Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
* Author for correspondence (e-mail: phillip.zamore{at}umassmed.edu)
SUMMARY
Discovered in nematodes in 1993, microRNAs (miRNAs) are non-coding RNAs that are related to small interfering RNAs (siRNAs), the small RNAs that guide RNA interference (RNAi). miRNAs sculpt gene expression profiles during plant and animal development. In fact, miRNAs may regulate as many as one-third of human genes. miRNAs are found only in plants and animals, and in the viruses that infect them. miRNAs function very much like siRNAs, but these two types of small RNAs can be distinguished by their distinct pathways for maturation and by the logic by which they regulate gene expression.
microHistory
The first miRNA, lin-4, was identified in 1993 in a genetic screen
for mutants that disrupt the timing of post-embryonic development in
Caenorhabditis elegans (Lee et
al., 1993). Cloning of the locus revealed that lin-4
produces a 22-nucleotide non-coding RNA, rather than a protein-coding mRNA
(Lee et al., 1993
).
lin-4 represses the expression of lin-14, which encodes a
nuclear protein (Lee et al.,
1993
; Wightman et al.,
1993
) whose concentration must be reduced for worms to progress
from their first larval stage to the second
(Rougvie, 2005
). The negative
regulation of lin-14 by lin-4 requires partial
complementarity between lin-4 and sites in the 3'-untranslated
region (UTR) of lin-14 mRNA (Ha
et al., 1996
; Olsen and
Ambros, 1999
). It was not until 2000 that a second miRNA,
let-7, was discovered, again in worms
(Reinhart et al., 2000
).
let-7 functions in a manner similar to lin-4, repressing the
expression of the lin-41 and hbl-1 mRNAs by binding to their
3' UTRs (Reinhart et al.,
2000
; Slack et al.,
2000
; Lin et al.,
2003
; Vella et al.,
2004
). let-7 is conserved throughout metazoans
(Pasquinelli et al., 2000
),
and the discovery of let-7
(Reinhart et al., 2000
),
together with the subsequent large-scale searches for additional miRNAs,
established miRNAs as a new and large class of ribo-regulators
(Lagos-Quintana et al., 2001
;
Lau et al., 2001
;
Lee and Ambros, 2001
), and
fueled speculation that tiny RNAs are a major feature of the gene regulatory
networks of animals. Now more than 1600 miRNAs have been identified in plants,
animals and viruses (Lai et al.,
2003
; Lim et al.,
2003a
; Lim et al.,
2003b
). The human genome alone may contain 800-1000 miRNAs, a
large portion of which may be specific to primates
(Bentwich et al., 2005
;
Berezikov et al., 2005
;
Xie et al., 2005
).
microMaturation
miRNAs are transcribed by RNA polymerase II as primary miRNAs (pri-miRNAs),
which range from hundreds to thousands of nucleotides in length
(Cai et al., 2004;
Lee et al., 2004
;
Parizotto et al., 2004
). Most
miRNAs are transcribed from regions of the genome that are distinct from
previously annotated protein-coding sequences
(Fig. 1). Some miRNA-encoding
loci reside well apart from other miRNAs, suggesting that they form their own
transcription units; others are clustered and share similar expression
patterns, implying that they are transcribed as polycistronic transcripts
(Lagos-Quintana et al., 2001
;
Lau et al., 2001
;
Lee et al., 2002
;
Reinhart et al., 2002
). About
half of the known mammalian miRNAs are within the introns of protein-coding
genes, or within either the introns or exons of non-coding RNAs, rather than
in their own unique transcription units
(Rodriguez et al., 2004
).
Intronic miRNAs usually lie in the same orientation as, and are coordinately
expressed with, the pre-mRNA in which they reside; that is, they share a
single primary transcript (Rodriguez et
al., 2004
; Baskerville and
Bartel, 2005
). A very few miRNAs reside in the untranslated
regions of protein-coding mRNAs; it is likely that these transcripts can make
either the miRNA or the protein, but not both, from a single molecule of mRNA
(Cullen, 2004
).
Animal microMaturation
In animals, two processing steps yield mature miRNAs
(Fig. 2A). Each step is
catalyzed by a ribonuclease III (RNase III) endonuclease together with a
double-stranded RNA-binding domain (dsRBD) protein partner. First, Drosha, a
nuclear RNase III, cleaves the flanks of pri-miRNA to liberate an
70-nucleotide stem loop, the precursor miRNA (pre-miRNA)
(Lee et al., 2002
;
Lee et al., 2003
;
Denli et al., 2004
;
Gregory et al., 2004
;
Han et al., 2004
;
Landthaler et al., 2004
). The
efficient processing of pri-miRNA by Drosha requires: a large terminal loop
(
10 nucleotides) in the hairpin; a stem region that is about one helical
turn longer than the slightly more than two helical turns of the stem of the
resulting pre-miRNA; and 5' and 3' single-stranded RNA extensions
at the base of the future pre-miRNA (Lee
et al., 2003
; Zeng and
Cullen, 2003
; Zeng and
Cullen, 2005
; Zeng et al.,
2005
). Accurate and efficient pri-miRNA processing by Drosha
requires a dsRBD protein, known as Pasha in Drosophila, Pash-1 C.
elegans and DGCR8 in mammals (Denli
et al., 2004
; Gregory et al.,
2004
; Han et al.,
2004
; Landthaler et al.,
2004
). The resulting pre-miRNA have 5' phosphate and
3' hydroxy termini, and two- or three-nucleotide 3'
single-stranded overhanging ends, all of which are characteristics of RNase
III cleavage of dsRNA. Thus, Drosha cleavage defines either the 5' or
the 3' end of the mature miRNA. (The mature miRNA resides in the
5' arm of some pre-miRNA and in the 3' arm in others.) The
pre-miRNA is then exported from nucleus to cytoplasm by Exportin 5/RanGTP,
which specifically recognizes the characteristic end structure of pre-miRNAs
(Yi et al., 2003
;
Bohnsack et al., 2004
;
Lund et al., 2004
;
Zeng and Cullen, 2004
).
