Circ2
The pull-down of cCD109 together with its partner miRNAs was performed according to the RNA Interactome MagIC Beads protocol (https://elementzero.bio/rna-interactome-magic-beads/). Briefly, 20 millions of CFBE41o- cells were harvested and biochemically cross-linked with 1% formaldehyde to allow the capture of the RNA-RNA complexes. Cell pellets (n=3) were then lysed and cCD109, together with its binding partners, was pulled down using cCD109-specific Magnetic Instant Capture (MagIC) Beads (Element Zero Biolab). RNAs from control beads and cCD109 beads were isolated using a modified version of phenol/chloroform extraction and enrichment efficiency was calculated via qRT-PCR of cCD109 (and the linear counterpart CD109) in control/cCD109 beads vs input RNA. Six samples (paired n=3 RNA pulled down with cCD109 beads vs control beads) were sent for miRNA sequencing using the Human microRNA Sequencing service from Arraystar Inc to identify the miRNAs binding to cCD109. Further bioinformatic analysis was carried out by Arraystar to infer the pathways and biological mechanisms potentially impacted by miRNAs potentially partnering with cCD109.