Tissue-specific disallowance of housekeeping genes

The other face of cell differentiation

L. Thorrez, I. Laudadio, K. Van Deun, R. Quintens, N. Hendrickx, M. Granvik, K. Lemaire, A. Schraenen, L. Van Lommel, S. Lehnert, C. Aguayo-mazzucato, R. Cheng-xue, P. Gilon, I. Van Mechelen, S. Bonner-weir, F. Lemaigre, F. Schuit

Research output: Contribution to journalArticleScientificpeer-review

Abstract

We report on a hitherto poorly characterized class of genes that are expressed in all tissues, except in one. Often, these genes have been classified as housekeeping genes, based on their nearly ubiquitous expression. However, the specific repression in one tissue defines a special class of “disallowed genes.” In this paper, we used the intersection-union test to screen for such genes in a multi-tissue panel of genome-wide mRNA expression data. We propose that disallowed genes need to be repressed in the specific target tissue to ensure correct tissue function. We provide mechanistic data of repression with two metabolic examples, exercise-induced inappropriate insulin release and interference with ketogenesis in liver. Developmentally, this repression is established during tissue maturation in the early postnatal period involving epigenetic changes in histone methylation. In addition, tissue-specific expression of microRNAs can further diminish these repressed mRNAs. Together, we provide a systematic analysis of tissue-specific repression of housekeeping genes, a phenomenon that has not been studied so far on a genome-wide basis and, when perturbed, can lead to human disease.
Original languageEnglish
Pages (from-to)95-105
JournalGenome Research
Volume21
Issue number1
DOIs
Publication statusPublished - 2011
Externally publishedYes

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Essential Genes
Cell Differentiation
MicroRNAs
Epigenomics
Histones
Liver

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Thorrez, L., Laudadio, I., Van Deun, K., Quintens, R., Hendrickx, N., Granvik, M., ... Schuit, F. (2011). Tissue-specific disallowance of housekeeping genes: The other face of cell differentiation. Genome Research, 21(1), 95-105. https://doi.org/10.1101/gr.109173.110
Thorrez, L. ; Laudadio, I. ; Van Deun, K. ; Quintens, R. ; Hendrickx, N. ; Granvik, M. ; Lemaire, K. ; Schraenen, A. ; Van Lommel, L. ; Lehnert, S. ; Aguayo-mazzucato, C. ; Cheng-xue, R. ; Gilon, P. ; Van Mechelen, I. ; Bonner-weir, S. ; Lemaigre, F. ; Schuit, F. / Tissue-specific disallowance of housekeeping genes : The other face of cell differentiation. In: Genome Research. 2011 ; Vol. 21, No. 1. pp. 95-105.
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abstract = "We report on a hitherto poorly characterized class of genes that are expressed in all tissues, except in one. Often, these genes have been classified as housekeeping genes, based on their nearly ubiquitous expression. However, the specific repression in one tissue defines a special class of “disallowed genes.” In this paper, we used the intersection-union test to screen for such genes in a multi-tissue panel of genome-wide mRNA expression data. We propose that disallowed genes need to be repressed in the specific target tissue to ensure correct tissue function. We provide mechanistic data of repression with two metabolic examples, exercise-induced inappropriate insulin release and interference with ketogenesis in liver. Developmentally, this repression is established during tissue maturation in the early postnatal period involving epigenetic changes in histone methylation. In addition, tissue-specific expression of microRNAs can further diminish these repressed mRNAs. Together, we provide a systematic analysis of tissue-specific repression of housekeeping genes, a phenomenon that has not been studied so far on a genome-wide basis and, when perturbed, can lead to human disease.",
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Thorrez, L, Laudadio, I, Van Deun, K, Quintens, R, Hendrickx, N, Granvik, M, Lemaire, K, Schraenen, A, Van Lommel, L, Lehnert, S, Aguayo-mazzucato, C, Cheng-xue, R, Gilon, P, Van Mechelen, I, Bonner-weir, S, Lemaigre, F & Schuit, F 2011, 'Tissue-specific disallowance of housekeeping genes: The other face of cell differentiation', Genome Research, vol. 21, no. 1, pp. 95-105. https://doi.org/10.1101/gr.109173.110

Tissue-specific disallowance of housekeeping genes : The other face of cell differentiation. / Thorrez, L.; Laudadio, I.; Van Deun, K.; Quintens, R.; Hendrickx, N.; Granvik, M.; Lemaire, K.; Schraenen, A.; Van Lommel, L.; Lehnert, S.; Aguayo-mazzucato, C.; Cheng-xue, R.; Gilon, P.; Van Mechelen, I.; Bonner-weir, S.; Lemaigre, F.; Schuit, F.

In: Genome Research, Vol. 21, No. 1, 2011, p. 95-105.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - Tissue-specific disallowance of housekeeping genes

T2 - The other face of cell differentiation

AU - Thorrez, L.

AU - Laudadio, I.

AU - Van Deun, K.

AU - Quintens, R.

AU - Hendrickx, N.

AU - Granvik, M.

AU - Lemaire, K.

AU - Schraenen, A.

AU - Van Lommel, L.

AU - Lehnert, S.

AU - Aguayo-mazzucato, C.

AU - Cheng-xue, R.

AU - Gilon, P.

AU - Van Mechelen, I.

AU - Bonner-weir, S.

AU - Lemaigre, F.

AU - Schuit, F.

PY - 2011

Y1 - 2011

N2 - We report on a hitherto poorly characterized class of genes that are expressed in all tissues, except in one. Often, these genes have been classified as housekeeping genes, based on their nearly ubiquitous expression. However, the specific repression in one tissue defines a special class of “disallowed genes.” In this paper, we used the intersection-union test to screen for such genes in a multi-tissue panel of genome-wide mRNA expression data. We propose that disallowed genes need to be repressed in the specific target tissue to ensure correct tissue function. We provide mechanistic data of repression with two metabolic examples, exercise-induced inappropriate insulin release and interference with ketogenesis in liver. Developmentally, this repression is established during tissue maturation in the early postnatal period involving epigenetic changes in histone methylation. In addition, tissue-specific expression of microRNAs can further diminish these repressed mRNAs. Together, we provide a systematic analysis of tissue-specific repression of housekeeping genes, a phenomenon that has not been studied so far on a genome-wide basis and, when perturbed, can lead to human disease.

AB - We report on a hitherto poorly characterized class of genes that are expressed in all tissues, except in one. Often, these genes have been classified as housekeeping genes, based on their nearly ubiquitous expression. However, the specific repression in one tissue defines a special class of “disallowed genes.” In this paper, we used the intersection-union test to screen for such genes in a multi-tissue panel of genome-wide mRNA expression data. We propose that disallowed genes need to be repressed in the specific target tissue to ensure correct tissue function. We provide mechanistic data of repression with two metabolic examples, exercise-induced inappropriate insulin release and interference with ketogenesis in liver. Developmentally, this repression is established during tissue maturation in the early postnatal period involving epigenetic changes in histone methylation. In addition, tissue-specific expression of microRNAs can further diminish these repressed mRNAs. Together, we provide a systematic analysis of tissue-specific repression of housekeeping genes, a phenomenon that has not been studied so far on a genome-wide basis and, when perturbed, can lead to human disease.

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DO - 10.1101/gr.109173.110

M3 - Article

VL - 21

SP - 95

EP - 105

JO - Genome Research

JF - Genome Research

SN - 1088-9051

IS - 1

ER -