Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags

Gorodkin, Jan; Cirera, Susanna; Hedegaard, Jakob; Gilchrist, Michael J.; Panitz, Frank; Jørgensen, Claus B.; Scheibye-Knudsen, Karsten; Arvin, Troels; Lumholdt, Steen; Sawera, Milena; Green, Trine; Nielsen, Bente J.; Havgaard, Jakob Hull; Rosenkilde, Carina; Wang, Junjun; Li, Heng; Li, Ruiqiang; Liu, Bin; Hu, Songnian; Dong, Wei; Wei, Li; Yu, Jun; Wang, Jian; Stærfeldt, Hans‐Henrik; Wernersson, Rasmus; Madsen, Lone Bruhn; Thomsen, Bo; Hornshøj, Henrik; Zhan, Bin; Wang, Xuegang; Wang, Xuefei; Bolund, Lars; Brunak, Søren; Yang, Huanming; Berthou, Christian; Fredholm, Merete

doi:10.1186/gb-2007-8-4-r45

Cited by 70 publications

(83 citation statements)

References 53 publications

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“…Previous attempts utilizing porcine-specific expressed sequence tags to define neuron-associated genes were limited based on the fact that whole tissue was used rather than isolated neurons (23,24). The relatively new Affymetrix Gene Chip 1 Porcine Genome Array represents 24,123 probe sets of Sus scrofa genes, while the new annotation file from Tsai et al (7) contains 12,124 unique genes.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Profile and Cytogenetic Analysis of Immortalized Neuronally Restricted Progenitor Cells Derived from the Porcine Olfactory Bulb

Uebing-Czipura

Dawson

Rutherford

et al. 2009

Animal Biotechnology

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Recently, we established and phenotypically characterized an immortalized porcine olfactory bulb neuroblast cell line, OBGF400 (1). To facilitate the future application of these cells in studies of neurological dysfunctions and neuronal pathogen interactions, a comprehensive knowledge of their genomic variability and overall gene expression capacity was pursued. Accordingly, the OBGF400 cells were subjected to karyotyping and more extensive transcriptome analyses. Cytogenetic characterization of these cells revealed a genetic mosaicism of neuronal hyperdiploidy. A direct comparison of the OBGF400 cell transcriptome pattern, generated by utilizing the Affymetrix GeneChip(R) Porcine Genome Array, to that of a non-neural, porcine epithelial cell line facilitated the identification of 831 probe sets preferentially hybridized by the neuroblast transcripts. Subsequent functional annotation of these OBGF400 RNAs using the Database for Annotation, Visualization and Integrated Discovery 2008 enabled their allocation to the corresponding gene ontology biological process term, thereby assisting the recognition of key elements involved in the regulation of neuronal signal transduction and neurogenesis.

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Section: Discussionmentioning

confidence: 99%

Transcriptome Profile and Cytogenetic Analysis of Immortalized Neuronally Restricted Progenitor Cells Derived from the Porcine Olfactory Bulb

Uebing-Czipura

Dawson

Rutherford

et al. 2009

Animal Biotechnology

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“…To further verify the pFcRn-S, the nucleotide sequence of the pFcRn-S (EF208068) was used to search the EST database using Megablast (optimized for highly similar sequences), (www.ncbi.nlm.hig.gov/blast). At least three EST sequences, BP142288.1, EW289930.1, and EW284029.1, were identified [34,35] and the nucleotides spanning α2 and α3 domain were perfectly aligned (Fig.2D). This suggests that the pFcRn-S lacks of α2 domain of the full length counterpart.…”

Section: Splicing Form Of Pfcrn Lacks α2 Domainmentioning

confidence: 99%

Identification and characterization of an alternatively spliced variant of the MHC class I-related porcine neonatal Fc receptor for IgG

