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Series GSE82199 Query DataSets for GSE82199
Status Public on Jun 29, 2017
Title LTR-retrotransposon control by tRNA-derived small RNA
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary Transposon reactivation is an inherent danger in cells that lose epigenetic silencing during developmental reprogramming. In the mouse, LTR-retrotransposons, or endogenous retroviruses (ERV), account for most novel insertions and are expressed in the absence of histone H3 Lysine 9 trimethylation in preimplantation stem cells. We found abundant, 18 nt tRNA-derived small RNA (tRF) in these cells, and ubiquitously expressed 22 nt tRFs, that include the 3' terminal CCA of mature tRNAs, and target the tRNA primer binding site (PBS) essential for ERV reverse transcription. We show that the two most active ERV families, IAP and MusD/ETn, are major targets and are strongly inhibited by tRFs in retrotransposition assays. 22 nt tRFs post-transcriptionally silence coding-competent ERVs, while 18 nt tRFs specifically interfere with reverse transcription and retrotransposon mobility. The PBS offers a unique target to specifically inhibit LTR-retrotransposons and tRF-targeting is a potentially highly conserved mechanism of small RNA-mediated transposon control.
Overall design small RNA profiling of mouse trophoblast (TS) stem cells, embryonic stem cells (ES wild-type, Dnmt1 KO, Setdb1 inducible KO), and mouse embryonic fibroblasts, transfected HeLa cells, 3-5 replicates (a/b technical rep., integer biological rep.); H3K9m3 native ChIPseq of trophoblast stem cells (TS), 4 replicates; transposon-specific RACE of uncapped, 5' RNA ends (2x2 conditions), 2 replicates per condition; sRNA libraries of transfected HeLa cells, 3 conditions, 3 replicates each
Contributor(s) Martienssen RA, Schorn A
Citation(s) 28666125
Submission date Jun 02, 2016
Last update date Jul 25, 2021
Contact name Robert A Martienssen
Organization name Cold Spring Harbor Laboratory
Department Delbruck Bldg.
Lab Martienssen
Street address 1 Bungtown Rd
City Cold Spring Harbor
State/province NY
ZIP/Postal code 11724
Country USA
Platforms (4)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL15520 Illumina MiSeq (Homo sapiens)
Samples (54)
GSM2186373 ES_wt_rep1a
GSM2186374 ES_wt_rep1b
GSM2186375 ES_wt_rep2a
BioProject PRJNA324286
SRA SRP076049

Download family Format
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Supplementary file Size Download File type/resource
GSE82199_RAW.tar 1008.5 Mb (http)(custom) TAR (of BEDGRAPH, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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