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A Supplementary Figure 1. ChIP-seq Sequencing Statistics b RNA-seq Sequencing Statistics Sample NameSequencing Depth Uniquely Mapped Reads Number of peaks.

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Presentation on theme: "A Supplementary Figure 1. ChIP-seq Sequencing Statistics b RNA-seq Sequencing Statistics Sample NameSequencing Depth Uniquely Mapped Reads Number of peaks."— Presentation transcript:

1 a Supplementary Figure 1

2 ChIP-seq Sequencing Statistics b RNA-seq Sequencing Statistics Sample NameSequencing Depth Uniquely Mapped Reads Number of peaks H3K4me329,607,43822,520,22013829 PolII186,897,451139,395,59411395 Input71,328,88454,200,494 c Supplementary Figure 1 Sample NameSequencing DepthUniquely Mapped Reads Basal3826038716146827 siCTRL_13407070415353237 siCTRL_23559003015965080 siUPF1_13099121215029160 siUPF1_24123836417146466 siCTRL_14620205423153491 siCTRL_25205607924794738 siEXOSC5_13506508417853409 siEXOSC5_24006219320404942 siCTRL3687620529287082 siSTAU1_13025672223896759 siSTAU1_23635320829049849

3 BRIC-seq Sequencing statistics d Sample NameSequencing DepthUniquely Mapped Reads siCTRL_1 0h3211398311795163 siCTRL_1 4h273326028410082 siCTRL_1 8h299101138223544 siCTRL_1 12h siUPF1 0h 29209782 35319906 4683418 11151822 siUPF1 4h408751197125974 siUPF1 8h324422016047454 siUPF1 12h303500334353768 siCTRL_1 0h1688984710067525 siCTRL_1 4h148501928384827 siCTRL_1 8h165700988854992 siCTRL_1 12h117552366132423 siCTRL_1 24h siEXOSC5 0h 14667835 18576472 5230211 9683224 siEXOSC5 4h174336158799438 siEXOSC5 8h154127917458473 siEXOSC5 12h175701579208784 siEXOSC5 24h3196987913096031 Supplementary Figure 1

4 Sample NameSequencing DepthUniquely Mapped Reads siCTRL_0min_113352159 10594823 siCTRL_0min_231670976 siCTRL_15min_118132028 13936994 siCTRL_15min_241093930 siCTRL_45min_116438439 12952619 siCTRL_45min_234245283 siCTRL_75min_19327364 6211525 siCTRL_75min_218999831 siCTRL_105min_114939127 11909083 siCTRL_105min_233708692 siCTRL_165min_112177919 8021772 siCTRL_165min_227973798 siCTRL_225min_111488756 7437648 siCTRL_225min_222130531 siCTRL_345min_112489096 6494652 siCTRL_345min_226268851 siCTRL_465min_118994160 8497967 siCTRL_465min_241189955 siCTRL_585min_119046004 7014734 siCTRL_585min_240260306 siCTRL_705min_118497524 6036560 siCTRL_705min_236250937 siSTAU1_0min_113599505 6053372 siSTAU1_0min_2 26876128 siSTAU1_15min_113918840 5826463 siSTAU1_15min_2 25039572 siSTAU1_45min_113340751 9828708 siSTAU1_45min_2 50151533 siSTAU1_75min_110229758 8666838 siSTAU1_75min_2 43411999 siSTAU1_105min_112541178 6163057 siSTAU1_105min_2 25791604 siSTAU1_165min_110176708 6399917 siSTAU1_165min_2 37987332 siSTAU1_225min_18809751 3633723 siSTAU1_225min_2 17219377 siSTAU1_345min_19236900 4375736 siSTAU1_345min_2 32321157 siSTAU1_465min_118482010 4631584 siSTAU1_465min_2 36820119 siSTAU1_585min_112695833 1731351 siSTAU1_585min_2 19272525 siSTAU1_705min_115785239 3747637 siSTAU1_705min_2 51642750 BRIC-seq Sequencing statistics (continued) Supplementary Figure 1

5 Supplementary Figure 2 a)b) c)d) Half-lives: BRIC: >24h ActD: >24h Half-lives: BRIC: >24h ActD: >24h Half-lives: BRIC: 1.72h ActD: 1.72h Half-lives: BRIC: 2.09h ActD: 1.70h