Tuo

Liu

et al. 2008

Developmental & Comparative Immunology

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The neonatal Fc receptor for IgG (FcRn) functions to transport maternal IgG to the fetal/neonatal animals and protects IgG from catabolism. The present study identified two pFcRn cDNAs (1.071 kb and 0.795 kb) from intestinal epithelial cells. The corresponding mRNA transcripts were detected in porcine kidney cell line LLC-PK1, peripheral blood mononuclear cells and porcine tissues by RT-PCR and Northern blot. Sequence analysis showed that the 1.071 kb cDNA encodes the full-length pFcRn (pFcRn-L); whereas the 0.795 kb cDNA codes for a truncated pFcRn (pFcRn-S) with deletion of 92 amino acids matching to the alpha2 domain of pFcRn-L. The pFcRn-L was constitutively expressed by epithelial cells; however, pFcRn-S was not detectable in porcine tissues and cell lines although its transcript was abundant. Despite of the lack of native pFcRn-S, pFcRn-S was readily detected in transfected cells. Recombinant pFcRn-L was confirmed to bind IgG at pH 6.0, but not pH 7.5; however, pFcRn-S failed to bind IgG at both pH 5.0-6.0 and 7.5. The pFcRn-L was expressed on the cell surface and mainly localized in early endosomes. In contrast, pFcRn-S was absent from cell surface and primarily localized in the lysosome and pFcRn-S trafficking to lysosomes was independent of β2m. The accumulation of pFcRn-S in the lysosome may explain the absence detection of native pFcRn-S protein expression. In addition, the trafficking of pFcRn-S to the lysosomal compartment suggests that in addition to sorting signals in its cytoplasmic tail, the FcRn structural integrity may be important for proper intracellular trafficking and function.

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“…Regarding technological aspects related to drycured high-quality products and the meat industry, an adequate layer of fat is required for the seasoning process of PDO products, such as dry-cured hams (Bosi & Russo 2004;Candek-Potokar & Skrlep 2012). During the last decade, pig transcriptomic data have been obtained initially by expressed sequence tag sequencing (Mikawa et al 2004;Uenishi et al 2004Uenishi et al , 2007Chen et al 2006;Gorodkin et al 2007) and microarrays (Hornshøj et al 2007;Ferraz et al 2008;Moon et al 2009), which allowed the comparison of gene expression levels in several pig tissues. More recently, the RNA-seq approach was used to compare the transcription profile of different pig fat tissues or different pig breeds (Chen et al 2011;Li et al 2012;Corominas et al 2013;Jiang et al 2013;Zhou et al 2013;Sodhi et al, 2014;Toedebusch et al 2014;Wang et al 2014).…”

mentioning

confidence: 99%

Transcriptional profiling of subcutaneous adipose tissue in Italian Large White pigs divergent for backfat thickness

Zambonelli¹,

Gaffo

Zappaterra³

et al. 2016

Animal Genetics

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Fat deposition is a widely studied trait in pigs because of its implications with animal growth efficiency, technological and nutritional characteristics of meat products, but the global framework of the biological and molecular processes regulating fat deposition in pigs is still incomplete. This study describes the backfat tissue transcription profile in Italian Large White pigs and reports genes differentially expressed between fat and lean animals according to RNA-seq data. The backfat transcription profile was characterised by the expression of 23 483 genes, of which 54.1% were represented by known genes. Of 63 418 expressed transcripts, about 80% were non-previously annotated isoforms. By comparing the expression level of fat vs. lean pigs, we detected 86 robust differentially expressed transcripts, 72 more highly expressed (e.g. ACP5, BCL2A1, CCR1, CD163, CD1A, EGR2, ENPP1, GPNMB, INHBB, LYZ, MSR1, OLR1, PIK3AP1, PLIN2, SPP1, SLC11A1, STC1) and 14 lower expressed (e.g. ADSSL1, CDO1, DNAJB1, HSPA1A, HSPA1B, HSPA2, HSPB8, IGFBP5, OLFML3) in fat pigs. The main functional categories enriched in differentially expressed genes were immune system process, response to stimulus, cell activation and skeletal system development, for the overexpressed genes, and unfolded protein binding and stress response, for the underexpressed genes, which included five heat shock proteins. Adipose tissue alterations and impaired stress response are linked to inflammation and, in turn, to adipose tissue secretory activity, similar to what is observed in human obesity. Our results provide the opportunity to identify biomarkers of carcass fat traits to improve the pig production chain and to identify genetic factors that regulate the observed differential expression.

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Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags

Cited by 70 publications

References 53 publications

Transcriptome Profile and Cytogenetic Analysis of Immortalized Neuronally Restricted Progenitor Cells Derived from the Porcine Olfactory Bulb

Transcriptome Profile and Cytogenetic Analysis of Immortalized Neuronally Restricted Progenitor Cells Derived from the Porcine Olfactory Bulb

Identification and characterization of an alternatively spliced variant of the MHC class I-related porcine neonatal Fc receptor for IgG

Transcriptional profiling of subcutaneous adipose tissue in Italian Large White pigs divergent for backfat thickness

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