In the cytoplasm, a second RNase III, Dicer, together with its dsRBD
protein partner, Loquacious (Loqs) in Drosophila or the
trans-activator RNA (tar)-binding protein (TRBP) in humans, makes a
pair of cuts that defines the other end of the mature miRNA, liberating an
21-nucleotide RNA duplex (Bernstein et
al., 2001
; Grishok et al.,
2001
; Hutvagner et al.,
2001
; Ketting et al.,
2001
; Chendrimada et al.,
2005
; Forstemann et al.,
2005
; Jiang et al.,
2005
; Saito et al.,
2005
). This RNA duplex has essentially the same structure as a
double-stranded siRNA, except that the mature miRNA is only partially paired
to the miRNA* the small RNA that resides on the side of the pre-miRNA
stem opposite the miRNA because the stems of pre-miRNAs are
imperfectly double stranded. From the miRNA/miRNA* duplex, one strand, the
miRNA, preferentially enters the protein complex that represses target gene
expression, the RNA-induced silencing complex (RISC), whereas the other
strand, the miRNA* strand, is degraded. The choice of strand relies on the
local thermodynamic stability of the miRNA/miRNA* duplex the strand
whose 5' end is less stably paired is loaded into the RISC
(Khvorova et al., 2003
;
Schwarz et al., 2003
). This
thermodynamic difference arises, in part, because miRNAs tend to begin with
uracil, and, in part, because miRNA/miRNA* duplexes contain mismatches and
bulges that favor the miRNA strand being loaded into the RISC.
|
The RISC directs gene silencing
The RISC carries out small RNA-directed gene silencing in both the miRNA
and the RNAi pathways in plants and animals
(Hammond et al., 2000;
Hammond et al., 2001
;
Hutvagner and Zamore, 2002
;
Zeng et al., 2002
;
Doench et al., 2003
). When the
small RNA guide in the RISC pairs extensively to a target mRNA, the RISC
functions as an endonuclease, cleaving the mRNA between the target nucleotides
paired to bases 10 and 11 of the miRNA or siRNA. The core component of every
RISC is a member of the Argonaute (Ago) protein family, whose members all
contain a central PAZ domain (named after the family member proteins Piwi,
Argonaute and Zwille) and a carboxy terminal PIWI domain. Structural studies
show that the PIWI domain binds to small RNAs at their 5' end, whereas
the PAZ domain binds to the 3' end of single-stranded RNAs
(Song et al., 2003
;
Yan et al., 2003
;
Lingel et al., 2004
;
Parker et al., 2004
;
Ma et al., 2005
;
Parker et al., 2005
).
Moreover, the three-dimensional structure of the PIWI domain closely resembles
that of RNase H, the enzyme that cleaves the RNA strand of an RNA-DNA hybrid
(Song et al., 2004
;
Nowotny et al., 2005
), and
both structural and biochemical studies have confirmed that Argonaute is the
target-cleaving endonuclease of the RISC
(Liu et al., 2004
;
Rand et al., 2004
;
Song et al., 2004
; Bamberger
and Baulcombe, 2005; Qi et al.,
2005
; Rivas et al.,
2005
). Notably, a subpopulation of Argonaute proteins do not
retain all the amino acids that are crucial for RISC catalytic activity, and
thus cannot cleave a target RNA even when the small RNA guide is sufficiently
complimentary to the target (Liu et al.,
2004
; Meister et al.,
2004b
; Rivas et al.,
2005
). The RISC-associated proteins include the putative
RNA-binding protein VIG (Vasa intronic gene), the Fragile-X related protein in
Drosophila, the exonuclease Tudor-SN, and several putative helicases
(Caudy et al., 2002
;
Hutvagner and Zamore, 2002
;
Ishizuka et al., 2002
;
Mourelatos et al., 2002
;
Caudy et al., 2003
). The
molecular function of these proteins in RNA silencing is not known.
|
miRNAs regulate their target genes via two main mechanisms: target mRNA cleavage and `translational repression'.
In plants, most miRNAs have perfect or near perfect complementarity to
their mRNA targets (Rhoades et al.,
2002). Upon binding to their mRNA targets, the miRNA-containing
RISCs function as endonucleases, cleaving the mRNA
(Llave et al., 2002
;
Tang et al., 2003
). Single
miRNA-binding motifs are found both in the coding regions, such as the
miR-166-targeting site in the PHABULOSA mRNA, and in the untranslated
regions of miRNA-regulated plant mRNAs, such as the miR-156-targeting site in
the SPL4 mRNA, albeit mainly in coding sequences, perhaps because
cleavage here most strongly inactivates translation of the mRNA into
functional protein (Rhoades et al.,
2002
). At least eight animal miRNA, miR-127, miR-136, miR-196,
miR-431, miR-433-3p, miR-433-5p, miR-434-3p and miR-434-5, and two viral
miRNAs, miR-BART2 and SVmiRNA, also act to cleave their targets
(Mansfield et al., 2004
;
Pfeffer et al., 2004
;
Yekta et al., 2004
;
Davis et al., 2005
;
Sullivan et al., 2005
).
In contrast to plant miRNAs, the complementarity between animal miRNAs and
their targets is usually restricted to the 5' region (nucleotides 2-8 or
2-7) of the miRNA, i.e. to the 3' region of the target site
(Lewis et al., 2003;
Lai, 2004
;
Brennecke et al., 2005
;
Lewis et al., 2005
;
Xie et al., 2005
). This
5' miRNA region has been called the `seed region' to describe its
disproportionate contribution to target-RNA binding. Because the seed region
of a miRNA is so short, miRNA are predicted to regulate surprisingly large
numbers of genes; the complete complement of human miRNAs may regulate as many
as one-third of the human protein-coding genes
(Lewis et al., 2005
;
Xie et al., 2005
)! In the
absence of extensive complementarity between the miRNA and the target, binding
of the RISC blocks translation of the target mRNA into protein, rather than
catalyzing its cleavage into two pieces
(Olsen and Ambros, 1999
).
Recent results suggest that regulation by miRNAs can direct target mRNA
degradation through a pathway that is distinct from small RNA-directed
endonucleolytic cleavage (Bagga et al.,
2005
; Lim et al.,
2005
). In human cells, the core component of the RISCs, Argonaute
proteins, together with mRNAs that are targeted for silencing by miRNAs are
concentrated in cytoplasmic foci called Processing bodies (P-bodies)
(Liu et al., 2005
;
Pillai et al., 2005
;
Sen and Blau, 2005
).
(P-bodies are also known as cytoplasmic bodies or GW-bodies.) miRNAs may
initially block translational initiation, causing the miRNA-programmed RISC
and the target mRNA to be re-localized to the P-body
(Pillai et al., 2005
). In
C. elegans, a P-body protein, AIN-1, interacts with the
miRNA-programmed RISC component ALG-1, an Argonaute protein, and is sufficient
to localize ALG-1 to the P-body (Ding et
al., 2005
). Thus, P-body-mediated miRNA-directed regulation may be
a general mechanism among animals.
microFunctions
miRNAs function in a broad range of biological processes in plants and
animals (Kidner and Martienssen,
2005; Alvarez-Garcia and Miska,
2005
). The first insight into their function came from phenotypic
studies of mutations that disrupt core components of the miRNA pathway.
dicer mutants show diverse developmental defects, including abnormal
embryogenesis in Arabidopsis, delayed germ-line stem-cell (GSC)
division in Drosophila, germ-line defects in C. elegans,
abnormal embryonic morphogenesis in zebrafish and stem-cell differentiation
defects in mice (Knight and Bass,
2001
; Park et al.,
2002
; Bernstein et al.,
2003
; Wienholds et al.,
2003
; Giraldez et al.,
2005
; Hatfield et al.,
2005
). Similarly, the disruption of Argonaute function causes
widespread developmental defects, such as defective stem-cell maintenance and
failure to form axillary meristem in an Arabidopsis mutant for
PINHEAD/ZWILLE (PNH/ZLL) or ARGONAUTE 1 (AGO1), a stem-cell
self-renewal defect in Drosophila piwi mutants, and defective early
development in C. elegans alg-1 and alg-2 mutants
(Bohmert et al., 1998
;
Cox et al., 1998
;
Moussian et al., 1998
;
Grishok et al., 2001
).
