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Series GSE106810 Query DataSets for GSE106810
Status Public on Jan 23, 2019
Title LINE-2 transposable elements are a source of functional human microRNAs and target sites
Organisms Homo sapiens; Mus musculus
Experiment type Non-coding RNA profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Transposable elements (TEs) are dynamically expressed at high levels in multiple human tissues, but the function of TE-derived transcripts remains largely unknown. In this study, we identify numerous TE-derived microRNAs (miRNAs) by conducting Argonaute2 RNA immunoprecipitation followed by small RNA sequencing (AGO2 RIP-seq) on human brain tissue. Many of these miRNAs originated from LINE-2 (L2) elements, which entered the human genome around 100-300 million years ago. We found that L2-miRNAs derive from the 3’ end of the L2 consensus sequence and thus share very similar sequences, indicating that L2-miRNAs could target transcripts with L2s in their 3’UTR. In line with this, we found that many protein-coding genes carry fragments of L2-derived sequences in their 3’UTR: these sequences serve as target sites for L2-miRNAs. L2-miRNAs and their targets were generally ubiquitously expressed at low levels in multiple human tissues, suggesting a role for this network in buffering transcriptional levels of housekeeping genes. Interestingly, we also found evidence that this network is perturbed in glioblastoma. In summary, our findings uncover a TE-based post-transcriptional network that shapes transcriptional regulation in human cells.
Overall design Small and total RNA sequencing data from AGO-RIPseq experiments on human glioblastoma and cortex tissue, mouse brain tissue and ESCs-derived neurons.
Contributor(s) Petri R, Brattås PL, Sharma Y, Jönsson ME, Pircs K, Bengzon J, Jakobsson J
Citation(s) 30865625
Submission date Nov 13, 2017
Last update date May 15, 2019
Contact name Per Brattas
Organization name Lund University
Lab Clinical Genomics
Street address Sölvegatan 17
City Lund
ZIP/Postal code 221 84
Country Sweden
Platforms (3)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (49)
GSM2850593 HumanCortex_AGO2RIP_B5_smallRNA
GSM2850594 HumanCortex_AGO2RIP_B8_smallRNA
GSM2850595 HumanCortex_AGO2RIP_B14_smallRNA
BioProject PRJNA418122
SRA SRP124840

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE106810_RAW.tar 35.3 Mb (http)(custom) TAR (of BW)
GSE106810_featC.3UTR.txt.gz 1.2 Mb (ftp)(http) TXT
GSE106810_featC.3UTRCells.txt.gz 351.3 Kb (ftp)(http) TXT
GSE106810_featC.RNR.txt.gz 1.1 Kb (ftp)(http) TXT
GSE106810_featC.hg38tRNA_minO.txt.gz 22.9 Kb (ftp)(http) TXT
GSE106810_featC.linc.txt.gz 408.5 Kb (ftp)(http) TXT
GSE106810_featC.miRbase2024_minoverlap.txt.gz 71.8 Kb (ftp)(http) TXT
GSE106810_featC.miRbaseminoverlap.txt.gz 73.3 Kb (ftp)(http) TXT
GSE106810_featC.piRNA2024minOverlap.txt.gz 11.9 Mb (ftp)(http) TXT
GSE106810_featC.piRNAminOverlap.txt.gz 11.9 Mb (ftp)(http) TXT
GSE106810_featC.refseq.txt.gz 2.9 Mb (ftp)(http) TXT
GSE106810_featC.repeatsONLYminOverlap.txt.gz 29.1 Kb (ftp)(http) TXT
GSE106810_featC.repeatsONLYminOverlap2024.txt.gz 23.5 Kb (ftp)(http) TXT
GSE106810_featC.small.hg38tRNAminO.txt.gz 15.4 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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