Experimental identification of microRNA targets

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    Review

    Experimental identification of microRNA targets

    Ulf Andersson rom 1, Anders H. Lund

    Biotech Research and Innovation Centre and Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark

    a b s t r a c ta r t i c l e i n f o

    Article history:

    Received 8 October 2009

    Received in revised form 10 November 2009

    Accepted 16 November 2009

    Available online 24 November 2009

    Received by A. J. Van Wijren

    Keywords:

    microRNA

    Target identification

    microRNAs are small RNAs that regulate protein synthesis post-transcriptionally. Animal microRNAs

    recognize their targets by incomplete base pairing to sequence motifs most often present in the 3

    untranslated region of their target mRNAs. This partial complementarity vastly expands the repertoire of

    potential targets and constitutes a problem for computational target prediction. Although computationalanalyses have shed light on important aspects of microRNA target recognition, several questions remain

    regarding how microRNAs can recognize and regulate their targets. Forward experimental approaches allow

    for an unbiased study of microRNA target recognition and may unveil novel, rare or uncommon target

    binding patterns. In this review we focus on animal microRNAs and the experimental approaches that have

    been described for identification of their targets.

    2009 Elsevier B.V. All rights reserved.

    1. Introduction

    microRNAs (miRNAs) are uncapped, unpolyadenylated small

    RNAs that are processed from primary transcripts in sequential

    steps by the RNase III endonucleases Drosha in the nucleus ( Lee et al.,

    2003) and Dicer in the cytoplasm (Hutvagner, 2005). Mature miRNAare incorporated into the RNA-induced silencing complex (RISC;

    Meister et al., 2004b) where they are bound by members of the

    Argonaute (Ago) family of proteins and constitute the target

    recognition module of RISC (Carthew and Sontheimer, 2009).

    Extensive research has revealed the existence of more than 700

    different human miRNAs (Griffiths-Jones et al., 2008) and numerous

    reports have demonstrated the importance of miRNA-mediated

    regulation in key processes, such as proliferation, apoptosis, differen-

    tiation and development, cellular identity and pathogenhost inter-

    actions (He et al., 2007; Parker and Sheth, 2007; Pillai et al., 2007;

    Carthew and Sontheimer, 2009). Despite of this, the mechanisms by

    which miRNAs act are still not resolved. The first step toward

    unraveling the function of a particular miRNA is the identification of

    its direct targets. This step has proven to be quite challenging in

    animals primarily due to the incomplete complementarity between

    miRNA and target mRNAs.

    Some key principles have emerged on the pattern of miRNA target

    recognition and these have been applied to computationally predict

    targets of miRNA regulation (Bartel, 2009). Examples of commonly

    used algorithms are miRanda (John et al., 2004), TargetScan (Lewis

    et al., 2003, 2005) and PicTar (Krek et al., 2005). The most general

    feature of miRNA regulation described is the recognition of sequence

    motifs complementary to the seed region (nucleotides 27 of the

    miRNA) in the 3 UTR of target mRNAs (Lewis et al., 2003), which

    together with criteria such as target sequence conservation make upthe basis for most target prediction algorithms. It is currently

    unknown which proportion of miRNA interactions follow these

    rules and functional recognition motifs outside of the 3 UTRs, not

    following the seed rule and target sequences that are not conserved

    between species, have been reported (Ha et al., 1996; Reinhart and

    Bartel, 2002; Vella et al., 2004b; Jopling et al., 2005; Krek et al., 2005;

    Didiano and Hobert, 2006; Easow et al., 2007; Orom et al., 2008; Tay

    et al., 2008; Tsai et al., 2009).

    Computational approaches to miRNA target identification are

    strong tools to narrow down the list of putative targets of miRNA

    regulation and have contributed significantly to the development of

    the miRNA field. However, a limitation of target predictions is that

    they rely on few established principles and as such cannot help in

    revealing novel aspects of miRNA target recognition. While several

    reports document the validity of predicted targets for miRNA

    regulation, many predicted targets do not recapitulate regulation in

    validation experiments (Nakamoto et al., 2005; Vinther et al., 2006;

    Frankel et al., 2008; Baek et al., 2008; Didiano and Hobert, 2008;

    Selbach et al., 2008; Jiang et al., 2009). A thorough study of miRNAs

    predicted to target CyclinD1 has addressed this using luciferase

    reporter assays (Jiang et al., 2009). Out of 45 miRNAs predicted to

    target the CyclinD1 3 UTR only 7 could be confirmed by the authors

    (16%). While false positive predictions can be eliminated by

    experimental validation studies, the number of false negative

    predictions remains unknown. An unbiased approach to study

    miRNA interactions with their targets would provide much insight

    Gene 451 (2010) 15

    Abbreviations: UTR, untranslated region; miRNA, microRNA; RISC, RNA-induced

    silencing complex; SILAC,stableisotope labeling by amino acids in cell culture; HITS-CLIP,

    high-throughput sequencing of RNAs isolated by cross-linking immunoprecipitation.