Arabidopsis plants mutant for ZIPPY (ZIP), an
Argonaute gene, and HASTY (HST), which encodes the miRNA
export receptor, exhibit a precocious vegetative phenotype and produce
abnormal flowers (Peragine et al.,
2004
). Overall, these phenotypes suggest that at least a subset of
miRNAs play important roles in early development.
Target prediction
The functional characterization of miRNAs relies largely on the
identification of their regulatory targets. In plants, because miRNAs are
almost perfectly complementary to their targets, target prediction is
straightforward (Rhoades et al.,
2002), and automated plant miRNA target prediction can now be
performed online (Zhang,
2005
). At least half of the predicted plant miRNA targets are
transcription factors, although transcription factors represent only 6% of
Arabidopsis protein-coding genes
(Riechmann et al., 2000
;
Rhoades et al., 2002
;
Jones-Rhoades et al., 2004). Typically, many members of a family of related
transcription factors are coordinately repressed by a single miRNA. These
miRNA-regulated transcription factors control developmental patterning, cell
proliferation, and environmental and hormonal responses
(Kidner and Martienssen,
2005
). DCL1 and AGO1 themselves are also miRNA
targets, suggesting a negative-feedback mechanism in which miRNAs tune their
own expression (Rhoades et al., 2002a;
Xie et al., 2003
;
Vaucheret et al., 2004
).
The bioinformatic prediction of animal miRNA targets is more complex
because animal miRNAs display only modest complementarity to their targets.
Different algorithms have been developed to predict animal miRNA targets,
using at least some of the following criteria: (1) perfect or nearly perfect
pairing of the `seed region' at the 5' end of the miRNAs and the
3' UTR of the target mRNA; (2) putative miRNA-binding site conservation
between closely related species; (3) multiple miRNA-binding sites in a single
target; and (4) lack of a strong secondary structure at the miRNA-binding site
on the target (Enright et al.,
2003; Lewis et al.,
2003
; Stark et al.,
2003
; Kiriakidou et al.,
2004
; Rajewsky and Socci,
2004
; Brennecke et al.,
2005
; Krek et al.,
2005
; Lewis et al.,
2005
; Zhao et al.,
2005
). The computational prediction of animal miRNA targets
suggests that the logic of miRNA regulation differs between animals and plants
(see Box 1). In animals, miRNA
has been proposed to fine-tune the expression of hundreds of genes, but to
dramatically downregulate the expression of a much smaller number of
transcripts (Bartel, 2004
);
such dramatic downregulation of transcript levels appears to be widespread for
plant miRNAs. Moreover, animal miRNAs, but perhaps not plant miRNAs, may act
combinatorially, with several miRNAs binding a single transcript. Thus, one
miRNA might be expressed early in development, reducing the steady-state level
of protein synthesis from a targeted mRNA by just a bit, a tuning function.
The subsequent expression of additional miRNAs targeting the same mRNA would
lower its expression still further (Bartel,
2004
). Cell culture experiments suggest that when multiple miRNAs
bind the same target, they act cooperatively, reducing mRNA translation by
more than the sum of their individual effects
(Doench et al., 2003
).
miRNA-target relationships can also be identified by beginning with a
target mRNA and searching for one or more regulatory miRNAs. In one case, the
earlier finding that GY-box, Brd-box and K-box motifs in the 3' UTR of
Notch mRNAs mediate their post-transcriptional repression helped to identify
three families of Drosophila miRNAs that are direct regulators of
Notch target genes (Lai and Posakony,
1997; Lai et al.,
1998
; Lai, 2002
;
Stark et al., 2003
;
Lai et al., 2005
). Another
example is the proposal that miR-16 in Drosophila plays a role in
AU-rich element (ARE)-mediated mRNA degradation
(Jing et al., 2005
). Because
depletion by RNAi of key RNA silencing proteins Dcr-1, Ago-1 and Ago-2
inhibited the rapid mRNA decay normally triggered by AREs, the authors
broke with `microOrthodoxy' and proposed that the ARE is a potential miRNA
target site, perhaps binding miR-16 in a unconventional mode that does not
require seed-sequence pairing.
microProfiling
miRNA profiling has also been used to identify miRNAs with potentially
important developmental roles. The rationale is that if a miRNA is highly
expressed in a tissue or cell type or at a specific developmental stage, it
may reasonably play a regulatory role in specifying tissue or cell identity,
or in regulating developmental timing. miRNA expression can be profiled by the
cloning and sequencing miRNAs from specific tissues or developmental states (a
labor-intensive method that has the benefit of uncovering new miRNAs), or by
microarray analysis (a more high-throughput method that can only reveal the
expression of known miRNAs). For example, miR-181, which is highly
expressed in mouse bone marrow B-lymphoid cells, but not in T-cells, was found
to promote hematopoietic differentiation towards the B-cell lineage
(Chen et al., 2004).
miR-375, an evolutionarily conserved, pancreatic islet-specific miRNA
identified by small RNA cloning from glucose-responsive murine pancreatic cell
lines, suppresses glucose-induced insulin secretion by repressing
myotrophin (Mtpn) expression
(Poy et al., 2004
). miRNA
expression profiling has also identified a zebrafish miRNA that regulates
brain morphogenesis, miR-430, whose expression peaks 4 hours after
fertilization (when most fish miRNAs are first expressed) and decreases after
24 hours (Chen et al., 2005
;
Giraldez et al., 2005
), and
also miR-1, a mouse miRNA whose expression is confined to cardiac and
skeletal muscle precursor cells, and which may control the balance between
differentiation and proliferation during cardiogenesis by regulating the
expression of Hand2 mRNA
(Wienholds et al., 2005
;
Zhao et al., 2005
).
To date, hundreds of miRNAs have been identified in different organisms,
which makes it possible to study their function individually by suppressing
their expression in cells. However, genetic depletion, i.e. making miRNA
mutants, is labor intensive. 2'-O-methyl antisense
oligonucleotides complementary to endogenous miRNAs provide an alternative to
genetic mutation. These antisense oligonucleotides transiently block miRNA
function (Hutvagner et al.,
2004; Meister et al.,
2004a
). Thus, injecting into worms a 2'-O-methyl
oligonucleotide that binds let-7 recapitulates the let-7
mutant phenotype (Hutvagner et al.,
2004
). In early syncitial Drosophila embryos, where
injection of oligonucleotides is straightforward, a panel of
2'-O-methyl oligonucleotides was used to reveal the embryonic
loss-of-function phenotypes of 46 miRNAs
(Leaman et al., 2005
). This
study suggests that miRNAs specifically regulate a broad range of
developmental events. In another study, Lecellier et al. used antisense
locked-nucleic acid (LNA) oligonucleotides, nucleic acid molecules that are
modified to dramatically increase their binding affinities, to block miR-32 in
cultured human cells, a miRNA proposed to mediate innate anti-viral defense
(Lecellier et al., 2005
). RNAi
itself has also been used to block miRNA expression in cultured cells, but its
broad utility is not yet established (Jing
et al., 2005
; Lee et al.,
2005
).
