNA targets. RNA (NEW YORK, N.Y.) 2014; 20:1090-102. [PMID: 24860013 PMCID: PMC4114688 DOI: 10.1261/rna.045005.114] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Recent studies implicated the RNA-binding protein with multiple splicing (RBPMS) family of proteins in oocyte, retinal ganglion cell, heart, and gastrointestinal smooth muscle development. These RNA-binding proteins contain a single RNA recognition motif (RRM), and their targets and molecular function have not yet been identified. We defined transcriptome-wide RNA targets using photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) in HEK293 cells, revealing exonic mature and intronic pre-mRNA binding sites, in agreement with the nuclear and cytoplasmic localization of the proteins. Computational and biochemical approaches defined the RNA recognition element (RRE) as a tandem CAC trinucleotide motif separated by a variable spacer region. Similar to other mRNA-binding proteins, RBPMS family of proteins relocalized to cytoplasmic stress granules under oxidative stress conditions suggestive of a support function for mRNA localization in large and/or multinucleated cells where it is preferentially expressed.
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Affiliation(s)
- Thalia A. Farazi
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Carl S. Leonhardt
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Neelanjan Mukherjee
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Aleksandra Mihailovic
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Song Li
- Biology Department, Duke University, Durham, North Carolina 27708, USA
| | - Klaas E.A. Max
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Cindy Meyer
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Masashi Yamaji
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Pavol Cekan
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Nicholas C. Jacobs
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Stefanie Gerstberger
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Claudia Bognanni
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Erik Larsson
- Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Uwe Ohler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
- Corresponding authorE-mail
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Kankare M, Salminen TS, Lampinen H, Hoikkala A. Sequence variation in couch potato and its effects on life-history traits in a northern malt fly, Drosophila montana. JOURNAL OF INSECT PHYSIOLOGY 2012; 58:256-264. [PMID: 22138635 DOI: 10.1016/j.jinsphys.2011.11.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 11/17/2011] [Accepted: 11/18/2011] [Indexed: 05/31/2023]
Abstract
Couch potato (cpo) has previously been connected to reproductive diapause in several insect species including Drosophila melanogaster, where it has been suggested to provide a link between the insulin signalling pathway and the hormonal control of diapause. In the first part of the study we sequenced nearly 3.6 kb of this gene in a northern Drosophila species (Drosophila montana) with a robust photoperiodically determined diapause and found several types of polymorphisms along the sequenced area. We also found variation among five Drosophila virilis group species in the length of the 5th exon of cpo and in the site of the stop codon at the end of this exon. The second part of the study was targeted on a deletion of six amino acids located in the last section of exon 5, which in D. melanogaster, is translated only in one short transcript lacking the following exons. The studied deletion appeared to be extremely rare in the wild D. montana population where it was found, but its frequency rapidly increased during laboratory culture. qPCR analyses showed the expression level of the deletion allele to be significantly downregulated in both the diapausing and non-diapausing females compared to the wild type allele. At the phenotypic level, the deletion and the decreased expression of cpo transcript involving it did not have direct effect on the incidence of female reproductive diapause, but it was associated with a reduction in development time under diapause-inducing conditions. This suggests that while the cpo transcript containing the prolonged version of the 5th exon with a stop codon is clearly associated with fly development time, the exons with RNA domains included in other transcripts of the gene may be more directly related to diapause regulation.
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Affiliation(s)
- Maaria Kankare
- Centre of Excellence in Evolutionary Research, Department of Biological and Environmental Science, P.O. Box 35, 40014 University of Jyväskylä, Finland.
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Zhang Q, Denlinger DL. Elevated couch potato transcripts associated with adult diapause in the mosquito Culex pipiens. JOURNAL OF INSECT PHYSIOLOGY 2011; 57:620-627. [PMID: 21315077 PMCID: PMC3104097 DOI: 10.1016/j.jinsphys.2011.02.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 01/31/2011] [Accepted: 02/01/2011] [Indexed: 05/30/2023]
Abstract
The couch potato (cpo) cDNA that we cloned from the northern house mosquito, Culex pipiens, encodes the C-terminus containing a highly conserved RNA recognition motif (RRM). Protein structure prediction indicates a canonical RRM structure with a βαββαβ topological structure. Northern blots indicate a single mRNA band over 9.49 kb, and Southern blot analysis suggests that the cpo gene contains large introns. Highest expression was noted in first instar larvae and pupae. A comparison of nondiapausing (long daylength) and diapausing (short daylength) adult females showed no difference immediately at adult eclosion, but by day 7 and thereafter, expression of cpo was much higher in diapausing adults. When 2-month old diapausing females were transferred from short daylength to diapausing-terminating conditions of long daylength and high temperature, expression of cpo declined. Similarly, when a topical application of JH III was used to terminate diapause abundance of the cpo transcript declined. Consistent with observations in Drosophila melanogaster and several other species levels of cpo in C. pipiens are influenced by the diapause program, although the direction of change is not the same in all species.