    Corresponding author.

    E-mail address: [email protected] (A.H. Lund).1 Present address: The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, USA.

    0378-1119/$ see front matter 2009 Elsevier B.V. All rights reserved.

    doi:10.1016/j.gene.2009.11.008

    Contents lists available at ScienceDirect

    Gene

    j o u r n a l h o m e p a g e : w w w. e l s e v i e r. c o m / l o c a t e / g e n e

    mailto:[email protected]://dx.doi.org/10.1016/j.gene.2009.11.008http://www.sciencedirect.com/science/journal/03781119http://www.sciencedirect.com/science/journal/03781119http://dx.doi.org/10.1016/j.gene.2009.11.008mailto:[email protected]
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    into additional recognition patterns and help as well to exclude false

    negative predictions. In this review, we describe the reported

    experimental approaches to identify the mRNA targets associated

    with specific miRNAs in animals (for overview, see Fig. 1).

    2. Experimental target identification

    2.1. Transcriptome analyses

    The realization that animal miRNAs down-regulate the level of a

    number of their target mRNAs (Bagga et al., 2005; Lim et al., 2005)

    paved the way for a series of overexpression and miRNA inhibition

    studies where miRNA targets were sought identified on a transcrip-

    tome-wide scale (Krutzfeldt et al., 2005; Christoffersen et al., 2007;

    Frankel et al., 2008; Grimson et al., 2007; Elmen et al., 2008a ). Initial

    studies transiently transfected the tissue specific miRNAs miR-1

    (muscle specific) and miR-124a (brain specific) into HeLa cells where

    they are normally not expressed and used microarray analyses to

    identify the cohort of mRNAs down-regulated as a consequence of

    miRNA overexpression (Lim et al., 2005). Subsequent analysis showed

    that target mRNA down-regulation is highly significantly associated

    with the presence of an miRNA seed complementary site in the mRNA

    3 UTR sequence. In addition, correlations between the mRNA targets

    and the miRNAs are shown: identified targets are primarily expressed

    at low levels in the tissues with high expression of the miRNAs ( Farh

    et al., 2005; Lim et al., 2005). Furthermore, introducing the tissue

    specific miRNAs into HeLa cells shifted the mRNA expression profile

    toward that of the tissue normally expressing the miRNA, suggesting

    a very important role for miRNAs in tissue development and

    maintenance (Lim et al., 2005). The option to identify a large set

    of miRNA targets using microarrays has prompted other groups to

    take similar approaches to unravel miRNA functions both in cell

    culture and in vivo. A modified approach, in part trying to avoid off-

    target effects resulting from miRNA overexpression, is to inhibit the

    miRNA of interest with oligonucleotides complementary to the

    miRNA (Hutvagner et al., 2004; Meister et al., 2004a; Orom et al.,

    2006) and analyze mRNA levels on microarrays. When inhibiting

    the miRNA a subset of its targets will increase at both the protein

    and mRNA levels and potential targets can thus be readily

    identified (Krutzfeldt et al., 2005; Frankel et al., 2008ff; Elmen et

    al., 2008b; Christoffersen et al., 2009). Two reports apply both

    overexpression and inhibition of miRNAs (Nicolas et al., 2008;

    Ziegelbauer et al., 2009). By analyzing the overlap between these

    two series of experiments the list of putative direct target is signi-ficantly reduced. When miR-140 was either overexpressed or

    inhibited (Nicolas et al., 2008) a list of 1236 and 466 genes were

    reported as differentially expressed, while the overlap between the

    two experiments was only 49 transcripts. Twenty-one of these 49

    mRNAs contain miR-140 seed complementary sites, yet none of them

    are predicted by commonly used miRNA target prediction algorithms,

    suggesting a significant number of false negative predictions by these

    algorithms.

    While these approaches can identify a subset of miRNA targets,

    they are limited to the mRNAs that are degraded to a certain extent by

    their targeting miRNAs, and the applications of such approaches have

    been highly dependent on computational analyses based on sequence

    complementarity. Such an approach yields many candidate target

    mRNAs that are differentially expressed upon exogenous introduction

    of miRNAs andmost likelymany false positive candidates areincluded

    due to downstream effects of the affected true miRNA mRNA targets.

    An approach to limit the number of false positives is to rely on seed

    site complementarity in the detected candidates. It is evident from

    these experiments that destabilization of target mRNAs is an

    important mechanism for miRNA function, on top of the strict

    translational repression without effects on mRNA levels.

