Promoter-associated noncoding RNA from the CCND1 promoter

Area of Science:

• Molecular Biology
• Genetics
• Epigenetics

Background:

• The human genome is extensively transcribed, with most transcripts being noncoding RNAs (ncRNAs).
• While small ncRNAs regulate translation and gene silencing, long ncRNAs (lncRNAs) are emerging as key regulators of transcription.
• The translocated in liposarcoma (TLS) protein binds to CBP/p300 and inhibits their histone acetyltransferase (HAT) activity, a process dependent on RNA binding.

Purpose of the Study:

• To identify naturally occurring RNA molecules that bind to TLS.
• To investigate the role of these RNA molecules in regulating gene transcription.
• To characterize novel long ncRNAs involved in transcriptional repression.

Main Methods:

• Systematic evolution of ligands by exponential enrichment (SELEX) to identify TLS-binding RNA sequences.
• Optimization of RT-PCR, chromatin immunoprecipitation (ChIP), RNA immunoprecipitation (RIP), and RNA gel-shift assays.
• Detection and characterization of promoter-associated ncRNAs (pncRNAs) from the CCND1 promoter.

Main Results:

• TLS specifically recognizes RNA oligonucleotides with a GGUG consensus sequence, though not strictly required.
• Long ncRNAs (pncRNAs) transcribed from the CCND1 promoter bind to TLS.
• CCND1 pncRNAs inhibit HAT activities of CBP/p300 at the CCND1 promoter, repressing CCND1 gene transcription, especially under genotoxic stress.

Conclusions:

• Novel long ncRNAs (pncRNAs) transcribed from the CCND1 promoter bind TLS and regulate its HAT inhibitory activity.
• These pncRNAs function as transcriptional repressors of the CCND1 gene.
• Developed methods successfully detect low-abundant lncRNAs and demonstrate their role in gene regulation.