CGGBP1-dependent CTCF-binding sites restrict ectopic transcription
| Autor: | Manthan Patel, Subhamoy Datta, Divyesh Patel, Umashankar Singh |
|---|---|
| Přispěvatelé: | Faculty of Medicine |
| Rok vydání: | 2021 |
| Předmět: |
CHROMATIN
CCCTC-Binding Factor INSULATOR RNA-sequencing PROTEIN RNA polymerase II ORGANIZATION Insulator (genetics) Genome Transcription (biology) ELEMENTS Humans Binding site Promoter Regions Genetic ChIP (chromatin immunoprecipitation) Molecular Biology Gene RNA polymerase 2 SV40 (simian virus 40) Binding Sites biology Genome Human SV40 ENHANCER HETEROCHROMATIN BARRIER Cell Biology GENE Chromatin Cell biology DNA-Binding Proteins GENOME CGGBP1-dependent CTCF-binding sites KD (anti-cggbp1 shRNA) CTCF biology.protein CT (control non-targeting shRNA) 1182 Biochemistry cell and molecular biology IMPRINTING CONTROL REGION transcription Research Paper Transcription Factors Developmental Biology |
| Zdroj: | Cell Cycle |
| ISSN: | 1551-4005 1538-4101 |
| DOI: | 10.1080/15384101.2021.1982508 |
| Popis: | Binding sites of the chromatin regulator protein CTCF function as important landmarks in the human genome. The recently characterized CTCF-binding sites at LINE-1 repeats depend on another repeat-regulatory protein CGGBP1. These CGGBP1-dependent CTCF-binding sites serve as potential barrier elements for epigenetic marks such as H3K9me3. Such CTCF-binding sites are associated with asymmetric H3K9me3 levels as well as RNA levels in their flanks. The functions of these CGGBP1-dependent CTCF-binding sites remain unknown. By performing targeted studies on candidate CGGBP1-dependent CTCF-binding sites cloned in an SV40 promoter-enhancer episomal system we show that these regions act as inhibitors of ectopic transcription from the SV40 promoter. CGGBP1-dependent CTCF-binding sites that recapitulate their genomic function of loss of CTCF binding upon CGGBP1 depletion and H3K9me3 asymmetry in immediate flanks are also the ones that show the strongest inhibition of ectopic transcription. By performing a series of strand-specific reverse transcription PCRs we demonstrate that this ectopic transcription results in the synthesis of RNA from the SV40 promoter in a direction opposite to the downstream reporter gene in a strand-specific manner. The unleashing of the bidirectionality of the SV40 promoter activity and a breach of the transcription barrier seems to depend on depletion of CGGBP1 and loss of CTCF binding proximal to the SV40 promoter. RNA-sequencing reveals that CGGBP1-regulated CTCF-binding sites act as barriers to transcription at multiple locations genome-wide. These findings suggest a role of CGGBP1-dependent binding sites in restricting ectopic transcription. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|