    2.2. Biochemical approaches

    Several known miRNA targets have been identified using bioinfor-

    matic analyses for seed complementarity and subsequent experi-

    mental and functional validation of the interaction. A more

    challenging task is to identify those targets regulated primarily at

    the level of translation, or recognized through non-seed base pairinginteractions. Toward this, several groups have reported progress using

    different experimental approaches. Three reports address experimen-

    tal miRNA target identification by immunoprecipitation of Ago

    proteins, either tagged or endogenous, to analyze the associated

    mRNAs as candidate miRNA targets.

    Karginov et al. used an epitope-tagged Ago2 in HEK293 to isolate

    targets of mir-124a, an miRNA not endogenously expressed in

    HEK293 cells (Karginov et al., 2007). Initial validation of the approach

    showed significant enrichment of three previously characterized

    targets of miR-124a, Ctdsp1, Plod3 and Vamp3, whereas a panel of

    housekeeping mRNAs was not enriched after immunoprecipitation of

    the myc-tagged Ago2. To identify a comprehensive set of miR-124a

    targets the myc-Ago2 immunoprecipitates were hybridized to

    microarrays along with determination of total mRNA levels. BothmRNA targets that are down-regulated in total mRNA and targets that

    are unaffected at the mRNA level by the miRNA were identified in the

    immunoprecipitates. Four of 4 down-regulated mRNA targets and 21

    of 30 tested mRNAs that were not affected at total mRNA level were

    validated in luciferase reporter 3 UTR assays, but a further

    characterization of the translationally regulated targets was not

    pursued. The paper shows that miRNA targets can be isolated and

    identified using Ago immunoprecipitation, identifying primarily those

    targets that are translationally repressed. Similar findings were

    demonstrated for miR-1 in a Drosophila system (Easow et al., 2007).

    Using immunoprecipitation of HA-tagged Ago1 proteins in S2 cells

    and subsequent microarray analysis, enrichments for mRNAs contain-

    ing miR-1 miRNA seed complementary sites in their 3 UTRs were

    demonstrated to correlate with the expression level of the specific

    Fig. 1. Overview of approaches for experimentally identifying microRNA targets.

    microRNA regulation of translation is a multi-facetted process that allows several

    entrances for experimentally identifying the targets regulated by a specific microRNA.

    Reports address this issue through: (1) Analysis of mRNAs degraded as a consequence

    of overexpressing the microRNA and subsequent analysis of sequence motifs, (2)

    immunoprecipitation of tagged or endogenous RISC complex and analysis of associated

    mRNAs, (3) Affinity purification of tagged microRNAs and microarray analysis of

    associated mRNAs, (4) by using the observation that some microRNA targets move in

    the polysomal distribution upon microRNA targeting and analyzing differences in

    polysomal associated mRNAs with and without the microRNA, (5) analyzing protein

    production following labeling of proteins and mass spectrometry.

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    miRNAs. The study shows as well the applicability of Ago immuno-

    precipitation for miRNA target identification, but lacks a thorough

    analysis of the identified targets. Rather the report focuses on the

    presence of miR-1 seeds in a subset of the identified potential targets

    of miR-1 regulation. Beitzinger et al. (2007) isolated endogenous Ago

    proteins from HEK293 cells using highly specific monoclonal

    antibodies against either human Ago1 or human Ago2 (Beitzinger

    et al., 2007). By purifying RNAs associated with either of the Ago

    proteins, cDNA synthesis and cloning, the associated mRNAs wereidentified. Analysis of the putative miRNA targets shows little overlap

    between Ago1- and Ago2-associated miRNA targets in human

    HEK293 cells, suggesting that specific pools of miRNAs or miRNA

    targets are associated to the different Ago proteins. About half of the

    suggested targets were predicted by at least one of the three applied

    target prediction methods: MiRanda (John et al., 2004), TargetScan

    (Lewis et al., 2003, 2005) or Pictar (Krek et al., 2005). For validation, 6

    mRNAs predicted to be targets of miRNA regulation were selected.

    Cloning of their 3 UTRs into a luciferase reporter vector and reporter

    assays with both miRNA overexpression or miRNA inhibition

    confirmed that these targets are regulated by the predicted miRNA

    through their 3 UTRs.

    While all three studies report the identification of miRNA targets

    using experimental approaches, none of them address miRNA target

    recognition directly but tend to rely on miRNA seed site interaction for

    validation. The three papers show the potential of Ago immunopre-

    cipitation as a means of identifying miRNA targets but at the same

    time they demonstrate the inherited difficulties in experimental

    miRNA target identification. While several thousands of mRNAs are

    hypothesized to be regulated by miRNAs, only a few are identified

    using these approaches.