Human viruses also express their own miRNAs
(Pfeffer et al., 2004;
Cai et al., 2005
;
Pfeffer et al., 2005
;
Sullivan et al., 2005
). Viral
miRNAs are proposed to regulate both viral and host gene expression
(Pfeffer et al., 2004
;
Cai et al., 2005
), but only
viral mRNA targets have been experimentally validated
(Pfeffer et al., 2004
).
Recently, Simian Virus 40-encoded miRNAs have been identified. These viral
miRNAs accumulate at late times in infection, and target early viral RNAs for
cleavage and reduce viral susceptibility to cytotoxic T cells
(Sullivan et al., 2005
).
Whether viral miRNAs always mediate the cleavage of viral mRNAs or whether
they can also act more like animal miRNAs to `tune' gene expression remains
unknown.
microPrognostication
A dozen years after their discovery, miRNAs represent a large class of regulators of gene expression that control a broad range of physiological and developmental processes in plants and animals. An immediate challenge is to tabulate the functions of each and every miRNA. For this, improved computational and experimental methods for the identification of miRNA targets will be essential. These efforts will no doubt be informed by our expanding knowledge of the mechanism by which miRNAs recognize and regulate their targets. The regulation of miRNA expression and maturation remains largely unknown, but many laboratories have begun to map where miRNAs are expressed and what factors regulate their transcription. Perhaps the most important goal in understanding miRNAs will be to describe how miRNAs function as a network, for it is in studying the coordinate action of multiple miRNAs on a single mRNA target that we are likely to reach a deeper understanding of the logic of these small but powerful ribo-regulators.
REFERENCES
Allen, E., Xie, Z., Gustafson, A. M. and Carrington, J. C. (2005). microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121,207 -221.[CrossRef][Medline]
Alvarez-Garcia, I. and Miska, E. A. (2005). MicroRNA function: animal development and human disease. Development 132,4653 -4662.[CrossRef]
Bagga, S., Bracht, J., Hunter, S., Massirer, K., Holtz, J., Eachus, R. and Pasquinelli, A. E. (2005). Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 122,553 -563.[CrossRef][Medline]
Bartel, D. P. (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116,281 -297.[CrossRef][Medline]
Baskerville, S. and Bartel, D. P. (2005).
Microarray profiling of microRNAs reveals frequent coexpression with
neighboring miRNAs and host genes. RNA
11,241
-247.
Baumberger, N. and Baulcombe, D. C. (2005).
Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs
and short interfering RNAs. Proc. Natl. Acad. Sci. USA
102,11928
-11933.
Bentwich, I., Avniel, A., Karov, Y., Aharonov, R., Gilad, S., Barad, O., Barzilai, A., Einat, P., Einav, U., Meiri, E. et al. (2005). Identification of hundreds of conserved and nonconserved human microRNAs. Nat. Genet. 37,766 -770.[CrossRef][Medline]
Berezikov, E., Guryev, V., van de Belt, J., Wienholds, E., Plasterk, R. H. and Cuppen, E. (2005). Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120,21 -24.[CrossRef][Medline]
Bernstein, E., Caudy, A. A., Hammond, S. M. and Hannon, G. J. (2001). Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409,363 -366.[CrossRef][Medline]
Bernstein, E., Kim, S. Y., Carmell, M. A., Murchison, E. P., Alcorn, H., Li, M. Z., Mills, A. A., Elledge, S. J., Anderson, K. V. and Hannon, G. J. (2003). Dicer is essential for mouse development. Nat. Genet. 35,215 -217.[CrossRef][Medline]
Bohmert, K., Camus, I., Bellini, C., Bouchez, D., Caboche, M.
and Benning, C. (1998). AGO1 defines a novel locus of
Arabidopsis controlling leaf development. EMBO J.
17,170
-180.
Bohnsack, M. T., Czaplinski, K. and Gorlich, D.
(2004). Exportin 5 is a RanGTP-dependent dsRNA-binding protein
that mediates nuclear export of pre-miRNAs. RNA
10,185
-191.
Boutet, S., Vazquez, F., Liu, J., Beclin, C., Fagard, M., Gratias, A., Morel, J. B., Crete, P., Chen, X. and Vaucheret, H. (2003). Arabidopsis HEN1: a genetic link between endogenous miRNA controlling development and siRNA controlling transgene silencing and virus resistance. Curr. Biol. 13,843 -848.[CrossRef][Medline]
Brennecke, J., Stark, A., Russell, R. B. and Cohen, S. M. (2005). Principles of microRNA-target recognition. PLoS Biol. 3,E85 .[CrossRef][Medline]
Cai, X., Hagedorn, C. H. and Cullen, B. R.
(2004). Human microRNAs are processed from capped, polyadenylated
transcripts that can also function as mRNAs. RNA
10,1957
-1966.
Cai, X., Lu, S., Zhang, Z., Gonzalez, C. M., Damania, B. and
Cullen, B. R. (2005). Kaposi's sarcoma-associated
herpesvirus expresses an array of viral microRNAs in latently infected cells.
Proc. Natl. Acad. Sci. USA
102,5570
-5575.
Calin, G. A., Sevignani, C., Dumitru, C. D., Hyslop, T., Noch,
E., Yendamuri, S., Shimizu, M., Rattan, S., Bullrich, F., Negrini, M.
et al. (2004). Human microRNA genes are frequently located at
fragile sites and genomic regions involved in cancers. Proc. Natl.
Acad. Sci. USA 101,2999
-3004.
Caudy, A. A., Myers, M., Hannon, G. J. and Hammond, S. M.
(2002). Fragile X-related protein and VIG associate with the RNA
interference machinery. Genes Dev.
16,2491
-2496.
Caudy, A. A., Ketting, R. F., Hammond, S. M., Denli, A. M., Bathoorn, A. M., Tops, B. B., Silva, J. M., Myers, M. M., Hannon, G. J. and Plasterk, R. H. (2003). A micrococcal nuclease homologue in RNAi effector complexes. Nature 425,411 -414.[CrossRef][Medline]
Chen, C. Z., Li, L., Lodish, H. F. and Bartel, D. P.
(2004). MicroRNAs modulate hematopoietic lineage differentiation.
Science 303,83
-86.
Chen, P. Y., Manninga, H., Slanchev, K., Chien, M., Russo, J.
J., Ju, J., Sheridan, R., John, B., Marks, D. S., Gaidatzis, D. et
al. (2005). The developmental miRNA profiles of zebrafish as
determined by small RNA cloning. Genes Dev.
19,1288
-1293.
