Table S1. CDE Sequences and Globin Reporter mrna Half-Lives in NIH3T3 Cells, Related to Figures 1 and 2 Construct Sequence t1/2 ± SD (hrs)

Size: px
Start display at page:

Download "Table S1. CDE Sequences and Globin Reporter mrna Half-Lives in NIH3T3 Cells, Related to Figures 1 and 2 Construct Sequence t1/2 ± SD (hrs)"

Transcription

1 Table S1. CDE Sequences and Globin Reporter mrna Half-Lives in NIH3T3 Cells, Related to Figures 1 and 2 Construct Sequence t 1/2 ± SD (hrs) n TNF -CDE 37 -V2 AGATCCTTCAGACAGACATGTTTTCTGTGAAAACGGAGCTGAGCTAGATCT 8.8 ± TNF -CDE 37 -V3 AGATCCAGTTCAGACAGACATGTTTTCTGTGAAAACGGAGCTGAGCTAGATCT 1.4 ± human TNF -CDE 37 -V3 AGATCCTGTTGGCTCAGACATGTTTTCCGTGAAAACGGAGCTGAACAAGATCT 2.0 ± TNF -CDE 37 -V3-M1 AGATCCAGTTCAGA TTTTCTGTGAAAACGGAGCTGAGCTAGATCT > 9.0* 1 TNF -CDE 37 -V3-M2 AGATCCAGTTCAGACAGACATGTTT GCTGAGCTAGATCT > 9.0* 2 TNF -CDE 37 -V3-M3 AGATCCAGTAGTGACAGACATGTTTTCTGTGAAAACGGAGCTGAGCTAGATCT 1.5 ± TNF -CDE 37 -V3-M4 AGATCCAGTTCAGACAGACATGTTTTCTGTGAAAACGGAGCACTGCTAGATCT 2.5 ± TNF -CDE 37 -V3-M5 AGATCCAGTAGTGACAGACATGTTTTCTGTGAAAACGGAGCACTGCTAGATCT 1.1* 2 TNF -CDE 37 -V3-M6 AGATCCAGTTCAGAGTGACATGTTTTCTGTGAAAACGGAGCTGAGCTAGATCT 1.4 ± TNF -CDE 37 -V3-M7 AGATCCAGTTCAGACAGACAACTTTTCTGTGAAAACGGAGCTGAGCTAGATCT > TNF -CDE 37 -V3-M8 AGATCCAGTTCAGAGTGACAACTTTTCTGTGAAAACGGAGCTGAGCTAGATCT > 9.0* 2 TNF -CDE 37 -V3-M9 AGATCCAGTTCAGACAGACATGTTTAGGCTGAAAACGGAGCTGAGCTAGATCT > TNF -CDE 37 -V3-M10 AGATCCAGTTCAGACAGACATGTTTTCTGTGAAAAGTCTGCTGAGCTAGATCT > 9.0* 1 TNF -CDE 37 -V3-M11 AGATCCAGTTCAGACAGACATGTTTAGGCTGAAAAGTCTGCTGAGCTAGATCT > 9.0* 1 TNF -CDE 37 -V3-M12 AGATCCAGTTCAGACAGACATGTTTTCTGTGAAAACGCTGCTGAGCTAGATCT 1.3 ± TNF -CDE 37 -V3-M13 AGATCCAGTTCAGACAGACATGTTTAGTGTGAAAACGCTGCTGAGCTAGATCT > TNF -CDE 37 -V3-M14 AGATCCAGTTCAGACAGACATGTTTTCTGTGAAAAGTGAGCTGAGCTAGATCT > TNF -CDE 37 -V3-M15 AGATCCAGTTCAGACAGACATGTTTTCGCTGAAAAGTGAGCTGAGCTAGATCT > TNF -CDE 37 -V3-M16 AGATCCAGTTCAGACAGACATGTTTTCTGTGAAATGGGAGCTGAGCTAGATCT > TNF -CDE 37 -V3-M17 AGATCCAGTTCAGACAGACATGTTTTCTCAGAAATGGGAGCTGAGCTAGATCT > TNF -CDE 37 -V3-M18 AGATCCAGTTCAGACAGAGTTGTTTTCTGTGAAAACGGAGCTGAGCTAGATCT 2.0 ± TNF -CDE 37 -V3-M19 AGATCCAGTTCAGACAGACATCATTTCTGTGAAAACGGAGCTGAGCTAGATCT > TNF -CDE 37 -V3-M20 AGATCCAGTTCAGACAGACATCATTTCTGTGAAATGGGAGCTGAGCTAGATCT 2.7 ± TNF -CDE 37 -V3-M21 AGATCCAGTTCAGACAGACATGTTTAGTGTGAAAACGGAGCTGAGCTAGATCT > TNF -CDE 37 -V3-M22 AGATCCAGTTCAGACAGACATGTTTTCTGTCTAAACGGAGCTGAGCTAGATCT > TNF -CDE 37 -V3-M23 AGATCCAGTTCAGACAGACATGTTTAGTGTCTAAACGGAGCTGAGCTAGATCT > TNF -CDE 37 -V3-M24 AGATCCAGTTCAGACAGACATGTTTTCTATGAAAACGGAGCTGAGCTAGATCT 2.2 ± TNF -CDE 37 -V3-M25 AGATCCAGTTCAGACAGACATGTTTTCACAGAAAACGGAGCTGAGCTAGATCT > TNF -CDE 37 -V3-M26 AGATCCAGTTCAGACAGACATGTATTCTGTGAATACGGAGCTGAGCTAGATCT 5.0 ± TNF -CDE 37 -V3-M27 AGATCCAGTTCAGACAGACATGTTATCTGTGATAACGGAGCTGAGCTAGATCT > TNF -CDE 17 -ds AGATCCAGTGTTTTCTGTGAAAACGCTAGATCT > TNF -CDE 17 -ss TCTAGATGTTTTCTGTGAAAACGACCGGT 1.1 ± ICOS-CDE 17 -ss TCTAGAAAATTTCTGTGAAATAAACCGGT 4.8 ± TNF -CDE 150 AGATCCTTTGGAAGGCCGGGGTGTCCTGGAGGACCCAGTGTGGGAAGCTGTCTTCAGACAG ACATGTTTTCTGTGAAAACGGAGCTGAGCTGTCCCCACCTGGCCTCTCTACCTTGTTGCCT CCTCTTTTGCTTATGTTTAAAACAAAATATTTATAGATCT 5.6 ± TNF -CDE 150 -M16 AGATCCTTTGGAAGGCCGGGGTGTCCTGGAGGACCCAGTGTGGGAAGCTGTCTTCAGACAG ACATGTTTTCTGTGAAATGGGAGCTGAGCTGTCCCCACCTGGCCTCTCTACCTTGTTGCCT > CCTCTTTTGCTTATGTTTAAAACAAAATATTTATAGATCT TNF -CDE 150 -M20 AGATCCTTTGGAAGGCCGGGGTGTCCTGGAGGACCCAGTGTGGGAAGCTGTCTTCAGACAG ACATCATTTCTGTGAAATGGGAGCTGAGCTGTCCCCACCTGGCCTCTCTACCTTGTTGCCT 5.6 ± CCTCTTTTGCTTATGTTTAAAACAAAATATTTATAGATCT XXX CDE sequence XXX nucleotides introduced into cloning context XXX mutation --- deletion XXX cloning sites XXX flanking TNF 3 UTR sequence in CDE 150 XXX primer sites * mrna half-lives determined upon stable transfection

2 Table S2. Proteins Enriched by CDE RNA Affinity Purification, Related to Figure 3 Name Symbol MW (kda) No of Peptides 4xS1m CDE-4xS1m Roquin, RING finger and CCCH zinc finger protein 1 Rc3h Cleavage and polyadenylation specificity factor subunit 7 Cpsf Ribosome biogenesis regulatory protein homolog Rrs Roquin2, RING finger and CCCH zinc finger protein 2 Rc3h Nucleophosmin Npm Splicing factor, proline- and glutamine-rich Sfpq Fragile X mental retardation syndrome-related protein 1 Fxr