    Tagging of the miRNA is another approach that has been employed

    to identify targets of miRNA regulation. By transfecting cells with

    miRNAs labeled with biotin and subsequently isolating the associated

    mRNAs, this method has been described for the well-characterized

    bantam/hid interaction in Drosophila both in reporter assays in

    HEK293 cells and for endogenous hid in S2 cells, where the hid 3 UTR

    could be affinity purified using a biotin-tagged bantam miRNA (Orom

    and Lund, 2007). The method has been used to validate individualmiRNA:target interactions (Kedde et al., 2007; Christoffersen et al.,

    2009) and to identify targets and suggest a novel function of the

    miRNA miR-10a (Orom et al., 2008). Surprisingly, it was found that

    miRNA-10a can target mRNAs encoding ribosomal proteins through

    their 5 UTRs via non-seed interactions to enhance their translation, as

    well as modulate mRNA targets through their 3 UTRs and repress

    their translation (Orom et al., 2008). Using this method, it was shown

    by cross-linking followed by primer extension mapping of the miRNA

    binding site that the non-canonical interaction is direct, which is also

    validated by mutating the miRNA target sequence and the

    corresponding bases in the miRNA to recover the enhancing effect

    observed of the miRNA.

    An in vitro procedure using digoxigenin-labeled miRNA precursors

    has also been employed (Hsu et al., 2009). By incubation with anti-DIG antiserum known miRNA targets from C. elegans and zebrafish

    were confirmed using qPCR. Additionally the approach identified

    hand2 as a miR-1 target.

    Controversy exists about miRNA target association to polysomes.

    mRNAs targeted by miRNAs are both reported associated to

    polysomes while bound by miRNAs and reported to shuttle in the

    polysomal spectrum as a consequence of miRNA regulation (Olsen

    and Ambros 1999; Nelson et al., 2004; Nakamoto et al., 2005; Pillai et

    al., 2005; Petersen et al., 2006; Thermann and Hentze, 2007).

    Nakamoto et al. have used the assumption that the position of a

    transcript in a polysome profile reflects, in part, the degree of its

    translation. Hence, shifts into heavier polysome fractions would

    reflect increased translation (Nakamoto et al., 2005). Using knock-

    down of endogenous miR-30a-3p and isolating polysomal and sub-

    polysomal fractions and comparing associated mRNAs on micro-

    arrays, 8 mRNAs translationally induced upon miR-30a-3p knock-

    down were identified and validated as being targets of miR-30a-3p

    regulation. Despite that all 8 mRNAs contain seed sites (including G:U

    wobble pairs), none of them were predicted to be targets of miR-30a-

    3p by the applied algorithms with a score above threshold. This study

    clearly demonstrates the applicability of forward approaches to

    identify miRNA targets. Even though only a few target candidates

    are identifi

    ed, none of them were previously predicted to be targets ofmiR-30a-3p.

    A recent report using purification of cross-linked RNA-binding

    proteins has shed more light on miRNA target recognition (Chi et al.,

    2009). This approach, termed HITS-CLIP, uses ultraviolet light to

    cross-link Ago proteins to associated RNA and miRNA. Ago protein

    complexes were immunoprecipitated and purified from mouse brains

    and the associated RNA identified by sequencing. Clusters of Ago

    binding sites were then identified, which provided not only thebound

    transcript but also the position of Ago binding. The study identifies

    1463 Ago clusters mapping to 829 transcripts. The identity of the

    miRNA bound to each target is not known with this approach. The

    authors use bioinformatics prediction to account for their presump-

    tion that the 20 most expressed miRNAs account for the majority of

    bound targets, however 27% of identified targets do not contain

    sequences corresponding to the 20 most expressed miRNAs. miRNAs

    are shown to bind mostly to 3 UTRs but also to a large degree to the

    open reading frames of the identified targets, although it is unclear if

    these binding sites are functional. The brain specific miRNA miR-124

    was used to compare to bioinformatics predictions for miR-124

    targets. Interestingly, there is a substantial overlap between targets

    identified for miR-124 using HITS-CLIP and computationally predicted

    transcripts, although the experimental approach identifies fewer

    binding sites for Agos in each transcript. This study provides insight

    on miRNA target recognition and can potentially assist in unraveling

    as yet uncharacterized patterns of miRNA target recognition, as the

    approach not only can help identify the targets of miRNA regulation

    but also define the region within which the interaction takes place.

    The option of studying single miRNAs with this approach would give

    even more insightful knowledge on the target recognition propertiesof a single miRNA without having to guess some of the interactions or

    make assumptions of which miRNAs are binding the identified target

    mRNA. Currently, further development of this method is ongoing in

    several laboratories.

    2.3. Proteome analyses

    Several proteomic approaches for studying miRNA target regula-

    tion using stable isotope labeling by amino acids in cell culture

    (SILAC) have been reported (Vinther et al., 2006; Baek et al., 2008;

    Selbach et al., 2008). This experimental approach is appealing as it

    may identify targets regulated both by transcript destabilization and

    translational repression. With SILAC, proteins are metabolically

    labeled by growing cells in medium containing heavy isotopes ofessential amino acids typically lysine and arginine. Using mass

    spectrometry, differences in protein synthesis can be determined by

    the ratio of peptide peak intensities from the light and heavy isotopes.

