Alternative Cleavage and Polyadenylation of RNA

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1 Developmental Cell 18 Supplemental Information The Spen Family Protein FPA Controls Alternative Cleavage and Polyadenylation of RNA Csaba Hornyik, Lionel C. Terzi, and Gordon G. Simpson Figure S1, related to Figure 4. FPA controls alternative polyadenylation of FPA premrna directly (A) Alternative polyadenylation of FPA mrna is unaffected by FLC. RNA gel blot analysis of alternative polyadenylation of FPA mrna in WT and autonomous pathway 1

2 mutants with elevated FLC levels: fve-3, ld-1, fca-9, fpa-7. FPA was detected with the same probe as used in Figure 1 and -TUBULIN was used as a loading control. (B) RNA gel blot analysis of alternative polyadenylation of FPA mrna in WT and fpa-7 compared with FLC null mutant flc-3 plants and fpa-7 flc-3 backgrounds. FPA was detected with the same probe as used in Figure 1 and -TUBULIN was used as a loading control. (C) Western blot analysis of different wild-type and fpa mutant backgrounds using anti- FPA antibodies. Coomassie staining of the corresponding proteins is shown as a loading control. (D) Association of Pol II with distal poly(a) sites in FPA chromatin is unaffected by genotypes with contrasting patterns of FPA poly(a) site selection. ChIP of Pol II at the FPA locus. Schematic depiction of FPA locus with exons shown as black rectangles and introns as gray lines. Poly(A) sites (PAS) are indicated. The chromatin regions analysed by qpcr are boxed. WT plants and lines expressing 35S::FPA:YFP and fpa-8 mutants were subjected to ChIP using anti-pol II antibodies (8WG16) followed by qpcr. Histograms show mean values SE obtained for four PCR amplifications. Figure S2, related to Figure 5. Changes in FPA activity correlate with differences in processing of antisense RNAs at the FLC locus 2

3 (A) Read-through defects in the gene upstream of FLC does not explain elevated FLC expression in fpa mutants. Schematic representation of FLC and adjacent loci. Rectangles represent exons and lines depict introns. Arrow heads and numbers identify position of primers used, and regions amplified in RT-qPCR. (B) RT-qPCR analysis of FLC, At5g10150 and intergenic transcription. Histograms show mean values SE for three independent PCR amplifications on three biological replicate samples. (C) Chromatograms of RT-PCR analysis of class I and class II antisense RNAs at the FLC locus from fpa-8 plants. The same primers used for RT-qPCR were used except that the forward primer was labeled with 6-FAM. The x axis shows size (bp) and the y axis the relative fluorescence signal. The position of the spliced variants identified by cloning (Figure 5a) are indicated. No RT controls are shown below. 3

4 Figure S3, related to Figure 6. Read-through from upstream Pol II gene explains AtSN1 up-regulation in fpa mutants (A) FPA does not play a generic role in silencing A. thaliana SINEs. RT-qPCR analysis of expression of the SINE, SB2-17 (At5TE38215), in WT, fpa-7 and a Pol V mutant background (drd3-7). Histograms show mean values SE for three independent PCR amplifications on three biological replicate samples. 4