3 Table S3. Proteins Purified with Roquin and Roquin2, Related to Figure 5 No of peptides Protein MW (kda) EGFP EGFP-Roquin EGFP-Roquin2 CNOT1 = Not RC3H1 = Roquin PABP TAB182 = TNKS1BP IF2B RC3H2 = Roquin PHB GBLP YBOX HNRPM IF2B MOV RCD1 = Not PABP STML PDIA DHX DBPA CNOTA = Not HNRPC P5CR CNOT2 = Not DDX VIME CB PAIRB AGAL IF2B LARP KCRB KPYM CNOT3 = Not RENT AFG ZCHC AL7A PCBP ILF PDIA DHB RBMX DDX3X AAAT CNO6L = Ccr4b CNOT8 = Caf1b

4 CNOT7 = Caf1a Blue: bait proteins Yellow: proteins of the Ccr4-Caf1-Not complex

5 Table S4. Bioinformatics Prediction of CDEs in Mouse 3 UTRs, Related to Figure 6 Name GeneID Genomic Coordinates CDE Sequence* Stem (nt) Conservation Bmpr1a chr14(-): GCTTTCTGTGAAAGC 6 41 Fos chr12(+): GTTTTCCATGAAAAC 6 40 D11Wsu99e chr11(-): CCTTCTGTGAAGG 5 38 Pdia chr12(+): AATTCTATGAATT 5 38 Prkg chr19(-): CATTTCTGTGAAATG 6 38 Fbxo chr17(-): TCTTTCTATGAAAGA 6 38 Slc25a chr2(-): CATTCTGTGAATG 5 37 Brwd chr16(-): TTTTCTATGAAAA 5 36 Nfkbiz chr16(-): TTGTTTCTATGAAACAA 7 36 Epc chr18(-): TCTCTTCTGTGAAGAGA 7 36 Adamts chr13(+): ACTTCTGTGAAGT 5 36 Baz2b chr2(-): TTTTCTGTGAAAA 5 36 Kpna chr3(-): TTTTCTATGAAAA 5 35 Dscaml chr9(+): TTTTTCTATGAAAAA 6 35 Bptf chr11(-): CTTTCTATGAAAG 5 35 Rc3h chr2(-): AACTTCTGTGAAGTT 6 34 Lpin chr17(+): TCTTTCTGTGAAAGA 6 34 Hmgxb chr18(-): CCCTTCTGTGAAGGG 6 34 Slc35f chr14(-): TATATTCTGTGAATATA A02Rik chr16(+): CCTTCTGTGAAGG 5 34 Frmd chr12(+): TCCTTTCTGTGAAAGGA 7 34 Rc3h chr1(+): AACTTCTGTGAAGTT 6 34 Phf chr4(-): GTTTCTGTGAAAC 5 33 Edem chr1(+): CATTCTGTGAATG 5 33 Tnf chr17(-): GTTTTCTGTGAAAAC 6 33 Aggf chr13(-): TTCTTCTGTGAAGAA 6 33 Uhrf1bp chr17(+): TGGTTCTGTGAACCA 6 33 Ctla chr1(+): ATTTTCCATGAAAAT 6 32 Lpin chr12(-): TCTTTCTGTGAAAGA 6 32 Prkd chr12(-): TGTTCTATGAACA 5 32 Gramd chr18(+): CATTTCTATGAAATG 6 32 Crispld chr8(+): TTTTTCTATGAAAAA 6 31 Plag chr4(-): GTTTCTATGAAAC 5 31 Mdga chr12(-): TTTTCTGTGAAAA 5 30 Wnt3a chr11(-): TTTCTTTCTATGAAAGAAA 8 30 Rbbp chr1(+): CCTTTCTGTGAAAGG 6 28 Slc25a chrx(+): TCTTCTGTGAAGA 5 28 Scmh chr4(+): GTCCTTCCATGAAGGAC 7 27 Efna chr3(-): GTCTTCTGTGAAGAC 6 27

6 Icos chr1(+): ATTTCTGTGAAAT 5 26 Atp2b chr10(+): ATTTCTGTGAAAT 5 26 Ppp1r chr17(+): TGTTTTCTATGAAAACA 7 26 Nfkbid chr7(+): GATTTCTGTGAAATC 6 25 Bcan chr3(-): TACTTCTGTGAAGTA 6 25 Nfkbid chr7(+): TGTTTCTGTGAAACA 6 23 Sertad chr7(+): CCTTCCGTGAAGG 5 23 Pdzk1ip chr4(+): TTATTTCTGTGAAATAA 7 21 Ier chr17(+): TGTTCTGTGAACA 5 21 Agap chr10(+): CCCTTTCCGTGAAAGGG 7 20 Kctd chr5(-): ATTTCTGTGAAAT 5 20 Shprh chr10(+): TCTTCTGTGAAGA 5 20 Pex chr11(-): GTTTCTATGAAAC 5 19 Prr chr17(-): TGTTTTCTGTGAAAACA 7 19 Zfp chr7(-): AACATTCTGTGAATGTT 7 15 Fam188b chr6(+): CCTTCCATGAAGG 5 13 Chic chrx(+): TTGTTTCCATGAAACAA 7 11 Dcaf chr4(-): ACTTTCTGTGAAAGT 6 9 Rps15a chr7(-): CATTTCTGTGAAATG 6 8 Fam63b chr9(-): ATTTCTGTGAAAT 5 5 Cdc14a chr3(-): TGTTCTATGAACA 5 4 Hes chr4(+): ACTTCTGCGAAGT K19Rik chr16(-): AGTTCTGTGAACT 5 3 Hdx chrx(-): TATTCTATGAATA 5 3 Arhgef chr3(+): CTTTCTACGAAAG 5 2 Tnks chr19(+): CTTTCCATGAAAG 5 2 Tcf chr9(-): ATTTCCATGAAAT 5 2 Tmem chr9(+): TATTCCATGAATA 5 2 Dagla chr19(-): TATTCTATGAATA 5 2 Ifi chr1(-): TTTTCTATGAAAA 5 2 Pxdn chr12(+): ACTTCTGTGAAGT 5 2 C330018D20Rik chr18(-): AGTTCTGTGAACT 5 2 Gpr chr5(+): CCTTCCGTGAAGG 5 2 Steap chr1(-): CCTTCTGCGAAGG 5 2 Pak chr7(+): CTGTTTCTACGAAACAG 7 2 Sftpb chr6(+): ATTTCTATGAAAT 5 2 Yipf chr17(+): TATTCCGCGAATA 5 2 Cnot chr8(-): TGTTCCGTGAACA 5 1 Pkib chr10(+): TTTTCTATGAAAA 5 1 Homez chr14(-): ATTTCTATGAAAT 5 1 Gng chr6(+): AAATTTCCGTGAAATTT 7 1

7 Gtf3c chr2(-): ATTTCTGTGAAAT 5 1 Tdg chr10(+): TGTTCTGTGAACA 5 1 Fyco chr9(-): CTTTCTATGAAAG 5 1 Kcnj chr16(-): CTTTCTGTGAAAG 5 1 Rpusd chr9(+): ATTTCTGTGAAAT 5 1 Msx chr13(-): ATTTCTATGAAAT 5 1 D630042F21Rik chr6(+): TGTTCTGTGAACA 5 1 Lrrcc chr3(+): CATTCCATGAATG B07Rik chr13(+): AGTTCTATGAACT 5 1 Mnda chr1(-): TTTTCTATGAAAA 5 1 Ccdc chr16(+): CCTCCTTCTGCGAAGGAGG 8 1 Sh3bp chr5(+): TTTTCTGTGAAAA 5 1 # Pdcd chr13(-): CAATTCTGTGAATTG 6 1 # Slc27a chr2(+): CTTTCTATGAAAG 5 1 # Zfp chr7(-): CTTTCTATGAAAG 5 1 # BC chr16(+): TGTTTCTATGAAACA 6 1 # Mndal chr1(-): TTTTCTATGAAAA 5 1 # Gvin chr7(-): ATTTTCTATGAAAAT 6 1 # Gm chr7(-): ATTTTCTATGAAAAT 6 1 # Mau chr8(-): CCTTCTGTGAAGG 5 1 # Dap chr3(-): TTTTCTGTGAAAA 5 1 # Slc7a chr3(+): TTATTCTATGAATAA 6 1 # Crispld chr1(+): TTTTCCATGAAAA 5 1 # Lrrtm chr6(+): ACTTTCTATGAAAGT 6 1 # A18Rik chr10(-): GTTTCTGTGAAAC 5 1 # Lilrb chr10(+): CATTCCATGAATG 5 1 # Gp49a chr10(+): CATTCCATGAATG 5 1 # Zfp chr8(-): ATTTCTGTGAAAT 5 1 # Afg3l chr8(+): CGTTCCGTGAACG 5 1 # * Stem depicted in black, loop depicted in red Number of species with a conserved CDE at this genomic position in the UCSC 46 vertebrate species alignment # Alignment at this genomic position was not available Yellow: CDEs conserved in > 10/46 vertebrate species