    Thefirststudy to apply SILAC formiRNAtarget identification found

    12 targets for the miRNA miR-1 in HeLa cells ( Vinther et al., 2006).

    Eight of the 12 identified targets contain seed complementary sites in

    their 3 UTRs. A comparison with mRNA microarray analysis studies of

    miR-1 targets in HeLa cells (Lim et al., 2005) showed that four of these

    targets overlap between the two studies using different approaches to

    address the same question. Luciferase reporter validation of 3 UTRs of

    the identified target genes supported 6 of the putative target mRNAs

    identified, underlining the applicability of the method for miRNA

    target identification. Following this report, two large-scale proteomics

    studies to identify miRNA targets have been published (Baek et al.,

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    2008; Selbach et al., 2008). Baek et al.studied themiRNAs miR-1,miR-

    124 and miR-181 in HeLa cells and the effect of removing miR-223 in

    mouse neutrophils. Selbach et al. used a slightly modified SILAC

    procedure where cells were pulse-labeled to incorporate the isotopes

    primarily into newly synthesized proteins, and studied the miRNAs

    miR-1,miR-30, miR-155, miR-16and let-7band knock-down of let-7b

    in HeLa cells.

    While one large-scale study reports primarily effects at the level of

    mRNA stability (Baek et al., 2008), another observes more instancesofspecific translational inhibition (Selbach et al., 2008).

    Common to the two reports is that they show effects of single

    miRNAs on hundreds of proteins, albeit with a bias toward the

    detection of proteins expressed at a higher level. Most of these effects

    are modest, making it hard to distinguish primary miRNA effects from

    secondary effects. Analyses for predicted binding sites in the 3 UTRs

    show enrichment for the presence of seed sites. The small effects

    observed lead theauthors to suggest that an important role of miRNAs

    might be the fine-tuning of the expression of many proteins.

    In addition, several putative targets show up-regulation of protein

    synthesis, suggesting a general enhancing effect of miRNAs (Selbach

    et al., 2008), either indirect or direct, on a large number of proteins.

    An example of a clinically applicable small-scale proteomics

    approach using reverse-phase protein miRNA analysis has been

    described (Iliopoulos et al., 2008). Comparison of miRNA expression

    and reverse-phase protein arrays probed with 214 antibodies in

    combination with miRNA target prediction identified a number of

    putative targets of miRNA regulation involved in the pathogenesis of

    osteoarthritis. The study identified and validated the regulation by

    miR-22 ofBMP7and PPARa. While the approach relies completely on

    target prediction algorithms, it is advantageous for analysis of clinical

    samples where the amount of sample is limited.

    3. Discussion

    When considering the several approaches reported to successfully

    identify mRNA targets of miRNA regulation only few experimentally

    identified and functionally validated miRNA targets exist. This likely

    reflects the challenge of miRNA target identification and subsequentuseful functional validation.

    miRNA target validation focusing on computationally predicted

    targets has been discussed recently (Kuhn et al., 2008; Bartel, 2009).

    For experimentally identified targets, functional validation is more

    relevant than computational analyses. Approaches such as calculation

    ofG values are mostly useful to narrow down the number of

    putative candidate target mRNAs from bioinformatics analyses and

    may also exclude true targets. Effects on endogenous target protein

    levels serve as good indicators for valid miRNA target interactions,

    although indirect effects cannot be excluded from these experiments.

    A more direct validation, although not in its natural context, can be

    obtained by cloning a sequence of the mRNA of interest into a

    luciferase reporter and do co-transfection reporter assays. By

    mutating the identified target site and subsequently introducingcomplementary mutations into the miRNA sequence, abrogation and

    restoration of the translational effect on the reporter should be

    observed for a true miRNA target. This approach suffers from the

    limitation that both target and miRNA are present at artificially high

    concentrations, which may affect the effect observed (Doench and

    Sharp, 2004). Furthermore, direct evidence that an mRNA is

    endogenously bound by an miRNA can be obtained by using either

    formaldehyde cross-linking of the miRNA to its targets (Vasudevan

    et al., 2007) or 4-thiouridine-modified miRNAs (Orom et al., 2008),

    that allows for subsequent mapping of the exact site of binding using

    primer extension.

    The data obtained from experimental approaches to identify

    miRNA targets should, in addition to identifying targets involved in

    the processesstudied, be used to characterize miRNA binding patterns

    further. Most of the approaches described in this review resort to

    using the proposed seed pattern of miRNA recognition of their targets

    as a validation criterion for the success of their approach, rather than

    asking which patterns of recognition can be deduced from their data.

    Flanking sequences outside of the miRNA recognition site have been

    suggested to have important regulatory functions for a number of

    miRNAs (Vella et al., 2004a; Didiano and Hobert, 2006; Grimson et al.,

    2007; Kertesz et al., 2007; Didiano and Hobert, 2008), but very little

    has been done so far toward identifying additional mRNA determi-nants for miRNA binding and function.