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Affiliation(s)
| | - David L. Denlinger
- Corresponding author. Tel.: +1 614 2926425; Fax: +1 614 2922180 (D.L. Denlinger)
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Miller BG, Stamatoyannopoulos JA. Integrative meta-analysis of differential gene expression in acute myeloid leukemia. PLoS One 2010; 5:e9466. [PMID: 20209125 PMCID: PMC2830886 DOI: 10.1371/journal.pone.0009466] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Accepted: 02/10/2010] [Indexed: 11/30/2022] Open
Abstract
Background Acute myeloid leukemia (AML) is a heterogeneous disease with an overall poor prognosis. Gene expression profiling studies of patients with AML has provided key insights into disease pathogenesis while exposing potential diagnostic and prognostic markers and therapeutic targets. A systematic comparison of the large body of gene expression profiling studies in AML has the potential to test the extensibility of conclusions based on single studies and provide further insights into AML. Methodology/Principal Findings In this study, we systematically compared 25 published reports of gene expression profiling in AML. There were a total of 4,918 reported genes of which one third were reported in more than one study. We found that only a minority of reported prognostically-associated genes (9.6%) were replicated in at least one other study. In a combined analysis, we comprehensively identified both gene sets and functional gene categories and pathways that exhibited significant differential regulation in distinct prognostic categories, including many previously unreported associations. Conclusions/Significance We developed a novel approach for granular, cross-study analysis of gene-by-gene data and their relationships with established prognostic features and patient outcome. We identified many robust novel prognostic molecular features in AML that were undetected in prior studies, and which provide insights into AML pathogenesis with potential diagnostic, prognostic, and therapeutic implications. Our database and integrative analysis are available online (http://gat.stamlab.org).
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Affiliation(s)
- Brady G. Miller
- Department of Hematology, University of Washington, Seattle, Washington, United States of America
| | - John A. Stamatoyannopoulos
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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Kwong JMK, Caprioli J, Piri N. RNA binding protein with multiple splicing: a new marker for retinal ganglion cells. Invest Ophthalmol Vis Sci 2010; 51:1052-8. [PMID: 19737887 PMCID: PMC3979483 DOI: 10.1167/iovs.09-4098] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Revised: 08/11/2009] [Accepted: 08/12/2009] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To characterize expression of the RNA binding protein (RBPMS) in the retina as a specific marker for retinal ganglion cells (RGCs). METHODS Optic nerve transection (ONT) was performed on adult male Wistar rats. Retrograde RGC labeling was performed with FluoroGold (FG) applied to the cut surface of the optic nerve. RBPMS mRNA and protein expression in the retina was analyzed by in situ hybridization and immunohistochemistry, respectively. The expression of RBPMS in various rat tissues was analyzed with semiquantitative RT-PCR. RESULTS RBPMS mRNA and protein expression was localized primarily to irregularly shaped cells in the ganglion cell layer of the retina. Quantitative analysis showed that almost 100% of RGCs labeled by FG were also RBPMS-positive, irrespective of their location relative to the optic nerve head. Approximately 94% to 97% of RBPMS-positive cells were also positive for Thy-1, neurofilament H, and III beta-tubulin. In 2-week ONT retinas, the remaining few RGCs were weakly stained with RBPMS compared with intact RGCs in control retinas. Outside the retina, expression of RBPMS was observed in the heart, kidney, liver, and lungs. No expression was detected in any neuronal tissues except the retina. CONCLUSIONS The data indicate that in the retina RBPMS is selectively expressed in RGCs and therefore could serve as a marker for RGC quantification in normal retinas and for estimation of RGC loss in ocular neuropathies.
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Affiliation(s)
| | - Joseph Caprioli
- From the
Jules Stein Eye Institute and
- Brain Research Institute, University of California Los Angeles, Los Angeles, California
| | - Natik Piri
- From the
Jules Stein Eye Institute and
- Brain Research Institute, University of California Los Angeles, Los Angeles, California
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22
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Hallstrom TC, Nevins JR. Balancing the decision of cell proliferation and cell fate. Cell Cycle 2009; 8:532-5. [PMID: 19182518 DOI: 10.4161/cc.8.4.7609] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The control of cellular proliferation is key in the proper development of a complex organism, the maintenance of tissue homeostasis and the ability to respond to various hormonal and other inducers. Key in the control of proliferation is the retinoblastoma (Rb) protein which regulates the activity of a family of transcription factors known as E2Fs. The E2F proteins are now recognized to regulate the expression of a large number of genes associated with cell proliferation including genes encoding DNA replication as well as mitotic activities. What has also become clear over the past several years is the intimate relationship between the control of cell proliferation and the control of cell fate, particularly the activation of apoptotic pathways. Central in this connection is the Rb/E2F pathway that not only provides the primary signals for proliferation but at the same time, connects with the p53-dependent apoptotic pathway. This review addresses this inter-connection and the molecular mechanisms that control the decision between proliferation and cell death.
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Affiliation(s)
- Timothy C Hallstrom
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
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23
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Iso T, Futami K, Iwamoto T, Furuichi Y. Modulation of the Expression of Bloom Helicase by Estrogenic Agents. Biol Pharm Bull 2007; 30:266-71. [PMID: 17268063 DOI: 10.1248/bpb.30.266] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We report that the expression of Bloom helicase (BLM) was up-regulated by 17beta-estradiol (E2) in estrogen receptor (ER)-positive mammary tumor MCF-7 cells, but was hardly modulated in ER-negative mammary tumor MDA-MB-231 cells. ER antagonist ICI182780 blocked the E2 effect on BLM expression in MCF-7 cells. From these results we conclude that ER participates in up-regulation of BLM expression in MCF-7 cells by means of E2. Similar results were obtained when MCF-7 cells were treated with bisphenol A (BPA), an endocrine-disrupting chemical having a weak estrogenic activity. The ER binding ability of BPA is estimated at 1/1000 of E2 ability, and in this study about 1000-times more BPA was needed for the same levels of estrogenic effect of E2. The expression of cell-cycle associated genes, cdc6, MCM5, MCM2, Myt1, PCNA and AuroraA were up-regulated by E2 and BPA treatment in MCF-7 cells accompanied by up-regulation of BLM. In this BLM promoter study, Sp1 elements in the upper region of BLM modulated transcription, but were not indispensable for E2 response. Our results suggested that up-regulation of BLM expression by E2 and BPA is ER-dependent and may be responsible for repair of DNA damage caused by the genotoxicity of these estrogenic agents.
