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Identification of TNF-α-responsive promoters and enhancers in the intestinal epithelial cell model Caco-2.

Boyd M, Coskun M, Lilje B, Andersson R, Hoof I, Bornholdt J, Dahlgaard K, Olsen J, Vitezic M, Bjerrum JT, Seidelin JB, Nielsen OH, Troelsen JT, Sandelin A - DNA Res. (2014)

Bottom Line: We found 520 promoters that significantly changed their usage level upon TNF-α stimulation; of these, 52% are not annotated.These enhancers share motif enrichments with similarly responding gene promoters.As a case example, we characterize an enhancer regulating the laminin-5 γ2-chain (LAMC2) gene by nuclear factor (NF)-κB binding.

View Article: PubMed Central - PubMed

Affiliation: The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaloes Vej 5, Copenhagen DK-2200, Denmark.

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Examples of loss of exons coding for protein domains due to alternative promoter usage. UCSC browser overview of the genes of interest: (A) NCK1, (B) COL16A1, (C) TRIM29, (D) BCL2L13 similar to Fig. 2. From top; (i) bar graph of normalized CAGE tag counts (TPM) from TNF-α(+) and TNF-α(−). Only tags on the relevant strand are shown; (ii) Pfam domains mapped to UCSC genes and (iii) RefSeq genes. Arrows indicate TSS clusters (core promoters) of interest and their direction of transcription. Sizes of arrows correspond to the CAGE signal strength. Grey regions indicate the part of the gene that is retained by usage of alternative promoters of interest. Lost, or partially lost, domains upstream of this region with dashed lines, while retained domains have a black background. Gene examples are commented in detail in the main text. This figure appears in colour in the online version of DNA Research.
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DSU022F3: Examples of loss of exons coding for protein domains due to alternative promoter usage. UCSC browser overview of the genes of interest: (A) NCK1, (B) COL16A1, (C) TRIM29, (D) BCL2L13 similar to Fig. 2. From top; (i) bar graph of normalized CAGE tag counts (TPM) from TNF-α(+) and TNF-α(−). Only tags on the relevant strand are shown; (ii) Pfam domains mapped to UCSC genes and (iii) RefSeq genes. Arrows indicate TSS clusters (core promoters) of interest and their direction of transcription. Sizes of arrows correspond to the CAGE signal strength. Grey regions indicate the part of the gene that is retained by usage of alternative promoters of interest. Lost, or partially lost, domains upstream of this region with dashed lines, while retained domains have a black background. Gene examples are commented in detail in the main text. This figure appears in colour in the online version of DNA Research.

Mentions: Our CAGE data make it possible to assess the frequency of these types of events in Caco-2 as a response to TNF-α. We found that 75 of the TNF-α(+) promoters are within an annotated coding region. These represent shorter RNA isoforms, which, if translated, would give rise to N-termini-truncated proteins. To identify cases similar to the LEF1 example above, we investigated if any of the intragenic TNF-α(+) promoters were located within or downstream of PFAM50 protein domains mapped to the coding sequence. In total, we found 39 promoters in 33 genes, where usage of the TNF-α(+) promoter would lead to RNAs that exclude one or more protein domains. Five of the promoters were within 100 bp from a known (alternative) RefSeq promoter, where all the gene products are annotated as protein coding. In these cases, it is likely that these TNF-α(+)-responsive promoters are producing proteins with truncated N-termini and loss of functional domains. For non-annotated alternative promoters, further validation is needed to prove that the produced RNAs are translated. We here show four examples of genes where exons containing domains are lost when using the TNF-α(+) promoters (Fig. 3).Figure 3.


Identification of TNF-α-responsive promoters and enhancers in the intestinal epithelial cell model Caco-2.

Boyd M, Coskun M, Lilje B, Andersson R, Hoof I, Bornholdt J, Dahlgaard K, Olsen J, Vitezic M, Bjerrum JT, Seidelin JB, Nielsen OH, Troelsen JT, Sandelin A - DNA Res. (2014)

Examples of loss of exons coding for protein domains due to alternative promoter usage. UCSC browser overview of the genes of interest: (A) NCK1, (B) COL16A1, (C) TRIM29, (D) BCL2L13 similar to Fig. 2. From top; (i) bar graph of normalized CAGE tag counts (TPM) from TNF-α(+) and TNF-α(−). Only tags on the relevant strand are shown; (ii) Pfam domains mapped to UCSC genes and (iii) RefSeq genes. Arrows indicate TSS clusters (core promoters) of interest and their direction of transcription. Sizes of arrows correspond to the CAGE signal strength. Grey regions indicate the part of the gene that is retained by usage of alternative promoters of interest. Lost, or partially lost, domains upstream of this region with dashed lines, while retained domains have a black background. Gene examples are commented in detail in the main text. This figure appears in colour in the online version of DNA Research.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263293&req=5

DSU022F3: Examples of loss of exons coding for protein domains due to alternative promoter usage. UCSC browser overview of the genes of interest: (A) NCK1, (B) COL16A1, (C) TRIM29, (D) BCL2L13 similar to Fig. 2. From top; (i) bar graph of normalized CAGE tag counts (TPM) from TNF-α(+) and TNF-α(−). Only tags on the relevant strand are shown; (ii) Pfam domains mapped to UCSC genes and (iii) RefSeq genes. Arrows indicate TSS clusters (core promoters) of interest and their direction of transcription. Sizes of arrows correspond to the CAGE signal strength. Grey regions indicate the part of the gene that is retained by usage of alternative promoters of interest. Lost, or partially lost, domains upstream of this region with dashed lines, while retained domains have a black background. Gene examples are commented in detail in the main text. This figure appears in colour in the online version of DNA Research.
Mentions: Our CAGE data make it possible to assess the frequency of these types of events in Caco-2 as a response to TNF-α. We found that 75 of the TNF-α(+) promoters are within an annotated coding region. These represent shorter RNA isoforms, which, if translated, would give rise to N-termini-truncated proteins. To identify cases similar to the LEF1 example above, we investigated if any of the intragenic TNF-α(+) promoters were located within or downstream of PFAM50 protein domains mapped to the coding sequence. In total, we found 39 promoters in 33 genes, where usage of the TNF-α(+) promoter would lead to RNAs that exclude one or more protein domains. Five of the promoters were within 100 bp from a known (alternative) RefSeq promoter, where all the gene products are annotated as protein coding. In these cases, it is likely that these TNF-α(+)-responsive promoters are producing proteins with truncated N-termini and loss of functional domains. For non-annotated alternative promoters, further validation is needed to prove that the produced RNAs are translated. We here show four examples of genes where exons containing domains are lost when using the TNF-α(+) promoters (Fig. 3).Figure 3.

Bottom Line: We found 520 promoters that significantly changed their usage level upon TNF-α stimulation; of these, 52% are not annotated.These enhancers share motif enrichments with similarly responding gene promoters.As a case example, we characterize an enhancer regulating the laminin-5 γ2-chain (LAMC2) gene by nuclear factor (NF)-κB binding.

View Article: PubMed Central - PubMed

Affiliation: The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaloes Vej 5, Copenhagen DK-2200, Denmark.

Show MeSH
Related in: MedlinePlus