    A major problem with an unbiased forward approach in target site

    analysis is the rather limited number of experimentally identified and

    validated targets each approach has revealed. With the recent, large-

    scale proteomic approaches, together with genome-wide mapping of

    miRNA binding regions coming from techniques such as HITS-CLIPS,

    this may no longer be a limitation.

    4. Conclusion

    Identifying targets of miRNA regulation remains a fundamental

    challenge and the lack of knowledge concerning the different

    mechanisms by which miRNAs work constitutes a major problem

    for experimental target identification. Hence, a combination of target

    identification methods may turn out to be necessary to reveal the full

    spectrum of miRNA target regulation. While the approaches applying

    Ago tagging and immunoprecipitation will likely miss degraded

    mRNAs, these are readily picked up by transfection and microarray

    approaches, which in turn cannot be used to identify targets that are

    exclusively regulated at the level of translation. The most compre-

    hensive approach described so far for miRNA target identification is

    the proteomics approach reported by three different groups (Vinther

    et al., 2006; Baek et al., 2008; Selbach et al., 2008), and such an

    approach should be able to pick up all kinds of repression by the

    miRNA, as theoutput is protein levels. Whileit remains problematic to

    distinguish primary and secondary effects without relying on

    extensive experimental validation or on computational predictions,

    global proteomics approaches could reveal new aspects of miRNA

    target site recognition and function. While repression is by far themost commonly reported effect of miRNA targeting of an mRNA,

    enhancement of translation by miRNAs has been observed by a

    handful of groups so far (Vasudevan et al., 2007; Henke et al., 2008;

    Orom et al., 2008; Selbach et al., 2008; Iwasaki and Tomari, 2009; Tsai

    et al., 2009), two of which are based on experimental target

    identification. This could be a consequence of different miRNA

    recognition motifs, of mRNA sequence context, or as recently

    suggested due to cell cycle-dependent differences in miRNA functions

    (Vasudevan et al., 2007).

    In summary, experimental identification of miRNA targets should

    to a higher extent be used to expand the current knowledge of miRNA

    target recognition and broadening of the spectrum of miRNA targets.

    Acknowledgments

    Work in the authors' laboratory is supported by EC FP7 funding

    (ONCOMIRS, Grant Agreement Number 201102. This publication

    reflects only the authors' views. The commission is not liable for any

    use that may be made of the information herein), the Novo Nordisk

    Foundation, the Danish National Research Foundation, the Danish

    Medical Research Council, the Danish Cancer Society and the Danish

    National Advanced Technology Foundation. UA is supported by a

    personal grant from the Danish Medical Research Council.

    References

    Baek, D., Villen, J., Shin, C., Camargo, F.D., Gygi, S.P., Bartel, D.P., 2008. The impact of

    microRNAs on protein output. Nature 455, 64

    71.

    4 U.A. rom, A.H. Lund / Gene 451 (2010) 15

  • 7/30/2019 Experimental identification of microRNA targets

    5/5

    Bagga, S., et al., 2005. Regulation by let-7 and lin-4 miRNAs results in target mRNAdegradation. Cell 122, 553563.

    Bartel, D.P., 2009. MicroRNAs: target recognition and regulatory functions. Cell 136,215233.

    Beitzinger, M., Peters, L., Zhu, J.Y., Kremmer, E., Meister, G., 2007. Identification ofhuman microRNA targets from isolated argonaute protein complexes. RNA Biol. 4,7684.

    Carthew, R.W., Sontheimer, E.J., 2009. Origins and mechanisms of miRNAs and siRNAs.Cell 136, 642655.

    Chi, S.W., Zang, J.B., Mele, A., Darnell, R.B., 2009. Argonaute HITS-CLIP decodesmicroRNAmRNA interaction maps. Nature 460, 479486.

    Christoffersen, N.R., et al., 2009. p53-independent upregulation of miR-34a duringoncogene-induced senescence represses MYC. Cell Death and Differentiation.doi:10.1038/cdd.2009.109.

    Christoffersen, N.R., Silahtaroglu, A., Orom, U.A., Kauppinen, S., Lund, A.H., 2007.miR-200b mediates post-transcriptional repression of ZFHX1B. Rna 13,11721178.

    Didiano, D., Hobert, O., 2006. Perfectseed pairing is nota generally reliable predictor formiRNA-target interactions. Nat. Struct. Mol. Biol. 13, 849851.

    Didiano, D., Hobert, O., 2008. Molecular architecture of a miRNA-regulated 3 UTR. Rna14, 12971317.

    Doench, J.G., Sharp, P.A., 2004. Specificity of microRNA target selection in translationalrepression. Genes Dev. 18, 504511.