6 Supplementary Figure 2 e)f) g)h) Half-lives: BRIC: >24h ActD: >24h Half-lives: BRIC: >24h ActD: >24h Half-lives: BRIC: 1.90h ActD: 4.62h Half-lives: BRIC: 1.61h ActD: 3.19h

7 b Predicted expression(log10) c 0.00.51.0 1.5 a Observed expression (log10) 0.0 0.5 1.0 1.5 Observed expression (log10) 0.00.51.0 1.5 0.0 0.5 1.0 1.5 Predicted expression(log10) Observed expression (log10) Supplementary Figure 3

8 Supplementary Figure 4 b HIC1 ZNF783 Remaining transcripts (%) Time (hours) Remaining transcripts (%) Time (hours) a c

9 a Supplementary Figure 5 Cell typeExperimental factorsURLLaboratory GM12878 H3k4me3 ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHiston eGm12878H3k04me3StdPkV2.broadPeak.gz Broad Pol2 ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChr omChipGm12878Pol2Pk.narrowPeak.gz UT-A H3k36me3 ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHiston eGm12878H3k36me3StdPk.broadPeak.gz Broad H1-hESC H3k4me3 ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHiston eH1hescH3k4me3StdPk.broadPeak.gz Broad Pol2 ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChr omChipH1hescPol2Pk.narrowPeak.gz UT-A H3k36me3 ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHiston eH1hescH3k36me3StdPk.broadPeak.gz Broad K562 H3k4me3 ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHiston eK562H3k4me3StdPk.broadPeak.gz Broad Pol2 ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHiston eK562Pol2bStdPk.broadPeak.gz Broad H3k36me3 ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHiston eK562H3k36me3StdPk.broadPeak.gz Broad HepG2 H3k4me3 ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHiston eHepg2H3k04me1StdPk.broadPeak.gz Broad Pol2 ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChr omChipHepg2Pol2Pk.narrowPeak.gz UT-A H3k36me3 ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHiston eHepg2H3k36me3StdPk.broadPeak.gz Broad HUVEC H3k4me3 ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHiston eHuvecH3k4me3StdPk.broadPeak.gz Broad Pol2 ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHiston eHuvecPol2bStdPk.broadPeak.gz Broad H3k36me3 ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHiston eHuvecH3k36me3StdPk.broadPeak.gz Broad MCF-7 H3k4me3 ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwHistone/wgEncodeUwHistoneMcf 7H3k4me3StdPkRep1.narrowPeak.gz USC Pol2 ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChr omChipMcf7Pol2PkRep1.narrowPeak.gz UT-A H3k36me3 ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhHistone/wgEncodeSydhHistone Mcf7H3k36me3bUcdPk.narrowPeak.gz USC NHEK H3k4me3 ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHiston eNhekH3k4me3StdPk.broadPeak.gz Broad Pol2 ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHiston eNhekPol2bStdPk.broadPeak.gz Broad H3k36me3 ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHiston eNhekH3k36me3StdPk.broadPeak.gz Broad DLD-1 H3k4me3 http://dbtss.hgc.jp/cgi-bin/downloader2.cgi/DLD1_H3k4me3_peaks.xls.gz DBTSS Pol2 http://dbtss.hgc.jp/cgi-bin/downloader2.cgi/DLD1_Pol2_peaks.xls.gz DBTSS H3k36me3 http://dbtss.hgc.jp/cgi-bin/downloader2.cgi/DLD1_H3k36me3_peaks.xls.gz DBTSS

