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Volumn 292, Issue 7, 2017, Pages 2586-2600

Functional transcriptomics in diverse intestinal epithelial cell types reveals robust MicroRNA sensitivity in intestinal stem cells to microbial status

Author keywords

[No Author keywords available]

Indexed keywords

CELLS; CYTOLOGY; DISEASE CONTROL; GENE EXPRESSION; GENES; STEM CELLS;

EID: 85013418941     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M116.770099     Document Type: Article
Times cited : (100)

References (60)
  • 1
    • 72949133888 scopus 로고
    • The turnover and shedding of epithelial cells
    • Creamer, B., Shorter, R. G., and Bamforth, J. (1961) The turnover and shedding of epithelial cells. Gut 2, 110-118
    • (1961) Gut , vol.2 , pp. 110-118
    • Creamer, B.1    Shorter, R.G.2    Bamforth, J.3
  • 2
    • 84923788626 scopus 로고    scopus 로고
    • Gut microbiome: The peacekeepers
    • Velasquez-Manoff, M. (2015) Gut microbiome: the peacekeepers. Nature 518, S3-S11
    • (2015) Nature , vol.518 , pp. S3-S11
    • Velasquez-Manoff, M.1
  • 4
    • 85013402072 scopus 로고    scopus 로고
    • Regulation of gastrointestinal mucosal growth (Granger, D. N., and Granger, J. P., eds) Morgan & claypool life sciences
    • CA
    • Jaladanki, R. N., and Wang, J.-Y. (2011) Regulation of gastrointestinal mucosal growth (Granger, D. N., and Granger, J. P., eds) Morgan & Claypool Life Sciences, San Rafael, CA
    • (2011) San Rafael
    • Jaladanki, R.N.1    Wang, J.-Y.2
  • 8
    • 84866973849 scopus 로고    scopus 로고
    • Gut microbiota metabolism of anthocyanin promotes reverse cholesterol transport in mice via repressing miRNA-10b
    • Wang, D., Xia, M., Yan, X., Li, D., Wang, L., Xu, Y., Jin, T., and Ling, W. (2012) Gut microbiota metabolism of anthocyanin promotes reverse cholesterol transport in mice via repressing miRNA-10b. Circ. Res. 111, 967-981
    • (2012) Circ. Res , vol.111 , pp. 967-981
    • Wang, D.1    Xia, M.2    Yan, X.3    Li, D.4    Wang, L.5    Xu, Y.6    Jin, T.7    Ling, W.8
  • 12
  • 13
    • 77951496399 scopus 로고    scopus 로고
    • Sox9 expression marks a subset of CD24-expressing small intestine epithelial stem cells that form organoids in vitro
    • Gracz, A. D., Ramalingam, S., and Magness, S. T. (2010) Sox9 expression marks a subset of CD24-expressing small intestine epithelial stem cells that form organoids in vitro. Am. J. Physiol. Gastrointest. Liver Physiol. 298, G590-G600
    • (2010) Am. J. Physiol. Gastrointest. Liver Physiol. , vol.298 , pp. G590-G600
    • Gracz, A.D.1    Ramalingam, S.2    Magness, S.T.3
  • 15
    • 84907060528 scopus 로고    scopus 로고
    • Impact of diet-induced obesity on intestinal stem cells: Hyperproliferation but impaired intrinsic function that requires insulin/IGF1
    • Mah, A. T., Van Landeghem, L., Gavin, H. E., Magness, S. T., and Lund, P. K. (2014) Impact of diet-induced obesity on intestinal stem cells: hyperproliferation but impaired intrinsic function that requires insulin/IGF1. Endocrinology 155, 3302-3314
    • (2014) Endocrinology , vol.155 , pp. 3302-3314
    • Mah, A.T.1    Van Landeghem, L.2    Gavin, H.E.3    Magness, S.T.4    Lund, P.K.5
  • 16
    • 84890462958 scopus 로고    scopus 로고
    • Insulin receptor isoform switching in intestinal stem cells, progenitors, differentiated lineages and tumors: Evidence that IR-B limits proliferation
    • Andres, S. F., Simmons, J. G., Mah, A. T., Santoro, M. A., Van Landeghem, L., and Lund, P. K. (2013) Insulin receptor isoform switching in intestinal stem cells, progenitors, differentiated lineages and tumors: evidence that IR-B limits proliferation. J. Cell Sci. 126, 5645-5656
