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  • 1
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    Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-10-09
    Description: Recent advances in next generation sequencing have made it possible to precisely characterize all somatic coding mutations that occur during the development and progression of individual cancers. Here we used these approaches to sequence the genomes (〉43-fold coverage) and transcriptomes of an oestrogen-receptor-alpha-positive metastatic lobular breast cancer at depth. We found 32 somatic non-synonymous coding mutations present in the metastasis, and measured the frequency of these somatic mutations in DNA from the primary tumour of the same patient, which arose 9 years earlier. Five of the 32 mutations (in ABCB11, HAUS3, SLC24A4, SNX4 and PALB2) were prevalent in the DNA of the primary tumour removed at diagnosis 9 years earlier, six (in KIF1C, USP28, MYH8, MORC1, KIAA1468 and RNASEH2A) were present at lower frequencies (1-13%), 19 were not detected in the primary tumour, and two were undetermined. The combined analysis of genome and transcriptome data revealed two new RNA-editing events that recode the amino acid sequence of SRP9 and COG3. Taken together, our data show that single nucleotide mutational heterogeneity can be a property of low or intermediate grade primary breast cancers and that significant evolution can occur with disease progression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shah, Sohrab P -- Morin, Ryan D -- Khattra, Jaswinder -- Prentice, Leah -- Pugh, Trevor -- Burleigh, Angela -- Delaney, Allen -- Gelmon, Karen -- Guliany, Ryan -- Senz, Janine -- Steidl, Christian -- Holt, Robert A -- Jones, Steven -- Sun, Mark -- Leung, Gillian -- Moore, Richard -- Severson, Tesa -- Taylor, Greg A -- Teschendorff, Andrew E -- Tse, Kane -- Turashvili, Gulisa -- Varhol, Richard -- Warren, Rene L -- Watson, Peter -- Zhao, Yongjun -- Caldas, Carlos -- Huntsman, David -- Hirst, Martin -- Marra, Marco A -- Aparicio, Samuel -- England -- Nature. 2009 Oct 8;461(7265):809-13. doi: 10.1038/nature08489.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Oncology, BC Cancer Agency, 675 West 10th Avenue, Vancouver V5Z 1L3, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19812674" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Vesicular Transport/genetics ; Breast Neoplasms/*genetics/metabolism/*pathology ; DNA Mutational Analysis ; Disease Progression ; Estrogen Receptor alpha/metabolism ; Evolution, Molecular ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Genes, Neoplasm/*genetics ; Genome, Human/genetics ; Germ-Line Mutation/genetics ; Humans ; Mutagenesis/*genetics ; Mutation/*genetics ; Neoplasm Metastasis ; Nucleotides/*genetics ; RNA Editing/genetics ; Signal Recognition Particle/genetics ; Time Factors
    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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  • 2
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    Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-07-29
    Description: Follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL) are the two most common non-Hodgkin lymphomas (NHLs). Here we sequenced tumour and matched normal DNA from 13 DLBCL cases and one FL case to identify genes with mutations in B-cell NHL. We analysed RNA-seq data from these and another 113 NHLs to identify genes with candidate mutations, and then re-sequenced tumour and matched normal DNA from these cases to confirm 109 genes with multiple somatic mutations. Genes with roles in histone modification were frequent targets of somatic mutation. For example, 32% of DLBCL and 89% of FL cases had somatic mutations in MLL2, which encodes a histone methyltransferase, and 11.4% and 13.4% of DLBCL and FL cases, respectively, had mutations in MEF2B, a calcium-regulated gene that cooperates with CREBBP and EP300 in acetylating histones. Our analysis suggests a previously unappreciated disruption of chromatin biology in lymphomagenesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3210554/" 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/PMC3210554/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Morin, Ryan D -- Mendez-Lago, Maria -- Mungall, Andrew J -- Goya, Rodrigo -- Mungall, Karen L -- Corbett, Richard D -- Johnson, Nathalie A -- Severson, Tesa M -- Chiu, Readman -- Field, Matthew -- Jackman, Shaun -- Krzywinski, Martin -- Scott, David W -- Trinh, Diane L -- Tamura-Wells, Jessica -- Li, Sa -- Firme, Marlo R -- Rogic, Sanja -- Griffith, Malachi -- Chan, Susanna -- Yakovenko, Oleksandr -- Meyer, Irmtraud M -- Zhao, Eric Y -- Smailus, Duane -- Moksa, Michelle -- Chittaranjan, Suganthi -- Rimsza, Lisa -- Brooks-Wilson, Angela -- Spinelli, John J -- Ben-Neriah, Susana -- Meissner, Barbara -- Woolcock, Bruce -- Boyle, Merrill -- McDonald, Helen -- Tam, Angela -- Zhao, Yongjun -- Delaney, Allen -- Zeng, Thomas -- Tse, Kane -- Butterfield, Yaron -- Birol, Inanc -- Holt, Rob -- Schein, Jacqueline -- Horsman, Douglas E -- Moore, Richard -- Jones, Steven J M -- Connors, Joseph M -- Hirst, Martin -- Gascoyne, Randy D -- Marra, Marco A -- 1U01CA114778/CA/NCI NIH HHS/ -- HHSN261200800001E/PHS HHS/ -- P50CA130805-01/CA/NCI NIH HHS/ -- TGT-53912/Canadian Institutes of Health Research/Canada -- U24 CA143866/CA/NCI NIH HHS/ -- U24 CA143866-01/CA/NCI NIH HHS/ -- U24 CA143866-02/CA/NCI NIH HHS/ -- U24 CA143866-03/CA/NCI NIH HHS/ -- England -- Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21796119" target="_blank"〉PubMed〈/a〉