    Easow, G., Teleman, A.A., Cohen, S.M., 2007. Isolation of microRNA targets by miRNPimmunopurification. Rna 13, 11981204.

    Elmen, J., et al., 2008a. LNA-mediated microRNA silencing in non-human primates.Nature 452, 896899.

    Elmen, J., et al., 2008b. Antagonism of microRNA-122 in mice by systemicallyadministered LNA-antimiR leads to up-regulation of a large set of predicted targetmRNAs in the liver. Nucleic Acids Res. 36, 11531162.

    Farh, K.K., Grimson, A., Jan, C., Lewis, B.P., Johnston, W.K., Lim, L.P., Burge, C.B., Bartel, D.P.,2005. The widespread impact of mammalian MicroRNAs on mRNA repression andevolution. Science 310, 18171821.

    Frankel, L.B., Christoffersen, N.R., Jacobsen, A., Lindow, M., Krogh, A., Lund, A.H., 2008.Programmed cell death 4 (PDCD4) is an important functional target of themicroRNA miR-21 in breast cancer cells. J. Biol. Chem. 283, 10261033.

    Griffiths-Jones, S., Saini, H.K., Dongen, S.V., Enright, A.J., 2008. miRBase: tools formicroRNA genomics. Nucleic Acids Res. 36, D154D158.

    Grimson, A., Farh, K.K., Johnston, W.K., Garrett-Engele, P., Lim, L.P., Bartel, D.P., 2007.MicroRNA targeting specificity in mammals: determinants beyond seed pairing.Mol. Cell 27, 91105.

    Ha,I., Wightman, B.,Ruvkun,G., 1996. A bulged lin-4/lin-14RNA duplexis sufficient forCaenorhabditis elegans lin-14 temporal gradient formation. Genes Dev. 10,30413050.

    He, L., He, X., Lowe, S.W., Hannon, G.J., 2007. microRNAs join the p53 networkanotherpiece in the tumour-suppression puzzle. Nat. Rev. Cancer 7, 819822.

    Henke, J.I., et al., 2008. microRNA-122 stimulates translation of hepatitis C virus RNA.EMBO J. 27, 33003310.

    Hsu, R.J., Yang, H.J., Tsai, H.J., 2009. Labeled microRNA pull-down assay system: anexperimental approach for high-throughput identification of microRNA-targetmRNAs. Nucleic Acids Res. 37, e77.

    Hutvagner, G., 2005. Small RNA asymmetry in RNAi: function in RISC assembly andgene regulation. FEBS Lett. 579, 58505857.

    Hutvagner, G., Simard, M.J., Mello, C.C., Zamore, P.D., 2004. Sequence-specific inhibitionof small RNA function. PLoS Biol. 2, E98.

    Iliopoulos, D., Malizos, K.N., Oikonomou, P., Tsezou, A., 2008. Integrative microRNA andproteomic approaches identify novel osteoarthritis genes and their collaborativemetabolic and inflammatory networks. PLoS One 3, e3740.

    Iwasaki, S., Tomari, Y., 2009. Argonaute-mediated translational repression (andactivation). Fly (Austin) 3, 204206.

    Jiang, Q., Feng, M., Mo, Y.Y., 2009. Systematic validation of predicted microRNAs forcyclin D1. BMC Cancer 9, 194.

    John, B., Enright, A.J., Aravin, A., Tuschl, T., Sander, C., Marks, D.S., 2004. HumanMicroRNA targets. PLoS Biol. 2, e363.

    Jopling, C.L., Yi, M., Lancaster, A.M., Lemon, S.M., Sarnow, P., 2005. Modulation ofhepatitis C virus RNA abundance by a liver-specific MicroRNA. Science 309,15771581.

    Karginov, F.V., et al., 2007. A biochemical approach to identifying microRNA targets.Proc. Natl. Acad. Sci. U S A 104, 1929119296.

    Kedde, M., et al., 2007. RNA-binding protein Dnd1 inhibits microRNA access to targetmRNA. Cell 131, 12731286.

    Kertesz, M., Iovino, N., Unnerstall, U., Gaul, U., Segal, E., 2007. The role of siteaccessibility in microRNA target recognition. Nat. Genet. 39, 12781284.

    Krek, A., et al., 2005. Combinatorial microRNA target predictions. Nat. Genet. 37,495500.

    Krutzfeldt, J., et al., 2005. Silencing of microRNAs in vivo with antagomirs. Nature 438,685689.

    Kuhn, D.E., Martin, M.M., Feldman, D.S., Terry, A.V., Jr., Nuovo, G.J., Elton, T.S., 2008.Experimental validation of miRNA targets. Methods 44, 4754.

    Lee, Y., et al., 2003. The nuclear RNase III Drosha initiates microRNA processing. Nature425, 415419.

