title: Extensive expression differences along porcine small intestine evidenced by transcriptome sequencing.
abstract: The aim of this study was to analyse gene expression along the small intestine (duodenum, jejunum, ileum) and in the ileal Peyer's patches in four young pigs with no clinical signs of disease by transcriptome sequencing. Multidimensional scaling evidenced that samples clustered by tissue type rather than by individual, thus prefiguring a relevant scenario to draw tissue-specific gene expression profiles. Accordingly, 1,349 genes were found differentially expressed between duodenum and jejunum, and up to 3,455 genes between duodenum and ileum. Additionally, a considerable number of differentially expressed genes were found by comparing duodenum (7,027 genes), jejunum (6,122 genes), and ileum (6,991 genes) with ileal Peyer's patches tissue. Functional analyses revealed that most of the significant differentially expressed genes along small intestinal tissues were involved in the regulation of general biological processes such as cell development, signalling, growth and proliferation, death and survival or cell function and maintenance. These results suggest that the intrinsic large turnover of intestinal tissues would have local specificities at duodenum, ileum and jejunum. In addition, in concordance with their biological function, enteric innate immune pathways were overrepresented in ileal Peyer's patches. The reported data provide an expression map of the cell pathway variation in the different small intestinal tissues. Furthermore, expression levels measured in healthy individuals could help to understand changes in gene expression that occur in dysbiosis or pathological states.
authors.affiliation: UMR1313 Génétique Animale et Biologie Intégrative, INRA, Jouy-en-Josas, France ; UMR1313 Génétique Animale et Biologie Intégrative, AgroParisTech, Jouy-en-Josas, France ; DSV/iRCM/SREIT/LREG, CEA, Jouy-en-Josas, France ; UMR1319 MICALIS, INRA, Jouy-en-Josas, France ; UMR1319 MICALIS, AgroParisTech, Jouy-en-Josas, France.
authors.forename: Núria
authors.initials: N
authors.lastname: Mach
authors.affiliation: UMR1282 ISP, INRA, Nouzilly, France ; UMR1282 ISP, Université de Tours, Tours, France.
authors.forename: Mustapha
authors.initials: M
authors.lastname: Berri
authors.affiliation: UMR444 LGC-Plateforme GET, INRA, Castanet-Tolosan, France.
authors.forename: Diane
authors.initials: D
authors.lastname: Esquerré
authors.affiliation: UMR1282 ISP, INRA, Nouzilly, France ; UMR1282 ISP, Université de Tours, Tours, France.
authors.forename: Claire
authors.initials: C
authors.lastname: Chevaleyre
authors.affiliation: UMR1313 Génétique Animale et Biologie Intégrative, INRA, Jouy-en-Josas, France ; UMR1313 Génétique Animale et Biologie Intégrative, AgroParisTech, Jouy-en-Josas, France ; DSV/iRCM/SREIT/LREG, CEA, Jouy-en-Josas, France.
authors.forename: Gaëtan
authors.initials: G
authors.lastname: Lemonnier
authors.affiliation: UE967 GEPA, INRA, Le Magneraud, France.
authors.forename: Yvon
authors.initials: Y
authors.lastname: Billon
authors.affiliation: UMR1319 MICALIS, INRA, Jouy-en-Josas, France ; UMR1319 MICALIS, AgroParisTech, Jouy-en-Josas, France.
authors.forename: Patricia
authors.initials: P
authors.lastname: Lepage
authors.affiliation: UMR1331 TOXALIM, INRA, Toulouse, France ; UMR1331 TOXALIM-INP, Université de Toulouse III, Toulouse, France.
authors.forename: Isabelle P
authors.initials: IP
authors.lastname: Oswald
authors.affiliation: UMR1319 MICALIS, INRA, Jouy-en-Josas, France ; UMR1319 MICALIS, AgroParisTech, Jouy-en-Josas, France.
authors.forename: Joël
authors.initials: J
authors.lastname: Doré
authors.affiliation: UMR1313 Génétique Animale et Biologie Intégrative, INRA, Jouy-en-Josas, France ; UMR1313 Génétique Animale et Biologie Intégrative, AgroParisTech, Jouy-en-Josas, France ; DSV/iRCM/SREIT/LREG, CEA, Jouy-en-Josas, France.
authors.forename: Claire
authors.initials: C
authors.lastname: Rogel-Gaillard
authors.affiliation: UMR1313 Génétique Animale et Biologie Intégrative, INRA, Jouy-en-Josas, France ; UMR1313 Génétique Animale et Biologie Intégrative, AgroParisTech, Jouy-en-Josas, France ; DSV/iRCM/SREIT/LREG, CEA, Jouy-en-Josas, France.
authors.forename: Jordi
authors.initials: J
authors.lastname: Estellé
mesh_terms: D000465:Algorithms; D000818:Animals; D015415:Biomarkers / Q000378:metabolism; D016000:Cluster Analysis; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D007107:Immune System; D007249:Inflammation; D007421:Intestine, Small / Q000378:metabolism*; D008297:Male; D015233:Models, Statistical; D010581:Peyer's Patches / Q000378:metabolism; D017423:Sequence Analysis, RNA; D015398:Signal Transduction; D012984:Software; D013552:Swine; D059467:Transcriptome
chemical_list: D015415:Biomarkers