publication . Article . Other literature type . 2012

Analysis of C. elegans intestinal gene expression and polyadenylation by fluorescence-activated nuclei sorting and 3′-end-seq

Zhe Ji; Mainul Hoque; Nigel Rust; Jane Mellor; Bin Tian; Michael O. Hengartner; Andre Furger; Cathy Browne; Helen E. Sharpe; Simon Haenni; ...
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  • Published: 01 Jul 2012 Journal: Nucleic Acids Research, volume 40, issue 13, pages 6,304-6,318 (issn: 0305-1048, eissn: 1362-4962, Copyright policy)
  • Publisher: Oxford University Press
Abstract
Despite the many advantages of Caenorhabditis elegans, biochemical approaches to study tissue-specific gene expression in post-embryonic stages are challenging. Here, we report a novel experimental approach for efficient determination of tissue-specific transcriptomes involving the rapid release and purification of nuclei from major tissues of post-embryonic animals by fluorescence-activated nuclei sorting (FANS), followed by deep sequencing of linearly amplified 3'-end regions of transcripts (3'-end-seq). We employed these approaches to compile the transcriptome of the developed C. elegans intestine and used this to analyse tissue-specific cleavage and polyaden...
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doi: 10.1093/nar/gks282 , 10.5167/uzh-61843
pmc: PMC3401467
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Subjects
free text keywords: RNA, Genetics, Institute of Molecular Life Sciences, 570 Life sciences; biology, Gene expression, Deep sequencing, Cell nucleus, medicine.anatomical_structure, medicine, Gene, Cell biology, Caenorhabditis elegans, biology.organism_classification, biology, Molecular biology, Transcriptome, Sequence analysis, Polyadenylation
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Funded by
SNSF| Apoptosis in the nematode C. elegans
Project
Apoptosis in the nematode C. elegans
  • Funder: Swiss National Science Foundation (SNSF)
  • Project Code: 3100A0B-128675
  • Funding stream: Project funding | Project funding (Div. I-III)
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54 references, page 1 of 4

Antoshechkin, I, Sternberg, PW. The versatile worm: genetic and genomic resources for Caenorhabditis elegans research. Nat. Rev. Genet.. 2007; 8: 518-532 [OpenAIRE] [PubMed]

McGhee, JD, Sleumer, MC, Bilenky, M, Wong, K, McKay, SJ, Goszczynski, B, Tian, H, Krich, ND, Khattra, J, Holt, RA. The ELT-2 GATA-factor and the global regulation of transcription in the C. elegans intestine. Dev. Biol.. 2007; 302: 627-645 [OpenAIRE] [PubMed]

Zhang, Y, Ma, C, Delohery, T, Nasipak, B, Foat, BC, Bounoutas, A, Bussemaker, HJ, Kim, SK, Chalfie, M. Identification of genes expressed in C. elegans touch receptor neurons. Nature. 2002; 418: 331-335 [PubMed]

Christensen, M, Estevez, A, Yin, X, Fox, R, Morrison, R, McDonnell, M, Gleason, C, Miller, DM, Strange, K. A primary culture system for functional analysis of C. elegans neurons and muscle cells. Neuron. 2002; 33: 503-514 [OpenAIRE] [PubMed]

Strange, K, Christensen, M, Morrison, R. Primary culture of Caenorhabditis elegans developing embryo cells for electrophysiological, cell biological and molecular studies. Nat. Protoc.. 2007; 2: 1003-1012 [PubMed]

Strange, K, Morrison, R. In vitro culture of C. elegans somatic cells. Methods Mol. Biol.. 2006; 351: 265-273 [PubMed]

Celniker, SE, Dillon, LA, Gerstein, MB, Gunsalus, KC, Henikoff, S, Karpen, GH, Kellis, M, Lai, EC, Lieb, JD, MacAlpine, DM. Unlocking the secrets of the genome. Nature. 2009; 459: 927-930 [OpenAIRE] [PubMed]

Roy, PJ, Stuart, JM, Lund, J, Kim, SK. Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature. 2002; 418: 975-979 [PubMed]

Pauli, F, Liu, Y, Kim, YA, Chen, PJ, Kim, SK. Chromosomal clustering and GATA transcriptional regulation of intestine-expressed genes in C. elegans. Development. 2006; 133: 287-295 [OpenAIRE] [PubMed]

Spencer, WC, Zeller, G, Watson, JD, Henz, SR, Watkins, KL, McWhirter, RD, Petersen, S, Sreedharan, VT, Widmer, C, Jo, J. A spatial and temporal map of C. elegans gene expression. Genome Res.. 2011; 21: 325-341 [OpenAIRE] [PubMed]

Minard, ME, Jain, AK, Barton, MC. Analysis of epigenetic alterations to chromatin during development. Genesis. 2009; 47: 559-572 [OpenAIRE] [PubMed]

D'Alessio, JA, Wright, KJ, Tjian, R. Shifting players and paradigms in cell-specific transcription. Mol. Cell. 2009; 36: 924-931 [OpenAIRE] [PubMed]

Wang, ET, Sandberg, R, Luo, S, Khrebtukova, I, Zhang, L, Mayr, C, Kingsmore, SF, Schroth, GP, Burge, CB. Alternative isoform regulation in human tissue transcriptomes. Nature. 2008; 456: 470-476 [OpenAIRE] [PubMed]

Neilson, JR, Sandberg, R. Heterogeneity in mammalian RNA 3' end formation. Exp. Cell Res.. 2010; 316: 1357-1364 [OpenAIRE] [PubMed]

Lutz, CS, Moreira, A. Alternative mRNA polyadenylation in eukaryotes: an effective regulator of gene expression. Wiley Interdiscip. Rev. RNA. 2011; 2: 23-31 [OpenAIRE] [PubMed]

54 references, page 1 of 4
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