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Affiliation(s)
- Takako Iso
- GeneCare Research Institute Co., Ltd., Kanagawa, Japan
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24
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Sun Y, Ding L, Zhang H, Han J, Yang X, Yan J, Zhu Y, Li J, Song H, Ye Q. Potentiation of Smad-mediated transcriptional activation by the RNA-binding protein RBPMS. Nucleic Acids Res 2006; 34:6314-26. [PMID: 17099224 PMCID: PMC1669761 DOI: 10.1093/nar/gkl914] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2006] [Revised: 10/15/2006] [Accepted: 10/16/2006] [Indexed: 11/25/2022] Open
Abstract
Smad2, Smad3 and Smad4 proteins are considered to be key mediators of transforming growth factor-beta (TGF-beta) signaling. However, the identities of the Smad partners mediating TGF-beta signaling are not fully understood. Here, we show that RNA-binding protein with multiple splicing (RBPMS), a member of the RNA-binding protein family, physically interacts with Smad2, Smad3 and Smad4 both in vitro and in vivo. The presence of TGF-beta increases the binding of RBPMS with these Smad proteins. Consistent with the binding results, overexpression of RBPMS enhances Smad-dependent transcriptional activity in a TGF-beta-dependent manner, whereas knockdown of RBPMS decreases this activity. RBPMS interacts with TGF-beta receptor type I (TbetaR-I), increases phosphorylation of C-terminal SSXS regions in Smad2 and Smad3, and promotes the nuclear accumulation of the Smad proteins. Moreover, RBPMS fails to enhance the transcriptional activity of Smad2 and Smad3 that lack the C-terminal phosphorylation sites. Our data provide the first evidence for an RNA-binding protein playing a role in regulation of Smad-mediated transcriptional activity and suggest that RBPMS stimulates Smad-mediated transactivation possibly through enhanced phosphorylation of Smad2 and Smad3 at the C-terminus and promotion of the nuclear accumulation of the Smad proteins.
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Affiliation(s)
- Yan Sun
- Beijing Institute of Biotechnology, Beijing 100850People's Republic of China
- The 307 Hospital, Beijing 100071People's Republic of China
- Beijing Institute of Radiation Medicine, Beijing 100850People's Republic of China
| | - Lihua Ding
- Beijing Institute of Biotechnology, Beijing 100850People's Republic of China
- The 307 Hospital, Beijing 100071People's Republic of China
- Beijing Institute of Radiation Medicine, Beijing 100850People's Republic of China
| | - Hao Zhang
- Beijing Institute of Biotechnology, Beijing 100850People's Republic of China
- The 307 Hospital, Beijing 100071People's Republic of China
- Beijing Institute of Radiation Medicine, Beijing 100850People's Republic of China
| | - Juqiang Han
- Beijing Institute of Biotechnology, Beijing 100850People's Republic of China
- The 307 Hospital, Beijing 100071People's Republic of China
- Beijing Institute of Radiation Medicine, Beijing 100850People's Republic of China
| | - Xiao Yang
- Beijing Institute of Biotechnology, Beijing 100850People's Republic of China
- The 307 Hospital, Beijing 100071People's Republic of China
- Beijing Institute of Radiation Medicine, Beijing 100850People's Republic of China
| | - Jinghua Yan
- Beijing Institute of Biotechnology, Beijing 100850People's Republic of China
- The 307 Hospital, Beijing 100071People's Republic of China
- Beijing Institute of Radiation Medicine, Beijing 100850People's Republic of China
| | - Yunfeng Zhu
- The 307 Hospital, Beijing 100071People's Republic of China
| | - Jiezhi Li
- Beijing Institute of Biotechnology, Beijing 100850People's Republic of China
- The 307 Hospital, Beijing 100071People's Republic of China
- Beijing Institute of Radiation Medicine, Beijing 100850People's Republic of China
| | - Haifeng Song
- Beijing Institute of Radiation Medicine, Beijing 100850People's Republic of China
| | - Qinong Ye
- To whom correspondence should be addressed. Tel: +8610 6818 0809; Fax: +8610 6824 8045;
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Jaatinen T, Hemmoranta H, Hautaniemi S, Niemi J, Nicorici D, Laine J, Yli-Harja O, Partanen J. Global gene expression profile of human cord blood-derived CD133+ cells. Stem Cells 2005; 24:631-41. [PMID: 16210406 DOI: 10.1634/stemcells.2005-0185] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Human cord blood (CB)-derived CD133+ cells carry characteristics of primitive hematopoietic cells and proffer an alternative for CD34+ cells in hematopoietic stem cell (HSC) transplantation. To characterize the CD133+ cell population on a genetic level, a global expression analysis of CD133+ cells was performed using oligonucleotide microarrays. CD133+ cells were purified from four fresh CB units by immunomagnetic selection. All four CD133+ samples showed significant similarity in their gene expression pattern, whereas they differed clearly from the CD133- control samples. In all, 690 transcripts were differentially expressed between CD133+ and CD133- cells. Of these, 393 were increased and 297 were decreased in CD133+ cells. The highest overexpression was noted in genes associated with metabolism, cellular physiological processes, cell communication, and development. A set of 257 transcripts expressed solely in the CD133+ cell population was identified. Colony-forming unit (CFU) assay was used to detect the clonal progeny of precursors present in the studied cell populations. The results demonstrate that CD133+ cells express primitive markers and possess clonogenic progenitor capacity. This study provides a gene expression profile for human CD133+ cells. It presents a set of genes that may be used to unravel the properties of the CD133+ cell population, assumed to be highly enriched in HSCs.