10 b Supplementary Figure 5 Cell typeExperimental factorsURLLaboratory GM12878 Cell ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLong RnaSeqGm12878CellPapGeneGencV7.gtf.gz CSHL Nucleus ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLong RnaSeqGm12878NucleusPapGeneGencV7.gtf.gz CSHL Cytosol ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLong RnaSeqGm12878CytosolPapGeneGencV7.gtf.gz CSHL H1-hESC Cell ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLong RnaSeqH1hescCellPapGeneGencV7.gtf.gz CSHL Nucleus ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLong RnaSeqH1hescNucleusPapGeneGencV7.gtf.gz CSHL Cytosol ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLong RnaSeqH1hescCytosolPapGeneGencV7.gtf.gz CSHL K562 Cell ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLong RnaSeqK562CellPapGeneGencV7.gtf.gz CSHL Nucleus ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLong RnaSeqK562NucleolusTotalGeneGencV7.gtf.gz CSHL Cytosol ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLong RnaSeqK562CytosolPapGeneGencV7.gtf.gz CSHL HepG2 Cell ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLong RnaSeqHepg2CellPapGeneGencV7.gtf.gz CSHL Nucleus ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLong RnaSeqHepg2NucleusPapGeneGencV7.gtf.gz CSHL Cytosol ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLong RnaSeqHepg2CytosolPapGeneGencV7.gtf.gz CSHL HUVEC Cell ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLong RnaSeqHuvecCellPapGeneGencV7.gtf.gz CSHL Nucleus ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLong RnaSeqHuvecNucleusPapGeneGencV7.gtf.gz CSHL Cytosol ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLong RnaSeqHuvecCytosolPapGeneGencV7.gtf.gz CSHL MCF-7 Cell ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLong RnaSeqMcf7CellPapGeneGencV7.gtf.gz CSHL Nucleus ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLong RnaSeqMcf7NucleusPapGeneGencV10.gtf.gz CSHL Cytosol ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLong RnaSeqMcf7CytosolPapGeneGencV10.gtf.gz CSHL NHEK Cell ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLong RnaSeqNhekCellPapGeneGencV7.gtf.gz CSHL Nucleus ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLong RnaSeqNhekNucleusPapGeneGencV7.gtf.gz CSHL Cytosol ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLong RnaSeqNhekCytosolPapGeneGencV7.gtf.gz CSHL DLD-1 http://dbtss.hgc.jp/cgi-bin/downloader2.cgi/DLD1_RNAseq.wig.gz DBTSS

11 R = 0.38 R = 0.32 R = 0.64R = 0.40 R = 0.57R = 0.34 R = 0.70 R = 0.60 R = 0.28 R = 0.36 R = 0.28 R = 0.32 R = 0.29 R = 0.31R = 0.40 R = 0.27 Supplementary Figure 6 RNA Expression H3K4me3 Intensities RNA Expression

12 Supplementary Figure 7 Refseq (mRNA) lincRNA Frequency in different cell types Frequency of Occurrences

13 Supplementary Figure 8 RT-qPCR and Western blot used to determine knockdown efficiencies b c a e f d siCTRL siEXOSC5_1 siEXOSC5_2 siCTRL siUPF1_1 UPF1 EXOSC5 α-tubulin siCTRL siSTAU1_1 STAU1 α-tubulin siSTAU1_2

14 siRNAs uesd for knock-down and oligonucleotides used for qPCR Name Sence sequece (5'-3') Antisense sequece (5'-3') siRNAs Control siRNA-1GTACCTGACTAGTCGCAGAAGTCTGCGACTAGTCAGGTACGG Control siRNA-2UUCUCCGAACGUGUCACGUTTACGUGACACGUUCGGAGAATT UPF1 siRNA-1GAUGCAGUUCCGCUCCAUUdTdTAAUGGAGCGGAACUGCAUCdTdT UPF1 siRNA-2AAUUUCUGUAACUUGUUUCCUGAAACAAGUUACAGAAAUUAC EXOSC5 siRNA-1CAACACGUCUUCCGUUUCUdTdTAGAAACGGAAGACGuGuuGdTdT EXOSC5 siRNA-2GCAAAGAGAUUUUCAACAAdTdTUUGUUGAAAAUCUCUUUGCdTdT siSTAU1-1CUCUGCGUGUGGUCCGUAUGGAUACGGACCACACGCAGAGCC siSTAU1-2CAGGGGAUCAAUCCGAUUAGCUAAUCGGAUUGAUCCCCUGGC Primer pairs for RT-qPCR GAPDHGCACCGTCAAGGCTGAGAACTGGTGAAGACGCCAGTGGA UPF1AGATCACGGCACAGCAGATTGGCAGAAGGGTTTTCCTT EXOSC5CCACACTCGAAGTGATCCTGCCGGCTCTTCTCTGCAAC STAU1TATCGGCAAGGATGTGGAGTTGGTCCAACTCAGACAGCAA HIC1GATGCTGGACACGATGGACTTGGTGCGCTGGTTGTT PVT1 CTCTTCCTGGTGAAGCATCTGATGGCTGTATGTGCCAAGGT XLOC_003734 TTTCAGAGGTTCTTTAGGGAAAAGACGTGCAAGAGGTCAAAGAAC XLOC_007604 GGACTGAGGCAACCCATCTATTCAAGATGAACCTTATGAGTGGT XLOC_013194 GGGGGCTCTGTGATATGCTATTCCTTTTCCTCTTGGGTTTAGT XLOC_000048 TGGAATATGGCTAATGTAAAGTTCAGCCCGTTCTTGTGGTAGAAG BAMBI CGCCACTCCAGCTACATCTTCACAGTAGCATCGAATTTCACC ZNF574 CGACGGCGAGAGCTAGAGCCTCTGATTCCTCAGTCATGG ZNF691 CCTTCCCTCGCCTACAGAGTCAGGCAGGTGTGGTTCTG ZBED5 TGAAGAGTGCATTTCAAGCTGTGGTACACCTTTTCTTAAAGGTAGATT MMP2 CCCCAAAACGGACAAAGAGCTTCAGCACAAACAGGTTGC SLC25A23 GAATTTTCCCGCTATCTGCCTGTTGGATCTCAGAGACATCAAT Supplementary Figure 9

