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REST regulates distinct transcriptional networks in embryonic and neural stem cells.

Johnson R, Teh CH, Kunarso G, Wong KY, Srinivasan G, Cooper ML, Volta M, Chan SS, Lipovich L, Pollard SM, Karuturi RK, Wei CL, Buckley NJ, Stanton LW - PLoS Biol. (2008)

Bottom Line: We investigated how these distinct biological roles are effected at a genomic level.In ESC, the REST regulatory network is highly integrated into that of pluripotency factors Oct4-Sox2-Nanog.We propose that an extensive, pluripotency-specific recruitment profile lends REST a key role in the maintenance of the ESC phenotype.

View Article: PubMed Central - PubMed

Affiliation: Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore.

ABSTRACT
The maintenance of pluripotency and specification of cellular lineages during embryonic development are controlled by transcriptional regulatory networks, which coordinate specific sets of genes through both activation and repression. The transcriptional repressor RE1-silencing transcription factor (REST) plays important but distinct regulatory roles in embryonic (ESC) and neural (NSC) stem cells. We investigated how these distinct biological roles are effected at a genomic level. We present integrated, comparative genome- and transcriptome-wide analyses of transcriptional networks governed by REST in mouse ESC and NSC. The REST recruitment profile has dual components: a developmentally independent core that is common to ESC, NSC, and differentiated cells; and a large, ESC-specific set of target genes. In ESC, the REST regulatory network is highly integrated into that of pluripotency factors Oct4-Sox2-Nanog. We propose that an extensive, pluripotency-specific recruitment profile lends REST a key role in the maintenance of the ESC phenotype.

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Diverse Outcomes of REST Function on ESC and NSC Gene Expression Profiles(A and B) The numbers of genes decreasing (“down”) and increasing (“up”) in response to DN:REST treatment are shown (p < 0.01 threshold for statistical significance) for (A) NSC and (B) ESC.(C and D) Genes with significant (p < 0.01) changes (≥3-fold) in expression were tabulated for (C) NSC and (D) ESC in response to DN:REST. Gray shaded genes are those with associated REST binding sites at the indicated distance (“Dist.”) from the TSS. Unshaded genes have no REST binding sites within 100 kbp. Common genes are printed in blue.
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pbio-0060256-g005: Diverse Outcomes of REST Function on ESC and NSC Gene Expression Profiles(A and B) The numbers of genes decreasing (“down”) and increasing (“up”) in response to DN:REST treatment are shown (p < 0.01 threshold for statistical significance) for (A) NSC and (B) ESC.(C and D) Genes with significant (p < 0.01) changes (≥3-fold) in expression were tabulated for (C) NSC and (D) ESC in response to DN:REST. Gray shaded genes are those with associated REST binding sites at the indicated distance (“Dist.”) from the TSS. Unshaded genes have no REST binding sites within 100 kbp. Common genes are printed in blue.

Mentions: Our mapping of REST binding sites in ESC and NSC indicated that there were distinct patterns of occupancy in the two cell types. We next asked which genes are transcriptionally repressed by REST in these cells. To this end, we profiled gene expression in ESC and NSC in which the activity of REST was blocked by a dominant-negative form of REST (DN:REST). DN:REST comprises the eight zinc fingers of the REST DNA binding domain, but lacks the N and C termini; it thus derepresses transcription of REST target genes [28]. An adenovirus was used to efficiently deliver DN:REST to the NSC. After 48 h of REST derepression, global changes in gene expression were measured by DNA microarray analysis. We detected expression of ∼21,000 genes, of which 911 genes were significantly altered (p < 0.01) in NSC in the presence of DN:REST (Dataset S5). Overall, 635 (3.0%) and 276 (1.3%) of the expressed genes showed statistically significant up- and down-regulation, respectively (Figure 5A). Given that REST is a transcriptional repressor, it is anticipated that, in response to the inhibition by DN:REST, direct target genes would be up-regulated. Thus, down-regulated genes are likely to be downstream, indirect targets of REST. We asked whether the most differentially expressed genes had evidence for genomic occupancy by REST. The gene nearest to each REST binding site was identified. There were 33 genes with expression elevated 3-fold or greater, of which 24 (73%) had an associated binding site (Figure 5C). Given that this number is far lower than the total number of expressed genes associated with a REST PET cluster, these data indicated that only a small proportion of bound genes are actually derepressed by DN:REST in NSC. However, among the derepressed genes, those that were most responsive to REST knock-down did have an associated REST binding site.