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Affiliation(s)
- Taina Jaatinen
- Finnish Red Cross Blood Service, Kivihaantie 7, 00310 Helsinki, Finland
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26
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Inoue A, Watanabe T, Tominaga K, Tsugawa K, Nishio K, Takahashi KP, Kaneda K. Association of hnRNP S1 proteins with vimentin intermediate filaments in migrating cells. J Cell Sci 2005; 118:2303-11. [PMID: 15870111 DOI: 10.1242/jcs.02345] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
S1 proteins C2 and D2 are multifunctional hnRNP proteins acting as transcriptional regulators in the nucleus. Immunofluorescence staining of various cells in culture revealed that S1 proteins also occur in the cytoplasm, often in association with vimentin intermediate filaments (VFs). Here, we verified the association of S1 proteins with vimentin using vimentin-deficient cells, crosslinking and immunoprecipitation, and further investigated the biological significance of this association. S1 proteins on VFs, referred to here as S1 fibers, were lost in highly confluent cells, where cell proliferation and cellular metabolic activity greatly decreased owing to cell density-dependent arrest. However, the disappearance of S1 fibers was not related to these reduced activities, but to inhibited cell migration. Although undetected in cells of non-migratory tissues as well as in confluent cultured cells, S1 fibers were found in all migratory cells examined, such as cultured cells in scratch/wound experiments, blood neutrophils and monocytes, and fibroblasts engaging in tissue healing. In addition, S1 fibers reappeared even in confluent cells when VFs were induced to reorganize with okadaic acid. We propose that S1 proteins occur in association with VFs in migratory cells. Possible participation of S1 proteins in the formation/reorganization of VFs is discussed.
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Affiliation(s)
- Akira Inoue
- Molecular Mechanisms of Biological Regulation, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka 545-8585, Japan.
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27
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Glasscock E, Tanouye MA. Drosophila couch potato mutants exhibit complex neurological abnormalities including epilepsy phenotypes. Genetics 2005; 169:2137-49. [PMID: 15687283 PMCID: PMC1449607 DOI: 10.1534/genetics.104.028357] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
RNA-binding proteins play critical roles in regulation of gene expression, and impairment can have severe phenotypic consequences on nervous system function. We report here the discovery of several complex neurological phenotypes associated with mutations of couch potato (cpo), which encodes a Drosophila RNA-binding protein. We show that mutation of cpo leads to bang-sensitive paralysis, seizure susceptibility, and synaptic transmission defects. A new cpo allele called cpo(EG1) was identified on the basis of a bang-sensitive paralytic mutant phenotype in a sensitized genetic background (sda/+). In heteroallelic combinations with other cpo alleles, cpo(EG1) shows an incompletely penetrant bang-sensitive phenotype with approximately 30% of flies becoming paralyzed. In response to electroconvulsive shock, heteroallelic combinations with cpo(EG1) exhibit seizure thresholds less than half that of wild-type flies. Finally, cpo flies display several neurocircuit abnormalities in the giant fiber (GF) system. The TTM muscles of cpo mutants exhibit long latency responses coupled with decreased following frequency. DLM muscles in cpo mutants show drastic reductions in following frequency despite exhibiting normal latency relationships. The labile sites appear to be the electrochemical GF-TTMn synapse and the chemical PSI-DLMn synapses. These complex neurological phenotypes of cpo mutants support an important role for cpo in regulating proper nervous system function, including seizure susceptibility.
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Affiliation(s)
- Edward Glasscock
- Department of Molecular and Cell Biology, Division of Neurobiology, University of California, Berkeley, 94720, USA
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28
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Zearfoss NR, Chan AP, Wu CF, Kloc M, Etkin LD. Hermes is a localized factor regulating cleavage of vegetal blastomeres in Xenopus laevis. Dev Biol 2004; 267:60-71. [PMID: 14975717 DOI: 10.1016/j.ydbio.2003.10.032] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2002] [Revised: 09/26/2003] [Accepted: 10/23/2003] [Indexed: 11/18/2022]
Abstract
We have identified the RNA-binding protein Hermes in a screen for vegetally localized RNAs in Xenopus oocytes. The RNA localizes to the vegetal cortex through both the message transport organizer (METRO) and late pathways. Hermes mRNA and protein are both detected at the vegetal cortex of the oocyte; however, the protein is degraded within a several hour period during oocyte maturation. Injection of antisense morpholino oligonucleotides (HE-MO) against Hermes caused a precocious reduction in Hermes protein present during maturation and resulted in a phenotype characterized by cleavage defects in vegetal blastomeres. The phenotype can be partially rescued by injecting Hermes mRNA. These results demonstrate that the localized RNA-binding protein Hermes functions during oocyte maturation to regulate the cleavage of specific vegetally derived cell lineages. Hermes most likely performs its function by regulating the translation or processing of one or more target RNAs. This is an important mechanism by which the embryo can generate unique cell lineages. The regulation of region-specific cell division is a novel function for a localized mRNA.
