Supplementary Figure S1 (A) Change of reporter activity levels after actinomycin D treatment. HEK293T cells were transiently transfected with the reporter and incubated with actinomycin D for the indicated times. (B) Schematic presentation of deletion constructs of mcry1 3UTR and their reporter activity. (C) Change of reporter mRNA levels after actinomycin D treatment. NIH3T3 cells were transiently transfected with the reporter and incubated with actinomycin D for the indicated times. (D) Each 3UTR in vitro transcribed with 32- α P-rUTP was subjected to in vitro binding and UV cross-linking assay with HEK 293T nuclear extract. The arrow indicates the proteins that shows differential binding. (E) wt 3UTR in vitro transcribed with 32- α P-rUTP was subjected to in vitro binding and UV cross-linking assay with HEK 293T cytoplasmic extract and unlabeled cold wtUTR. The arrow indicates the proteins that shows differential binding. (F) Each 3UTR in vitro transcribed with 32- α P-rUTP was subjected to in vitro binding and UV cross-linking assay with NIH-3T3 cytoplasmic extract. The arrow indicates the proteins that shows differential binding. (G) wt 3UTR in vitro transcribed with 32- α P-rUTP was subjected to in vitro binding and UV cross-linking assay with HEK 293T cytoplasmic extract and homo-oligoribonucleotide A, C, and U. The arrow indicates the proteins that shows differential binding. (H) Alignment of conserved U-tract sequences among various species compared with between 252 and 280 in mcry1 3'UTR.

NAT activity pcNAT pcNAT_wt610 pcNAT_N201 pcNAT_N mcry1_3UTR CMVNAT Woo et al_ Supplementary Fig. S1 B A C Act.D 0h Act.D 5h AANAT activity (%of Act.D 0h) pcNAT pcNAT_wt Time after Act.D [h] pcNAT-N401 pcNAT-N201 Relative mRNA level (aanat/rpl32)

homopolymer HEK_cyto ++ ACU ++ mCry1_3UTR F G Woo et al_ Supplementary Fig. S1 H N401 wt610 N201 NIH_cyto N401 wt610 N201 HEK_nuc Cold 37.5 wt610 HEK_cyto DE

Sequence(5=>3) Endo-mcry1 F CCT TGA AAA GCC TGG GAA AT Endo-mcry1 R TCC GCT GCG TCT ATA TCC TC Endo-mper2 F GCC TTC AGA CTC ATG ATG ACA GA Endo-mper2 R TTT GTG TGC GTC AGC TTT GG mRPL32 F AAC CCA GAG GCA TTG ACA AC mRPL32 R CAC CTC CAG CTC CTT GAC AT aanat F TTT GAG ATT GAG CGC GAA G aanat R TCG AAC CAG CCC AGT GAC mGAPDH F GCC ATC AAT GAC CCC TTC ATT mGAPDH R GCT CCT GGA AGA TGG TGA TGG mTBP F CAG CCT TCC ACC TTA TGC TC mTBP R TTG CTG CTG CTG TCT TTG TT Supplementary Table primer sequences for real time PCR