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Comprehensive annotation of splice junctions supports pervasive alternative splicing at the BRCA1 locus: a report from the ENIGMA consortium (2014)

Colombo, M., Blok, M. J., Whiley, P., Santamarina, M., Gutierrez-Enriquez, S., Romero, A., Garre, P., Becker, A., Smith, L. D., De Vecchi, G., Brandao, R. D., Tserpelis, D., Brown, M., Blanco, A., Bonache, S., Menendez, M., Houdayer, C., Foglia, C., Fackenthal, J. D., Baralle, D., Wappenschmidt, B., k; Con; Fa; B Investigators, Diaz-Rubio, E., Caldes, T., Walker, L., Diez, O., Vega, A., Spurdle, A. B., Radice, P., De La Hoya, M.

Oxford University Press

In: Human Molecular Genetics

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Publication Date: 2014-06-21

Description: Loss-of-function germline mutations in BRCA1 (MIM #113705) confer markedly increased risk of breast and ovarian cancer. The full-length transcript codifies for a protein involved in DNA repair pathways and cell-cycle checkpoints. Several BRCA1 splicing isoforms have been described in public domain databases, but the physiological role (if any) of BRCA1 alternative splicing remains to be established. An accurate description of ‘naturally occurring’ alternative splicing at this locus is a prerequisite to understand its biological significance. However, a systematic analysis of alternative splicing at the BRCA1 locus is yet to be conducted. Here, the Evidence-Based Network for the Interpretation of Germ-Line Mutant Alleles consortium combines RT-PCR, exon scanning, cloning, sequencing and relative semi-quantification to describe naturally occurring BRCA1 alternative splicing with unprecedented resolution. The study has been conducted in blood-related RNA sources, commonly used for clinical splicing assays, as well as in one healthy breast tissue. We have characterized a total of 63 BRCA1 alternative splicing events, including 35 novel findings. A minimum of 10 splicing events (1Aq, 5, 5q, 8p, 9, (9,10), 9_11, 11q, 13p and 14p) represent a substantial fraction of the full-length expression level (ranging from 5 to 100%). Remarkably, our data indicate that BRCA1 alternative splicing is similar in blood and breast, a finding supporting the clinical relevance of blood-based in vitro splicing assays. Overall, our data suggest an alternative splicing model in which most non-mutually exclusive alternative splicing events are randomly combined into individual mRNA molecules to produce hundreds of different BRCA1 isoforms.

Print ISSN: 0964-6906

Electronic ISSN: 1460-2083

Topics: Biology , Medicine

Published by Oxford University Press

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Linking the p53 tumour suppressor pathway to somatic cell reprogramming (2009)

T. Kawamura ; J. Suzuki ; Y. V. Wang ; [et al.]

Nature Publishing Group (NPG)

In: Nature. 460(7259): 1140-4. doi: 10.1038/nature08311.

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Publication Date: 2009-08-12

Description: Reprogramming somatic cells to induced pluripotent stem (iPS) cells has been accomplished by expressing pluripotency factors and oncogenes, but the low frequency and tendency to induce malignant transformation compromise the clinical utility of this powerful approach. We address both issues by investigating the mechanisms limiting reprogramming efficiency in somatic cells. Here we show that reprogramming factors can activate the p53 (also known as Trp53 in mice, TP53 in humans) pathway. Reducing signalling to p53 by expressing a mutated version of one of its negative regulators, by deleting or knocking down p53 or its target gene, p21 (also known as Cdkn1a), or by antagonizing reprogramming-induced apoptosis in mouse fibroblasts increases reprogramming efficiency. Notably, decreasing p53 protein levels enabled fibroblasts to give rise to iPS cells capable of generating germline-transmitting chimaeric mice using only Oct4 (also known as Pou5f1) and Sox2. Furthermore, silencing of p53 significantly increased the reprogramming efficiency of human somatic cells. These results provide insights into reprogramming mechanisms and suggest new routes to more efficient reprogramming while minimizing the use of oncogenes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735889/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735889/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kawamura, Teruhisa -- Suzuki, Jotaro -- Wang, Yunyuan V -- Menendez, Sergio -- Morera, Laura Batlle -- Raya, Angel -- Wahl, Geoffrey M -- Izpisua Belmonte, Juan Carlos -- 5 R01 CA061449/CA/NCI NIH HHS/ -- 5 R01 CA100845/CA/NCI NIH HHS/ -- R01 CA061449/CA/NCI NIH HHS/ -- R01 CA061449-30/CA/NCI NIH HHS/ -- R01 CA100845/CA/NCI NIH HHS/ -- R01 CA100845-05/CA/NCI NIH HHS/ -- R33 HL088293/HL/NHLBI NIH HHS/ -- R33 HL088293-03/HL/NHLBI NIH HHS/ -- England -- Nature. 2009 Aug 27;460(7259):1140-4. doi: 10.1038/nature08311. Epub 2009 Aug 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19668186" target="_blank"〉PubMed〈/a〉