8 Table S5. Functional Categories of Genes Containing Conserved 3 UTR CDEs, Related to Figure 6 Gene ontology term (biological process) observed Number of genes expected Regulation of developmental process Transcription, DNA-dependent Regulation of RNA metabolic process RNA biosynthetic process Nucleic acid metabolic process Negative regulation of T-cell differentiation

9 Table S6. mrnas Significantly Enriched by Roquin-IP, Related to Figure 6 Name GeneID CDE p-value (Roquin-IP vs control-ip) fold enrichment (Roquin-IP / control-ip) fold enrichment (Roquin-IP / input) Nfkbid UTR, conserved (2) 2.1E Tnf (TNFα) UTR, conserved 1.1E Irf E Gm E D5Ertd579e ORF (2) 3.7E Rc3h1 (Roquin) UTR, conserved 1.8E Tcf7l E Csf3 (G-CSF) E Id E Slc39a E Zfp E Calcrl E Rc3h2 (Roquin2) UTR, conserved 6.0E Ptger E Ptpre E Id E Mgat E Adamts E Clk E Nfkbiz UTR, conserved 4.9E Ap1g E Usp E B630005N14Rik E Map3k E Id E Pex E Smek E C07Rik E Bmpr1a UTR, conserved 1.5E Icos UTR, conserved 1.7E Zbtb E Ier UTR, conserved 8.1E Fbxo E Pik3ca E Rybp E Tigd E Ss18l E Lfng E Pptc E Rsf E Lysmd E Mlec E Fam160b E

10 D030056L22Rik E Sec24c E Tmem E F09Rik E Cenpf E Etaa E Nedd E Ipo ORF (2) 9.3E Ppan E Ppp1r UTR, conserved 2.1E Tm2d E Ndst E Slc35e E Prr UTR, conserved 5.6E Agbl E Msl E Hinfp E Kctd E Nuf E Cgrrf E Rbm E Aggf UTR, conserved 3.7E Pole ORF 2.2E Papolg E Tfap E Fam76b E Cdc E D21Rik E Dnajc E Cdon E Ap1s E Nfxl E Sacm1l E Zfp E Hcst E Dcun1d E Fbxo UTR, conserved 8.8E B4galt ORF 7.4E Mthfd E Mrps E Rbbp UTR, conserved 2.9E Ube2q E E20Rik E D19Rik E Rabl E Hmgxb UTR, conserved 1.6E Lig E Fam84b E Epc UTR, conserved 7.0E

11 Dpy19l E AI E Pik3cb E Purple: mrna significantly enriched by Roquin-IP that contains a conserved CDE in the 3 UTR Green: mrna significantly enriched by Roquin-IP that contains a CDE in the ORF

12 Table S7. DNA Oligonucleotides, Related to Experimental Procedures Name Sequence Description G078 GGTGGTCGGAAAGCTATC S7 probe F G083 TTACAAAGTCACTCAGGATG Ncl probe R G314 TTAAGCTAGCAGGGAATGGG mouse TNF probe F G316 GCCGATTTAGGTGACACTATAGAATACTGGCTCTGTGAGG mouse TNF probe R G1000 GTGCATCTGTCCAGTG globin probe R G1001 GCCGATTTAGGTGACACTATAGAATACCCTGAAGTTCTC globin probe F G1008 GCCGATTTAGGTGACACTATAGAATACTATAGACACCAG S7 probe R G1009 GCCGATTTAGGTGACACTATAGAATACTTAGCGTCTTCG Ncl probe F G1706 AGGGGGCAGAAATTGATGGACGAT mouse Ncl qpcr F G1707 TGGGTTCTGGGGCACTTTG mouse Ncl qpcr R G1712 GAGCGGGCCGTGGTGTC mouse Ier3 qpcr F G1713 CTTGGCAATGTTGGGTTCCTC mouse Ier3 qpcr R G1844 TGCCTATGTCTCAGCCTCTTC mouse TNFα qpcr F G1845 GAGGCCATTTGGGAACTTCT mouse TNFα qpcr R G2053 ACTCCACTCACGGCAAATTCAACG mouse Gapdh qpcr F G2054 AAGACACCAGTAGACTCCACGACA mouse Gapdh qpcr R G2181 CAGGTGAACACCACGGATT mouse Nfkbiz qpcr F G2182 CTCACAGCTCCCTTCTGGAT mouse Nfkbiz qpcr R G2199 ATATTCGTGAACATAAAGGCAAGA mouse Nfkbid qpcr F G2200 TCAGTGGCGTTAGGCTCTG mouse Nfkbid qpcr R G2234 CCAAGTAATACGACTCACTATAGGCCTGGCTCACAAATACCACTG pt7-in-line F G2235 AATTTTTGGCAGAGGGAAAAAG in-line R G2332 CCAAGTAATACGACTCACTATAGGTTTGGAAGGCCGGGGT pt7-cde 150 mouse in-line F G2333 ATAAATATTTTGTTTTAAACATAAGCAAAAGAG CDE 150 mouse in-line R G2364 CATGGCTGCAACACTTACACAGCA mouse Nupl1 qpcr F G2365 ATTGCAAGCCAGTGCCAATACCTG mouse Nupl1 qpcr R G2392 TTGTACCTGAAGCCACTCAGCAGT mouse Roquin qpcr F G2393 TCCACTAGCTGGCAATGAACCAGA mouse Roquin qpcr R G2394 TGCCCATTCTCAGGAAGAGCTTGA mouse Roquin2 qpcr F G2395 GCTGTGGTTGTGACAGTGCTGTTT mouse Roquin2 qpcr R G1612 CCCAAGCTTGATATCATCCACCATGGTGAGCAAG EGFP F, HindIII-EcoRV G1613 TTAAGGTACCCTTGTACAGCTCGTCCATGCCGAG EGFP R, KpnI G2421 TGGACACAGTATCATACCCAGAAAACACCTGTCTCTTCAACTCTTCCTGTGGCCA mouse Roquin2 cdna F G2427 GATCATCGATTCAGCTGTTAACCATCTTCCCA mouse Roquin2-ClaI cdna R G2495 GATCGGATCCTTTGGAAGGCCGGGGT CDE 150 -BamHI-outF G2496 GATCAGATCTATAAATATTTTGTTTTAAACATAAGCAAAAGAG CDE 150 -outr-bglii G2497 TTCTGTGAAATGGGAGCTGAG CDE 150 -M16 F G2498 TTTCACAGAAAACATGTCTGTCTGA CDE 150 -M16 R G2501 GACAGACATCATTTCTGTGAAATGGGA CDE 150 -M20 F G2502 ATGTCTGTCTGAAGACAGCTTCC CDE 150 -M20 R G2554 AAACTAGTATGCGCCGAGATTTACGA Roquin2 cdna C413R F G2555 CATACTAGTTTTATACTTGCTGTTTGGCTG Roquin2 cdna C413R R G2556 GATCCAATTGTTTTGCAGCGAACTG Roquin2-MfeI cdna F G2576 AACATACATGCGTCGAGATATGAAG Roquin cdna C419R F