    • (2013) J. Cell Sci. , vol.126 , pp. 5645-5656
    • Andres, S.F.1    Simmons, J.G.2    Mah, A.T.3    Santoro, M.A.4    Van Landeghem, L.5    Lund, P.K.6
  • 17
    • 84945566808 scopus 로고    scopus 로고
    • SOX9 maintains reserve stem cells and preserves radioresistance in mouse small intestine
    • Roche, K. C., Gracz, A. D., Liu, X. F., Newton, V., Akiyama, H., and Magness, S. T. (2015) SOX9 maintains reserve stem cells and preserves radioresistance in mouse small intestine. Gastroenterology 149, 1553-1563.e10
    • (2015) Gastroenterology , vol.149 , pp. 1553-1563e10
    • Roche, K.C.1    Gracz, A.D.2    Liu, X.F.3    Newton, V.4    Akiyama, H.5    Magness, S.T.6
  • 21
    • 0028109959 scopus 로고
    • Microflora modulates endocrine cells in the gastrointestinal mucosa of the rat
    • Uribe, A., Alam, M., Johansson, O., Midtvedt, T., and Theodorsson, E. (1994) Microflora modulates endocrine cells in the gastrointestinal mucosa of the rat. Gastroenterology 107, 1259-1269
    • (1994) Gastroenterology , vol.107 , pp. 1259-1269
    • Uribe, A.1    Alam, M.2    Johansson, O.3    Midtvedt, T.4    Theodorsson, E.5
  • 22
    • 0029848867 scopus 로고    scopus 로고
    • The diet and gut microflora influence the distribution of enteroendocrine cells in the rat intestine
    • Sharma, R., and Schumacher, U. (1996) The diet and gut microflora influence the distribution of enteroendocrine cells in the rat intestine. Experientia 52, 664-670
    • (1996) Experientia , vol.52 , pp. 664-670
    • Sharma, R.1    Schumacher, U.2
  • 23
    • 84876414806 scopus 로고    scopus 로고
    • The gut microbiota: Masters of host development and physiology
    • Sommer, F., and Bäckhed, F. (2013) The gut microbiota: masters of host development and physiology. Nat. Rev. Microbiol. 11, 227-238
    • (2013) Nat. Rev. Microbiol. , vol.11 , pp. 227-238
    • Sommer, F.1    Bäckhed, F.2
  • 24
    • 84940624027 scopus 로고
    • Influence of conventionalization on small-intestinal mucosa of germ-free Wistar rats: Quantitative light microscopic observations
    • Ishikawa, K., Satoh, Y., Tanaka, H., and Ono, K. (1986) Influence of conventionalization on small-intestinal mucosa of germ-free Wistar rats: quantitative light microscopic observations. Acta Anat. 127, 296-302
    • (1986) Acta Anat. , vol.127 , pp. 296-302
    • Ishikawa, K.1    Satoh, Y.2    Tanaka, H.3    Ono, K.4
  • 25
    • 0014958605 scopus 로고
    • Action de la microflore totale du rat sur i'activité mitotique des cryptes de lieberkühn C. R
    • Paris
    • Guenet, J. L., Sacquet, E., Gueneau, G., and Meslin, J. C. (1970) Action de la microflore totale du rat sur i'activité mitotique des cryptes de lieberkühn. C. R. Acad. Sci. (Paris) 270, 3087-3090
    • (1970) Acad. Sci. , vol.270 , pp. 3087-3090
    • Guenet, J.L.1    Sacquet, E.2    Gueneau, G.3    Meslin, J.C.4
  • 26
    • 84946735654 scopus 로고    scopus 로고
    • Gene ontology consortium: Going forward
    • Gene Ontology Consortium. (2015) Gene Ontology Consortium: going forward. Nucleic Acids Res. 43, D1049-D1056
    • (2015) Nucleic Acids Res. , vol.43 , pp. D1049-D1056
    • Gene, O.C.1
  • 29
    • 84883651731 scopus 로고    scopus 로고
    • Beta cell 5'-shifted isomiRs are candidate regulatory hubs in type 2 diabetes
    • Baran-Gale, J., Fannin, E. E., Kurtz, C. L., and Sethupathy, P. (2013) Beta cell 5'-shifted isomiRs are candidate regulatory hubs in type 2 diabetes. PLoS ONE 8, e73240
    • (2013) PLoS ONE , vol.8 , pp. e73240
