LINE-2 transposable elements are a source of functional human microRNAs and target sites
(2019) In PLoS Genetics 15(3). p.1008036-1008036- Abstract
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. L2-miRNAs derived from the 3' end of the L2 consensus sequence and thus shared very similar sequences, indicating that L2-miRNAs could target transcripts with L2s in their 3'UTR. In line with this, many protein-coding genes carried fragments of L2-derived sequences in... (More)
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. L2-miRNAs derived from the 3' end of the L2 consensus sequence and thus shared very similar sequences, indicating that L2-miRNAs could target transcripts with L2s in their 3'UTR. In line with this, many protein-coding genes carried fragments of L2-derived sequences in their 3'UTR: these sequences served 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. In addition, 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.
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- author
- Petri, Rebecca LU ; Brattås, Per Ludvik LU ; Sharma, Yogita LU ; Jönsson, Marie E. LU ; Pircs, Karolina LU ; Bengzon, Johan LU and Jakobsson, Johan LU
- organization
- publishing date
- 2019
- type
- Contribution to journal
- publication status
- published
- subject
- in
- PLoS Genetics
- volume
- 15
- issue
- 3
- pages
- 1008036 - 1008036
- publisher
- Public Library of Science (PLoS)
- external identifiers
-
- pmid:30865625
- scopus:85063712282
- ISSN
- 1553-7404
- DOI
- 10.1371/journal.pgen.1008036
- language
- English
- LU publication?
- yes
- id
- ad159d99-2f7b-47a1-aa0f-d8a4b02b7fa1
- date added to LUP
- 2019-04-10 10:57:33
- date last changed
- 2024-10-15 22:03:41
@article{ad159d99-2f7b-47a1-aa0f-d8a4b02b7fa1, abstract = {{<p>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. L2-miRNAs derived from the 3' end of the L2 consensus sequence and thus shared very similar sequences, indicating that L2-miRNAs could target transcripts with L2s in their 3'UTR. In line with this, many protein-coding genes carried fragments of L2-derived sequences in their 3'UTR: these sequences served 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. In addition, 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.</p>}}, author = {{Petri, Rebecca and Brattås, Per Ludvik and Sharma, Yogita and Jönsson, Marie E. and Pircs, Karolina and Bengzon, Johan and Jakobsson, Johan}}, issn = {{1553-7404}}, language = {{eng}}, number = {{3}}, pages = {{1008036--1008036}}, publisher = {{Public Library of Science (PLoS)}}, series = {{PLoS Genetics}}, title = {{LINE-2 transposable elements are a source of functional human microRNAs and target sites}}, url = {{http://dx.doi.org/10.1371/journal.pgen.1008036}}, doi = {{10.1371/journal.pgen.1008036}}, volume = {{15}}, year = {{2019}}, }