15 Assumed differential equation: RNA half-life: Supplementary Figure 10

16 Supplementary Figure 11 Experimental factorsCell typeGM12878H1-hESCK562HepG2HUVECMCF-7NHEKDLD-1 H3K4me3 No. of peaks73,95233,27052,422138,70940,94869,52551,31016,917 No. of peaks (>= fold10)6,03522,30326,06311,33323,28267,45828,42811,498 Pol2 No. of peaks33,71035,87754,27741,66638,86250,97343,49632,865 No. of peaks (>= fold10)0025,315047,713028,3549,167 H3K36me3 No. of peaks141,174173,09162,502252,66090,694157,26756,505101,691 No. of peaks (>= fold10)14,12310,72726,46821,61516,0956,29121,42927,693 Experimental factorsCell typeGM12878H1-hESCK562HepG2HUVECMCF-7NHEKDLD-1 H3K4me3No. of genes14,81714,83413,71816,06214,25814,18614,87411,954 Pol2No. of genes14,64214,54513,69213,48013,69213,09313,15312,306 H3K36me3No. of genes11,50811,57111,52411,42011,7827,54212,21410,996 all positive No. of genes10,61110,19410,56910,90210,6407,28610,9719,706 No. of genes (>= fold10)2,2468,9067,9142999,4857,2779,3669,464 No. of genes (< 1RPKM)1,5821,3211,5221,4701,4502471,488121 No. of genes (>= 1RPKM)9,0298,8739,0479,4329,1907,0399,4839,585 No. of genes (>= fold10 & < 1RPKM)1481,068787531,1212451,01486 No. of genes (>= fold10 & >= 1RPKM)2,0987,8387,1272468,3647,0328,3529,378 No. of genes (>= fold25 & < 1RPKM)413034340222711742 No. of genes (>= fold25 & >= 1RPKM)81,47677073,6117,0022,2007,830 Experimental factorsCell typeGM12878H1-hESCK562HepG2HUVECMCF-7NHEKDLD-1 H3K4me3No. of genes5,0233,6684,0156,8023,7843,5594,5812,022 Pol2No. of genes4,8244,1414,5293,1754,5542,6254,1482,894 H3K36me3No. of genes2,2932,1432,5931,9152,0262012,4911,077 all positive No. of genes1,2588801,7421,2331,197951,605379 No. of genes (>= fold10)3526971,19963972951,192341 No. of genes (< 1RPKM)8225711,210824923431,21455 No. of genes (>= 1RPKM)43630953240927452391324 No. of genes (>= fold10 & < 1RPKM)213423769487344388450 No. of genes (>= fold10 & >= 1RPKM)1392744301523852308291 No. of genes (>= fold25 & < 1RPKM)7664603194019435 No. of genes (>= fold25 & >= 1RPKM)0534931214196248

17 Cell TypeP Value Gm128780.42 H1hesc3.73E-14 K5620.40 Hepg20.17 Huvec0.31 Mcf70.37 Nhek0.008 ChIP+/ RNA- OtherChIP+/ RNA- OtherChIP+/ RNA- Other ChIP+/ RNA- Other ChIP+/ RNA- Other ChIP+/ RNA- Other ChIP+/ RNA- Other Nuclear to Cytoplasm ratio (N/C) Supplementary Figure 12

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