Chendrimada, T. P., Gregory, R. I., Kumaraswamy, E., Norman, J., Cooch, N., Nishikura, K. and Shiekhattar, R. (2005). TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 436.740 -744.[CrossRef][Medline]
Cox, D. N., Chao, A., Baker, J., Chang, L., Qiao, D. and Lin,
H. (1998). A novel class of evolutionarily conserved genes
defined by piwi are essential for stem cell self-renewal. Genes
Dev. 12,3715
-3727.
Cullen, B. R. (2004). Transcription and processing of human microRNA precursors. Mol. Cell 16,861 -865.[CrossRef][Medline]
Davis, E., Caiment, F., Tordoir, X., Cavaille, J., Ferguson-Smith, A., Cockett, N., Georges, M. and Charlier, C. (2005). RNAi-mediated allelic trans-interaction at the imprinted Rtl1/Peg11 locus. Curr. Biol. 15,743 -749.[CrossRef][Medline]
Denli, A. M., Tops, B. B., Plasterk, R. H., Ketting, R. F. and Hannon, G. J. (2004). Processing of primary microRNAs by the Microprocessor complex. Nature 432,231 -235.[CrossRef][Medline]
Ding, L., Spencer, A., Morita, K. and Han, M. (2005). The developmental timing regulator AIN-1 interacts with miRISCs and may target the Argonaute protein ALG-1 to cytoplasmic P Bodies in C. elegans. Mol. Cell 19,437 -447.[CrossRef][Medline]
Doench, J. G., Petersen, C. P. and Sharp, P. A.
(2003). siRNAs can function as miRNAs. Genes
Dev. 17,438
-442.
Eis, P. S., Tam, W., Sun, L., Chadburn, A., Li, Z., Gomez, M.
F., Lund, E. and Dahlberg, J. E. (2005). Accumulation of
miR-155 and BIC RNA in human B cell lymphomas. Proc. Natl. Acad.
Sci. USA 102,3627
-3632.
Enright, A. J., John, B., Gaul, U., Tuschl, T., Sander, C. and Marks, D. S. (2003). MicroRNA targets in Drosophila. Genome Biol. 5,R1 .[CrossRef][Medline]
Forstemann, K., Tomari, Y., Du, T., Vagin, V. V., Denli, A. M., Bratu, D. P., Klattenhoff, C., Theurkauf, W. E. and Zamore, P. D. (2005). Normal microRNA maturation and germ-line stem cell maintenance requires Loquacious, a double-stranded RNA-binding domain protein. PLoS Biol. 3,E236 .[CrossRef][Medline]
Giraldez, A. J., Cinalli, R. M., Glasner, M. E., Enright, A. J.,
Thomson, J. M., Baskerville, S., Hammond, S. M., Bartel, D. P. and
Schier, A. F. (2005). MicroRNAs regulate brain morphogenesis
in zebrafish. Science
308,833
-838.
Gregory, R. I., Yan, K. P., Amuthan, G., Chendrimada, T., Doratotaj, B., Cooch, N. and Shiekhattar, R. (2004). The Microprocessor complex mediates the genesis of microRNAs. Nature 432,235 -240.[CrossRef][Medline]
Grishok, A., Pasquinelli, A. E., Conte, D., Li, N., Parrish, S., Ha, I., Baillie, D. L., Fire, A., Ruvkun, G. and Mello, C. C. (2001). Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106,23 -34.[CrossRef][Medline]
Ha, I., Wightman, B. and Ruvkun, G. (1996). A bulged lin-4/lin-14 RNA duplex is sufficient for Caenorhabditis elegans lin-14 temporal gradient formation. Genes Dev. 10,3041 -3050.[Abstract]
Hammond, S. M., Bernstein, E., Beach, D. and Hannon, G. J. (2000). An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404,293 -296.[CrossRef][Medline]
Hammond, S. M., Boettcher, S., Caudy, A. A., Kobayashi, R. and
Hannon, G. J. (2001). Argonaute2, a link between
genetic and biochemical analyses of RNAi. Science
293,1146
-1150.
Han, J., Lee, Y., Yeom, K. H., Kim, Y. K., Jin, H. and Kim, V.
N. (2004). The Drosha-DGCR8 complex in primary microRNA
processing. Genes Dev.
18,3016
-3027.
Hatfield, S. D., Shcherbata, H. R., Fischer, K. A., Nakahara, K., Carthew, R. W. and Ruohola-Baker, H. (2005). Stem cell division is regulated by the microRNA pathway. Nature 435,974 -978.[CrossRef][Medline]
He, L., Thomson, J. M., Hemann, M. T., Hernando-Monge, E., Mu, D., Goodson, S., Powers, S., Cordon-Cardo, C., Lowe, S. W., Hannon, G. J. et al. (2005). A microRNA polycistron as a potential human oncogene. Nature 435,828 -833.[CrossRef][Medline]
Hutvagner, G. and Zamore, P. D. (2002). A
microRNA in a multiple-turnover RNAi enzyme complex.
Science 297,2056
-2060.
Hutvagner, G., McLachlan, J., Pasquinelli, A. E., Balint, E.,
Tuschl, T. and Zamore, P. D. (2001). A cellular
function for the RNA-interference enzyme Dicer in the maturation of the let-7
small temporal RNA. Science
293,834
-838.
Hutvagner, G., Simard, M. J., Mello, C. C. and Zamore, P. D. (2004). Sequence-specific inhibition of small RNA function. PLoS Biol. 2,E98 .[Medline]
Ishizuka, A., Siomi, M. C. and Siomi, H.
(2002). A Drosophila fragile X protein interacts with components
of RNAi and ribosomal proteins. Genes Dev.
16,2497
-2508.
Jiang, F., Ye, X., Liu, X., Fincher, L., McKearin, D. and Liu,
Q. (2005). Dicer-1 and R3D1-L catalyze microRNA maturation in
Drosophila. Genes Dev.
19,1674
-1679.
Jing, Q., Huang, S., Guth, S., Zarubin, T., Motoyama, A., Chen, J., Di Padova, F., Lin, S. C., Gram, H. and Han, J. (2005). Involvement of microRNA in AU-rich element-mediated mRNA instability. Cell 120,623 -634.[CrossRef][Medline]
Jones-Rhoades, M. W. and Bartel, D. P. (2004). Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell 14,787 -799.[CrossRef][Medline]
Ketting, R. F., Fischer, S. E., Bernstein, E., Sijen, T.,
Hannon, G. J. and Plasterk, R. H. (2001). Dicer
functions in RNA interference and in synthesis of small RNA involved in
developmental timing in C. elegans. Genes Dev.
15,2654
-2659.
Khvorova, A., Reynolds, A. and Jayasena, S. D. (2003). Functional siRNAs and miRNAs exhibit strand bias. Cell 115,209 -216.[CrossRef][Medline]
Kidner, C. A. and Martienssen, R. A. (2005). The developmental role of microRNA in plants. Curr. Opin. Plant Biol. 8,38 -44.[CrossRef][Medline]
Kiriakidou, M., Nelson, P. T., Kouranov, A., Fitziev, P.,
Bouyioukos, C., Mourelatos, Z. and Hatzigeorgiou, A.
