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Alsulami M, Munawar N, Dillon E, Oliviero G, Wynne K, Alsolami M, Moss C, Ó Gaora P, O'Meara F, Cotter D, Cagney G. SETD1A Methyltransferase Is Physically and Functionally Linked to the DNA Damage Repair Protein RAD18. Mol Cell Proteomics 2019; 18:1428-1436. [PMID: 31076518 PMCID: PMC6601208 DOI: 10.1074/mcp.ra119.001518] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Indexed: 12/13/2022] Open
Abstract
SETD1A is a SET domain-containing methyltransferase involved in epigenetic regulation of transcription. It is the main catalytic component of a multiprotein complex that methylates lysine 4 of histone H3, a histone mark associated with gene activation. In humans, six related protein complexes with partly nonredundant cellular functions share several protein subunits but are distinguished by unique catalytic SET-domain proteins. We surveyed physical interactions of the SETD1A-complex using endogenous immunoprecipitation followed by label-free quantitative proteomics on three subunits: SETD1A, RBBP5, and ASH2L. Surprisingly, SETD1A, but not RBBP5 or ASH2L, was found to interact with the DNA damage repair protein RAD18. Reciprocal RAD18 immunoprecipitation experiments confirmed the interaction with SETD1A, whereas size exclusion and protein network analysis suggested an interaction independent of the main SETD1A complex. We found evidence of SETD1A and RAD18 influence on mutual gene expression levels. Further, knockdown of the genes individually showed a DNA damage repair phenotype, whereas simultaneous knockdown resulted in an epistatic effect. This adds to a growing body of work linking epigenetic enzymes to processes involved in genome stability.
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Affiliation(s)
- Manal Alsulami
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Nayla Munawar
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; ¶Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan
| | - Eugene Dillon
- §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Giorgio Oliviero
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kieran Wynne
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; ‖Maine Medical Center Research Institute, 81 Research Drive, Scarborough, Maine 04074
| | - Mona Alsolami
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Catherine Moss
- §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Peadar Ó Gaora
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Fergal O'Meara
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - David Cotter
- **Department of Psychiatry, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Gerard Cagney
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland;.
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Alsulami M, Munawar N, Dillon E, Oliviero G, Wynne K, Alsolami M, Moss C, Ó Gaora P, O'Meara F, Cotter D, Cagney G. SETD1A Methyltransferase Is Physically and Functionally Linked to the DNA Damage Repair Protein RAD18. Mol Cell Proteomics 2019. [DOI: https://doi.org/10.1074/mcp.ra119.001518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Yu Z, Gunn L, Brennan E, Reid R, Wall PG, Gaora PÓ, Hurley D, Bolton D, Fanning S. Complete Genome Sequence of Clostridium estertheticum DSM 8809, a Microbe Identified in Spoiled Vacuum Packed Beef. Front Microbiol 2016; 7:1764. [PMID: 27891116 PMCID: PMC5104964 DOI: 10.3389/fmicb.2016.01764] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 10/20/2016] [Indexed: 11/13/2022] Open
Abstract
Blown pack spoilage (BPS) is a major issue for the beef industry. Etiological agents of BPS involve members of a group of Clostridium species, including Clostridium estertheticum which has the ability to produce gas, mostly carbon dioxide, under anaerobic psychotrophic growth conditions. This spore-forming bacterium grows slowly under laboratory conditions, and it can take up to 3 months to produce a workable culture. These characteristics have limited the study of this commercially challenging bacterium. Consequently information on this bacterium is limited and no effective controls are currently available to confidently detect and manage this production risk. In this study the complete genome of C. estertheticum DSM 8809 was determined by SMRT® sequencing. The genome consists of a circular chromosome of 4.7 Mbp along with a single plasmid carrying a potential tellurite resistance gene tehB and a Tn3-like resolvase-encoding gene tnpR. The genome sequence was searched for central metabolic pathways that would support its biochemical profile and several enzymes contributing to this phenotype were identified. Several putative antibiotic/biocide/metal resistance-encoding genes and virulence factors were also identified in the genome, a feature that requires further research. The availability of the genome sequence will provide a basic blueprint from which to develop valuable biomarkers that could support and improve the detection and control of this bacterium along the beef production chain.
