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Extensive remodeling of DC function by rapid maturation-induced transcriptional silencing.

Seguín-Estévez Q, Dunand-Sauthier I, Lemeille S, Iseli C, Ibberson M, Ioannidis V, Schmid CD, Rousseau P, Barras E, Geinoz A, Xenarios I, Acha-Orbea H, Reith W - Nucleic Acids Res. (2014)

Bottom Line: This silencing response is a rapid primary event distinct from repression mechanisms known to operate at later stages of DC maturation.The repressed genes function in pivotal processes--including antigen-presentation, extracellular signal detection, intracellular signal transduction and lipid-mediator biosynthesis--underscoring the central contribution of the silencing mechanism to rapid reshaping of DC function.Interestingly, promoters of the repressed genes exhibit a surprisingly high frequency of PU.1-occupied sites, suggesting a novel role for this lineage-specific transcription factor in marking genes poised for inducible repression.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology and Immunology, University of Geneva Medical School, CH-1211 Geneva, Switzerland.

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Related in: MedlinePlus

Transcriptome profiling by nascent-transcript sequencing. (A) Schematic representation of the strategy used for purifying and sequencing chromatin-bound nascent transcripts. mRNA was purified and sequenced in parallel. (B and C) Nascent-transcript-sequencing profiles are shown for representative silenced (B) and induced (C) genes: results are expressed as numbers of reads mapping to the genes in untreated and 1 h-LPS-treated Mo-DCs; schematic maps of the genes are depicted; exons are indicated as boxes; positions of mature microRNA sequences are indicated for microRNA genes; mRNA-sequencing profiles from untreated Mo-DCs are included as controls for protein-coding genes.
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Figure 4: Transcriptome profiling by nascent-transcript sequencing. (A) Schematic representation of the strategy used for purifying and sequencing chromatin-bound nascent transcripts. mRNA was purified and sequenced in parallel. (B and C) Nascent-transcript-sequencing profiles are shown for representative silenced (B) and induced (C) genes: results are expressed as numbers of reads mapping to the genes in untreated and 1 h-LPS-treated Mo-DCs; schematic maps of the genes are depicted; exons are indicated as boxes; positions of mature microRNA sequences are indicated for microRNA genes; mRNA-sequencing profiles from untreated Mo-DCs are included as controls for protein-coding genes.

Mentions: To assess global transcriptional consequences of histone-deacetylation, we explored the possibility of exploiting published microarray-based mRNA-expression data. A comparison of seven datasets for LPS-treated Mo-DCs (29–32) indicated that mRNA-profiling is not reliable for studying gene silencing. Reproducibility was significantly lower for silenced genes than induced genes: whereas most induced genes (75%) were reproduced in at least two experiments, most down-regulated genes (60%) were observed in only one experiment (Supplementary Figure S3E). Furthermore, key genes silenced in activated Mo-DCs, including CIITA, MARCH1 and CD1A (Figure 1, Figure 3C and Supplementary Figure S3A and F) (20,21), were not found to be down-regulated in the microarray experiments, probably because of low expression-levels and/or mRNA half-life issues. We therefore developed a genome-wide approach for measuring global transcription rates, based on high-throughput sequencing of chromatin-bound primary transcripts (Figure 4A). Primary-transcript and mRNA preparations from immature Mo-DCs and 1 h-LPS-treated Mo-DCs were sequenced in parallel. Reproducibility between biological repeats was excellent as evidenced by examining global transcription profiles (Supplementary Figure S4A), spatial patterns of sequence-reads mapping to individual genes (Supplementary Figure S4B), and transcriptional changes observed for representative genes (Supplementary Figure S4C).


Extensive remodeling of DC function by rapid maturation-induced transcriptional silencing.

Seguín-Estévez Q, Dunand-Sauthier I, Lemeille S, Iseli C, Ibberson M, Ioannidis V, Schmid CD, Rousseau P, Barras E, Geinoz A, Xenarios I, Acha-Orbea H, Reith W - Nucleic Acids Res. (2014)

Transcriptome profiling by nascent-transcript sequencing. (A) Schematic representation of the strategy used for purifying and sequencing chromatin-bound nascent transcripts. mRNA was purified and sequenced in parallel. (B and C) Nascent-transcript-sequencing profiles are shown for representative silenced (B) and induced (C) genes: results are expressed as numbers of reads mapping to the genes in untreated and 1 h-LPS-treated Mo-DCs; schematic maps of the genes are depicted; exons are indicated as boxes; positions of mature microRNA sequences are indicated for microRNA genes; mRNA-sequencing profiles from untreated Mo-DCs are included as controls for protein-coding genes.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4150779&req=5

Figure 4: Transcriptome profiling by nascent-transcript sequencing. (A) Schematic representation of the strategy used for purifying and sequencing chromatin-bound nascent transcripts. mRNA was purified and sequenced in parallel. (B and C) Nascent-transcript-sequencing profiles are shown for representative silenced (B) and induced (C) genes: results are expressed as numbers of reads mapping to the genes in untreated and 1 h-LPS-treated Mo-DCs; schematic maps of the genes are depicted; exons are indicated as boxes; positions of mature microRNA sequences are indicated for microRNA genes; mRNA-sequencing profiles from untreated Mo-DCs are included as controls for protein-coding genes.
Mentions: To assess global transcriptional consequences of histone-deacetylation, we explored the possibility of exploiting published microarray-based mRNA-expression data. A comparison of seven datasets for LPS-treated Mo-DCs (29–32) indicated that mRNA-profiling is not reliable for studying gene silencing. Reproducibility was significantly lower for silenced genes than induced genes: whereas most induced genes (75%) were reproduced in at least two experiments, most down-regulated genes (60%) were observed in only one experiment (Supplementary Figure S3E). Furthermore, key genes silenced in activated Mo-DCs, including CIITA, MARCH1 and CD1A (Figure 1, Figure 3C and Supplementary Figure S3A and F) (20,21), were not found to be down-regulated in the microarray experiments, probably because of low expression-levels and/or mRNA half-life issues. We therefore developed a genome-wide approach for measuring global transcription rates, based on high-throughput sequencing of chromatin-bound primary transcripts (Figure 4A). Primary-transcript and mRNA preparations from immature Mo-DCs and 1 h-LPS-treated Mo-DCs were sequenced in parallel. Reproducibility between biological repeats was excellent as evidenced by examining global transcription profiles (Supplementary Figure S4A), spatial patterns of sequence-reads mapping to individual genes (Supplementary Figure S4B), and transcriptional changes observed for representative genes (Supplementary Figure S4C).

Bottom Line: This silencing response is a rapid primary event distinct from repression mechanisms known to operate at later stages of DC maturation.The repressed genes function in pivotal processes--including antigen-presentation, extracellular signal detection, intracellular signal transduction and lipid-mediator biosynthesis--underscoring the central contribution of the silencing mechanism to rapid reshaping of DC function.Interestingly, promoters of the repressed genes exhibit a surprisingly high frequency of PU.1-occupied sites, suggesting a novel role for this lineage-specific transcription factor in marking genes poised for inducible repression.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology and Immunology, University of Geneva Medical School, CH-1211 Geneva, Switzerland.

Show MeSH
Related in: MedlinePlus