HCT116 cells were rinsed with ice-cold PBS and cross-linked under UV light at 254 nm with a total E of 4000 J/m² using a UVP cross-linker CL-3000 (Analytik Jena). Cross-linked cells were lysed in CLIP lysis buffer (20.3 mM Na2HPO4, 3.5 mM KH2PO4, 6.8 mM KCl, 342.5 mM NaCl, 0.1% SDS, 0.5% sodium deoxycholate, and 0.5% NP-40) and kept on ice for 10 min. The lysates were treated with RNase-free DNase I (Thermo Scientific; EN0523) at 37°C for 5 min, followed by the addition of 0.1 ng of RNase A (Thermo Scientific; EN0531) and incubation at 37°C for 10 min. After centrifugation at 13,000 g at 4°C for 20 min, the supernatants were divided for use as input or immunoprecipitation (IP) using mouse monoclonal SAF-A antibody (Santa Cruz Biotechnology; sc-32315) conjugated to Dynabeads™ Protein A (Invitrogen; 10002D). IP was carried out at 4°C for 3 h. The beads were washed twice with CLIP lysis buffer and subsequently with PNK buffer [50 mM Tris-HCl (pH 7.4), 10 mM MgCl2, and 0.5% NP-40]. To dephosphorylate the ends of RNA fragments, the beads were incubated with 40 U/mL alkaline phosphatase (Roche; 10108138001) at 37°C for 10 min. Next, the RNA 5' ends were phosphorylated by incubation with 0.5 U/μl T4 polynucleotide kinase (New England Biolabs; M0201L) and 0.125 mM ATP at 37°C for 10 min. Ribonucleoprotein complexes were finally eluted from the beads using 4X lithium dodecyl sulfate sample buffer (Invitrogen; NP0008). For RNA isolation from both input and IP samples, the RNA-protein complex was separated by SDS-PAGE in a 7.5% Mini-PROTEAN® TGX™ Precast Protein Gels (BIO-RAD; 456-1024) and transferred to a 0.45 μm NC blotting membrane (Cytiva; 10600003). Membrane regions corresponding to the molecular weight of SAF-A plus ~20 kDa above was excised and incubated with PK buffer [100 mM Tris-HCl (pH 7.4), 50 mM NaCl, and 10 mM EDTA] containing 4 mg/mL proteinase K (Roche; 3115836001) at 37°C for 20 min, followed by an additional 20 min incubation with PK/Urea buffer [100 mM Tris-HCl (pH 7.4), 50 mM NaCl, 10 mM EDTA, and 7 M urea] at 37°C. Supernatants were then subjected to organic extraction and ethanol precipitation with GlycoBlue (Invitrogen; AM9515) for efficient recovery of RNA fragments. CLIP libraries were constructed using the SMARTer® smRNA-Seq Kit for Illumina®.