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Affiliation(s)
- Zhongyi Yu
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, School of Biomedical and Biomolecular Science, University College Dublin Dublin, Ireland
| | - Lynda Gunn
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, School of Biomedical and Biomolecular Science, University College Dublin Dublin, Ireland
| | - Evan Brennan
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, School of Biomedical and Biomolecular Science, University College Dublin Dublin, Ireland
| | | | - Patrick G Wall
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, School of Biomedical and Biomolecular Science, University College Dublin Dublin, Ireland
| | - Peadar Ó Gaora
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, School of Biomedical and Biomolecular Science, University College Dublin Dublin, Ireland
| | - Daniel Hurley
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, School of Biomedical and Biomolecular Science, University College Dublin Dublin, Ireland
| | | | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, School of Biomedical and Biomolecular Science, University College Dublin Dublin, Ireland
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Varešlija D, McBryan J, Fagan A, Redmond AM, Hao Y, Sims AH, Turnbull A, Dixon JM, Ó Gaora P, Hudson L, Purcell S, Hill ADK, Young LS. Adaptation to AI Therapy in Breast Cancer Can Induce Dynamic Alterations in ER Activity Resulting in Estrogen-Independent Metastatic Tumors. Clin Cancer Res 2016; 22:2765-77. [PMID: 26763249 DOI: 10.1158/1078-0432.ccr-15-1583] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 12/20/2015] [Indexed: 11/16/2022]
Abstract
PURPOSE Acquired resistance to aromatase inhibitor (AI) therapy is a major clinical problem in the treatment of breast cancer. The detailed mechanisms of how tumor cells develop this resistance remain unclear. Here, the adapted function of estrogen receptor (ER) to an estrogen-depleted environment following AI treatment is reported. EXPERIMENTAL DESIGN Global ER chromatin immuno-precipitation (ChIP)-seq analysis of AI-resistant cells identified steroid-independent ER target genes. Matched patient tumor samples, collected before and after AI treatment, were used to assess ER activity. RESULTS Maintained ER activity was observed in patient tumors following neoadjuvant AI therapy. Genome-wide ER-DNA-binding analysis in AI-resistant cell lines identified a subset of classic ligand-dependent ER target genes that develop steroid independence. The Kaplan-Meier analysis revealed a significant association between tumors, which fail to decrease this steroid-independent ER target gene set in response to neoadjuvant AI therapy, and poor disease-free survival and overall survival (n = 72 matched patient tumor samples, P = 0.00339 and 0.00155, respectively). The adaptive ER response to AI treatment was highlighted by the ER/AIB1 target gene, early growth response 3 (EGR3). Elevated levels of EGR3 were detected in endocrine-resistant local disease recurrent patient tumors in comparison with matched primary tissue. However, evidence from distant metastatic tumors demonstrates that the ER signaling network may undergo further adaptations with disease progression as estrogen-independent ER target gene expression is routinely lost in established metastatic tumors. CONCLUSIONS Overall, these data provide evidence of a dynamic ER response to endocrine treatment that may provide vital clues for overcoming the clinical issue of therapy resistance. Clin Cancer Res; 22(11); 2765-77. ©2016 AACR.
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Affiliation(s)
- Damir Varešlija
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Jean McBryan
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Ailís Fagan
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Aisling M Redmond
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Yuan Hao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Andrew H Sims
- University of Edinburgh Cancer Research Centre, Carrington Crescent, Edinburgh, EH4 2XU, United Kingdom
| | - Arran Turnbull
- University of Edinburgh Cancer Research Centre, Carrington Crescent, Edinburgh, EH4 2XU, United Kingdom
| | - J M Dixon
- University of Edinburgh Cancer Research Centre, Carrington Crescent, Edinburgh, EH4 2XU, United Kingdom
| | - Peadar Ó Gaora
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Lance Hudson
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Siobhan Purcell
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Arnold D K Hill
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Leonie S Young
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin 2, Ireland.
