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Updated: Jul 5, 2026

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions
Published on: June 28, 2018
The 5' untranslated regions (UTRs) of CCN1, CCN2, and CCN4 exhibit cryptic promoter activity
Bau-Lin Huang1, Lisa M Dornbach, Karen M Lyons
1Department of Oral Biology, School of Dentistry at UCLA, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Abstract:
CCNs are structurally related matricellular proteins that are highly expressed in many embryonic and adult tissues, including the skeletal system and tumors, where canonical cap-dependent translation is suppressed under hypoxic environments. CCNs are encoded by mRNAs containing long G/C rich 5'-untranslated regions (5'-UTRs). Given that they are expressed under conditions of cellular stress, it has been suggested that the long G/C-rich regions contain internal ribosomal entry sites (IRES) that allow these mRNAS to be translated under conditions where cap-dependent translation is suppressed. Previously published work supported this possibility. However, recent studies have shown that a number of previously reported cellular IRES elements do not in fact possess IRES activity. Here we aimed to reveal whether the 5'UTRs of CCNs harbor IRES activities. The 5'UTRs of CCN1, 2, and 4 were tested in this study. Our results showed that the 5'UTRs of these genes do not contain IRES elements, but instead appear to contain cryptic promoters. Both promoterless and hairpin-containing dicistronic tests showed that transcription was initiated by cryptic promoter elements in 5'UTRs of CCN1, 2, and 4. When dicistronic mRNAs were translated in vitro or in vivo, no IRES activities were detected in the 5'UTRs of CCN1, 2, and 4. Furthermore, these cryptic promoter activities from 5'UTRs of CCN1, 2, and 4 could be detected in various cell types, including chondrocytes, osteoblasts, and endothelial cells, where the cryptic promoter permitted varying degrees of activation. In addition, the core promoter element of the CCN2 5'UTR was identified. CCNs are expressed under conditions of cellular stress, and it has been suggested that some CCN family members utilize IRES-mediated translation initiation to facilitate this expression. We found no evidence for IRES activity, but rather found that the unusually long 5'UTRs of CCNs 1, 2, and 4 harbor cryptic promoters that showed varying degrees of activity in different cell types. These results suggest that these promoters may contribute to the regulation of CCN genes in vivo.
Insights
Cellular communication network (CCN) gene 5' untranslated regions (5' UTRs) do not use internal ribosomal entry sites (IRES) for translation. Instead, these CCN 5' UTRs contain cryptic promoters that regulate gene expression under cellular stress.
Area of Science:
- Molecular Biology
- Gene Regulation
- Cellular Stress Response
Background:
- Cellular communication network (CCN) proteins are matricellular proteins crucial in embryonic and adult tissues, including skeletal systems and tumors.
- CCNs are expressed during cellular stress, with their long, G/C-rich 5'-untranslated regions (5'-UTRs) previously hypothesized to contain internal ribosomal entry sites (IRES) for cap-independent translation.
- Recent findings question the activity of previously identified IRES elements, necessitating re-evaluation of CCN translation mechanisms.
Purpose of the Study:
- To investigate whether the 5'-UTRs of CCN1, CCN2, and CCN4 contain functional IRES elements.
- To determine the mechanism by which CCN mRNAs are translated under conditions of cellular stress and suppressed cap-dependent translation.
Main Methods:
- Utilized promoterless and hairpin-containing dicistronic reporter assays to test for IRES activity and cryptic promoter function in CCN 5'-UTRs.
- Performed in vitro and in vivo translation assays using dicistronic mRNAs.
- Analyzed cryptic promoter activity in various cell types, including chondrocytes, osteoblasts, and endothelial cells.
- Identified the core promoter element within the CCN2 5'-UTR.
Main Results:
- The 5'-UTRs of CCN1, CCN2, and CCN4 lack IRES activity.
- Cryptic promoter elements were identified within the 5'-UTRs of CCN1, CCN2, and CCN4, initiating transcription.
- These cryptic promoters demonstrated varying levels of activity across different cell types.
- No IRES activity was detected in the tested CCN 5'-UTRs, contrary to previous hypotheses.
Conclusions:
- The long 5'-UTRs of CCN1, CCN2, and CCN4 do not function as IRES elements.
- Cryptic promoters within these 5'-UTRs play a significant role in regulating CCN gene expression.
- These findings suggest an alternative mechanism for CCN gene regulation during cellular stress, distinct from IRES-mediated translation.
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