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Affiliation(s)
- N R Zearfoss
- Department of Molecular Genetics, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
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29
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Kalish JA, Willis DJ, Li C, Link JJ, Deutsch ER, Contreras MA, Quist WC, Logerfo FW. Temporal genomics of vein bypass grafting through oligonucleotide microarray analysis. J Vasc Surg 2004; 39:645-54. [PMID: 14981462 DOI: 10.1016/j.jvs.2003.10.049] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OBJECTIVE Autologous vein is the conduit of choice for small artery reconstruction. Despite excellent patency, these conduits undergo remodeling over time. The purpose of this study was to identify temporal gene expression in vein grafts versus control veins through microarray analysis. METHOD Cephalic vein grafts (n = 12) were used to bypass femoral arteries in canines. Vein grafts were harvested after 1, 7, 14, and 30 days. Normal contralateral cephalic vein served as control. Total RNA was isolated; its quantity and quality were confirmed with spectrophotometry and gel electrophoresis. Affymetrix U133A GeneChips, comprising approximately 15,000 genes, were used to analyze differential gene expression at each time point. Statistical analysis was performed with Affymetrix and dChip software to identify consistently upregulated and downregulated genes. Real-time, quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) and immunohistochemistry were used to validate microarray data. RESULTS Statistical analysis revealed that 49 genes were consistently upregulated and 31 genes were consistently downregulated in all three animals at various time points. qRT-PCR to quantitatively assess messenger RNA expression was performed on specific genes to validate the microarray data. Immunohistochemistry to qualitatively assess protein expression was used for further validation. Hierarchical clustering with dChip identified additional genes with similar temporal or functional expression patterns. CONCLUSIONS This is the first study to use microarray analysis with confirmatory qRT-PCR to identify altered genes after vein bypass grafting. Oligonucleotide microarrays and hierarchical clustering are powerful tools to generate hypotheses as the basis for additional research on gene expression in vein graft remodeling. Ultimately, identification of a temporal sequence of differential gene expression may provide insights not preferred into the molecular mechanisms of vein graft remodeling, but also into the pathways leading to intimal hyperplasia.
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Affiliation(s)
- Jeffrey A Kalish
- Department of Surgery, Division of Vascular Surgery, Beth Israel Deacones Medical Center, Boston, MA 02115, USA.
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30
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Chaib H, MacDonald JW, Vessella RL, Washburn JG, Quinn JE, Odman A, Rubin MA, Macoska JA. Haploinsufficiency and reduced expression of genes localized to the 8p chromosomal region in human prostate tumors. Genes Chromosomes Cancer 2003; 37:306-13. [PMID: 12759929 DOI: 10.1002/gcc.10226] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Cytogenetic and molecular studies have suggested that deletion or rearrangement of sequences that map to the short arm of chromosome 8 may be permissive for tumorigenesis in several organ systems, and in human prostate tumors in particular. In this study, we hypothesized that genes deleted for one copy and localized to the 8p chromosomal region may be transcriptionally down-regulated or ablated in affected human prostate tumor tissues. To test this hypothesis, we used cDNA microarray analysis to determine the transcriptional profiles for 259 transcribed sequences mapping to the 8p chromosomal region for seven human prostate tumor xenografts, completely characterized for numerical and structural alterations on chromosome 8, and five normal human prostate tissues. These experiments identified 33 genes differentially expressed between normal and malignant prostate tissues, the majority of which (28/33, 85%) were transcriptionally down-regulated in malignant compared to normal human prostate tissues. These findings, that haploinsufficiency and transcriptional down-regulation for genes mapping to 8p are largely coincident in human prostate tumors, should provide a powerful tool for the identification of tumor-suppressor genes associated with human prostate cancer initiation and progression.
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Affiliation(s)
- Hassan Chaib
- Department of Urology, The University of Michigan, Ann Arbor 48109, USA
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31
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Sahasrabudhe PV, Xiao R, Montelione GT. Resonance assignments for the N-terminal domain from human RNA-binding protein with multiple splicing (RBP-MS). JOURNAL OF BIOMOLECULAR NMR 2001; 19:285-286. [PMID: 11330819 DOI: 10.1023/a:1011264512393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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32
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Kitao S, Lindor NM, Shiratori M, Furuichi Y, Shimamoto A. Rothmund-thomson syndrome responsible gene, RECQL4: genomic structure and products. Genomics 1999; 61:268-76. [PMID: 10552928 DOI: 10.1006/geno.1999.5959] [Citation(s) in RCA: 118] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
RECQL4 is the fourth gene identified as a member of the human DNA helicase RecQ gene family including the genes for Werner syndrome (WRN) and Bloom syndrome, both of which are characterized by genomic instability. Recently, RECQL4 was identified as the gene responsible for some cases of Rothmund-Thomson syndrome (RTS), a rare autosomal recessive genetic disorder that shows chromosomal instability, premature aging, and a high risk of mesenchymal tumors. In this study, we show the genomic organization of the RECQL4 gene, including the exon-intron boundaries, the transcription initiation sites, and the potential promoter sequences, which facilitates further mutation analysis of the RECQL4 gene and studies to elucidate the pathogenesis behind RTS. The RECQL4 gene is in a small genome of 6.5 kb and consists of 21 exons. In the 5' upstream region, one Sp1 site and several AP 2 sites exist near the capping site, suggesting that the expression of RECQL4 is regulated by a housekeeping-type promoter similar to WRN. By comparative Northern blot analysis, we show that the RECQL4 transcripts are severely down-regulated in the cells from RTS patients, similar to our previous observation for WRN transcripts in cells from Werner patients. Immunocytochemical analysis indicated that the RECQL4 protein expressed in HeLa cells is in the nucleus and appears to be localized mainly in the nucleoplasm similar to WRN helicase.