(2004). A combined computational-experimental approach predicts
human microRNA targets. Genes Dev.
18,1165
-1178.
Knight, S. W. and Bass, B. L. (2001). A role
for the RNase III enzyme DCR-1 in RNA interference and germ line development
in Caenorhabditis elegans. Science
293,2269
-2271.
Krek, A., Grun, D., Poy, M. N., Wolf, R., Rosenberg, L., Epstein, E. J., MacMenamin, P., da Piedade, I., Gunsalus, K. C., Stoffel, M. et al. (2005). Combinatorial microRNA target predictions. Nat. Genet. 37,495 -500.[CrossRef][Medline]
Lagos-Quintana, M., Rauhut, R., Lendeckel, W. and Tuschl, T.
(2001). Identification of novel genes coding for small expressed
RNAs. Science 294,853
-858.
Lai, E. C. (2002). Micro RNAs are complementary to 3' UTR sequence motifs that mediate negative post-transcriptional regulation. Nat. Genet. 30,363 -364.[CrossRef][Medline]
Lai, E. C. (2004). Predicting and validating microRNA targets. Genome Biol. 5, 115.[CrossRef][Medline]
Lai, E. C. and Posakony, J. W. (1997). The
Bearded box, a novel 3' UTR sequence motif, mediates negative
post-transcriptional regulation of Bearded and Enhancer of split Complex gene
expression. Development
124,4847
-4856.
Lai, E. C., Burks, C. and Posakony, J. W.
(1998). The K box, a conserved 3' UTR sequence motif,
negatively regulates accumulation of enhancer of split complex transcripts.
Development 125,4077
-4088.
Lai, E. C., Tomancak, P., Williams, R. W. and Rubin, G. M. (2003). Computational identification of Drosophila microRNA genes. Genome Biol. 4,R42 .[CrossRef][Medline]
Lai, E. C., Tam, B. and Rubin, G. M. (2005).
Pervasive regulation of Drosophila Notch target genes by GY-box-, Brd-box-,
and K-box-class microRNAs. Genes Dev.
19,1067
-1080.
Landthaler, M., Yalcin, A. and Tuschl, T. (2004). The human DiGeorge syndrome critical region gene 8 and Its D. melanogaster homolog are required for miRNA biogenesis. Curr. Biol. 14,2162 -2167.[CrossRef][Medline]
Lau, N. C., Lim, L. P., Weinstein, E. G. and Bartel, D. P.
(2001). An abundant class of tiny RNAs with probable regulatory
roles in Caenorhabditis elegans. Science
294,858
-862.
Leaman, D., Chen, P. Y., Fak, J., Yalcin, A., Pearce, M., Unnerstall, U., Marks, D. S., Sander, C., Tuschl, T. and Gaul, U. (2005). Antisense-mediated depletion reveals essential and specific functions of microRNAs in Drosophila development. Cell 121,1097 -1108.[CrossRef][Medline]
Lecellier, C. H., Dunoyer, P., Arar, K., Lehmann-Che, J.,
Eyquem, S., Himber, C., Saib, A. and Voinnet, O.
(2005). A cellular microRNA mediates antiviral defense in human
cells. Science 308,557
-560.
Lee, R. C. and Ambros, V. (2001). An extensive
class of small RNAs in Caenorhabditis elegans. Science
294,862
-864.
Lee, R. C., Feinbaum, R. L. and Ambros, V. (1993). The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75,843 -854.[CrossRef][Medline]
Lee, Y., Jeon, K., Lee, J. T., Kim, S. and Kim, V. N.
(2002). MicroRNA maturation: stepwise processing and subcellular
localization. EMBO J.
21,4663
-4670.
Lee, Y., Ahn, C., Han, J., Choi, H., Kim, J., Yim, J., Lee, J., Provost, P., Radmark, O., Kim, S. et al. (2003). The nuclear RNase III Drosha initiates microRNA processing. Nature 425,415 -419.[CrossRef][Medline]
Lee, Y., Kim, M., Han, J., Yeom, K. H., Lee, S., Baek, S. H. and
Kim, V. N. (2004). MicroRNA genes are transcribed by
RNA polymerase II. EMBO J.
23,4051
-4060.
Lee, Y. S., Kim, H. K., Chung, S., Kim, K. S. and Dutta, A.
(2005). Depletion of human micro-RNA miR-125b reveals that it is
critical for the proliferation of differentiated cells but not for the
down-regulation of putative targets during differentiation. J.
Biol. Chem. 280,16635
-16641.
Lewis, B. P., Shih, I. H., Jones-Rhoades, M. W., Bartel, D. P. and Burge, C. B. (2003). Prediction of mammalian microRNA targets. Cell 115,787 -798.[CrossRef][Medline]
Lewis, B. P., Burge, C. B. and Bartel, D. P. (2005). Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120,15 -20.[CrossRef][Medline]
Lim, L. P., Glasner, M. E., Yekta, S., Burge, C. B. and Bartel,
D. P. (2003a). Vertebrate microRNA genes.
Science 299,1540
.
Lim, L. P., Lau, N. C., Weinstein, E. G., Abdelhakim, A., Yekta,
S., Rhoades, M. W., Burge, C. B. and Bartel, D. P.
(2003b). The microRNAs of Caenorhabditis elegans.
Genes Dev. 17,991
-1008.
Lim, L. P., Lau, N. C., Garrett-Engele, P., Grimson, A., Schelter, J. M., Castle, J., Bartel, D. P., Linsley, P. S. and Johnson, J. M. (2005). Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433,769 -773.[CrossRef][Medline]
Lin, S. Y., Johnson, S. M., Abraham, M., Vella, M. C., Pasquinelli, A., Gamberi, C., Gottlieb, E. and Slack, F. J. (2003). The C. elegans hunchback homolog, hbl-1, controls temporal patterning and is a probable microRNA target. Dev. Cell 4,639 -650.[CrossRef][Medline]
Lingel, A., Simon, B., Izaurralde, E. and Sattler, M. (2004). Nucleic acid 3'-end recognition by the Argonaute2 PAZ domain. Nat. Struct. Mol. Biol. 11,576 -577.[CrossRef][Medline]
Liu, J., Carmell, M. A., Rivas, F. V., Marsden, C. G., Thomson,
J. M., Song, J. J., Hammond, S. M., Joshua-Tor, L. and Hannon, G.
J. (2004). Argonaute2 is the catalytic engine of mammalian
RNAi. Science 305,1437
-1441.
Liu, J., Valencia-Sanchez, M. A., Hannon, G. J. and Parker, R. (2005). MicroRNA-dependent localization of targeted mRNAs to mammalian P-bodies. Nat. Cell Biol. 7, 719-723[CrossRef][Medline]
Llave, C., Xie, Z., Kasschau, K. D. and Carrington, J. C.