13 G2577 CATGTATGTTTTGTATTTGCTATGCTGT Roquin cdna C419R R G2579 GATCCACATGGTGGTGGAGTATAGTACATACC Roquin-DraIII cdna R G2592 TTCCCCCTGTTGAAGTTCC mouse Ppp1r10 qpcr F G2593 CTTGCGAGTCAGCTGGTTG mouse Ppp1r10 qpcr R G2622 GATACTGTGTCCACTGATCTGGC BstXI-Roquin2 cdna R G2623 TCATTTGCACAGAGTGTTCAGG Roquin-DraIII cdna F G2723 TGACCTGGGCCTAGCTGTTA mouse Bmpr1a qpcr F G2724 TTCAGGCTTTCATCCAGCA mouse Bmpr1a qpcr R G2729 CTCACATCCTGGACACTGGA mouse Pdia6 qpcr F G2730 ACTGGGCTCCAGCTTCTGT mouse Pdia6 qpcr R G2737 TGTTGGCCCTCTATGAATCTG mouse Hmgxb3 qpcr F G2738 TGGAACCACAGACCACCTG mouse Hmgxb3 qpcr R G2747 TTCATCGTATTGGAAGATCAGG mouse Rck qpcr F G2748 TTGGGATGGGTTTGATCTCT mouse Rck qpcr R G2788 AGGGACCGGTGTCGACC AgeI-SalI-Roquin flanking fr1 F G2789 AGAGCAATTGTTAGCTCCTGAACA MfeI-Roquin flanking fr2 R G2790 GTGACCGAACTGATTCTCCAGCACCAG sirna-resistant Roquin fr2 F G2791 CAGTTCGGTCACTGTGCGTTCACCTAAAG sirna-resistant Roquin fr1 R G2840 ATTAATCGATCTATTCCTGTGAATGTG ClaI-Stop-N-term R G2842 TTATACCGGTGGAACTGGAAAAG Roquin C-term F G2843 GTCCCACGTGGAATCAGTTG Roquin C-term R G2855 TTATACCGGTGCGCCCAATGCAGAGGAA ROQ-AgeI F G2856 TATAATCGATGAGTAACTCCAAATGGGGTCTTAG ROQ-ClaI R

Roquin Promotes Constitutive mrna Decay via a Conserved Class of Stem-Loop Recognition Motifs

Roquin Promotes Constitutive mrna Decay via a Conserved Class of Stem-Loop Recognition Motifs Roquin Promotes Constitutive mrna Decay via a Conserved Class of Stem-Loop Recognition Motifs Kathrin Leppek, 1 Johanna Schott, 1 Sonja Reitter, 1 Fabian Poetz, 1 Ming C. Hammond, 2 and Georg Stoecklin

More information

Supplemental Information For: The genetics of splicing in neuroblastoma

Supplemental Information For: The genetics of splicing in neuroblastoma Supplemental Information For: The genetics of splicing in neuroblastoma Justin Chen, Christopher S. Hackett, Shile Zhang, Young K. Song, Robert J.A. Bell, Annette M. Molinaro, David A. Quigley, Allan Balmain,

More information

Molecular Biology (BIOL 4320) Exam #2 May 3, 2004

Molecular Biology (BIOL 4320) Exam #2 May 3, 2004 Molecular Biology (BIOL 4320) Exam #2 May 3, 2004 Name SS# This exam is worth a total of 100 points. The number of points each question is worth is shown in parentheses after the question number. Good

More information

Supplemental Figure S1. Expression of Cirbp mrna in mouse tissues and NIH3T3 cells.

Supplemental Figure S1. Expression of Cirbp mrna in mouse tissues and NIH3T3 cells. SUPPLEMENTAL FIGURE AND TABLE LEGENDS Supplemental Figure S1. Expression of Cirbp mrna in mouse tissues and NIH3T3 cells. A) Cirbp mrna expression levels in various mouse tissues collected around the clock

More information

Supplementary information

Supplementary information Supplementary information Human Cytomegalovirus MicroRNA mir-us4-1 Inhibits CD8 + T Cell Response by Targeting ERAP1 Sungchul Kim, Sanghyun Lee, Jinwook Shin, Youngkyun Kim, Irini Evnouchidou, Donghyun

More information

SUPPLEMENTARY INFORMATION

SUPPLEMENTARY INFORMATION doi: 1.138/nature89 IFN- (ng ml ) 5 4 3 1 Splenocytes NS IFN- (ng ml ) 6 4 Lymph node cells NS Nfkbiz / Nfkbiz / Nfkbiz / Nfkbiz / IL- (ng ml ) 3 1 Splenocytes IL- (ng ml ) 1 8 6 4 *** ** Lymph node cells

More information

SUPPLEMENTARY INFORMATION. Supp. Fig. 1. Autoimmunity. Tolerance APC APC. T cell. T cell. doi: /nature06253 ICOS ICOS TCR CD28 TCR CD28

SUPPLEMENTARY INFORMATION. Supp. Fig. 1. Autoimmunity. Tolerance APC APC. T cell. T cell. doi: /nature06253 ICOS ICOS TCR CD28 TCR CD28 Supp. Fig. 1 a APC b APC ICOS ICOS TCR CD28 mir P TCR CD28 P T cell Tolerance Roquin WT SG Icos mrna T cell Autoimmunity Roquin M199R SG Icos mrna www.nature.com/nature 1 Supp. Fig. 2 CD4 + CD44 low CD4

More information

a) List of KMTs targeted in the shrna screen. The official symbol, KMT designation,

a) List of KMTs targeted in the shrna screen. The official symbol, KMT designation, Supplementary Information Supplementary Figures Supplementary Figure 1. a) List of KMTs targeted in the shrna screen. The official symbol, KMT designation, gene ID and specifities are provided. Those highlighted

More information

SUPPLEMENTARY MATERIAL

SUPPLEMENTARY MATERIAL SYPPLEMENTARY FIGURE LEGENDS SUPPLEMENTARY MATERIAL Figure S1. Phylogenic studies of the mir-183/96/182 cluster and 3 -UTR of Casp2. (A) Genomic arrangement of the mir-183/96/182 cluster in vertebrates.

More information

Circular RNAs (circrnas) act a stable mirna sponges

Circular RNAs (circrnas) act a stable mirna sponges Circular RNAs (circrnas) act a stable mirna sponges cernas compete for mirnas Ancestal mrna (+3 UTR) Pseudogene RNA (+3 UTR homolgy region) The model holds true for all RNAs that share a mirna binding

More information

Soft Agar Assay. For each cell pool, 100,000 cells were resuspended in 0.35% (w/v)

Soft Agar Assay. For each cell pool, 100,000 cells were resuspended in 0.35% (w/v) SUPPLEMENTARY MATERIAL AND METHODS Soft Agar Assay. For each cell pool, 100,000 cells were resuspended in 0.35% (w/v) top agar (LONZA, SeaKem LE Agarose cat.5004) and plated onto 0.5% (w/v) basal agar.

More information

Supplementary information: Forstner, Hofmann et al.

Supplementary information: Forstner, Hofmann et al. Supplementary information: Forstner, Hofmann et al., Genome-wide analysis implicates micrornas and their target genes in the development of bipolar disorder Table of contents Supplementary Figure 1: Regional

More information

Supplementary Figure 1. SC35M polymerase activity in the presence of Bat or SC35M NP encoded from the phw2000 rescue plasmid.

Supplementary Figure 1. SC35M polymerase activity in the presence of Bat or SC35M NP encoded from the phw2000 rescue plasmid. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Supplementary Figure 1. SC35M polymerase activity in the presence of Bat or SC35M NP encoded from the phw2000 rescue plasmid. HEK293T

More information

he micrornas of Caenorhabditis elegans (Lim et al. Genes & Development 2003)

he micrornas of Caenorhabditis elegans (Lim et al. Genes & Development 2003) MicroRNAs: Genomics, Biogenesis, Mechanism, and Function (D. Bartel Cell 2004) he micrornas of Caenorhabditis elegans (Lim et al. Genes & Development 2003) Vertebrate MicroRNA Genes (Lim et al. Science

More information

Molecular Cell Biology - Problem Drill 10: Gene Expression in Eukaryotes

Molecular Cell Biology - Problem Drill 10: Gene Expression in Eukaryotes Molecular Cell Biology - Problem Drill 10: Gene Expression in Eukaryotes Question No. 1 of 10 1. Which of the following statements about gene expression control in eukaryotes is correct? Question #1 (A)

More information

Translation. Host Cell Shutoff 1) Initiation of eukaryotic translation involves many initiation factors

Translation. Host Cell Shutoff 1) Initiation of eukaryotic translation involves many initiation factors Translation Questions? 1) How does poliovirus shutoff eukaryotic translation? 2) If eukaryotic messages are not translated how can poliovirus get its message translated? Host Cell Shutoff 1) Initiation

More information

Supplementary Figure 1. AdipoR1 silencing and overexpression controls. (a) Representative blots (upper and lower panels) showing the AdipoR1 protein

Supplementary Figure 1. AdipoR1 silencing and overexpression controls. (a) Representative blots (upper and lower panels) showing the AdipoR1 protein Supplementary Figure 1. AdipoR1 silencing and overexpression controls. (a) Representative blots (upper and lower panels) showing the AdipoR1 protein content relative to GAPDH in two independent experiments.