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McBryan J, Fagan A, McCartan D, Bane FT, Varešlija D, Cocchiglia S, Byrne C, Bolger J, McIlroy M, Hudson L, Tibbitts P, Ó Gaora P, Hill AD, Young LS. Transcriptomic Profiling of Sequential Tumors from Breast Cancer Patients Provides a Global View of Metastatic Expression Changes Following Endocrine Therapy. Clin Cancer Res 2015; 21:5371-9. [DOI: 10.1158/1078-0432.ccr-14-2155] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 07/21/2015] [Indexed: 11/16/2022]
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Maillo V, Gaora PÓ, Forde N, Besenfelder U, Havlicek V, Burns GW, Spencer TE, Gutierrez-Adan A, Lonergan P, Rizos D. Oviduct-Embryo Interactions in Cattle: Two-Way Traffic or a One-Way Street? Biol Reprod 2015; 92:144. [PMID: 25926440 DOI: 10.1095/biolreprod.115.127969] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 04/22/2015] [Indexed: 12/19/2022] Open
Abstract
This study examined the effect of the presence of single or multiple embryos on the transcriptome of the bovine oviduct. In experiment 1, cyclic (nonbred, n = 6) and pregnant (artificially inseminated, n = 11) heifers were slaughtered on Day 3 after estrus, and the ampulla and isthmic regions of the oviduct ipsilateral to the corpus luteum were separately flushed. Oviductal epithelial cells from the isthmus region, in which all oocytes/embryos were located, were snap-frozen for microarray analysis. In experiment 2, heifers were divided into cyclic (nonbred, n = 6) or pregnant (multiple embryo transfer, n = 10) groups. In vitro-produced presumptive zygotes were transferred endoscopically to the ipsilateral oviduct on Day 1.5 postestrus (n = 50 zygotes/heifer). Heifers were slaughtered on Day 3, and oviductal isthmus epithelial cells were recovered for RNA sequencing. Microarray analysis in experiment 1 failed to detect any difference in the transcriptome of the oviductal isthmus induced by the presence of a single embryo. In experiment 2, following multiple embryo transfer, RNA sequencing revealed 278 differentially expressed genes, of which 123 were up-regulated and 155 were down-regulated in pregnant heifers. Most of the down-regulated genes were related to immune function. In conclusion, the presence of multiple embryos in the oviduct resulted in the detection of differentially expressed genes in the oviductal isthmus; failure to detect changes in the oviduct transcriptome in the presence of a single embryo may be due to the effect being local and undetectable under the conditions of this study.
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Affiliation(s)
| | - Peadar Ó Gaora
- School of Biomolecular and Biomedical Sciences, University College Dublin, Belfield, Dublin, Ireland
| | - Niamh Forde
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland
| | - Urban Besenfelder
- Reproduction Centre-Wieselburg, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Vitezslav Havlicek
- Reproduction Centre-Wieselburg, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Gregory W Burns
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, Washington
| | - Thomas E Spencer
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, Washington
| | | | - Patrick Lonergan
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland
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O'Hara J, Vareslija D, McBryan J, Bane F, Tibbitts P, Byrne C, Conroy RM, Hao Y, Gaora PÓ, Hill ADK, McIlroy M, Young LS. AIB1:ERα transcriptional activity is selectively enhanced in aromatase inhibitor-resistant breast cancer cells. Clin Cancer Res 2012; 18:3305-15. [PMID: 22550166 DOI: 10.1158/1078-0432.ccr-11-3300] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The use of aromatase inhibitors (AI) in the treatment of estrogen receptor (ER)-positive, postmenopausal breast cancer has proven efficacy. However, inappropriate activation of ER target genes has been implicated in the development of resistant tumors. The ER coactivator protein AIB1 has previously been associated with initiation of breast cancer and resistance to endocrine therapy. EXPERIMENTAL DESIGN Here, we investigated the role of AIB1 in the deregulation of ER target genes occurring as a consequence of AI resistance using tissue microarrays of patients with breast cancer and cell line models of resistance to the AI letrozole. RESULTS Expression of AIB1 associated with disease recurrence (P = 0.025) and reduced disease-free survival time (P = 0.0471) in patients treated with an AI as first-line therapy. In a cell line model of resistance to letrozole (LetR), we found ERα/AIB1 promoter recruitment and subsequent expression of the classic ER target genes pS2 and Myc to be constitutively upregulated in the presence of both androstenedione and letrozole. In contrast, the recruitment of the ERα/AIB1 transcriptional complex to the nonclassic ER target cyclin D1 and its subsequent expression remained sensitive to steroid treatment and could be inhibited by treatment with letrozole. Molecular studies revealed that this may be due in part to direct steroid regulation of c-jun-NH(2)-kinase (JNK), signaling to Jun and Fos at the cyclin D1 promoter. CONCLUSION This study establishes a role for AIB1 in AI-resistant breast cancer and describes a new mechanism of ERα/AIB1 gene regulation which could contribute to the development of an aggressive tumor phenotype.