5 (B) RT-qPCR signal detected at AtSN1 in fpa mutants arises from the same strand as At3g Strand-specific RT-PCR analysis of transcription at AtSN1. RT-PCR products were separated on agarose gels and stained with ethidium bromide. ACTIN2 and no RT and no RNA controls are included. (C) Estimation of percentage read-through at At3g qpcr analysis of read-through and mrna in WT and fpa-8 mutant background. Absolute amounts of RNA were derived from a standard curve prepared from amplification of cloned At3g44010 and downstream sequences. (D) Total amount of read-through RNA depicted in C, showing that there is an increase in the amount of read-through RNA in fpa-8 plants comparing to WT plants. Table S1, related to Figure 5. Antisense FLC RNA isoform sequences Isoform Sequence 5-3 Class I i Class I ii Class II i CTCGATGCAATTCTCACACGAATAAGGTGGCTAATTAAGTAGTGGGAGAGTCACCGGA AGATTGTCGGAGATTTGTCCAGCAGGTGACATCTCCATCTCAGCTTCTGCTCCCACATG ATGATTATTCTCCATCTGTACGATAATCATAGGTCAAAATCACTATTCACTTTCTCTTTTT GTCTTCTATCCAAGGA CTCGATGCAATTCTCACACGAATAAGGTACAAAGTTCATCAACCTTTTGTCTTAAAACAG ATAGTATTGACTTAGTTCCGTCTACTTAAGTATCACACACAAAGTCTCTTGGCCAAAGAG AGAGTATTAAGATATACAAACGCTCGCCCTTATCAGCGGAATAATTACATATCTTATTTT TTTTTTCTTCATAATTATATATGTTTTGGATTTTGATTTCAACCGCCGATTTAAGGTGGCT AATTAAGTAGTGGGAGAGTCACCGGAAGATTGTCGGAGATTTGTCCAGCAGGTGACAT CTCCATCTCAGCTTCTGCTCCCACATGATGATTATTCTCCATCTGTACGATAATCATAGG TCAAAATCACTATTCACTTTCTCTTTTTGTCTTCTATCCAAGGA CTCGATGCAATTCTCACACGAATAAGAAAAGTAAAAGAGCACAAAACAGAAGATAAAAG GGGGAACAAATGAAAACCCAGGTAAGGAAAAGGCGTACTTATCGCCGGAGGAGAA Class II ii CTCGATGCAATTCTCACACGAATAAGGTGGCTAATTAAGTAGTGGGAGAGTCACCGGA AGATTGTCGGAGATTTGTCCAGCAGGTGACATCTCCATCTCAGCTTCTGCTCCCACATG ATGATTATTCTCCATCTGTACGATAATCATAGAAAAGTAAAAGAGCACAAAACAGAAGAT AAAAGGGGGAACAAATGAAAACCCAGGTAAGGAAAAGGCGTACTTATCGCCGGAGGA GAA Class II iii CTCGATGCAATTCTCACACGAATAAGGTGGCTAATTAAGTAGTGGGAGAGTCACCGGA AGATTGTCGGAGATTTGTCCAGCAGAAAAGTAAAAGAGCACAAAACAGAAGATAAAAG GGGGAACAAATGAAAACCCAGGTAAGGAAAGGGCGTACTTATCGCCGGAGGAGAA Class II iv CTCGATGCAATTCTCACACGAATAAGAAAAAAACACAAACAAACACAGAACCGAGAAAC AACAAGAGATCCGCCGGAAAAAAACCAAACGGTAAGGAAAAGACGTACTTATCGCCGG AGGAGAA 5

6 SUPPLEMENTAL EXPERIMENTAL PROCEDURES Plant strains fpa-3, fpa-7 (SALK_021959), flc-3, 35S::FPA fca-1 were provided by R. Amasino (Madison). fca-9, fpa-8, 35S::FPA:YFP fpa-8, were provided by C. Dean (John Innes Centre), fve-3 was provided by J. Martinez-Zapater (Madrid). The Pol V mutant, drd3-7, was provided by M. Matzke (Vienna). The wild-type strains Col-0 and Ler and ld-1, fpa- 1, fpa-2, fca-1, fy-1 were obtained from NASC (UK). 35S::FPA was made by crossing 35S::FPA fca-1 to Ler. fpa-3 has been described (Meier et al., 2001), but our analysis revealed a different mutation to that reported; fpa-3 contains a single deletion corresponding to G 3553 in exon 6. A. thaliana seeds were sown aseptically in MS10 or MS10+Kanamycin (35S::FPA) plates. Seeds were stratified for 2 days at 4 o C. Plants were grown at constant 24 o C under 16 h light/ 8 h dark conditions. Seedlings were harvested 14 days after transfer to 24 o C. Detection of FLC antisense RNA isoforms using RT-PCR with 6-FAM labelled primer For detection of FLC antisense RNA isoforms we used an RT-PCR based method (Simpson et al., 2008). Total RNA was extracted from 100mg seedlings using TRIzol reagent (Invitrogen) and treated with DNaseI (Roche). 2.5 g of total RNA was used for first strand synthesis (MMLV reverse transcriptase, Promega) according to the manufacturer. We used 6-carboxyfluoresceine (6-FAM) labelled forward primer (antisense FLC Class I and Class II) and reverse primer (antisense FLC Class I and Class II) to amplify FLC antisense RNAs with Taq polymerase (Roche). 1 l of 25 l reaction was mixed with 9 l of HiDi formamide containing 0.05 l of GeneScan-500 LIZ (Applied Biosystems) internal size standard. Amplified fragments were separated on a 3730 DNA Analyser (Applied Biosystems); results were analysed using GeneMapper software (Applied Biosystems). 6