More information

SUPPLEMENTARY FIGURES

SUPPLEMENTARY FIGURES SUPPLEMENTARY FIGURES 1 Supplementary Figure 1, Adult hippocampal QNPs and TAPs uniformly express REST a-b) Confocal images of adult hippocampal mouse sections showing GFAP (green), Sox2 (red), and REST

More information

Supplement Figure S1. Real Time PCR analysis of mrna levels of C/EBPα and PU.1 in wild type (WT) and NQO1-null (NQO1-/-) mice.

Supplement Figure S1. Real Time PCR analysis of mrna levels of C/EBPα and PU.1 in wild type (WT) and NQO1-null (NQO1-/-) mice. competes with 20S proteasome for binding with C/EBP leading to its stabilization and Relative mrna levels Supplement Figure S1. Real Time PCR analysis of mrna levels of C/EBPα and PU.1 in wild type (WT)

More information

7SK ChIRP-seq is specifically RNA dependent and conserved between mice and humans.

7SK ChIRP-seq is specifically RNA dependent and conserved between mice and humans. Supplementary Figure 1 7SK ChIRP-seq is specifically RNA dependent and conserved between mice and humans. Regions targeted by the Even and Odd ChIRP probes mapped to a secondary structure model 56 of the

More information

Supplementary Figure 1 Role of Raf-1 in TLR2-Dectin-1-mediated cytokine expression

Supplementary Figure 1 Role of Raf-1 in TLR2-Dectin-1-mediated cytokine expression Supplementary Figure 1 Supplementary Figure 1 Role of Raf-1 in TLR2-Dectin-1-mediated cytokine expression. Quantitative real-time PCR of indicated mrnas in DCs stimulated with TLR2-Dectin-1 agonist zymosan

More information

Host Double Strand Break Repair Generates HIV-1 Strains Resistant to CRISPR/Cas9

Host Double Strand Break Repair Generates HIV-1 Strains Resistant to CRISPR/Cas9 Host Double Strand Break Repair Generates HIV-1 Strains Resistant to CRISPR/Cas9 Kristine E. Yoder, a * and Ralf Bundschuh b a Department of Molecular Virology, Immunology and Medical Genetics, Center

More information

RNA SEQUENCING AND DATA ANALYSIS

RNA SEQUENCING AND DATA ANALYSIS RNA SEQUENCING AND DATA ANALYSIS Download slides and package http://odin.mdacc.tmc.edu/~rverhaak/package.zip http://odin.mdacc.tmc.edu/~rverhaak/rna-seqlecture.zip Overview Introduction into the topic

More information

Prediction of micrornas and their targets

Prediction of micrornas and their targets Prediction of micrornas and their targets Introduction Brief history mirna Biogenesis Computational Methods Mature and precursor mirna prediction mirna target gene prediction Summary micrornas? RNA can

More information

genomics for systems biology / ISB2020 RNA sequencing (RNA-seq)

genomics for systems biology / ISB2020 RNA sequencing (RNA-seq) RNA sequencing (RNA-seq) Module Outline MO 13-Mar-2017 RNA sequencing: Introduction 1 WE 15-Mar-2017 RNA sequencing: Introduction 2 MO 20-Mar-2017 Paper: PMID 25954002: Human genomics. The human transcriptome

More information

Molecular Biology (BIOL 4320) Exam #2 April 22, 2002

Molecular Biology (BIOL 4320) Exam #2 April 22, 2002 Molecular Biology (BIOL 4320) Exam #2 April 22, 2002 Name SS# This exam is worth a total of 100 points. The number of points each question is worth is shown in parentheses after the question number. Good

More information

Scaffold function of long noncoding RNA HOTAIR in protein ubiquitination

Scaffold function of long noncoding RNA HOTAIR in protein ubiquitination Yoon et al, page Scaffold function of long noncoding RNA HOTAIR in protein ubiquitination Je-Hyun Yoon,, Kotb Abdelmohsen, Jiyoung Kim, Xiaoling Yang, Jennifer L. Martindale, Kumiko Tominaga-Yamanaka,

More information

Co-expressed Cyclin D variants cooperate to regulate proliferation of germline nuclei in. Accession number

Co-expressed Cyclin D variants cooperate to regulate proliferation of germline nuclei in. Accession number SUPPLEMENTARY MATERIAL Co-expressed Cyclin D variants cooperate to regulate proliferation of germline nuclei in a syncytium. Subramaniam et al. Table S1. Cyclin accession numbers Gene Human Cyclin D1a

More information

Supplemental Figure S1. Tertiles of FKBP5 promoter methylation and internal regulatory region

Supplemental Figure S1. Tertiles of FKBP5 promoter methylation and internal regulatory region Supplemental Figure S1. Tertiles of FKBP5 promoter methylation and internal regulatory region methylation in relation to PSS and fetal coupling. A, PSS values for participants whose placentas showed low,

More information

Nature Genetics: doi: /ng.3731

Nature Genetics: doi: /ng.3731 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

More information

Supplementary Figure 1 ITGB1 and ITGA11 increase with evidence for heterodimers following HSC activation. (a) Time course of rat HSC activation

Supplementary Figure 1 ITGB1 and ITGA11 increase with evidence for heterodimers following HSC activation. (a) Time course of rat HSC activation Supplementary Figure 1 ITGB1 and ITGA11 increase with evidence for heterodimers following HSC activation. (a) Time course of rat HSC activation indicated by the detection of -SMA and COL1 (log scale).

More information

Computational Identification and Prediction of Tissue-Specific Alternative Splicing in H. Sapiens. Eric Van Nostrand CS229 Final Project

Computational Identification and Prediction of Tissue-Specific Alternative Splicing in H. Sapiens. Eric Van Nostrand CS229 Final Project Computational Identification and Prediction of Tissue-Specific Alternative Splicing in H. Sapiens. Eric Van Nostrand CS229 Final Project Introduction RNA splicing is a critical step in eukaryotic gene

More information

RNA SEQUENCING AND DATA ANALYSIS

RNA SEQUENCING AND DATA ANALYSIS RNA SEQUENCING AND DATA ANALYSIS Length of mrna transcripts in the human genome 5,000 5,000 4,000 3,000 2,000 4,000 1,000 0 0 200 400 600 800 3,000 2,000 1,000 0 0 2,000 4,000 6,000 8,000 10,000 Length

More information

Identification of mirnas in Eucalyptus globulus Plant by Computational Methods

Identification of mirnas in Eucalyptus globulus Plant by Computational Methods International Journal of Pharmaceutical Science Invention ISSN (Online): 2319 6718, ISSN (Print): 2319 670X Volume 2 Issue 5 May 2013 PP.70-74 Identification of mirnas in Eucalyptus globulus Plant by Computational

More information

The autoimmune disease-associated PTPN22 variant promotes calpain-mediated Lyp/Pep

The autoimmune disease-associated PTPN22 variant promotes calpain-mediated Lyp/Pep SUPPLEMENTARY INFORMATION The autoimmune disease-associated PTPN22 variant promotes calpain-mediated Lyp/Pep degradation associated with lymphocyte and dendritic cell hyperresponsiveness Jinyi Zhang, Naima

More information

SUPPLEMENTARY FIGURES

SUPPLEMENTARY FIGURES SUPPLEMENTARY FIGURES Figure S1. Clinical significance of ZNF322A overexpression in Caucasian lung cancer patients. (A) Representative immunohistochemistry images of ZNF322A protein expression in tissue

More information

RNA sequencing of cancer reveals novel splicing alterations

RNA sequencing of cancer reveals novel splicing alterations RNA sequencing of cancer reveals novel splicing alterations Jeyanthy Eswaran, Anelia Horvath, Sucheta Godbole, Sirigiri Divijendra Reddy, Prakriti Mudvari, Kazufumi Ohshiro, Dinesh Cyanam, Sujit Nair,

More information

iclip Predicts the Dual Splicing Effects of TIA-RNA Interactions

iclip Predicts the Dual Splicing Effects of TIA-RNA Interactions iclip Predicts the Dual Splicing Effects of TIA-RNA Interactions Zhen Wang 1., Melis Kayikci 1., Michael Briese 1, Kathi Zarnack 2, Nicholas M. Luscombe 2,3, Gregor Rot 4, Blaž Zupan 4, Tomaž Curk 4, Jernej

More information

Figure S1! CrFK! DNA Synthesis! Copies viral DNA/ 100 ng DNA (Log 10 ) % Infected (GFP+) cells! 100! 80! 60! 40! 20! 0! 1! 10! 100! 1000!

