ChIA-PET
In-silico masking of repetitive elements.
ChIA-PET法は、クロマチン免疫沈降法(Kuo & Allis, 1999)および3C法を組み合わせた手法である(The ChIA-PET method combines ChIP-based methods (Kuo & Allis, 1999), and Chromosome_conformation_capture (3C), to extend the capabilities of both approaches.)。 ChIP-Seq法が転写因子結合領域(TFBS)を決定するのに広く用いられる手法である一方、染色体間の大域的相互作用の測定には3C法が用いられていた(Dekker et al., 2002)(ChIP-Sequencing (ChIP-Seq) is a popular method used to identify TFBS while 3C has been used to identify long-range chromatin interactions (Dekker et al., 2002).)。 However, both suffer from limitations when used independently to identify de-novo long-range interactions genome wide.
While ChIP-Seq is typically used for genome-wide identification of TFBS (Barski et al., 2007; Wei et al., 2006), it provides only linear information of protein binding sites along the chromosomes (but not interactions between them), and suffers from high genomic background noise (false positives). Additionally, only a small amount of sequences generated by ChIP-Seq uniquely map to the genome, and an even smaller amount are functional TFBS (Johnson et al., 2007).
While 3C is capable of analyzing long-range chromatin interactions, it cannot be used genome wide and, like ChIP-Seq, also suffers from high levels of background noise. Since the noise increases in relation to the distance between interacting regions (max 100kb), laborious and tedious controls are required for accurate characterization of chromatin interactions (Dekker et al., 2006).
Satellite regions and binding sites present in regions with severe structural variations are removed.
PETs which are mapped to different chromosomes are called interchromosomal inter-ligation PETs.
Figure 9. Proposed mechanism showing how distal regulatory elements can initiate long-range chromatin interactions involving promoter regions of target genes.
The interactions form DNA loop structures with multiple TFBS at the anchoring center. Small loops might package genes near the anchoring center in a tight sub-compartment, which could increase the local concentration of regulatory proteins for enhanced transcriptional activation.
This mechanism might also enhance transcription efficiency, allowing RNA pol II to cycle the tight circular gene templates. The large interaction loops are more likely to link together distant genes at either end of the loop residing near anchor sites for coordinated regulation, or could separate genes in long loops to prevent their activation. Adapted from Fullwood et al. (2009).