miR-128 represses L1 retrotransposition by binding directly to L1 RNA

Abstract

VOLUME 22 NUMBER 10 OCTOBER 2015 nature structural & molecular biology a r t i c l e s microRNAs (miRs) are a class of small (~22-nt) genomically encoded molecules that inhibit translational initiation and stimulate decay of mRNA targets 1,2 . miRs are transcribed by RNA polymerase II and processed by the RNase III enzymes-Dicer and Drosha with its binding partner, DGCR8-to produce short double-stranded RNAs in the nucleus. One strand associates with the Argonaute (Ago) protein, thus forming the miR-mediated silencing complex (miRISC). miRs guide the pairing of miRISC, with imperfect complementarity, to sequences in target mRNAs, thus resulting in their subsequent destabilization and translational repression of the target 3 . The 'seed sequence' , at nucleotides 2-8, is a key determinant for miRISC-target recognition 4,5 . Recent data have shown that 35-40% of miR-binding sites are found in 3′ untranslated regions (UTRs), 40-50% in coding regions and <5% in 5′-UTR regions of mRNAs 6,7 . More than 60% of the human transcriptome has been predicted to be under miR regulation, thus making this post-transcriptional control pathway as important as protein pathways in the regulation of cell functions 2 . It is clear that miRs have essential roles in regulating diverse functions in normal and diseased cells 8,9 .L1 belongs to the most abundant class of autonomous transposable elements 10 . Human L1 contains two open reading frames, ORF1 and ORF2, which encode a protein with RNA-binding and nucleotide acid-chaperone activity (ORF1) 11 and a protein with endonuclease and reverse-transcriptase activities (ORF2) 12-15 , respectively. L1 mobilizes replicatively from one location in the genome to another by a 'copy-and-paste' mechanism, and it has been proposed to be a remnant of an ancient retrovirus 12,16 . Active and inactive L1s have been implicated in the evolution of mammalian genomes and are linked to cell-based diseases, including cancer [17][18][19] . In addition, somatic L1 insertions are biased toward regions of cancer-specific DNA hypomethylation, thus suggesting that L1 insertions may provide a selective advantage during tumorigenesis 20 . Mechanisms that operate at different levels in gene-expression hierarchies have been selected to control transposition-mediated mutagenesis and mitigate the potential negative effects of newly inserted elements. In germ cells, a specific small-RNA subtype (piwi-interacting RNAs (piRNAs)) efficiently counteracts L1 activity, but these RNAs are not expressed in nongerm cells 21,22 . Somatic cells attenuate element mobilization by DNA methylation of the L1 promoter 23 . Other methods of regulation are mediated by APOBEC proteins 24,25 , microprocessor interactions 26 and Ago-mediated RNA interference in mouse embryonic stem cells 27 . L1-promoter silencing is greatly attenuated, and L1 transcription is reactivated in hypomethylated cells, such as cancer cells and tumor-initiating cells, and is also reactivated during reprogramming [28][29][30] . Because miRs act as regulators of g...

Dicer, a new regulator of pluripotency exit and LINE‐1 elements in mouse embryonic stem cells

“…Nevertheless, our work, together with other studies performed in human cultured cells, indicates a role of DICER as a player in L1s regulation [77,82,83]. How DICER controls L1s still remains unclear and further investigations are needed.…”

“…How DICER controls L1s still remains unclear and further investigations are needed. Recently, a study performed in human cells indicated that a particular microRNA, miR‐128, was involved in the direct regulation of L1s transcripts . Nevertheless, miR‐128 is not expressed in mESCs (data not shown) and therefore cannot explain the regulation of L1s by DICER.…”

What Doesn't Kill You Makes You Stronger: Transposons as Dual Players in Chromatin Regulation and Genomic Variation

“…The HUSH complex and MORC2 have also been shown to target evolutionarily young euchromatic LINE1 elements for silencing by deposition of H3K9me3 . Posttranscriptional silencing of LINE1 RNA is mediated via RNA interference by small RNAs, such as piRNAs and rasiRNAs . PIWI proteins use piRNAs to guide the cleavage of LINE1 RNA in germ cells.…”

miR-128 inhibits telomerase activity by targeting TERT mRNA

“…We have recently established that miRs (miR-128) can repress the activity of key enzymes in our cells, such as reverse transcriptase (RT) encoded by transposable elements (long-interspaced element-1, LINE-1 or L1) [29]. With this in mind we turned our attention to the most famous RT in human cells -telomerase -an enzyme which plays a crucial role in cancer, stem cells and aging [7][8][9].…”

“…Most studies have, however, found it to act as a tumor suppressor and downregulation has been documented in a long list of human malignancies, including glioma, prostate, head and neck, lung and colorectal cancer, where it has been shown to function as an inhibitor of cancer cell growth and metastasis [22,[24][25][26][27][28]. We recently demonstrated that miR-128 regulates another cellular reverse transcriptase, namely the Long-Interspaced Element-1 (LINE-1 or L1) by directly interacting with ORF2 L1 RNA, which encodes L1 RT [29]. Derepression of L1 elements have been demonstrated to function as driver mutations during tumor initiation, as well as during tumor progression [30][31][32][33][34][35][36].…”