(2002). Cleavage of Scarecrow-like mRNA targets directed by a
class of Arabidopsis miRNA. Science
297,2053
-2056.
Lund, E., Guttinger, S., Calado, A., Dahlberg, J. E. and Kutay,
U. (2004). Nuclear export of microRNA precursors.
Science 303,95
-98.
Ma, J. B., Yuan, Y. R., Meister, G., Pei, Y., Tuschl, T. and Patel, D. J. (2005). Structural basis for 5'-end-specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature 434,666 -670.[CrossRef][Medline]
Mansfield, J. H., Harfe, B. D., Nissen, R., Obenauer, J., Srineel, J., Chaudhuri, A., Farzan-Kashani, R., Zuker, M., Pasquinelli, A. E., Ruvkun, G. et al. (2004). MicroRNA-responsive `sensor' transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression. Nat. Genet. 36,1079 -1083.[CrossRef][Medline]
Meister, G., Landthaler, M., Dorsett, Y. and Tuschl, T.
(2004a). Sequence-specific inhibition of microRNA- and
siRNA-induced RNA silencing. RNA
10,544
-550.
Meister, G., Landthaler, M., Patkaniowska, A., Dorsett, Y., Teng, G. and Tuschl, T. (2004b). Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol. Cell 15,185 -197.[CrossRef][Medline]
Mourelatos, Z., Dostie, J., Paushkin, S., Sharma, A., Charroux,
B., Abel, L., Rappsilber, J., Mann, M. and Dreyfuss, G.
(2002). miRNPs: a novel class of ribonucleoproteins containing
numerous microRNAs. Genes Dev.
16,720
-728.
Moussian, B., Schoof, H., Haecker, A., Jurgens, G. and Laux,
T. (1998). Role of the ZWILLE gene in the regulation of
central shoot meristem cell fate during Arabidopsis embryogenesis.
EMBO J. 17,1799
-1809.
Nowotny, M., Gaidamakov, S. A., Crouch, R. J. and Yang, W. (2005). Crystal structures of RNase H Bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis. Cell 121,1005 -1016.[CrossRef][Medline]
Olsen, P. H. and Ambros, V. (1999). The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Dev. Biol. 216,671 -680.[CrossRef][Medline]
Papp, I., Mette, M. F., Aufsatz, W., Daxinger, L., Schauer, S.
E., Ray, A., van der Winden, J., Matzke, M. and Matzke, A. J.
(2003). Evidence for nuclear processing of plant micro RNA and
short interfering RNA precursors. Plant Physiol.
132,1382
-1390.
Parizotto, E. A., Dunoyer, P., Rahm, N., Himber, C. and Voinnet,
O. (2004). In vivo investigation of the transcription,
processing, endonucleolytic activity, and functional relevance of the spatial
distribution of a plant miRNA. Genes Dev.
18,2237
-2242.
Park, M. Y., Wu, G., Gonzalez-Sulser, A., Vaucheret, H. and
Poethig, R. S. (2005). Nuclear processing and export
of microRNAs in Arabidopsis. Proc. Natl. Acad. Sci.
USA 102,3691
-3696.
Park, W., Li, J., Song, R., Messing, J. and Chen, X. (2002). CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr. Biol. 12,1484 -1495.[CrossRef][Medline]
Parker, J. S., Roe, S. M. and Barford, D.
(2004). Crystal structure of a PIWI protein suggests mechanisms
for siRNA recognition and slicer activity. EMBO J.
23,4727
-4737.
Parker, J. S., Roe, S. M. and Barford, D. (2005). Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex. Nature 434,663 -666.[CrossRef][Medline]
Pasquinelli, A. E., Reinhart, B. J., Slack, F., Martindale, M. Q., Kuroda, M. I., Maller, B., Hayward, D. C., Ball, E. E., Degnan, B., Muller, P. et al. (2000). Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408,86 -89.[CrossRef][Medline]
Peragine, A., Yoshikawa, M., Wu, G., Albrecht, H. L. and
Poethig, R. S. (2004). SGS3 and SGS2/SDE1/RDR6 are required
for juvenile development and the production of trans-acting siRNAs in
Arabidopsis. Genes Dev.
18,2368
-2379.
Pfeffer, S., Zavolan, M., Grasser, F. A., Chien, M., Russo, J.
J., Ju, J., John, B., Enright, A. J., Marks, D., Sander, C. et al.
(2004). Identification of virus-encoded microRNAs.
Science 304,734
-736.
Pfeffer, S., Sewer, A., Lagos-Quintana, M., Sheridan, R., Sander, C., Grasser, F. A., van Dyk, L. F., Ho, C. K., Shuman, S., Chien, M. et al. (2005). Identification of microRNAs of the herpesvirus family. Nat. Methods 2, 269-276.[CrossRef][Medline]
Pillai, R. S., Bhattacharyya, S. N., Artus, C. G., Zoller, T.,
Cougot, N., Basyuk, E., Bertrand, E. and Filipowicz, W.
(2005). Inhibition of translational initiation by let-7 microRNA
in human cells. Science
309,1573
-1576.
Poy, M. N., Eliasson, L., Krutzfeldt, J., Kuwajima, S., Ma, X., Macdonald, P. E., Pfeffer, S., Tuschl, T., Rajewsky, N., Rorsman, P. et al. (2004). A pancreatic islet-specific microRNA regulates insulin secretion. Nature 432,226 -230.[CrossRef][Medline]
Qi, Y., Denli, A. M. and Hannon, G. J. (2005). Biochemical Specialization within Arabidopsis RNA Silencing Pathways. Mol. Cell 19,421 -428.[CrossRef][Medline]
Rajewsky, N. and Socci, N. D. (2004). Computational identification of microRNA targets. Dev. Biol. 267,529 -535.[CrossRef][Medline]
Rand, T. A., Ginalski, K., Grishin, N. V. and Wang, X.
(2004). Biochemical identification of Argonaute 2 as the sole
protein required for RNA-induced silencing complex activity. Proc.
Natl. Acad. Sci. USA 101,14385
-14389.
Reinhart, B. J., Slack, F. J., Basson, M., Pasquinelli, A. E., Bettinger, J. C., Rougvie, A. E., Horvitz, H. R. and Ruvkun, G. (2000). The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403,901 -906.[CrossRef][Medline]
Reinhart, B. J., Weinstein, E. G., Rhoades, M. W., Bartel, B.
and Bartel, D. P. (2002). MicroRNAs in plants.
Genes Dev. 16,1616
-1626.
Rhoades, M. W., Reinhart, B. J., Lim, L. P., Burge, C. B., Bartel, B. and Bartel, D. P. (2002). Prediction of plant microRNA targets. Cell 110,513 -520.[CrossRef][Medline]
Riechmann, J. L., Heard, J., Martin, G., Reuber, L., Jiang, C.,
Keddie, J., Adam, L., Pineda, O., Ratcliffe, O. J., Samaha, R. R. et
al. (2000). Arabidopsis transcription factors: genome-wide
comparative analysis among eukaryotes. Science
290,2105
-2110.