Figure S1! CrFK! DNA Synthesis! Copies viral DNA/ 100 ng DNA (Log 10 ) % Infected (GFP+) cells! 100! 80! 60! 40! 20! 0! 1! 10! 100! 1000! Figure S1! A! B! % Infected (GFP+) cells! 100! 80! 60! 40! 20! 0! 1! 10! 100! 1000! Dose μl! CrFK! B-MLV! N-MLV! Template:! Water! Ube2V2! Ube2V1! Primers:! V2! V1! V2! V1! V2! V1! bp! 500! 300! 200! 150!

More information

A putative MYB35 ortholog is a candidate for the sex-determining genes in Asparagus

A putative MYB35 ortholog is a candidate for the sex-determining genes in Asparagus Supplementary figures for: A putative MYB35 ortholog is a candidate for the sex-determining genes in Asparagus officinalis Daisuke Tsugama, Kohei Matsuyama, Mayui Ide, Masato Hayashi, Kaien Fujino, and

More information

SUPPLEMENTAL DATA RESULTS

SUPPLEMENTAL DATA RESULTS SUPPLEMENTAL DATA RESULTS Ded1-mediated ribosomal scanning is less leaky than scanning promoted by eifs 4A/4B/4F. The efficiency of leaky scanning in the presence of Ded1 or of eifs 4A/4B/4F was investigated

More information

Supplementary Figure 1 Transcription assay of nine ABA-responsive PP2C. Transcription assay of nine ABA-responsive PP2C genes. Total RNA was isolated

Supplementary Figure 1 Transcription assay of nine ABA-responsive PP2C. Transcription assay of nine ABA-responsive PP2C genes. Total RNA was isolated Supplementary Figure 1 Transcription assay of nine ABA-responsive PP2C genes. Transcription assay of nine ABA-responsive PP2C genes. Total RNA was isolated from 7 day-old seedlings treated with or without

More information

Supplementary Figure 1

Supplementary Figure 1 Supplementary Figure 1 Asymmetrical function of 5p and 3p arms of mir-181 and mir-30 families and mir-142 and mir-154. (a) Control experiments using mirna sensor vector and empty pri-mirna overexpression

More information

Transduction of lentivirus to human primary CD4+ T cells

Transduction of lentivirus to human primary CD4+ T cells Transduction of lentivirus to human primary CD4 + T cells Human primary CD4 T cells were stimulated with anti-cd3/cd28 antibodies (10 µl/2 5 10^6 cells of Dynabeads CD3/CD28 T cell expander, Invitrogen)

More information

SUPPLEMENTARY INFORMATION

SUPPLEMENTARY INFORMATION SUPPLEMENTARY INFORMATION doi:1.138/nature11986 relative IL-6 expression Viable intracellular Bp per well 18 16 1 1 5 5 3 1 6 +DG 8 8 8 Control DG Time (h) hours B. pertussis IL-6 (pg/ml) 15 Control DG

More information

reads observed in trnas from the analysis of RNAs carrying a 5 -OH ends isolated from cells induced to express

reads observed in trnas from the analysis of RNAs carrying a 5 -OH ends isolated from cells induced to express Supplementary Figure 1. VapC-mt4 cleaves trna Ala2 in E. coli. Histograms representing the fold change in reads observed in trnas from the analysis of RNAs carrying a 5 -OH ends isolated from cells induced

More information

Comparison of open chromatin regions between dentate granule cells and other tissues and neural cell types.

Comparison of open chromatin regions between dentate granule cells and other tissues and neural cell types. Supplementary Figure 1 Comparison of open chromatin regions between dentate granule cells and other tissues and neural cell types. (a) Pearson correlation heatmap among open chromatin profiles of different

More information

Alpha thalassemia mental retardation X-linked. Acquired alpha-thalassemia myelodysplastic syndrome

Alpha thalassemia mental retardation X-linked. Acquired alpha-thalassemia myelodysplastic syndrome Alpha thalassemia mental retardation X-linked Acquired alpha-thalassemia myelodysplastic syndrome (Alpha thalassemia mental retardation X-linked) Acquired alpha-thalassemia myelodysplastic syndrome Schematic

More information

Supplemental Materials and Methods Plasmids and viruses Quantitative Reverse Transcription PCR Generation of molecular standard for quantitative PCR

Supplemental Materials and Methods Plasmids and viruses Quantitative Reverse Transcription PCR Generation of molecular standard for quantitative PCR Supplemental Materials and Methods Plasmids and viruses To generate pseudotyped viruses, the previously described recombinant plasmids pnl4-3-δnef-gfp or pnl4-3-δ6-drgfp and a vector expressing HIV-1 X4

More information

well for 2 h at rt. Each dot represents an individual mouse and bar is the mean ±

well for 2 h at rt. Each dot represents an individual mouse and bar is the mean ± Supplementary data: Control DC Blimp-1 ko DC 8 6 4 2-2 IL-1β p=.5 medium 8 6 4 2 IL-2 Medium p=.16 8 6 4 2 IL-6 medium p=.3 5 4 3 2 1-1 medium IL-1 n.s. 25 2 15 1 5 IL-12(p7) p=.15 5 IFNγ p=.65 4 3 2 1

More information

Accessing and Using ENCODE Data Dr. Peggy J. Farnham

Accessing and Using ENCODE Data Dr. Peggy J. Farnham 1 William M Keck Professor of Biochemistry Keck School of Medicine University of Southern California How many human genes are encoded in our 3x10 9 bp? C. elegans (worm) 959 cells and 1x10 8 bp 20,000

More information

Nature Medicine: doi: /nm.4322

Nature Medicine: doi: /nm.4322 1 2 3 4 5 6 7 8 9 10 11 Supplementary Figure 1. Predicted RNA structure of 3 UTR and sequence alignment of deleted nucleotides. (a) Predicted RNA secondary structure of ZIKV 3 UTR. The stem-loop structure

More information

SUPPLEMENTARY INFORMATION. Divergent TLR7/9 signaling and type I interferon production distinguish

SUPPLEMENTARY INFORMATION. Divergent TLR7/9 signaling and type I interferon production distinguish SUPPLEMENTARY INFOATION Divergent TLR7/9 signaling and type I interferon production distinguish pathogenic and non-pathogenic AIDS-virus infections Judith N. Mandl, Ashley P. Barry, Thomas H. Vanderford,

More information

Palindromic amplification of the ERBB2 oncogene in human primary breast tumors. A common pattern of copy number transition of chromosome 17 in HER2-

Palindromic amplification of the ERBB2 oncogene in human primary breast tumors. A common pattern of copy number transition of chromosome 17 in HER2- Supplemental Figures Table of Contents Palindromic amplification of the ERBB2 oncogene in human primary breast tumors Michael Marotta 1,5, Taku Onodera 3,5, Jeffrey Johnson 4, Thomas Budd 2, Takaaki Watanabe

More information

Mechanisms of alternative splicing regulation

Mechanisms of alternative splicing regulation Mechanisms of alternative splicing regulation The number of mechanisms that are known to be involved in splicing regulation approximates the number of splicing decisions that have been analyzed in detail.

More information

Fig. S1. Validation of ChIP-seq binding sites by single gene ChIP-PCR Fig. S2. Transactivation potential of PPAR

Fig. S1. Validation of ChIP-seq binding sites by single gene ChIP-PCR Fig. S2. Transactivation potential of PPAR Fig. S1. Validation of ChIP-seq binding sites by single gene ChIP-PCR ChIP-PCR was performed on PPARγ and RXR-enriched chromatin harvested during adipocyte differentiation at day and day 6 as described

More information

Nature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1

Nature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1 Supplementary Figure 1 U1 inhibition causes a shift of RNA-seq reads from exons to introns. (a) Evidence for the high purity of 4-shU-labeled RNAs used for RNA-seq. HeLa cells transfected with control

More information

Supplementary Information

Supplementary Information Supplementary Information Supplementary Figure 1. EBV-gB 23-431 mainly exists as trimer in HEK 293FT cells. (a) Western blotting analysis for DSS crosslinked FLAG-gB 23-431. HEK 293FT cells transfected

More information

Nature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1. Generation and validation of mtef4-knockout mice.

