Supporting Information for Warkocki et al 2018

Uridilation by TUT4/7 restricts retrotransposition of human Line-1





Scripts used for the analysis of presented data can be found in the GitHub repository https://github.com/smaegol/LINE_1_RACE_seq_analysis.
In the same place more detailed description of samples in each sequencing run can be also found.

This page contains links to the raw data used for the paper.

FilenameMD5FileSizeContentssamples
180413_M01788_0119_000000000-BP85V.tar.gz (seq_5) 762c3c49c23b80c3fa1ac5cde70e3465 108GB RACE seq libraries for control transcripts (GAPDH,ACTB,PABPC4,SOGA2). Conditions tested included RNAi depletion of TUTases, MOV10 or TUT1 in PA-1 cell line
Illumina intensity files (CIF) included.		 Reporter LINE1 in HEK293 FLPIN cells:
  • overexpression of TUT1, TENT5C or CNTRL (Fig. 2F);
  • siRNA depletion of TUT1 or CNTRL (Fig. S2I);

Control transcripts (ACTB,GAPDH,PABPC4,SOGA2) in HEK293 FLPIN cells:
  • overexpression of TUT1, TENT5C or CNTRL;
  • siRNA depletion of TUT1, TUT4+TUT7 or CNTRL; (Fig. S2G)

Control transcripts (ACTB,GAPDH,PABPC4,SOGA2) in PA-1 cells:
  • siRNA depletion of MOV10, TUT4+TUT7 or CNTRL (Fig. S2C);
180302_M01788_0117_000000000-BKKGK.tar.gz (seq_4) f0c1c33b2dc59cfba6d14058549625cd 96GB
RACE seq libraries for control transcripts (GAPDH,ACTB,PABPC4,SOGA2). Conditions tested included RNAi depletion of TUTases, MOV10 or TUT1 in in HEK293 Flp-IN cell lines. Illumina intensity files (CIF) included.		 Control transcripts (ACTB, GAPDH, PABPC4,SOGA2) in HEK293 FLPIN cell line:
  • Overexpression of MOV10, TUT4WT, TUT4MT, TUT7WT, TUT7MT, TUT1, CNTRL (Fig. S2F)
  • siRNA depletion of TUT4+TUT7, TUT1 or CNTRL (Fig. S2G)

Endogenous LINE1s from mouse testes (Fig. 2AB, S2A)
180115_M01788_0113_000000000-BKMF4.tar.gz (seq_3) 3b91bd85189cbf5aa1e5c42a67ae377f 114GB RACE seq libraries for reporter LINE1 seqeunces, in HEK293 Flp-IN cell lines. Conditions tested included TUT4, TUT7 or MOV10 overexpression.
Illumina intensity files (CIF) included.		 Reporter LINE1:
  •   overexpression of MOV10, TUT4WT, TUT4MT, TUT7WT, TUT7MT, TUT1, TENT5C, CTRL in HEK293 FLPIN cell line (Fig. 2DE, S2D)
Control transcripts (ACTB, GAPDH, PABPC4, SOGA2):
  •   overexpression of MOV10, TUT4WT, TUT4MT, TUT7WT, TUT7MT, TUT1, TENT5C, CTRL in HEK293 FLPIN cell line (Fig. S2F)
Endogenous LINE1 from H9 cell line:
  •   untreated (NT) cells (Fig. 2AB, S2A)
Control transcript (GAPDH) from mouse testes
170614_M01788_0098_000000000-AVGUP.tar.gz (seq_2) 8e7d504d90868d0c6a56ad87982470a8 80GB RACE seq libraries for genomic-encoded LINE1 and control transcripts (GAPDH,ACTB,PABPC4,SOGA2), in HEK293 Flp-IN, PA1, H9 or NPC cell lines. Conditions tested included TUT4, TUT7 or MOV10 overexpression or RNAi depletion.
Illumina intensity files (CIF) included.		 Endogenous LINE1:
  •   PA-1 cell line:
    •     siRNA depletion of MOV10, TUT4+TUT7, CNTRL (Fig. 2C, S2B)
    •     untreated (NT) cells (Fig. 2AB, S2A)
    •     fractionation (cyto/nuc) (Fig. 2I)
  •   H9 and NPC cell lines: untreated (NT) cells (Fig. 2AB, S2A)
Control transcripts (ACTB, GAPDH, PABPC4, SOGA2):
  •   PA-1 cell line:
    •     siRNA depletion of MOV10, TUT4+TUT7, CNTRL (Fig. S2C)
    •     untreated (NT) cells (Fig. S2A)
    •     fractionation (cyto/nuc) (Fig. 2I)
  •   H9 and NPC cell lines: untreated (NT) cells (Fig. S2A)
151104_M01788_0064_000000000-D0KK1.tar.gz (seq_1) e584e16f3168064130186838e6889cfe 2.5GB RACE seq libraries for reporter LINE1 seqeunces, in HEK293 Flp-IN cell lines. Conditions tested included TUT4, TUT7 or MOV10 overexpression or RNAi depletion.
Illumina intensity files (CIF) included.		 Reporter LINE1 in HEK293 FLPIN cell line:
  •   overexpression of MOV10, TUT4WT, TUT4MT, TUT7WT, TUT7MT, CTRL; (Fig. 2DE, S2D)
  •   siRNA depletion of TUT4, TUT7, TUT4+TUT7, MOV10, CNTRL (Fig. 2GH, S2H)

RNA sequencing data can be found at GEO (currently available only to reviewers)







Additional data - control length accuracy plots, as produced by tailseeker3 for the PCR or SSDNA spike-ins.
We've tested 2 approaches for spike-in preparation and found out that PCR amplification has an important impact on the quality of longer spike-ins. Hence, we decided to perform all tailseq-based analyses using only the synthesized spike-in samples.