Skip to main content

Lund University Publications

LUND UNIVERSITY LIBRARIES

LINE-2 transposable elements are a source of functional human microRNAs and target sites

Petri, Rebecca LU ; Brattås, Per Ludvik LU ; Sharma, Yogita LU ; Jönsson, Marie E. LU ; Pircs, Karolina LU orcid ; Bengzon, Johan LU and Jakobsson, Johan LU orcid (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.

(Less)
Please use this url to cite or link to this publication:
author
; ; ; ; ; and
organization
publishing date
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
2024-06-11 08:06:27
@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}},
}