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Affiliation(s)
- Jane O'Hara
- Endocrine Oncology Research Group, Department of Surgery and Epidemiology, Royal College of Surgeons in Ireland, University College Dublin, Dublin, Ireland
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Brennan EP, Morine MJ, Walsh DW, Roxburgh SA, Lindenmeyer MT, Brazil DP, Gaora PÓ, Roche HM, Sadlier DM, Cohen CD, Godson C, Martin F. Next-generation sequencing identifies TGF-β1-associated gene expression profiles in renal epithelial cells reiterated in human diabetic nephropathy. Biochim Biophys Acta Mol Basis Dis 2012; 1822:589-99. [PMID: 22266139 DOI: 10.1016/j.bbadis.2012.01.008] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 01/06/2012] [Accepted: 01/08/2012] [Indexed: 01/09/2023]
Abstract
Transforming growth factor-beta (TGF-β1) is implicated in the onset and progression of renal fibrosis and diabetic nephropathy (DN), leading to a loss of epithelial characteristics of tubular cells. The transcriptional profile of renal tubular epithelial cells stimulated with TGF-β1 was assessed using RNA-Seq, with 2027 differentially expressed genes identified. Promoter analysis of transcription factor binding sites in the TGF-β1 responsive gene set predicted activation of multiple transcriptional networks, including NFκB. Comparison of RNA-Seq with microarray data from identical experimental conditions identified low abundance transcripts exclusive to RNA-Seq data. We compared these findings to human disease by analyzing transcriptomic data from renal biopsies of patients with DN versus control groups, identifying a shared subset of 179 regulated genes. ARK5, encoding an AMP-related kinase, and TGFBI - encoding transforming growth factor, beta-induced protein were induced by TGF-β1 and also upregulated in human DN. Suppression of ARK5 attenuated fibrotic responses of renal epithelia to TGF-β1 exposure; and silencing of TGFBI induced expression of the epithelial cell marker - E-cadherin. We identified low abundance transcripts in sequence data and validated expression levels of several transcripts (ANKRD56, ENTPD8) in tubular enriched kidney biopsies of DN patients versus living donors. In conclusion, we have defined a TGF-β1-driven pro-fibrotic signal in renal epithelial cells that is also evident in the DN renal transcriptome.
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Affiliation(s)
- Eoin P Brennan
- UCD Diabetes Research Centre, UCD Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin 4, Ireland
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McCartan D, Bolger JC, Fagan A, Byrne C, Hao Y, Qin L, McIlroy M, Xu J, Hill AD, Gaora PÓ, Young LS. Global characterization of the SRC-1 transcriptome identifies ADAM22 as an ER-independent mediator of endocrine-resistant breast cancer. Cancer Res 2011; 72:220-9. [PMID: 22072566 DOI: 10.1158/0008-5472.can-11-1976] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The development of breast cancer resistance to endocrine therapy results from an increase in cellular plasticity that permits the emergence of a hormone-independent tumor. The steroid coactivator protein SRC-1, through interactions with developmental proteins and other nonsteroidal transcription factors, drives this tumor adaptability. In this discovery study, we identified ADAM22, a non-protease member of the ADAM family of disintegrins, as a direct estrogen receptor (ER)-independent target of SRC-1. We confirmed SRC-1 as a regulator of ADAM22 by molecular, cellular, and in vivo studies. ADAM22 functioned in cellular migration and differentiation, and its levels were increased in endocrine resistant-tumors compared with endocrine-sensitive tumors in mouse xenograft models of human breast cancer. Clinically, ADAM22 was found to serve as an independent predictor of poor disease-free survival. Taken together, our findings suggest that SRC-1 switches steroid-responsive tumors to a steroid-resistant state in which the SRC-1 target gene ADAM22 has a critical role, suggesting this molecule as a prognostic and therapeutic drug target that could help improve the treatment of endocrine-resistant breast cancer.
