2021
DOI: 10.3390/ijms22158337
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Regulation Network of Colorectal-Cancer-Specific Enhancers in the Progression of Colorectal Cancer

Abstract: Enhancers regulate multiple genes via higher-order chromatin structures, and they further affect cancer progression. Epigenetic changes in cancer cells activate several cancer-specific enhancers that are silenced in normal cells. These cancer-specific enhancers are potential therapeutic targets of cancer. However, the functions and regulation networks of colorectal-cancer-specific enhancers are still unknown. In this study, we profile colorectal-cancer-specific enhancers and reveal their regulation network thr… Show more

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Cited by 8 publications
(8 citation statements)
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“…We set out to understand which of these changes in RNA abundance could be directly controlled by TBX3. To this aim, we integrated the TBX3 genomic distribution with the network of active CRC-enhancers obtained by HiChIP targeting the marker of open chromatin H3K27ac in HCT116 50 . The 155 differentially expressed CAGE-seq regions were anchored to 230 H3K27ac-mediated DNA-DNA interaction loops (Figure 4C; note that each CAGE-seq region could be anchored to >1 H3K27ac loop), supporting the notion that they correspond to active regulatory elements 51 .…”
Section: Resultsmentioning
confidence: 99%
“…We set out to understand which of these changes in RNA abundance could be directly controlled by TBX3. To this aim, we integrated the TBX3 genomic distribution with the network of active CRC-enhancers obtained by HiChIP targeting the marker of open chromatin H3K27ac in HCT116 50 . The 155 differentially expressed CAGE-seq regions were anchored to 230 H3K27ac-mediated DNA-DNA interaction loops (Figure 4C; note that each CAGE-seq region could be anchored to >1 H3K27ac loop), supporting the notion that they correspond to active regulatory elements 51 .…”
Section: Resultsmentioning
confidence: 99%
“…HiChIP of H3K27ac in HCT116 data was performed by Chen et al. ( 53 ). bedpe files containing unfiltered loops downstream of HiChipper were downloaded from GEO GSE173699.…”
Section: Methodsmentioning
confidence: 99%
“…This raises the prediction that β-catenin binding event probability could be associated with differential functionally relevant regulatory events. To test our prediction, we focused on active cis-regulatory three-dimensional chromatin interactions by employing published HiChIP of H3K27ac in HCT116 31 . This assay uncovers distant regions that are engaging in gene regulation events and that are marked by the open chromatin mark often found in active enhancer regions 31 .…”
Section: Peak Probability Identified By Iceberg Predicts Cis-regulato...mentioning
confidence: 99%
“…To test our prediction, we focused on active cis-regulatory three-dimensional chromatin interactions by employing published HiChIP of H3K27ac in HCT116 31 . This assay uncovers distant regions that are engaging in gene regulation events and that are marked by the open chromatin mark often found in active enhancer regions 31 . We focused on H3K27ac mediated loops that overlap with a βcatenin ICEBERG peak in at least one anchor and assessed the correlation between β-catenin peak detection frequency and 1) number of loops associated to each probability group, 2) loop strength in terms of counts and 3) loop size in terms of linear genomic distance between the two anchors.…”
Section: Peak Probability Identified By Iceberg Predicts Cis-regulato...mentioning
confidence: 99%
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