    • Baran-Gale, J.1    Fannin, E.E.2    Kurtz, C.L.3    Sethupathy, P.4
  • 30
    • 45749135780 scopus 로고    scopus 로고
    • Inducible expression of microRNA-194 is regulated by HNF-1 during intestinal epithelial cell differentiation
    • Hino, K., Tsuchiya, K., Fukao, T., Kiga, K., Okamoto, R., Kanai, T., and Watanabe, M. (2008) Inducible expression of microRNA-194 is regulated by HNF-1 during intestinal epithelial cell differentiation. RNA 14, 1433-1442
    • (2008) RNA , vol.14 , pp. 1433-1442
    • Hino, K.1    Tsuchiya, K.2    Fukao, T.3    Kiga, K.4    Okamoto, R.5    Kanai, T.6    Watanabe, M.7
  • 34
    • 84946075782 scopus 로고    scopus 로고
    • The microRNA repertoire in enteroendocrine cells: Identification of miR-375 as a potential regulator of the enteroendocrine lineage
    • Knudsen, L. A., Petersen, N., Schwartz, T. W., and Egerod, K. L. (2015) The microRNA repertoire in enteroendocrine cells: Identification of miR-375 as a potential regulator of the enteroendocrine lineage. Endocrinology 156, 3971-3983
    • (2015) Endocrinology , vol.156 , pp. 3971-3983
    • Knudsen, L.A.1    Petersen, N.2    Schwartz, T.W.3    Egerod, K.L.4
  • 37
    • 84924629414 scopus 로고    scopus 로고
    • Moderated estimation offold change and dispersion for RNA-seq data with DESeq2
    • Love, M. I., Huber, W., and Anders, S. (2014) Moderated estimation offold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550
    • (2014) Genome Biol. , vol.15 , pp. 550
    • Love, M.I.1    Huber, W.2    Anders, S.3
  • 38
    • 84902548164 scopus 로고    scopus 로고
    • The emerging role of miR-375 in cancer
    • Yan, J.-W., Lin, J.-S., and He, X.-X. (2014) The emerging role of miR-375 in cancer. Int. J. Cancer 135, 1011-1018
    • (2014) Int. J. Cancer , vol.135 , pp. 1011-1018
    • Yan, J.-W.1    Lin, J.-S.2    He, X.-X.3
  • 39
    • 84876068310 scopus 로고    scopus 로고
    • MiR-375 regulates rat alveolar epithelial cell trans-differentiation by inhibiting Wnt/-catenin pathway
    • Wang, Y., Huang, C., Reddy Chintagari, N., Bhaskaran, M., Weng, T., Guo, Y., Xiao, X., and Liu, L. (2013) miR-375 regulates rat alveolar epithelial cell trans-differentiation by inhibiting Wnt/-catenin pathway. Nucleic Acids Res. 41, 3833-3844
    • (2013) Nucleic Acids Res , vol.41 , pp. 3833-3844
    • Wang, Y.1    Huang, C.2    Reddy Chintagari, N.3    Bhaskaran, M.4    Weng, T.5    Guo, Y.6    Xiao, X.7    Liu, L.8
  • 40
    • 84890479052 scopus 로고    scopus 로고
    • miR-375 inhibits proliferation of mouse pancreatic progenitor cells by targeting YAP1
    • Zhang, Z.-W., Men, T., Feng, R.-C., Li, Y.-C., Zhou, D., and Teng, C.-B. (2013) miR-375 inhibits proliferation of mouse pancreatic progenitor cells by targeting YAP1. Cell. Physiol. Biochem. 32, 1808-1817
    • (2013) Cell. Physiol. Biochem. , vol.32 , pp. 1808-1817
    • Zhang, Z.-W.1    Men, T.2    Feng, R.-C.3    Li, Y.-C.4    Zhou, D.5    Teng, C.-B.6
  • 41
    • 84892795457 scopus 로고    scopus 로고
    • MicroRNA 375 mediates palmitate-induced enteric neuronal damage and high-fat diet-induced delayed intestinal transit in mice
    • Nezami, B. G., Mwangi, S. M., Lee, J. E., Jeppsson, S., Anitha, M., Yarandi, S. S., Farris, A. B., 3rd, and Srinivasan, S. (2014) MicroRNA 375 mediates palmitate-induced enteric neuronal damage and high-fat diet-induced delayed intestinal transit in mice. Gastroenterology 146, 473- 483.e3
    • (2014) Gastroenterology , vol.146 , pp. 473-483e3
    • Nezami, B.G.1    Mwangi, S.M.2    Lee, J.E.3    Jeppsson, S.4    Anitha, M.5    Yarandi, S.S.6    Farris, A.B.7    Srinivasan, S.8
  • 43
  • 45
