Extract for J2-IP experiments was made from young adult animals grown on solid plates at 15°C. Worms used for TDP-1 immunoprecipitation followed by RT-PCR were crosslinked according to (Zisoulis et al, 2010). Worms used for J2-IP were not crosslinked. Extract was prepared by bead beating as described in (Saldi et al, 2007). Extracts were used immediately for immunoprecipitations or dissolved in TRizol (for input RNA). RNA for poly(A) and total RNA sequencing libraries was extracted from whole animals by TRIzol extraction. Genomic DNA was removed using turboDNase (Invitrogen). For total RNA libraries, 5μg of RNA was run through a Ribozero column (Epicenter, #R2C1046) to remove ribosomal RNA. For poly(A)-selected libraries, RNA was selected using sera-mag magnetic oligo dT beads (Therma Scientific). Libraries were created using Illumina TruSeq kits (RS-122-2001). RNA recovered by immunoprecipitation with the J2 antibody (three biologically independent lysates) of young adult worms as well as input material (as a loading control) were converted into strand-specific total RNA libraries using V2 Scriptseq (Epicenter #SSV21106) kits following manufacturer's instructions, except reverse transcription was done with SuperScript III (Invitrogen #18080-044) using incrementally increasing temperatures from 42°C-59°C to allow for transcription though structured RNAs. rRNA was not removed from J2-IP RNA samples. Immunoprecipitated DNA from ChIP samples was converted in sequencing libraries using ChIP-Seq DNA Sample Prep Kit (IP-102-1001). Libraries were sequenced on Illumina HiSeq 2000 platforms.