    Keywords: Chromatin/genetics/metabolism ; DNA-Binding Proteins/genetics/metabolism ; Genome, Human/genetics ; Histone Acetyltransferases/genetics/metabolism ; Histone-Lysine N-Methyltransferase/genetics/metabolism ; Histones/*metabolism ; Humans ; Loss of Heterozygosity/genetics ; Lymphoma, Follicular/enzymology/genetics ; Lymphoma, Large B-Cell, Diffuse/enzymology/genetics ; Lymphoma, Non-Hodgkin/enzymology/*genetics ; MADS Domain Proteins/genetics/metabolism ; MEF2 Transcription Factors ; Mutation/*genetics ; Myogenic Regulatory Factors/genetics/metabolism ; Neoplasm Proteins/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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  • 3
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    Conserved role of intragenic DNA methylation in regulating alternative promoters (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-07-09
    Description: Although it is known that the methylation of DNA in 5' promoters suppresses gene expression, the role of DNA methylation in gene bodies is unclear. In mammals, tissue- and cell type-specific methylation is present in a small percentage of 5' CpG island (CGI) promoters, whereas a far greater proportion occurs across gene bodies, coinciding with highly conserved sequences. Tissue-specific intragenic methylation might reduce, or, paradoxically, enhance transcription elongation efficiency. Capped analysis of gene expression (CAGE) experiments also indicate that transcription commonly initiates within and between genes. To investigate the role of intragenic methylation, we generated a map of DNA methylation from the human brain encompassing 24.7 million of the 28 million CpG sites. From the dense, high-resolution coverage of CpG islands, the majority of methylated CpG islands were shown to be in intragenic and intergenic regions, whereas less than 3% of CpG islands in 5' promoters were methylated. The CpG islands in all three locations overlapped with RNA markers of transcription initiation, and unmethylated CpG islands also overlapped significantly with trimethylation of H3K4, a histone modification enriched at promoters. The general and CpG-island-specific patterns of methylation are conserved in mouse tissues. An in-depth investigation of the human SHANK3 locus and its mouse homologue demonstrated that this tissue-specific DNA methylation regulates intragenic promoter activity in vitro and in vivo. These methylation-regulated, alternative transcripts are expressed in a tissue- and cell type-specific manner, and are expressed differentially within a single cell type from distinct brain regions. These results support a major role for intragenic methylation in regulating cell context-specific alternative promoters in gene bodies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998662/" 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/PMC3998662/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Maunakea, Alika K -- Nagarajan, Raman P -- Bilenky, Mikhail -- Ballinger, Tracy J -- D'Souza, Cletus -- Fouse, Shaun D -- Johnson, Brett E -- Hong, Chibo -- Nielsen, Cydney -- Zhao, Yongjun -- Turecki, Gustavo -- Delaney, Allen -- Varhol, Richard -- Thiessen, Nina -- Shchors, Ksenya -- Heine, Vivi M -- Rowitch, David H -- Xing, Xiaoyun -- Fiore, Chris -- Schillebeeckx, Maximiliaan -- Jones, Steven J M -- Haussler, David -- Marra, Marco A -- Hirst, Martin -- Wang, Ting -- Costello, Joseph F -- U01 ES017154/ES/NIEHS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Jul 8;466(7303):253-7. doi: 10.1038/nature09165.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20613842" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Brain/anatomy & histology/cytology/*metabolism ; Carrier Proteins/genetics ; Cell Line ; Conserved Sequence/*genetics ; CpG Islands/genetics ; *DNA Methylation ; DNA, Intergenic/genetics/metabolism ; Frontal Lobe/metabolism ; Gene Expression Regulation ; Histones/genetics/metabolism ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; Middle Aged ; Nerve Tissue Proteins ; Organ Specificity ; Promoter Regions, Genetic/*genetics ; Transcription, Genetic/genetics
    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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