Identification of Novel Genes Selectively Expressed in the Follicle-Associated Epithelium from the Meta-Analysis of Transcriptomics Data from Multiple Mouse Cell and Tissue Populations

Atsushi Kobayashi; David S Donaldson; Takashi Kanaya; Shinji Fukuda; J Kenneth Baillie; Tom C Freeman; Hiroshi Ohno; Ifor R Williams; Neil A Mabbott

doi:10.1093/dnares/dss022

Identification of Novel Genes Selectively Expressed in the Follicle-Associated Epithelium from the Meta-Analysis of Transcriptomics Data from Multiple Mouse Cell and Tissue Populations

Atsushi Kobayashi, David S Donaldson, Takashi Kanaya, Shinji Fukuda, J Kenneth Baillie, Tom C Freeman, Hiroshi Ohno, Ifor R Williams, Neil A Mabbott

Research output: Contribution to journal › Article › peer-review

Abstract

The follicle-associated epithelium (FAE) overlying the Peyer's patches and the microfold cells (M cells) within it are important sites of antigen transcytosis across the intestinal epithelium. Using a meta-analysis approach, we identified a transcriptional signature that distinguished the FAE from a large collection of mouse cells and tissues. A co-expressed cluster of 21 FAE-specific genes was identified, and the analysis of the transcription factor binding site motifs in their promoter regions indicated that these genes shared an underlying transcriptional programme. This cluster contained known FAE- (Anxa10, Ccl20, Psg18 and Ubd) and M-cell-specific (Gp2) genes, suggesting that the others were novel FAE-specific genes. Some of these novel candidate genes were expressed highly by the FAE and M cells (Calcb, Ces3b, Clca2 and Gjb2), and others only by the FAE (Ascl2, Cftr, Fgf15, Gpr133, Kcna1, Kcnj15, Mycl1, Pgap1 and Rps6kl). We also identified a subset of novel FAE-related genes that were induced in the intestinal epithelium after receptor activator of nuclear factor (NF)-κB ligand stimulation. These included Mfge8 which was specific to FAE enterocytes. This study provides new insight into the FAE transcriptome. Further characterization of the candidate genes identified here will aid the identification of novel regulators of cell function in the FAE.

Original language	English
Pages (from-to)	407-422
Number of pages	16
Journal	DNA Research
Volume	19
Issue number	5
DOIs	https://doi.org/10.1093/dnares/dss022
Publication status	Published - 2012

Keywords / Materials (for Non-textual outputs)

follicle-associated epithelium
M cells
intestine
meta-analysis
clustering

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10.1093/dnares/dss022

Identification of Novel Genes Selectively Expressed in the Follicle-Associated Epithelium from the Meta-Analysis of Transcriptomics Data from Multiple Mouse Cell and Tissue Populations
© The Author 2012. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Final published version, 899 KBLicence: Creative Commons: Attribution Non-Commercial (CC-BY-NC)

http://dnaresearch.oxfordjournals.org/content/19/5/407

Innate immunity and endemic diseases in livestock species
Collie, D. (Principal Investigator), Beard, P. (Co-investigator), Bishop, S. (Co-investigator), Bronsvoort, M. (Co-investigator), Burt, D. (Co-investigator), Fitzgerald, R. (Co-investigator), Freeman, T. (Co-investigator), Gally, D. (Co-investigator), Gill, A. (Co-investigator), Glass, E. (Co-investigator), Hocking, P. (Co-investigator), Hope, J. (Co-investigator), Hume, D. (Co-investigator), Kaiser, P. (Co-investigator), Mabbott, N. (Co-investigator), McLachlan, G. (Co-investigator), Morrison, L. (Co-investigator), Stevens, J. (Co-investigator), Stevens, M. (Co-investigator) & Watson, M. (Co-investigator)
BBSRC
1/04/12 → 31/03/17
Project: Research
Chareterisation of the development of the NALT and GALT in lymphotoxin-deficient mice.
Mabbott, N. (Principal Investigator)
BBSRC
1/06/09 → 30/11/10
Project: Research
The infuence of galt in tse agent in neuroinvasion from the large intestine
Mabbott, N. (Principal Investigator)
BBSRC
5/05/09 → 31/10/12
Project: Research

