Total RNA was extracted from cells and tissues using TRIzol (Invitrogen, Carlsbad, CA, USA) and protein-RNA complexes were isolated with antibody. Libraries were prepared according to NEB's instructions accompanying the NEBNext® Ultra™ RNA Library Prep Kit  (E7530L). Briefly, to deplete rRNA(MeRIP-seq and RIP-seq), we used 1,000 ng of fragmented  RNA , with the NEBNext rRNA remove kit(E6310X) following the manufacturer's instructions  and to isolate poly(A)+ mRNA(RNA-seq and polysome-seq), we used 5 μg of polysome total RNA with the PolyATtract®mRNA Isolation Systems (Promega) following manufacturer's standard protocol.