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Affiliation(s)
- S Kitao
- AGENE Research Institute, Kamakura, 247-0063, Japan
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33
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Chughtai SA, Crundwell MC, Cruickshank NR, Affie E, Armstrong S, Knowles MA, Takle LA, Kuo M, Khan N, Phillips SM, Neoptolemos JP, Morton DG. Two novel regions of interstitial deletion on chromosome 8p in colorectal cancer. Oncogene 1999; 18:657-65. [PMID: 9989816 DOI: 10.1038/sj.onc.1202340] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have investigated interstitial deletions of chromosome 8 in 70 colorectal carcinomas and 11 colonic adenomas using 11 microsatellite markers, including eight spanning the centromeric region of chromosome 8p (p11.2-p12). Allelic loss or imbalance was observed in 38 (54%) cancers and four (36%) adenomas. Twenty-eight (40%) of the cancers had deletions of 8p11.2-p12. Two distinct and independent regions of interstitial loss were found within this region. Fluorescent in situ hybridization, using an alpha satellite repeat probe to the centromere of 8p and two probes to the P1 region, was performed in four tumours that demonstrated allelic imbalance. Localized heterozygous deletions were confirmed in all four tumours. Eleven (16%) cancers had localized deletion in the region ANK-1 to D8S255 (P1) and a further eleven (16%) cancers had a less well localized deletion in the region defined by the markers D8S87 to D8S259 (P2). Loss of both centromeric loci was identified in a further six (9%) tumours. A functional significance for these two deletion regions was sought by correlation with primary and secondary tumour characteristics. Isolated P2 deletion was associated with 'early' T1 cancers (2p=0.0002), and were also identified in 3/11 adenomas. Conversely, interstitial deletions of the P1 locus were more frequently seen in 'locally invasive' T3/4 cancers (2p=0.015), and isolated P1 deletions were also associated with the presence of liver metastases (2p=0.016). Our data provide evidence of at least two genes within the 8p11.2-p12 region, mutations in which may confer different and independent roles in the pathogenesis of colorectal cancer.
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Affiliation(s)
- S A Chughtai
- Department of Surgery, University of Birmingham, Edgbaston, UK
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Gerber WV, Yatskievych TA, Antin PB, Correia KM, Conlon RA, Krieg PA. The RNA-binding protein gene, hermes, is expressed at high levels in the developing heart. Mech Dev 1999; 80:77-86. [PMID: 10096065 DOI: 10.1016/s0925-4773(98)00195-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In a screen for novel sequences expressed during embryonic heart development we have isolated a gene which encodes a putative RNA-binding protein. This protein is a member of one of the largest families of RNA-binding proteins, the RRM (RNA Recognition Motif) family. The gene has been named hermes (for HEart, RRM Expressed Sequence). The hermes protein is 197-amino acids long and contains a single RRM domain. In situ hybridization analysis indicates that hermes is expressed at highest levels in the myocardium of the heart and to a lesser extent in the ganglion layer of the retina, the pronephros and epiphysis. Expression of hermes in each of these tissues begins at approximately the time of differentiation and is maintained throughout development. Analysis of the RNA expression of the hermes orthologues from chicken and mouse reveals that, like Xenopus, the most prominent tissue of expression is the developing heart. The sequence and expression pattern of hermes suggests a role in post-transcriptional regulation of heart development.
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Affiliation(s)
- W V Gerber
- Institute for Cell and Molecular Biology, University of Texas at Austin 78712, USA
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Kitao S, Ohsugi I, Ichikawa K, Goto M, Furuichi Y, Shimamoto A. Cloning of two new human helicase genes of the RecQ family: biological significance of multiple species in higher eukaryotes. Genomics 1998; 54:443-52. [PMID: 9878247 DOI: 10.1006/geno.1998.5595] [Citation(s) in RCA: 194] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Two new human DNA helicase genes, RecQ4 and RecQ5, that belong to the RecQ helicase family were cloned and characterized. The addition of these genes increases the total to five helicase genes in the human RecQ family, which includes helicases involved in Bloom and Werner syndromes, the genetic diseases manifesting the distinctive but overlapping clinical phenotypes of immunodeficiency, premature aging, and an enhanced risk of cancer. The RecQ4 helicase is as large as the Bloom (BLM) and Werner (WRN) helicases, and its gene expression profile is organ-specific, resembling that of BLM helicase. In contrast, the RecQ5 helicase has a low molecular weight, similar to the human progenitor RecQ1 helicase, and is expressed in all the organs examined. All five human helicase genes are expressed in cultured K562 leukemia and fibroblast cells. Synchronized K562 cell cultures showed that the genes RecQ4 and BLM, and RecQ1 and WRN, seem to be upregulated at the G1/S and G2/M phases, respectively, of the cell cycle. The biological significance of multiple species of human RecQ helicases, which are apparently nonessential for life but may be related to distinct diseases, is discussed in light of the fact that unicellular organisms, like Escherichia coli and yeast, contain only one species of helicase of this particular family.