Nature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1. Generation and validation of mtef4-knockout mice. Supplementary Figure 1 Generation and validation of mtef4-knockout mice. (a) Alignment of EF4 (E. coli) with mouse, yeast and human EF4. (b) Domain structures of mouse mtef4 compared to those of EF4 (E.

More information

Supplementary Figures

Supplementary Figures Supplementary Figures Supplementary Figure 1. Confirmation of Dnmt1 conditional knockout out mice. a, Representative images of sorted stem (Lin - CD49f high CD24 + ), luminal (Lin - CD49f low CD24 + )

More information

Nature Immunology doi: /ni Supplementary Figure 1. Raf-1 inhibition does not affect TLR4-induced type I IFN responses.

Nature Immunology doi: /ni Supplementary Figure 1. Raf-1 inhibition does not affect TLR4-induced type I IFN responses. Supplementary Figure 1 Raf-1 inhibition does not affect TLR4-induced type I IFN responses. Real-time PCR analyses of IFNB, ISG15, TRIM5, TRIM22 and APOBEC3G mrna in modcs 6 h after stimulation with TLR4

More information

Supplementary Figure 1 IL-27 IL

Supplementary Figure 1 IL-27 IL Tim-3 Supplementary Figure 1 Tc0 49.5 0.6 Tc1 63.5 0.84 Un 49.8 0.16 35.5 0.16 10 4 61.2 5.53 10 3 64.5 5.66 10 2 10 1 10 0 31 2.22 10 0 10 1 10 2 10 3 10 4 IL-10 28.2 1.69 IL-27 Supplementary Figure 1.

More information

Alternative RNA processing: Two examples of complex eukaryotic transcription units and the effect of mutations on expression of the encoded proteins.

Alternative RNA processing: Two examples of complex eukaryotic transcription units and the effect of mutations on expression of the encoded proteins. Alternative RNA processing: Two examples of complex eukaryotic transcription units and the effect of mutations on expression of the encoded proteins. The RNA transcribed from a complex transcription unit

More information

The functional investigation of the interaction between TATA-associated factor 3 (TAF3) and p53 protein

The functional investigation of the interaction between TATA-associated factor 3 (TAF3) and p53 protein THESIS BOOK The functional investigation of the interaction between TATA-associated factor 3 (TAF3) and p53 protein Orsolya Buzás-Bereczki Supervisors: Dr. Éva Bálint Dr. Imre Miklós Boros University of

More information

MicroRNA in Cancer Karen Dybkær 2013

MicroRNA in Cancer Karen Dybkær 2013 MicroRNA in Cancer Karen Dybkær RNA Ribonucleic acid Types -Coding: messenger RNA (mrna) coding for proteins -Non-coding regulating protein formation Ribosomal RNA (rrna) Transfer RNA (trna) Small nuclear

More information

SUPPLEMENTARY INFORMATION

SUPPLEMENTARY INFORMATION SUPPLEMENTARY INFORMATION doi:10.1038/nature12864 Supplementary Table 1 1 2 3 4 5 6 7 Peak Gene code Screen Function or Read analysis AMP reads camp annotation reads minor Tb927.2.1810 AMP ISWI Confirmed

More information

Molecular Detection of BCR/ABL1 for the Diagnosis and Monitoring of CML

Molecular Detection of BCR/ABL1 for the Diagnosis and Monitoring of CML Molecular Detection of BCR/ABL1 for the Diagnosis and Monitoring of CML Imran Mirza, MD, MS, FRCPC Pathology & Laboratory Medicine Institute Sheikh Khalifa Medical City, Abu Dhabi, UAE. imirza@skmc.ae

More information

Chapter II. Functional selection of intronic splicing elements provides insight into their regulatory mechanism

Chapter II. Functional selection of intronic splicing elements provides insight into their regulatory mechanism 23 Chapter II. Functional selection of intronic splicing elements provides insight into their regulatory mechanism Abstract Despite the critical role of alternative splicing in generating proteomic diversity

More information

Supplementary Information. Supplementary Figure 1

Supplementary Information. Supplementary Figure 1 Supplementary Information Supplementary Figure 1 1 Supplementary Figure 1. Functional assay of the hcas9-2a-mcherry construct (a) Gene correction of a mutant EGFP reporter cell line mediated by hcas9 or

More information

Cross species analysis of genomics data. Computational Prediction of mirnas and their targets

Cross species analysis of genomics data. Computational Prediction of mirnas and their targets 02-716 Cross species analysis of genomics data Computational Prediction of mirnas and their targets Outline Introduction Brief history mirna Biogenesis Why Computational Methods? Computational Methods

More information

Designer Affinity Reagents. Reagents. Types of Affinity. M13 Bacteriophage. 900 nm x 10 nm. Brian Kay Src SH3 domain.

Designer Affinity Reagents. Reagents. Types of Affinity. M13 Bacteriophage. 900 nm x 10 nm. Brian Kay Src SH3 domain. Designer Affinity Reagents Brian Kay bkay@uic.edu Types of Affinity Reagents Src SH3 domain Lysozyme Src SH3 domain FN3 monobody Peptide Ligand Antibody Fragment Scaffold M13 Bacteriophage 900 nm 10 nm

More information

sirna count per 50 kb small RNAs matching the direct strand Repeat length (bp) per 50 kb repeats in the chromosome

sirna count per 50 kb small RNAs matching the direct strand Repeat length (bp) per 50 kb repeats in the chromosome Qi et al. 26-3-2564C Qi et al., Figure S1 sirna count per 5 kb small RNAs matching the direct strand sirna count per 5 kb small RNAs matching the complementary strand Repeat length (bp) per 5 kb repeats

More information

levels of genes were separated by their expression levels; 2,000 high, medium, and low

levels of genes were separated by their expression levels; 2,000 high, medium, and low Figure S1. Histone modification profiles near transcription start sites. The overall histone modification around transcription start sites (TSSs) was calculated. Histone modification levels of genes were

More information

Somatic intronic microsatellite loci differentiate glioblastoma from lower-grade gliomas

Somatic intronic microsatellite loci differentiate glioblastoma from lower-grade gliomas 1 Somatic intronic microsatellite loci differentiate glioblastoma from lower-grade gliomas 2 3 FIGURE S1: Sensitivity & Specificity receiver operator characteristics (ROC) of Signature Cancer-Associated

More information

Nature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1

Nature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1 Supplementary Figure 1 Effect of HSP90 inhibition on expression of endogenous retroviruses. (a) Inducible shrna-mediated Hsp90 silencing in mouse ESCs. Immunoblots of total cell extract expressing the

More information

Supplementary Figure 1: Hsp60 / IEC mice are embryonically lethal (A) Light microscopic pictures show mouse embryos at developmental stage E12.

Supplementary Figure 1: Hsp60 / IEC mice are embryonically lethal (A) Light microscopic pictures show mouse embryos at developmental stage E12. Supplementary Figure 1: Hsp60 / IEC mice are embryonically lethal (A) Light microscopic pictures show mouse embryos at developmental stage E12.5 and E13.5 prepared from uteri of dams and subsequently genotyped.