    • 84904397909 scopus 로고    scopus 로고
    • GATA4 and GATA6 regulate intestinal epithelial cytodifferentiation during development
    • Walker, E. M., Thompson, C. A., and Battle, M. A. (2014) GATA4 and GATA6 regulate intestinal epithelial cytodifferentiation during development. Dev. Biol. 392, 283-294
    • (2014) Dev. Biol. , vol.392 , pp. 283-294
    • Walker, E.M.1    Thompson, C.A.2    Battle, M.A.3
  • 48
    • 84979776395 scopus 로고    scopus 로고
    • miR-30 family controls proliferation and differentiation of intestinal epithelial cell models by directing a broad gene expression program that includes SOX9 and the ubiquitin ligase pathway
    • Peck, B. C., Sincavage, J., Feinstein, S., Mah, A. T., Simmons, J. G., Lund, P. K., and Sethupathy, P. (2016) miR-30 family controls proliferation and differentiation of intestinal epithelial cell models by directing a broad gene expression program that includes SOX9 and the ubiquitin ligase pathway. J. Biol. Chem. 291, 15975-15984
    • (2016) J. Biol. Chem. , vol.291 , pp. 15975-15984
    • Peck, B.C.1    Sincavage, J.2    Feinstein, S.3    Mah, A.T.4    Simmons, J.G.5    Lund, P.K.6    Sethupathy, P.7
  • 49
    • 84983663590 scopus 로고    scopus 로고
    • Interplay between microbial d-amino acids and host d-amino acid oxidase modifies murine mucosal defence and gut microbiota
    • Sasabe, J., Miyoshi, Y., Rakoff-Nahoum, S., Zhang, T., Mita, M., Davis, B. M., Hamase, K., and Waldor, M. K. (2016) Interplay between microbial d-amino acids and host d-amino acid oxidase modifies murine mucosal defence and gut microbiota. Nat. Microbiol. 1, 16125
    • (2016) Nat. Microbiol. , vol.1 , pp. 16125
    • Sasabe, J.1    Miyoshi, Y.2    Rakoff-Nahoum, S.3    Zhang, T.4    Mita, M.5    Davis, B.M.6    Hamase, K.7    Waldor, M.K.8
  • 50
    • 84945182619 scopus 로고    scopus 로고
    • Colonic MUC2 mucin regulates the expression and antimicrobial activity of β-defensin 2
    • Cobo, E. R., Kissoon-Singh, V., Moreau, F., and Chadee, K. (2015) Colonic MUC2 mucin regulates the expression and antimicrobial activity of β-defensin 2. Mucosal Immunol. 8, 1360-1372
    • (2015) Mucosal Immunol , vol.8 , pp. 1360-1372
    • Cobo, E.R.1    Kissoon-Singh, V.2    Moreau, F.3    Chadee, K.4
  • 54
    • 84905049901 scopus 로고    scopus 로고
    • Trimmomatic: A flexible trimmer for Illumina sequence data
    • Bolger, A. M., Lohse, M., and Usadel, B. (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120
    • (2014) Bioinformatics , vol.30 , pp. 2114-2120
    • Bolger, A.M.1    Lohse, M.2    Usadel, B.3
  • 55
    • 84943820623 scopus 로고    scopus 로고
    • Creating reference gene annotation for the mouse C57BL6/J genome assembly
    • Mudge, J. M., and Harrow, J. (2015) Creating reference gene annotation for the mouse C57BL6/J genome assembly. Mamm. Genome 26, 366-378
    • (2015) Mamm. Genome , vol.26 , pp. 366-378
    • Mudge, J.M.1    Harrow, J.2
  • 59
    • 84962854536 scopus 로고    scopus 로고
    • Salmon: Accurate, versatile and ultrafast quantification from rna-seq data using lightweight alignment
    • Patro, R., Duggal, G., and Kingsford, C. (2015) Salmon: Accurate, versatile and ultrafast quantification from rna-seq data using lightweight alignment. bioRxiv 10.1101/021592
    • (2015) BioRxiv
    • Patro, R.1    Duggal, G.2    Kingsford, C.3
  • 60
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders, S., and Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biol. 11, R106
    • (2010) Genome Biol. , vol.11 , pp. R106
    • Anders, S.1    Huber, W.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.