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Affiliation(s)
- Damian McCartan
- Endocrine Oncology Research, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
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Krampe B, Fagan A, Gaora PÓ, Al-Rubeai M. Chemostat-based transcriptional analysis of growth rate change and BCL-2 over-expression in NS0 cells. Biotechnol Bioeng 2011; 108:1603-15. [DOI: 10.1002/bit.23100] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 01/14/2011] [Accepted: 02/01/2011] [Indexed: 01/22/2023]
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Cederlund ML, Vendrell V, Morrissey ME, Yin J, Gaora PÓ, Smyth VA, Higgins DG, Kennedy BN. mab21l2 transgenics reveal novel expression patterns of mab21l1 and mab21l2, and conserved promoter regulation without sequence conservation. Dev Dyn 2011; 240:745-54. [PMID: 21360786 DOI: 10.1002/dvdy.22573] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2010] [Indexed: 11/10/2022] Open
Abstract
mab21l1 and mab21l2 paralogs have widespread and dynamic expression patterns during vertebrate development. Both genes are expressed in the developing eye, midbrain, neural tube, and branchial arches. Our goal was to identify promoter regions with activity in mab21l2 expression domains. Assays of mab21l2 promoter-EGFP constructs in zebrafish embryos confirm that constructs containing 7.2 or 4.9 kb of mab21l2 promoter region are sufficient to drive expression in known (e.g., tectum, branchial arches) and unexpected domains (e.g., lens and retinal amacrine cells). A comparative analysis identifies complementary and novel expression domains of endogenous mab21l2 (e.g., lens and ventral iridocorneal canal) and mab21l1 (e.g., retinal amacrine and ganglion cells). Interestingly, therefore, despite the absence of conserved non-coding elements, a 4.9-kb mab21l2 promoter is sufficient to recapitulate expression in tissues unique to mab21l1 or mab21l2.
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Affiliation(s)
- Maria L Cederlund
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute, University College Dublin, Dublin, Ireland.
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Jennings P, Aydin S, Bennett J, McBride R, Weiland C, Tuite N, Gruber LN, Perco P, Gaora PÓ, Ellinger-Ziegelbauer H, Ahr HJ, Kooten CV, Daha MR, Prieto P, Ryan MP, Pfaller W, McMorrow T. Inter-laboratory comparison of human renal proximal tubule (HK-2) transcriptome alterations due to Cyclosporine A exposure and medium exhaustion. Toxicol In Vitro 2009; 23:486-99. [DOI: 10.1016/j.tiv.2008.12.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2008] [Revised: 12/22/2008] [Accepted: 12/23/2008] [Indexed: 11/27/2022]
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Power KA, McRedmond JP, de Stefani A, Gallagher WM, Ó Gaora P. High-throughput proteomics detection of novel splice isoforms in human platelets. PLoS One 2009; 4:e5001. [PMID: 19308253 PMCID: PMC2654914 DOI: 10.1371/journal.pone.0005001] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Accepted: 02/20/2009] [Indexed: 12/16/2022] Open
Abstract
Alternative splicing (AS) is an intrinsic regulatory mechanism of all metazoans. Recent findings suggest that 100% of multiexonic human genes give rise to splice isoforms. AS can be specific to tissue type, environment or developmentally regulated. Splice variants have also been implicated in various diseases including cancer. Detection of these variants will enhance our understanding of the complexity of the human genome and provide disease-specific and prognostic biomarkers. We adopted a proteomics approach to identify exon skip events - the most common form of AS. We constructed a database harboring the peptide sequences derived from all hypothetical exon skip junctions in the human genome. Searching tandem mass spectrometry (MS/MS) data against the database allows the detection of exon skip events, directly at the protein level. Here we describe the application of this approach to human platelets, including the mRNA-based verification of novel splice isoforms of ITGA2, NPEPPS and FH. This methodology is applicable to all new or existing MS/MS datasets.
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Affiliation(s)
- Karen A. Power
- UCD Conway Institute and UCD School of Biomolecular & Biomedical Sciences, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - James P. McRedmond
- UCD Conway Institute and UCD School of Biomolecular & Biomedical Sciences, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | | | - William M. Gallagher
- UCD Conway Institute and UCD School of Biomolecular & Biomedical Sciences, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Peadar Ó Gaora
- UCD Conway Institute and UCD School of Medicine & Medical Sciences, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
- * E-mail:
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