More information

RECAP (1)! In eukaryotes, large primary transcripts are processed to smaller, mature mrnas.! What was first evidence for this precursorproduct

RECAP (1)! In eukaryotes, large primary transcripts are processed to smaller, mature mrnas.! What was first evidence for this precursorproduct RECAP (1) In eukaryotes, large primary transcripts are processed to smaller, mature mrnas. What was first evidence for this precursorproduct relationship? DNA Observation: Nuclear RNA pool consists of

More information

Bioinformation by Biomedical Informatics Publishing Group

Bioinformation by Biomedical Informatics Publishing Group Predicted RNA secondary structures for the conserved regions in dengue virus Pallavi Somvanshi*, Prahlad Kishore Seth Bioinformatics Centre, Biotech Park, Sector G, Jankipuram, Lucknow 226021, Uttar Pradesh,

More information

DOI: 10.1038/ncb2210 b. ICAM1 ng ml -1 P = 0.0001 Small RNA (15-30nts) ng ml -1 Cell Lysate Exosome HDL Plasma HDL Normal Human HDL mirnas R = 0.45 P < 0.0001 Normal Human Exosome mirnas Figure S1. Characterization

More information

Tel: ; Fax: ;

Tel: ; Fax: ; Tel.: +98 216 696 9291; Fax: +98 216 696 9291; E-mail: mrasadeghi@pasteur.ac.ir Tel: +98 916 113 7679; Fax: +98 613 333 6380; E-mail: abakhshi_e@ajums.ac.ir A Soluble Chromatin-bound MOI 0 1 5 0 1 5 HDAC2

More information

Supporting Information

Supporting Information Supporting Information Zhu et al. 1.173/pnas.11167618 SI Materials and Methods DNA Construction. The plasmid pcdna4to/myc-rzap, which expresses myc-tagged full-length rat ZAP, has been described previously

More information

Mouse Meda-4 : chromosome 5G bp. EST (547bp) _at. 5 -Meda4 inner race (~1.8Kb)

Mouse Meda-4 : chromosome 5G bp. EST (547bp) _at. 5 -Meda4 inner race (~1.8Kb) Supplemental.Figure1 A: Mouse Meda-4 : chromosome 5G3 19898bp I II III III IV V a b c d 5 RACE outer primer 5 RACE inner primer 5 RACE Adaptor ORF:912bp Meda4 cdna 2846bp Meda4 specific 5 outer primer

More information

Supplemental Figure S1. PLAG1 kidneys contain fewer glomeruli (A) Quantitative PCR for Igf2 and PLAG1 in whole kidneys taken from mice at E15.

Supplemental Figure S1. PLAG1 kidneys contain fewer glomeruli (A) Quantitative PCR for Igf2 and PLAG1 in whole kidneys taken from mice at E15. Supplemental Figure S1. PLAG1 kidneys contain fewer glomeruli (A) Quantitative PCR for Igf2 and PLAG1 in whole kidneys taken from mice at E15.5, E18.5, P4, and P8. Values shown are means from four technical

More information

Editorial Type 2 Diabetes and More Gene Panel: A Predictive Genomics Approach for a Polygenic Disease

Editorial Type 2 Diabetes and More Gene Panel: A Predictive Genomics Approach for a Polygenic Disease Cronicon OPEN ACCESS EC DIABETES AND METABOLIC RESEARCH Editorial Type 2 Diabetes and More Gene Panel: A Predictive Genomics Approach for a Polygenic Disease Amr TM Saeb* University Diabetes Center, College

More information

Supplemental Figure 1. Genes showing ectopic H3K9 dimethylation in this study are DNA hypermethylated in Lister et al. study.

Supplemental Figure 1. Genes showing ectopic H3K9 dimethylation in this study are DNA hypermethylated in Lister et al. study. mc mc mc mc SUP mc mc Supplemental Figure. Genes showing ectopic HK9 dimethylation in this study are DNA hypermethylated in Lister et al. study. Representative views of genes that gain HK9m marks in their

More information

Designer Affinity Reagents. Brian Kay

Designer Affinity Reagents. Brian Kay Designer Affinity Reagents Brian Kay bkay@uic.edu Types of Affinity Reagents Src SH3 domain Lysozyme Src SH3 domain FN3 monobody Peptide Ligand Antibody Fragment Scaffold M13 Bacteriophage 900 nm x 10

More information

Mouse Clec9a ORF sequence

Mouse Clec9a ORF sequence Mouse Clec9a gene LOCUS NC_72 13843 bp DNA linear CON 1-JUL-27 DEFINITION Mus musculus chromosome 6, reference assembly (C57BL/6J). ACCESSION NC_72 REGION: 129358881-129372723 Mouse Clec9a ORF sequence

More information

Supplementary information. The proton-sensing G protein-coupled receptor T-cell death-associated gene 8

Supplementary information. The proton-sensing G protein-coupled receptor T-cell death-associated gene 8 1 Supplementary information 2 3 The proton-sensing G protein-coupled receptor T-cell death-associated gene 8 4 (TDAG8) shows cardioprotective effects against myocardial infarction 5 Akiomi Nagasaka 1+,

More information

qpcr-array Analysis Service

qpcr-array Analysis Service qpcr-array Analysis Service Customer Name Institute Telephone Address E-mail PO Number Service Code Report Date Service Laboratory Department Phalanx Biotech Group, Inc 6 Floor, No.6, Technology Road 5,

More information

Identification of Mutation(s) in. Associated with Neutralization Resistance. Miah Blomquist

Identification of Mutation(s) in. Associated with Neutralization Resistance. Miah Blomquist Identification of Mutation(s) in the HIV 1 gp41 Subunit Associated with Neutralization Resistance Miah Blomquist What is HIV 1? HIV-1 is an epidemic that affects over 34 million people worldwide. HIV-1

More information

The Alternative Choice of Constitutive Exons throughout Evolution

The Alternative Choice of Constitutive Exons throughout Evolution The Alternative Choice of Constitutive Exons throughout Evolution Galit Lev-Maor 1[, Amir Goren 1[, Noa Sela 1[, Eddo Kim 1, Hadas Keren 1, Adi Doron-Faigenboim 2, Shelly Leibman-Barak 3, Tal Pupko 2,

More information

Supplementary Information

Supplementary Information Supplementary Information mediates STAT3 activation at retromer-positive structures to promote colitis and colitis-associated carcinogenesis Zhang et al. a b d e g h Rel. Luc. Act. Rel. mrna Rel. mrna

More information

Rho GTPase activating protein 8 /// PRR5- ARHGAP8 fusion

Rho GTPase activating protein 8 /// PRR5- ARHGAP8 fusion Probe Set ID RefSeq Transcript ID Gene Title Gene Symbol 205980_s_at NM_001017526 /// NM_181334 /// NM_181335 Rho GTPase activating protein 8 /// PRR5- ARHGAP8 fusion ARHGAP8 /// LOC553158 FC ALK shrna

More information

Supplemental Material for:

Supplemental Material for: Supplemental Material for: Transcriptional silencing of γ-globin by BCL11A involves long-range interactions and cooperation with SOX6 Jian Xu, Vijay G. Sankaran, Min Ni, Tobias F. Menne, Rishi V. Puram,

More information

Supplementary Material. Table S1. Summary of mapping results

Supplementary Material. Table S1. Summary of mapping results Supplementary Material Table S1. Summary of mapping results Sample Total reads Mapped (%) HNE0-1 99687516 80786083 (81.0%) HNE0-2 94318720 77047792 (81.7%) HNE0-3 104033900 84348102 (81.1%) HNE15-1 94426598

More information

RAW264.7 cells stably expressing control shrna (Con) or GSK3b-specific shrna (sh-

RAW264.7 cells stably expressing control shrna (Con) or GSK3b-specific shrna (sh- 1 a b Supplementary Figure 1. Effects of GSK3b knockdown on poly I:C-induced cytokine production. RAW264.7 cells stably expressing control shrna (Con) or GSK3b-specific shrna (sh- GSK3b) were stimulated

More information

pplementary Figur Supplementary Figure 1. a.

pplementary Figur Supplementary Figure 1. a. pplementary Figur Supplementary Figure 1. a. Quantification by RT-qPCR of YFV-17D and YFV-17D pol- (+) RNA in the supernatant of cultured Huh7.5 cells following viral RNA electroporation of respective

More information

oocytes were pooled for RT-PCR analysis. The number of PCR cycles was 35. Two

oocytes were pooled for RT-PCR analysis. The number of PCR cycles was 35. Two Supplementary Fig. 1 a Kdm3a Kdm4b β-actin Oocyte Testis Oocyte Testis Oocyte Testis b 1.8 Relative expression.6.4.2 Kdm3a Kdm4b RT-PCR analysis of Kdm3a and Kdm4b expression in oocytes and testes. Twenty

More information

Studying Alternative Splicing

Studying Alternative Splicing Studying Alternative Splicing Meelis Kull PhD student in the University of Tartu supervisor: Jaak Vilo CS Theory Days Rõuge 27 Overview Alternative splicing Its biological function Studying splicing Technology

More information

Supplementary Figure 1. Quantile-quantile (Q-Q) plots. (Panel A) Q-Q plot graphical

Supplementary Figure 1. Quantile-quantile (Q-Q) plots. (Panel A) Q-Q plot graphical Supplementary Figure 1. Quantile-quantile (Q-Q) plots. (Panel A) Q-Q plot graphical representation using all SNPs (n= 13,515,798) including the region on chromosome 1 including SORT1 which was previously

More information