REST regulates distinct transcriptional networks in embryonic and neural stem cells.

Johnson R, Teh CH, Kunarso G, Wong KY, Srinivasan G, Cooper ML, Volta M, Chan SS, Lipovich L, Pollard SM, Karuturi RK, Wei CL, Buckley NJ, Stanton LW - PLoS Biol. (2008)

Diverse Outcomes of REST Function on ESC and NSC Gene Expression Profiles(A and B) The numbers of genes decreasing (“down”) and increasing (“up”) in response to DN:REST treatment are shown (p < 0.01 threshold for statistical significance) for (A) NSC and (B) ESC.(C and D) Genes with significant (p < 0.01) changes (≥3-fold) in expression were tabulated for (C) NSC and (D) ESC in response to DN:REST. Gray shaded genes are those with associated REST binding sites at the indicated distance (“Dist.”) from the TSS. Unshaded genes have no REST binding sites within 100 kbp. Common genes are printed in blue.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2573930&req=5

pbio-0060256-g005: Diverse Outcomes of REST Function on ESC and NSC Gene Expression Profiles(A and B) The numbers of genes decreasing (“down”) and increasing (“up”) in response to DN:REST treatment are shown (p < 0.01 threshold for statistical significance) for (A) NSC and (B) ESC.(C and D) Genes with significant (p < 0.01) changes (≥3-fold) in expression were tabulated for (C) NSC and (D) ESC in response to DN:REST. Gray shaded genes are those with associated REST binding sites at the indicated distance (“Dist.”) from the TSS. Unshaded genes have no REST binding sites within 100 kbp. Common genes are printed in blue.
Mentions: Our mapping of REST binding sites in ESC and NSC indicated that there were distinct patterns of occupancy in the two cell types. We next asked which genes are transcriptionally repressed by REST in these cells. To this end, we profiled gene expression in ESC and NSC in which the activity of REST was blocked by a dominant-negative form of REST (DN:REST). DN:REST comprises the eight zinc fingers of the REST DNA binding domain, but lacks the N and C termini; it thus derepresses transcription of REST target genes [28]. An adenovirus was used to efficiently deliver DN:REST to the NSC. After 48 h of REST derepression, global changes in gene expression were measured by DNA microarray analysis. We detected expression of ∼21,000 genes, of which 911 genes were significantly altered (p < 0.01) in NSC in the presence of DN:REST (Dataset S5). Overall, 635 (3.0%) and 276 (1.3%) of the expressed genes showed statistically significant up- and down-regulation, respectively (Figure 5A). Given that REST is a transcriptional repressor, it is anticipated that, in response to the inhibition by DN:REST, direct target genes would be up-regulated. Thus, down-regulated genes are likely to be downstream, indirect targets of REST. We asked whether the most differentially expressed genes had evidence for genomic occupancy by REST. The gene nearest to each REST binding site was identified. There were 33 genes with expression elevated 3-fold or greater, of which 24 (73%) had an associated binding site (Figure 5C). Given that this number is far lower than the total number of expressed genes associated with a REST PET cluster, these data indicated that only a small proportion of bound genes are actually derepressed by DN:REST in NSC. However, among the derepressed genes, those that were most responsive to REST knock-down did have an associated REST binding site.

Bottom Line: We investigated how these distinct biological roles are effected at a genomic level.In ESC, the REST regulatory network is highly integrated into that of pluripotency factors Oct4-Sox2-Nanog.We propose that an extensive, pluripotency-specific recruitment profile lends REST a key role in the maintenance of the ESC phenotype.

View Article: PubMed Central - PubMed

Affiliation: Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore.

ABSTRACT
The maintenance of pluripotency and specification of cellular lineages during embryonic development are controlled by transcriptional regulatory networks, which coordinate specific sets of genes through both activation and repression. The transcriptional repressor RE1-silencing transcription factor (REST) plays important but distinct regulatory roles in embryonic (ESC) and neural (NSC) stem cells. We investigated how these distinct biological roles are effected at a genomic level. We present integrated, comparative genome- and transcriptome-wide analyses of transcriptional networks governed by REST in mouse ESC and NSC. The REST recruitment profile has dual components: a developmentally independent core that is common to ESC, NSC, and differentiated cells; and a large, ESC-specific set of target genes. In ESC, the REST regulatory network is highly integrated into that of pluripotency factors Oct4-Sox2-Nanog. We propose that an extensive, pluripotency-specific recruitment profile lends REST a key role in the maintenance of the ESC phenotype.

Show MeSH