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Affiliation(s)
- S Kitao
- AGENE Research Institute, 200 Kajiwara, Kamakura, 247, Japan
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Sahasrabudhe PV, Tejero R, Kitao S, Furuichi Y, Montelione GT. Homology modeling of an RNP domain from a human RNA-binding protein: Homology-constrained energy optimization provides a criterion for distinguishing potential sequence alignments. Proteins 1998. [DOI: 10.1002/(sici)1097-0134(19981201)33:4<558::aid-prot8>3.0.co;2-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Yamabe Y, Shimamoto A, Goto M, Yokota J, Sugawara M, Furuichi Y. Sp1-mediated transcription of the Werner helicase gene is modulated by Rb and p53. Mol Cell Biol 1998; 18:6191-200. [PMID: 9774636 PMCID: PMC109206 DOI: 10.1128/mcb.18.11.6191] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The regulation of Werner's syndrome gene (WRN) expression was studied by characterizing the cis-regulatory elements in the promoter region and the trans-activating factors that bind to them. First, we defined the transcription initiation sites and the sequence of the 5' upstream region (2.8 kb) of WRN that contains a number of cis-regulatory elements, including 7 Sp1, 9 retinoblastoma control element (RCE), and 14 AP2 motifs. A region consisting of nucleotides -67 to +160 was identified as the principal promoter of WRN by reporter gene assays in HeLa cells, using a series of WRN promoter-luciferase reporter (WRN-Luc) plasmids that contained the 5'-truncated or mutated WRN upstream regions. In particular, two Sp1 elements proximal to the transcription initiation site are indispensable for WRN promoter activity and bind specifically to Sp1 proteins. The RCE enhances WRN promoter activity. Coexpression of the WRN-Luc plasmids with various dosages of plasmids expressing Rb or p53 in Saos2 cells lacking active Rb and p53 proteins showed that the introduced Rb upregulates WRN promoter activity a maximum of 2. 5-fold, while p53 downregulates it a maximum of 7-fold, both dose dependently. Consistently, the overexpressed Rb and p53 proteins also affected the endogenous WRN mRNA levels in Saos2 cells, resulting in an increase with Rb and a decrease with p53. These findings suggest that WRN expression, like that of other housekeeping genes, is directed mainly by the Sp1 transcriptional control system but is also further modulated by transcription factors, including Rb and p53, that are implicated in the cell cycle, cell senescence, and genomic instability.
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Affiliation(s)
- Y Yamabe
- AGENE Research Institute, Kamakura, Kanagawa 247, Japan
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38
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Adélaïde J, Chaffanet M, Imbert A, Allione F, Geneix J, Popovici C, van Alewijk D, Trapman J, Zeillinger R, Børresen-Dale AL, Lidereau R, Birnbaum D, Pébusque MJ. Chromosome region 8p11-p21: refined mapping and molecular alterations in breast cancer. Genes Chromosomes Cancer 1998; 22:186-99. [PMID: 9624530 DOI: 10.1002/(sici)1098-2264(199807)22:3<186::aid-gcc4>3.0.co;2-s] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Several genes, most of them unknown, of the short arm of chromosome 8 are involved in malignant diseases. Numerous studies have implicated a portion of the 8p11-p21 region as the location of one or more tumor suppressor genes involved in a variety of human cancers, including breast cancer. We and others have reported linkage analyses suggesting the presence of a putative breast cancer susceptibility gene. Furthermore, several oncogenes of the 8p11-p12 region are involved in reciprocal translocations in myeloproliferative and myelodysplastic disorders and in amplification in breast cancer. To facilitate the analysis of the 8p11-p21 region and the cloning of candidate oncogenes and tumor suppressor genes, a high-resolution physical and transcriptional map was established with 39 yeast artificial chromosomes and 94 markers, including so-called sequence-tagged sites and expressed sequence-tagged sites derived from either known genes or expressed sequence tags corresponding to unidentified transcripts. In addition, four novel transcripts were identified and localized precisely within the map. This transcription map provides a detailed description of gene order for the 8p11-p21 region and will be helpful in the identification of candidate genes for diseases. From this basis, we refined the mapping of two types of molecular alterations that occur at 8p11-p21 in sporadic breast cancers, i.e., amplification and deletion.
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Affiliation(s)
- J Adélaïde
- Laboratoire de Biologie des Tumeurs, Institut Paoli-Calmettes, Marseille, France
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39
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Burke J, Wang H, Hide W, Davison DB. Alternative gene form discovery and candidate gene selection from gene indexing projects. Genome Res 1998; 8:276-90. [PMID: 9521931 PMCID: PMC310695 DOI: 10.1101/gr.8.3.276] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/1997] [Accepted: 02/06/1998] [Indexed: 02/06/2023]
Abstract
Several efforts are under way to partition single-read expressed sequence tag (EST), as well as full-length transcript data, into large-scale gene indices, where transcripts are in common index classes if and only if they share a common progenitor gene. Accurate gene indexing facilitates gene expression studies, as well as inexpensive and early gene sequence discovery through assembly of ESTs that are derived from genes that have not been sequenced by classical methods. We extend, correct, and enhance the information obtained from index groups by splitting index classes into subclasses based on sequence dissimilarity (diversity). Two applications of this are highlighted in this report. First it is shown that our method can ameliorate the damage that artifacts, such as chimerism, inflict on index integrity. Additionally, we demonstrate how the organization imposed by an effective subpartition can greatly increase the sensitivity of gene expression studies by accounting for the existence and tissue- or pathology-specific regulation of novel gene isoforms and polymorphisms. We apply our subpartitioning treatment to the UniGene gene indexing project to measure a marked increase in information quality and abundance (in terms of assembly length and insertion/deletion error) after treatment and demonstrate cases where new levels of information concerning differential expression of alternate gene forms, such as regulated alternative splicing, are discovered. [Tables 2 and 3 can be viewed in their entirety as Online Supplements at http://www.genome.org.]
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Affiliation(s)
- J Burke
- Department of Biochemical and Biophysical Sciences, University of Houston, Houston, Texas 77004-5934, USA.
