Supplementary Figure 1 Circadian profiles of Adarb1 transcript and ADARB1 protein in mouse tissues. (a) Overlap of rhythmic transcripts identified in the previous transcriptome analyses. The mouse liver samples were prepared under DD conditions in Yoshitane et al. 6, Koike et al. 4 and Vollmers et al. 7 and under LD conditions in Menet et al. 5. (b) Circadian expression profiles of two isoforms of Adar p15 and p11 in the mouse liver examined by qrt-pcr analysis. The signals were normalized to Rps29 (mean ± SEM; n = 3). (c) Temporal profiles of Arntl and Adarb1 mrnas (determined by qrt-pcr) and the editing levels at the Flnb Q/R site (determined by direct sequencing analysis) in mouse liver through 3 days in DD. (d) Temporal expression profiles of Adarb1, Adarb1 long isoform, Adar p15, Adar p11, Adarb2, Dbp and Arntl in mouse tissues. The signals were normalized to Rps29 (mean ± SEM; n = 3). (e) Temporal profiles of the editing levels at the Q/R site of Flnb, the Y/C and I/M sites of Cacna1d and the A and B sites of Htr2c in direct sequencing analysis (mean ± SEM; n = 3). (f) Temporal profiles of ADARB1 protein levels (top panel, indicated by an arrowhead) in control and Adarb1-KO liver nuclear extracts. Non-specific bands were indicated by asterisks. TBP served as a loading control (bottom panel). (b, d, e) The temporal changes were analyzed by one-way ANOVA, * p <.5, ** p <.1, *** p <.1 and n.s. p.5.
Supplementary Figure 2 Circadian regulation of A-to-I RNA editing in mouse liver. (a) Direct sequencing chromatograms from RT-PCR products of Cdk13 mrna at various times of the day. (b) Circadian profiles of editing levels at the Cdk13 Q/R site in direct sequencing analysis (mean ± SEM; n = 3). (c) Regulation of alternative splicing of Adarb1 transcripts by Adarb1-mediated editing. The self-editing site is shown as a closed circle, and the indicated PCR primer set amplifies only the long isoform. (d) Circadian expression profiles of the long (top) and short isoforms (middle) of Adarb1 transcripts, determined by RT-PCR analyses. The relative band intensities [long / (long + short) (%)] were plotted (bottom). The gene specific primers used in this RT-PCR were described in Supplementary Table 6. (e) Direct sequencing chromatograms from RT-PCR products of Cog3 and Copa mrnas at various times of the day. (f) Circadian profiles of editing levels [G / (A+G) (%)] at the indicated editing sites in RNA-Seq analysis (top and 3rd panels) and in direct sequencing analysis (2nd and bottom panels, mean ± SEM; n = 3). (g) Neighbor preferences of ADAR and ADARB1 represented by Two Sample Logo sequence motifs. Logo displays enriched bases above the upper line and depleted bases below the lower line on both sides of the central edited adenosine. (h) Trinucleotide preferences of ADAR and ADARB1. (b, f) The temporal changes were analyzed by one-way ANOVA, * p <.5, ** p <.1, *** p <.1, n.s. p.5 and N.D. not detected.
Supplementary Figure 3 Gene expression rhythms revealed by RNA-seq in Adarb1-knockout mice. (a) Comparison between two biological replicates of transcript expression levels (FPKM) exhibited a high degree of reproducibility with an average R 2 value of.98. (b) Overlap of rhythmic transcripts between control (black) and Adarb1-KO liver (yellow). A solid line circle indicates rhythmic transcripts with strong rhythmic expression, and a dotted circle indicates those with weak rhythmic expression. (c) Temporal expression profiles of Slcola4 and Aim1l in qrt-pcr analysis. The signals were normalized to Rps29 (mean ± SEM; n = 3). The temporal changes were analyzed by one-way ANOVA, * p <.5, ** p <.1 and n.s. p.5. (d) Temporal expression profiles of Cpeb2, Hmgxb4 and Gmeb1 in RNA-Seq analysis (Data are mean; n = 2). (e) Pie charts showing the enrichment of transcripts that were defined as arrhythmic at nascent RNA levels in the previous study 5. (f, g) Circadian expression profiles of typical clock genes in RNA-Seq analysis (f) and in qrt-pcr analysis (g) of control and Adarb1-KO mouse liver. In panel g, the signals were normalized to Rps29 (mean ± SEM; n = 3). (h) A heat map of rhythmically expressed genes both in control and Adarb1-KO mice (n = 659). Gene expression levels of two biological replicates across time points were shown in each lane corresponding to one gene, ordered by the phases. High expression levels were displayed in yellow and low in blue. (i) A histogram of acrophase (circadian peak phase) of the 659 rhythmic genes in both genotypes.
Supplementary Figure 4 Short-period phenotype of ADARB1 deficiency. (a) Differences in circadian peak phase (Δacrophase) of the 659 rhythmic genes between control and Adarb1-KO mouse liver (*** p <.1 by Paired t-test). The acrophase in control was set to. (b) In NIH3T3 cells transiently transfected with an shrna expression vector (control sh, Adarb1_sh1, Adarb1_sh2 or Adarb1_sh3), Adarb1 mrna levels were examined by qrt-pcr. The signals were normalized to Rps29 (mean ± SEM; n = 3; ** p <.1 by Student's t-test). (c) Unsynchronized NIH3T3 cells were transiently transfected with a Flag-ADARB1 expression vector in combination with an shrna expression vector (control sh, Adarb1_sh1, Adarb1_sh2 or Adarb1_sh3). The cell lysates were subjected to immunoblotting. ACTB served as a loading control. (d, e) A representative set of bioluminescence rhythms of Fig.4c (d) and 4d (e) was shown. (f) Circadian profiles of CRY1 (arrowhead), PER2, CLOCK and ARNTL proteins in control and Adarb1-KO mice liver nuclear extracts (mean ± SEM; n = 3; * p <.5 by Student's t-test). Nonspecific bands are indicated by asterisks. (g) Dual luciferase reporter assay in unsynchronized NIH3T3 cells transiently transfected with a luciferase- Cry2 3 -UTR reporter (nt 1-2177) in combination with a let-7g expression vector (mean ± SEM; n = 3; * p <.5, ** p <.1 and n.s. p.5 by Student's t-test). The relative luciferase activities were normalized to the signals from the cells transiently transfected with an empty pcdna3.1/v5-his plasmid, and the mean value of the empty luciferase reporter was set to 1. (h) Circadian periods of synchronized NIH3T3 cells transiently transfected with a Arntl-luciferase reporter in combination with control sh, Adarb1 shrna and let- 7g expression vectors (mean ± SEM; n = 6; * p <.5, *** p <.1 by Student's t-test). (i) A model for the ADARB1-mediated regulations of the rhythmical A-to-I RNA editing events and global circadian outputs. The circadian expression of Adarb1 by CLOCKdependent transactivation produces the rhythmic profiles of ADARB1-dependent A-to-I RNA editing. ADARB1 plays an essential role for the robust circadian oscillation by suppressing CRY2 expression through the regulation of mirna biogenesis. ADARB1-mediated post-transcriptional regulation contributed to circadian profiles of steady-state mrna levels and global circadian outputs.
Terajima et al., Table S4 Repeat families B1 B2 B4 ERV1 ERVK ERVL ERVL_MaLR L1 L2 Registered editing sites (8,41) 3,357 1,678 473 36 1 125 352 443 1 Editing sites in this study (389) 165 32 29 1 1 6 12 1 Rhythmic Editing sites in this study (132) 57 5 1 3 2