Cite this

Kobayashi, A., Donaldson, D. S., Kanaya, T., Fukuda, S., Baillie, J. K., Freeman, T. C., Ohno, H., Williams, I. R., & Mabbott, N. A. (2012). Identification of Novel Genes Selectively Expressed in the Follicle-Associated Epithelium from the Meta-Analysis of Transcriptomics Data from Multiple Mouse Cell and Tissue Populations. DNA Research, 19(5), 407-422. https://doi.org/10.1093/dnares/dss022

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title = "Identification of Novel Genes Selectively Expressed in the Follicle-Associated Epithelium from the Meta-Analysis of Transcriptomics Data from Multiple Mouse Cell and Tissue Populations",

abstract = "The follicle-associated epithelium (FAE) overlying the Peyer's patches and the microfold cells (M cells) within it are important sites of antigen transcytosis across the intestinal epithelium. Using a meta-analysis approach, we identified a transcriptional signature that distinguished the FAE from a large collection of mouse cells and tissues. A co-expressed cluster of 21 FAE-specific genes was identified, and the analysis of the transcription factor binding site motifs in their promoter regions indicated that these genes shared an underlying transcriptional programme. This cluster contained known FAE- (Anxa10, Ccl20, Psg18 and Ubd) and M-cell-specific (Gp2) genes, suggesting that the others were novel FAE-specific genes. Some of these novel candidate genes were expressed highly by the FAE and M cells (Calcb, Ces3b, Clca2 and Gjb2), and others only by the FAE (Ascl2, Cftr, Fgf15, Gpr133, Kcna1, Kcnj15, Mycl1, Pgap1 and Rps6kl). We also identified a subset of novel FAE-related genes that were induced in the intestinal epithelium after receptor activator of nuclear factor (NF)-κB ligand stimulation. These included Mfge8 which was specific to FAE enterocytes. This study provides new insight into the FAE transcriptome. Further characterization of the candidate genes identified here will aid the identification of novel regulators of cell function in the FAE.",

keywords = "follicle-associated epithelium , M cells, intestine , meta-analysis, clustering",

author = "Atsushi Kobayashi and Donaldson, {David S} and Takashi Kanaya and Shinji Fukuda and Baillie, {J Kenneth} and Freeman, {Tom C} and Hiroshi Ohno and Williams, {Ifor R} and Mabbott, {Neil A}",

year = "2012",

doi = "10.1093/dnares/dss022",

language = "English",

volume = "19",

pages = "407--422",

journal = "DNA Research",

issn = "1340-2838",

publisher = "Oxford University Press",

number = "5",

}

Kobayashi, A, Donaldson, DS, Kanaya, T, Fukuda, S, Baillie, JK, Freeman, TC, Ohno, H, Williams, IR & Mabbott, NA 2012, 'Identification of Novel Genes Selectively Expressed in the Follicle-Associated Epithelium from the Meta-Analysis of Transcriptomics Data from Multiple Mouse Cell and Tissue Populations', DNA Research, vol. 19, no. 5, pp. 407-422. https://doi.org/10.1093/dnares/dss022

Identification of Novel Genes Selectively Expressed in the Follicle-Associated Epithelium from the Meta-Analysis of Transcriptomics Data from Multiple Mouse Cell and Tissue Populations. / Kobayashi, Atsushi; Donaldson, David S; Kanaya, Takashi et al.
In: DNA Research, Vol. 19, No. 5, 2012, p. 407-422.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - Identification of Novel Genes Selectively Expressed in the Follicle-Associated Epithelium from the Meta-Analysis of Transcriptomics Data from Multiple Mouse Cell and Tissue Populations