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40
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Imamura O, Sugawara M, Furuichi Y. Cloning and characterization of a putative human RNA helicase gene of the DEAH-box protein family. Biochem Biophys Res Commun 1997; 240:335-40. [PMID: 9388478 DOI: 10.1006/bbrc.1997.7585] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A human RNA helicase gene, DBP1, was cloned by PCR methodsusing degenerate oligonucleotide primers corresponding to highly conserved motifs among known members of the DEAH-box protein family. The full-length DBP1 contains 3028 nucleotides and codes for a protein of 813 amino acids with a calculated mol. wt. of 92723 daltons. The predicted amino acid sequence shares extensive homology with Prp2, Prp16, and Prp22 proteins, which are required to splice mRNA precursors in budding yeast. The protein encoded by DBP1 has RGD, RD, and HS(A/T) repeat motifs close to the N-terminus. Southern blot analysis suggested the presence of a homologue of the DBP1 genes in other species, and Northern blot analysis showed that DBP1 is expressed ubiquitously in various human organs investigated. The DBP1 gene was found to be on chromosome 4p15.3 and encodes a putative nuclear ATP-dependent RNA helicase.
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Affiliation(s)
- O Imamura
- AGENE Research Institute, Kamakura, Japan
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41
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Edwalds-Gilbert G, Veraldi KL, Milcarek C. Alternative poly(A) site selection in complex transcription units: means to an end? Nucleic Acids Res 1997; 25:2547-61. [PMID: 9185563 PMCID: PMC146782 DOI: 10.1093/nar/25.13.2547] [Citation(s) in RCA: 410] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Many genes have been described and characterized which result in alternative polyadenylation site use at the 3'-end of their mRNAs based on the cellular environment. In this survey and summary article 95 genes are discussed in which alternative polyadenylation is a consequence of tandem arrays of poly(A) signals within a single 3'-untranslated region. An additional 31 genes are described in which polyadenylation at a promoter-proximal site competes with a splicing reaction to influence expression of multiple mRNAs. Some have a composite internal/terminal exon which can be differentially processed. Others contain alternative 3'-terminal exons, the first of which can be skipped in some cells. In some cases the mRNAs formed from these three classes of genes are differentially processed from the primary transcript during the cell cycle or in a tissue-specific or developmentally specific pattern. Immunoglobulin heavy chain genes have composite exons; regulated production of two different Ig mRNAs has been shown to involve B cell stage-specific changes in trans -acting factors involved in formation of the active polyadenylation complex. Changes in the activity of some of these same factors occur during viral infection and take-over of the cellular machinery, suggesting the potential applicability of at least some aspects of the Ig model. The differential expression of a number of genes that undergo alternative poly(A) site choice or polyadenylation/splicing competition could be regulated at the level of amounts and activities of either generic or tissue-specific polyadenylation factors and/or splicing factors.
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Affiliation(s)
- G Edwalds-Gilbert
- Department of Molecular Genetics and Biochemistry and the Graduate Program in Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261-2072, USA
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42
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Ichikawa K, Yamabe Y, Imamura O, Kuromitsu J, Sugawara K, Suzuki N, Shimamoto A, Matsumoto T, Tokutake Y, Kitao S, Kataoka H, Satoh M, Sugimoto M, Goto M, Sugawara M, Furuichi Y. Cloning and characterization of a novel gene, WS-3, in human chromosome 8p11-p12. Gene 1997; 189:277-87. [PMID: 9168138 DOI: 10.1016/s0378-1119(96)00863-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A novel human gene referred to as the WS-3 gene, in the short arm of human chromosome 8, was cloned by a combination of exon trapping, thermal asymmetric interlaced-PCR (TAIL-PCR) and the Marathon-Ready cDNA amplification method. The gene consists of 7 exons separated by 6 introns, and is at the telomere side of the STS marker, D8S1055. The full-length WS-3 gene contains 1052 nucleotides and codes for a protein of 190 amino acids with a calculated mol. wt. of 20,747. Southern blot experiments showed that the WS-3 gene exists as a single copy in the human genome. A protein encoded by the WS-3 gene has an R-G-D (Arg-Gly-Asp) motif in the N-terminal region, which seems to confer adhesive properties to macromolecular proteins like fibronectin. Although WS-3 is a small gene with unknown biological function, its ubiquitous expression in various tissues and organs suggests that the encoded protein is one of the essential components of all organs and tissues.
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Affiliation(s)
- K Ichikawa
- AGENE Research Institute, Kamakura-shi, Kanagawa, Japan
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Suzuki N, Sugawara M, Sugimoto M, Oshimura M, Furuichi Y. Gene expressions of transferred human chromosome 8 in mouse cell lines. Biochem Biophys Res Commun 1997; 230:315-9. [PMID: 9016774 DOI: 10.1006/bbrc.1996.5953] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Gene expressions were studied for the human chromosome 8 which were introduced by microcell fusion to three mouse tumor cell lines: A9, mouse melanoma B16F10 and SCVA2 derived from SV40-transformed scid fibroblasts. Nineteen genes in the human chromosome 8 were chosen, and the presence of their transcripts in these cells was examined by RT-PCR. The data showed that most of the human genes were expressed, with a few exceptions: the indoleamine 2, 3-dioxygenase gene was expressed in none of these cell lines, while two other genes, calbindin and neuronal nicotinic acetylcholine receptor subunit (Ach Rbeta3) genes, were not expressed in the A9 and SCVA2 cell lines, respectively, suggesting some cell- or species-specific transcriptional regulations exist. These results show that the mouse cell lines carrying a human chromosome are powerful tools for chromosome-specific cDNA cloning.
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Affiliation(s)
- N Suzuki
- AGENE Research Institute, Kamakura-shi, Japan
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