ChIRP-seq (Chromatin Isolation by RNA Purification) is a relatively new method developed to map the functional association of novel RNA to distinct regions of the genome to gain a better understanding of their function. A huge repertoire of non-coding transcripts is highly essential for proper gene regulation involved in many biological processes. Long, no-coding RNAs (lncRNA) regulate chromatin states and serve as landing platforms for chromatin-modifying complexes. ChIRP provides a powerful tool to map IncRNA binding sites on chromatin and can be combined with sequencing methods for a genome-wide resolution.
There are currently many challenges involved with ChIRP. IncRNAs display a focal, interspersed, and gene-selective binding making the identification of binding sites challenging and therefore requires optimal fixation and shearing parameters. Gentle shearing conditions are required to restore complete complexes that use IncRNAs as landing platforms on chromatin. Additionally, proper shearing of chromatin is required to identify genome-wide, high-resolution binding patterns for IncRNAs as well as binding motifs.
Our Adaptive Focused Acoustics® (AFA®) technology offers a gentle and tunable shearing method with many advantages including reduced glutaraldehyde fixation times. This enables shorter shearing times with better epitope preservation, higher restoration of big complexes bound to chromatin, and better detection of IncRNAs with very few distinct binding site because of the good epitope preservations.
Are you interested in working with Covaris for your ChIRP-seq research? Contact [email protected] today!