AU - Kobayashi, Atsushi

AU - Donaldson, David S

AU - Kanaya, Takashi

AU - Fukuda, Shinji

AU - Baillie, J Kenneth

AU - Freeman, Tom C

AU - Ohno, Hiroshi

AU - Williams, Ifor R

AU - Mabbott, Neil A

PY - 2012

Y1 - 2012

N2 - The follicle-associated epithelium (FAE) overlying the Peyer's patches and the microfold cells (M cells) within it are important sites of antigen transcytosis across the intestinal epithelium. Using a meta-analysis approach, we identified a transcriptional signature that distinguished the FAE from a large collection of mouse cells and tissues. A co-expressed cluster of 21 FAE-specific genes was identified, and the analysis of the transcription factor binding site motifs in their promoter regions indicated that these genes shared an underlying transcriptional programme. This cluster contained known FAE- (Anxa10, Ccl20, Psg18 and Ubd) and M-cell-specific (Gp2) genes, suggesting that the others were novel FAE-specific genes. Some of these novel candidate genes were expressed highly by the FAE and M cells (Calcb, Ces3b, Clca2 and Gjb2), and others only by the FAE (Ascl2, Cftr, Fgf15, Gpr133, Kcna1, Kcnj15, Mycl1, Pgap1 and Rps6kl). We also identified a subset of novel FAE-related genes that were induced in the intestinal epithelium after receptor activator of nuclear factor (NF)-κB ligand stimulation. These included Mfge8 which was specific to FAE enterocytes. This study provides new insight into the FAE transcriptome. Further characterization of the candidate genes identified here will aid the identification of novel regulators of cell function in the FAE.

AB - The follicle-associated epithelium (FAE) overlying the Peyer's patches and the microfold cells (M cells) within it are important sites of antigen transcytosis across the intestinal epithelium. Using a meta-analysis approach, we identified a transcriptional signature that distinguished the FAE from a large collection of mouse cells and tissues. A co-expressed cluster of 21 FAE-specific genes was identified, and the analysis of the transcription factor binding site motifs in their promoter regions indicated that these genes shared an underlying transcriptional programme. This cluster contained known FAE- (Anxa10, Ccl20, Psg18 and Ubd) and M-cell-specific (Gp2) genes, suggesting that the others were novel FAE-specific genes. Some of these novel candidate genes were expressed highly by the FAE and M cells (Calcb, Ces3b, Clca2 and Gjb2), and others only by the FAE (Ascl2, Cftr, Fgf15, Gpr133, Kcna1, Kcnj15, Mycl1, Pgap1 and Rps6kl). We also identified a subset of novel FAE-related genes that were induced in the intestinal epithelium after receptor activator of nuclear factor (NF)-κB ligand stimulation. These included Mfge8 which was specific to FAE enterocytes. This study provides new insight into the FAE transcriptome. Further characterization of the candidate genes identified here will aid the identification of novel regulators of cell function in the FAE.

KW - follicle-associated epithelium

KW - M cells

KW - intestine

KW - meta-analysis

KW - clustering

U2 - 10.1093/dnares/dss022

DO - 10.1093/dnares/dss022

M3 - Article

C2 - 22991451

SN - 1340-2838

VL - 19

SP - 407

EP - 422

JO - DNA Research

JF - DNA Research

IS - 5

ER -

Identification of Novel Genes Selectively Expressed in the Follicle-Associated Epithelium from the Meta-Analysis of Transcriptomics Data from Multiple Mouse Cell and Tissue Populations

Abstract

Keywords / Materials (for Non-textual outputs)

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Projects

Innate immunity and endemic diseases in livestock species

Chareterisation of the development of the NALT and GALT in lymphotoxin-deficient mice.

The infuence of galt in tse agent in neuroinvasion from the large intestine

Cite this