    Lewis, B.P., Burge, C.B., Bartel, D.P., 2005. Conserved seed pairing, often flanked by

    adenosines, indicates that thousands of human genes are microRNA targets. Cell120, 1520.Lewis, B.P., Shih, I.H., Jones-Rhoades, M.W., Bartel, D.P., Burge, C.B., 2003. Prediction of

    mammalian microRNA targets. Cell 115, 787798.Lim, L.P., et al., 2005. Microarray analysis shows that some microRNAs downregulate

    large numbers of target mRNAs. Nature 433, 769773.Meister, G., Landthaler, M., Dorsett, Y., Tuschl, T., 2004a. Sequence-specific inhibition of

    microRNA- and siRNA-induced RNA silencing. Rna 10, 544550.Meister, G., Landthaler, M., Patkaniowska, A., Dorsett, Y., Teng, G., Tuschl, T., 2004b.

    Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol.Cell 15, 185197.

    Nakamoto, M., Jin, P., O'Donnell, W.T., Warren, S.T., 2005. Physiological identification ofhuman transcripts translationally regulated by a specific microRNA. Hum. Mol.Genet. 14, 38133821.

    Nelson, P.T., Hatzigeorgiou, A.G., Mourelatos, Z., 2004. miRNP:mRNA association inpolyribosomes in a human neuronal cell line. Rna 10, 387394.

    Nicolas, F.E., et al., 2008. Experimental identification of microRNA-140 targets bysilencing and overexpressing miR-140. Rna 14, 25132520.

    Olsen, P.H., Ambros, V., 1999. The lin-4 regulatory RNA controls developmental timing

    in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiationof translation. Dev Biol 216, 671680.

    Orom, U.A., Kauppinen, S., Lund, A.H., 2006. LNA-modified oligonucleotides mediatespecific inhibition of microRNA function. Gene 372, 137141.

    Orom, U.A., Lund, A.H., 2007. Isolation of microRNA targets using biotinylated syntheticmicroRNAs. Methods 43, 162165.

    Orom, U.A., Nielsen, F.C., Lund, A.H., 2008. MicroRNA-10a binds the 5UTR of ribosomalprotein mRNAs and enhances their translation. Mol. Cell 30, 460471.

    Parker, R., Sheth, U., 2007. P bodies and the control of mRNA translation anddegradation. Mol. Cell 25, 635646.

    Petersen, C.P., Bordeleau, M.E., Pelletier, J., Sharp, P.A., 2006. Short RNAs represstranslation after initiation in mammalian cells. Mol Cell 21, 533542.

    Pillai, R.S., Bhattacharyya, S.N., Artus, C.G., Zoller, T., Cougot, N., Basyuk, E., Bertrand, E.,Filipowicz, W., 2005. Inhibition of translational initiation by Let-7 MicroRNA inhuman cells. Science 309, 15731676.

    Pillai, R.S., Bhattacharyya, S.N., Filipowicz, W., 2007. Repression of protein synthesis bymiRNAs: how many mechanisms? Trends Cell Biol. 17, 118126.

    Reinhart, B.J., Bartel, D.P., 2002. Small RNAs correspond to centromere heterochromaticrepeats. Science 297, 1831.

    Selbach, M., Schwanhausser, B., Thierfelder, N., Fang, Z., Khanin, R., Rajewsky, N., 2008.Widespreadchanges in proteinsynthesisinduced by microRNAs. Nature455, 5863.

    Tay, Y., Zhang, J., Thomson, A.M., Lim, B., Rigoutsos, I., 2008. MicroRNAs to Nanog, Oct4and Sox2 coding regions modulate embryonic stem cell differentiation. Nature 455,11241128.

    Thermann, R., Hentze, M.W., 2007. Drosophila miR2 induces pseudo-polysomes andinhibits translation initiation. Nature 447, 875878.

    Tsai, N.P., Lin, Y.L., Wei, L.N., 2009. Micro-RNA mir346 targets the 5 UTR of RIP140mRNA and up-regulates its protein expression. Biochem. J. 424, 411418.

    Vasudevan, S., Tong, Y., Steitz, J.A., 2007. Switching from repression to activation:microRNAs can up-regulate translation. Science 318, 19311934.

    Vella, M.C., Choi, E.Y.,Lin, S.Y.,Reinert, K., Slack, F.J., 2004a. The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3 UTR. Genes Dev.18, 132137.

    Vella, M.C., Reinert, K., Slack, F.J., 2004b. Architecture of a validated microRNA:targetinteraction. Chem. Biol. 11, 16191623.

    Vinther, J., Hedegaard, M.M., Gardner, P.P., Andersen, J.S., Arctander, P., 2006.Identification of miRNA targets with stable isotope labeling by amino acids in cell

    culture. Nucleic Acids Res. 34, e107.Ziegelbauer, J.M., Sullivan, C.S., Ganem, D., 2009. Tandem array-based expression

    screens identify host mRNA targets of virus-encoded microRNAs. Nat. Genet. 41,130134.

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