7 Table of Primers AMPLICON NAME USED IN FORWARD (F) and REVERSE (R) PRIMER (5' to 3') UBIQUITIN Figures 5 and 6 F: gttggaggatggcagaactc R: tcccagtcaacgtcttaacg FLC Figure S2 - qpcr1 F: gagccaagaagaccgaactc R: ttctgctcccacatgatga FLC_UpIR Figure S2 - qpcr2 F: ataagcattaggttgttcc R: gatagcgagtaagaaacg At5g10150 Figure S2 - qpcr3 F: tatcgacggagacaatggaa R: gagtcaaatcggacgagtca Anti-sense FLC Class I Figures 5b and 5e F: ctcgatgcaattctcacacg R: tccttggatagaagacaaaaagaga Anti-sense FLC Class II Figures 5b and 5e F: ctcgatgcaattctcacacg R: ttctcctccggcgataagta SB2-17 Figure S3a F: ttacatgatgtggtttcgg R: aacatttatccatttccaatg At3TE63855 Figure 6b - qpcr 1 F: cgaccaatgctggagttgta R: aacatcagaacagaacgacca AtSN1_DownIR Figure 6b - qpcr 2 F: tggtacagtgaacgccaaat R: ttggtcctctgtccaattca AtSN1 (At3TE63860) Figure 6b - qpcr 3 F: aaagaagatgaatttctggtatgg R: agcctagttttaattctacggatca AtSN1_UpIR Figure 6b - qpcr 4 F: cactccagctccatgtcatt R: agaaaaagtgacggcaaaaa At3g44005 Figure 6b - qpcr 5 F: ccgaccaccttaaagattttcc R: ccacagccatgcctaacc At3g44006 Figure 6b - qpcr 6 F: aaatgctggcacttcacc R: caccgtttcaggactaacc At3g44010_DownIR Figure 6b - qpcr 7 F: ttttgctttgttaccgttcg R: ggctgcgactgaagtaaaca At3g44010 Figure 6b - qpcr 8, S3 F: aagttggtgcttgattaacg R: ggaagtatggtttgaactgc At3g44010_UpIR Figure 6b - qpcr 9 F: gtcacgatgatgaagaagc R: catgtggatggagaagaaag At3g44010_PCR1 Figure 6d, S3c,d F: cttggattggagacgcatta R: tgatgttttggctattctcgt At3g44010_PCR2 Figure 6d F: cttggattggagacgcatta R: ggaagtatggtttgaactgc ACT2 Figure S3b F: tcatactagtctcgagagatgactcagatcatgtttgag R: tcattctagaggcgcgccacaatttcccgttctgcggtag AtSN1_PCR 1 Figures 6f, S3b F: aaaataagtggtggttgtacaagc R: accaacgtgctgttggcccagtggtaaatc AtSN1_PCR 2 Figure 6f F: aaaataagtggtggttgtacaagc R: agaaaaagtgacggcaaaaa AtSN1_PCR 3 Figure 6f F: cggctttgatttgatgtgaa R: accaacgtgctgttggcccagtggtaaatc ACTIN Figure 4b, 5d, S1c F: gagagattcagatgcccagaagtc R: tggattccagcagcttcca FPA 1 Figure 4b, S1c F: acgtatcatcgcacaattcg R: ccaaaattccaatcccagaa FPA 2 Figure 4b F: ttcgtttgttctctaactttgattg R: tttttggactaaacaagcatca FPA 3 Figure 4b F: ttgacttcttcacaaccattctg R: ccaaataaaccaatccctgaa FPA 4 Figure 4b F: tggggaggtcgataagaatc R: ttgctgctgtttctgctgta FPA 5 Figure 4b, S1c F: ttctaccctctgcctgatga 7

8 FLC-H3 FLC-Mid Figure 5d Figure 5d R: aaatgctccagtttcaacga F: ggttgttatttggtggtgtga R: cttctgctcccacatgatga F: caactggaggaacaccttga R: cacggttgttctcagcaaa SUPPLEMENTAL REFERENCES Meier, C., Bouquin, T., Nielsen, M.E., Raventos, D., Mattsson, O., Rocher, A., Schomburg, F., Amasino, R.M., and Mundy, J. (2001). Gibberellin response mutants identified by luciferase imaging. Plant J 25, Simpson, C.G., Fuller, J., Maronova, M., Kalyna, M., Davidson, D., McNicol, J., Barta, A., and Brown, J.W. (2008). Monitoring changes in alternative precursor messenger RNA splicing in multiple gene transcripts. Plant J 53,

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