Keywords: Animals ; Cells, Cultured ; Cellular Reprogramming/*physiology ; Cyclin-Dependent Kinase Inhibitor p21/deficiency/genetics/metabolism ; Down-Regulation ; Embryo, Mammalian/cytology ; Female ; Fibroblasts/cytology/metabolism ; Humans ; Keratinocytes ; Male ; Mice ; Mice, Inbred C57BL ; Pluripotent Stem Cells/*cytology/*metabolism ; Tumor Suppressor Protein p53/deficiency/genetics/*metabolism

Print ISSN: 0028-0836

Electronic ISSN: 1476-4687

Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics

Published by Nature Publishing Group (NPG)

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The histone variant macroH2A suppresses melanoma progression through regulation of CDK8 (2010)

A. Kapoor ; M. S. Goldberg ; L. K. Cumberland ; [et al.]

Nature Publishing Group (NPG)

In: Nature. 468(7327): 1105-9. doi: 10.1038/nature09590.

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Publication Date: 2010-12-24

Description: Cancer is a disease consisting of both genetic and epigenetic changes. Although increasing evidence demonstrates that tumour progression entails chromatin-mediated changes such as DNA methylation, the role of histone variants in cancer initiation and progression currently remains unclear. Histone variants replace conventional histones within the nucleosome and confer unique biological functions to chromatin. Here we report that the histone variant macroH2A (mH2A) suppresses tumour progression of malignant melanoma. Loss of mH2A isoforms, histone variants generally associated with condensed chromatin and fine-tuning of developmental gene expression programs, is positively correlated with increasing malignant phenotype of melanoma cells in culture and human tissue samples. Knockdown of mH2A isoforms in melanoma cells of low malignancy results in significantly increased proliferation and migration in vitro and growth and metastasis in vivo. Restored expression of mH2A isoforms rescues these malignant phenotypes in vitro and in vivo. We demonstrate that the tumour-promoting function of mH2A loss is mediated, at least in part, through direct transcriptional upregulation of CDK8. Suppression of CDK8, a colorectal cancer oncogene, inhibits proliferation of melanoma cells, and knockdown of CDK8 in cells depleted of mH2A suppresses the proliferative advantage induced by mH2A loss. Moreover, a significant inverse correlation between mH2A and CDK8 expression levels exists in melanoma patient samples. Taken together, our results demonstrate that mH2A is a critical component of chromatin that suppresses the development of malignant melanoma, a highly intractable cutaneous neoplasm.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057940/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057940/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kapoor, Avnish -- Goldberg, Matthew S -- Cumberland, Lara K -- Ratnakumar, Kajan -- Segura, Miguel F -- Emanuel, Patrick O -- Menendez, Silvia -- Vardabasso, Chiara -- Leroy, Gary -- Vidal, Claudia I -- Polsky, David -- Osman, Iman -- Garcia, Benjamin A -- Hernando, Eva -- Bernstein, Emily -- 5P30CA016087-27/CA/NCI NIH HHS/ -- CA109388/CA/NCI NIH HHS/ -- R21 CA150117/CA/NCI NIH HHS/ -- R21 CA150117-01/CA/NCI NIH HHS/ -- R21 CA150117-02/CA/NCI NIH HHS/ -- R21CA150117/CA/NCI NIH HHS/ -- England -- Nature. 2010 Dec 23;468(7327):1105-9. doi: 10.1038/nature09590.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Oncological Sciences, Mount Sinai School of Medicine, 1425 Madison Avenue, New York, New York 10029, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21179167" target="_blank"〉PubMed〈/a〉

Keywords: Animals ; Cell Line, Tumor ; Cell Movement ; Cell Proliferation ; Cyclin-Dependent Kinase 8/*metabolism ; Disease Progression ; Gene Expression Profiling ; *Gene Expression Regulation, Neoplastic ; Gene Knockdown Techniques ; HCT116 Cells ; Histones/deficiency/genetics/*metabolism ; Humans ; Melanoma/*pathology/physiopathology ; Melanoma, Experimental ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Neoplasm Metastasis/*pathology/physiopathology ; Rats ; Up-Regulation

Print ISSN: 0028-0836

Electronic ISSN: 1476-4687

Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics

Published by Nature Publishing Group (NPG)

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The leukemogenicity of AML1-ETO is dependent on site-specific lysine acetylation (2011)

L. Wang ; A. Gural ; X. J. Sun ; [et al.]

American Association for the Advancement of Science (AAAS)

In: Science. 333(6043): 765-9. doi: 10.1126/science.1201662.

