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Antibody binding was visualised using a secondary antibody (polyclonal, Cy5TM-conjugated anti-mouse IgG from goat; Zymed).

Finally, antibody binding was visualised using DAB as the chromogen and the sections mounted in Mowiol for observation under a Nikon 90i microscope.

OPG binding was visualised using TMB Pierce Chemical Coo).

Antibody binding was visualised using AEC-solution (for LSAB2-Kit).

Antibody binding was visualised using 3-diaminobenzidine (Sigma-Aldrich).

Antibody binding was visualised using Vectastain reagents and protocols performed on a Dako immunostainer.

After blocking (3% BSA, 1.5% normal goat serum in PBS), cells were incubated with primary antibodies against BHMT (mouse monoclonal, ab52144, AbCam, 1 500 dilution) and Nox4 (rabbit polyclonal; 1 200 dilution [1]. Antibody bindings were visualised using Alexa 568-conjugated anti-mouse IgG and 488-conjugated anti-rabbit IgG secondary antibodies (Invitrogen Molecular Probes; 1 200 dilution).

Membranes were incubated with an anti-rabbit secondary antibody conjugated to alkaline phosphatase (Sigma-Aldrich), and binding to PG1 was visualised using 1-Step NBT/BCIP (Pierce).

Specific binding of antibodies was visualised using appropriate horseradish peroxidase-linked secondary antibody followed by detection of chemoluminescence using an enhanced chemoluminescence detection kit (Roche) according to manufacturer's instructions.

When the top 10 RNA targets with the largest number of crosslink sites were listed according to each RNA segment, the position of SAFB1 binding within each gene was visualised using the UCSC Genome Browser (Supplementary Figure  2).

Nuclear morphology and total cell number was visualised using the DNA binding dyes Hoechst 33342 (1 μg/mL; Sigma, B2261).