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Publication Date: 2011-07-19

Description: The chromosomal translocations found in acute myelogenous leukemia (AML) generate oncogenic fusion transcription factors with aberrant transcriptional regulatory properties. Although therapeutic targeting of most leukemia fusion proteins remains elusive, the posttranslational modifications that control their function could be targetable. We found that AML1-ETO, the fusion protein generated by the t(8;21) translocation, is acetylated by the transcriptional coactivator p300 in leukemia cells isolated from t(8;21) AML patients, and that this acetylation is essential for its self-renewal-promoting effects in human cord blood CD34(+) cells and its leukemogenicity in mouse models. Inhibition of p300 abrogates the acetylation of AML1-ETO and impairs its ability to promote leukemic transformation. Thus, lysine acetyltransferases represent a potential therapeutic target in AML.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3251012/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3251012/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Lan -- Gural, Alexander -- Sun, Xiao-Jian -- Zhao, Xinyang -- Perna, Fabiana -- Huang, Gang -- Hatlen, Megan A -- Vu, Ly -- Liu, Fan -- Xu, Haiming -- Asai, Takashi -- Xu, Hao -- Deblasio, Tony -- Menendez, Silvia -- Voza, Francesca -- Jiang, Yanwen -- Cole, Philip A -- Zhang, Jinsong -- Melnick, Ari -- Roeder, Robert G -- Nimer, Stephen D -- GM62437/GM/NIGMS NIH HHS/ -- R01 GM062437/GM/NIGMS NIH HHS/ -- R01 GM062437-12/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2011 Aug 5;333(6043):765-9. doi: 10.1126/science.1201662. Epub 2011 Jul 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Pharmacology and Chemistry Program, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21764752" target="_blank"〉PubMed〈/a〉

Keywords: Acetylation ; Animals ; Cell Line ; Cell Line, Tumor ; *Cell Transformation, Neoplastic ; Core Binding Factor Alpha 2 Subunit/chemistry/*metabolism ; E1A-Associated p300 Protein/antagonists & inhibitors/*metabolism ; Fetal Blood/cytology ; Gene Expression Profiling ; Hematopoietic Stem Cells/*cytology/physiology ; Humans ; Leukemia, Myeloid, Acute/*metabolism/pathology ; Lysine/*metabolism ; Mice ; Mice, Inbred C57BL ; Mutant Proteins/metabolism ; Oncogene Proteins, Fusion/chemistry/*metabolism ; Preleukemia/metabolism/pathology ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Processing, Post-Translational ; Transcriptional Activation ; Tumor Cells, Cultured

Print ISSN: 0036-8075

Electronic ISSN: 1095-9203

Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics

Published by American Association for the Advancement of Science (AAAS)

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3, 4-Dimethylpyrazole phosphate reduces nitrous oxide emissions from grassland after slurry application (2005)

Merino, P. ; Menéndez, S. ; Pinto, M. ; [et al.]

Oxford, UK : Blackwell Publishing Ltd

Soil use and management 21 (2005), S. 0

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ISSN: 1475-2743

Source: Blackwell Publishing Journal Backfiles 1879-2005

Topics: Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition

Notes: Abstract. A field study was conducted to assess the effect of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP), applied at a rate of 1 kg ha−1, on nitrous oxide (N2O) emissions, forage production and N extraction from a grassland soil after cattle slurry applications in autumn and spring. Nitrous oxide emissions were measured daily or weekly using the closed chamber technique. DMPP efficiency after slurry application was lower in spring (16.7 °C mean soil temperature) than in autumn (11.4 °C mean soil temperature). Thus, DMPP was able to maintain soil mineral N in the ammonium form for 22 days and reduce cumulative N2O emissions by 69% in autumn, while in spring its effect on soil mineral N lasted for 7–14 days, reducing cumulative N2O losses by 48%. Furthermore, application of DMPP after slurry did not decrease biomass yield or N uptake.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1111/j.1475-2743.2005.tb00106.x

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REMOVAL OF LISTERIA SPP. IN A CHEESE FACTORY (1997)

MENENDEZ, S. ; GODINEZ, Ma.R. ; RODRIGUEZ-OTERO, J.L. ; [et al.]

Oxford, UK : Blackwell Publishing Ltd

Journal of food safety 17 (1997), S. 0

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ISSN: 1745-4565

Source: Blackwell Publishing Journal Backfiles 1879-2005

Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Process Engineering, Biotechnology, Nutrition Technology

Notes: A total of 311 samples of 10 mL for liquids and 400-cm2 for surfaces were analyzed in a cheese plant in Galicia (Spain) within a period of 10 months (Feb.-Nov. 1996). Forty-six samples were positive for Listeria spp., 36 of which corresponded to L. innocua, 8 to L. monocytogenes and 2 to L. welshimeri. Twenty percent of raw milk samples were Listeria-positive. Listeria was initially detected on some surfaces of production and ripening rooms, but was never detected after replacing old iron machinery with stainless steel machinery, avoiding the movement of the plant equipment outside the factory building, eliminating wooden boards in the ripening chambers and modifying the disinfection system.; Accepted for Publication May 23, 1997

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1111/j.1745-4565.1997.tb00182.x

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