Rivas, F. V., Tolia, N. H., Song, J. J., Aragon, J. P., Liu, J., Hannon, G. J. and Joshua-Tor, L. (2005). Purified Argonaute2 and an siRNA form recombinant human RISC. Nat. Struct. Mol. Biol. 12,340 -349.[CrossRef][Medline]
Rodriguez, A., Griffiths-Jones, S., Ashurst, J. L. and Bradley,
A. (2004). Identification of mammalian microRNA host genes
and transcription units. Genome Res.
14,1902
-1910.
Rougvie, A. D. (2005). Keeping time with
microRNAs. Development,
132.3787
-3798.
Saito, K., Ishizuka, A., Siomi, H. and Siomi, M. C. (2005). Processing of pre-microRNAs by the dicer-1-loquacious complex in Drosophila cells. PLoS Biol. 3, E235.[CrossRef][Medline]
Schwarz, D. S., Hutvagner, G., Du, T., Xu, Z., Aronin, N. and Zamore, P. D. (2003). Asymmetry in the assembly of the RNAi enzyme complex. Cell 115,199 -208.[CrossRef][Medline]
Sen, G. L. and Blau, H. M. (2005). Argonaute 2/RISC resides in sites of mammalian mRNA decay known as cytoplasmic bodies. Nat. Cell. Biol. 7,633 -636.[CrossRef][Medline]
Slack, F. J., Basson, M., Liu, Z., Ambros, V., Horvitz, H. R. and Ruvkun, G. (2000). The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor. Mol. Cell 5, 659-669.[CrossRef][Medline]
Song, J. J., Liu, J., Tolia, N. H., Schneiderman, J., Smith, S. K., Martienssen, R. A., Hannon, G. J. and Joshua-Tor, L. (2003). The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nat. Struct. Biol. 10,1026 -1032.[CrossRef][Medline]
Song, J. J., Smith, S. K., Hannon, G. J. and Joshua-Tor, L.
(2004). Crystal structure of Argonaute and its implications for
RISC slicer activity. Science
305,1434
-1437.
Stark, A., Brennecke, J., Russell, R. B. and Cohen, S. M. (2003). Identification of Drosophila MicroRNA targets. PLoS Biol. 1,E60 .[Medline]
Sullivan, C. S., Grundhoff, A. T., Tevethia, S., Pipas, J. M. and Ganem, D. (2005). SV40-encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells. Nature 435,682 -686.[CrossRef][Medline]
Tang, G., Reinhart, B. J., Bartel, D. P. and Zamore, P. D.
(2003). A biochemical framework for RNA silencing in plants.
Genes Dev. 17,49
-63.
Tomari, Y. and Zamore, P. D. (2005).
Perspective: machines for RNAi. Genes Dev.
19,517
-529.
Vaucheret, H., Vazquez, F., Crete, P. and Bartel, D. P.
(2004). The action of ARGONAUTE1 in the miRNA pathway and its
regulation by the miRNA pathway are crucial for plant development.
Genes Dev. 18,1187
-1197.
Vazquez, F., Gasciolli, V., Crete, P. and Vaucheret, H. (2004a). The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing. Curr. Biol. 14,346 -351.[CrossRef][Medline]
Vazquez, F., Vaucheret, H., Rajagopalan, R., Lepers, C., Gasciolli, V., Mallory, A. C., Hilbert, J. L., Bartel, D. P. and Crete, P. (2004b). Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol. Cell 16, 69-79.[CrossRef][Medline]
Vella, M. C., Choi, E. Y., Lin, S. Y., Reinert, K. and Slack, F.
J. (2004). The C. elegans microRNA let-7 binds to imperfect
let-7 complementary sites from the lin-41 3'UTR. Genes
Dev. 18,132
-137.
Wienholds, E., Koudijs, M. J., van Eeden, F. J., Cuppen, E. and Plasterk, R. H. (2003). The microRNA-producing enzyme Dicer1 is essential for zebrafish development. Nat. Genet. 35,217 -218.[CrossRef][Medline]
Wienholds, E., Kloosterman, W. P., Miska, E., Alvarez-Saavedra,
E., Berezikov, E., de Bruijn, E., Horvitz, R. H., Kauppinen, S. and
Plasterk, R. H. (2005). MicroRNA expression in zebrafish
embryonic development. Science
309,310
-311.
Wightman, B., Ha, I. and Ruvkun, G. (1993). Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75,855 -862.[CrossRef][Medline]
Xie, X., Lu, J., Kulbokas, E. J., Golub, T. R., Mootha, V., Lindblad-Toh, K., Lander, E. S. and Kellis, M. (2005). Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature 434,338 -345.[CrossRef][Medline]
Xie, Z., Kasschau, K. D. and Carrington, J. C. (2003). Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradation. Curr. Biol. 13,784 -789.[CrossRef][Medline]
Xie, Z., Johansen, L. K., Gustafson, A. M., Kasschau, K. D., Lellis, A. D., Zilberman, D., Jacobsen, S. E. and Carrington, J. C. (2004). Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2, E104.[CrossRef][Medline]
Yan, K. S., Yan, S., Farooq, A., Han, A., Zeng, L. and Zhou, M. M. (2003). Structure and conserved RNA binding of the PAZ domain. Nature 426,468 -474.[CrossRef][Medline]
Yekta, S., Shih, I. H. and Bartel, D. P.
(2004). MicroRNA-directed cleavage of HOXB8 mRNA.
Science 304,594
-596.
Yi, R., Qin, Y., Macara, I. G. and Cullen, B. R.
(2003). Exportin-5 mediates the nuclear export of pre-microRNAs
and short hairpin RNAs. Genes Dev.
17,3011
-3016.
Yu, B., Yang, Z., Li, J., Minakhina, S., Yang, M., Padgett, R.
W., Steward, R. and Chen, X. (2005). Methylation as a
crucial step in plant microRNA biogenesis. Science
307,932
-935.
Zeng, Y. and Cullen, B. R. (2003). Sequence
requirements for micro RNA processing and function in human cells.
RNA 9,112
-123.
Zeng, Y. and Cullen, B. R. (2004). Structural
requirements for pre-microRNA binding and nuclear export by Exportin 5.
Nucleic Acids Res. 32,4776
-4785.
Zeng, Y. and Cullen, B. R. (2005). Efficient
processing of primary microRNA hairpins by Drosha requires flanking
non-structured RNA sequences. J. Biol. Chem.
280,27595
-27603.
Zeng, Y., Wagner, E. J. and Cullen, B. R. (2002). Both natural and designed micro RNAs can inhibit the expression of cognate mRNAs when expressed in human cells. Mol. Cell 9,1327 -1333.[CrossRef][Medline]
Zeng, Y., Yi, R. and Cullen, B. R. (2005).
Recognition and cleavage of primary microRNA precursors by the nuclear
processing enzyme Drosha. EMBO J.
24,138
-148.
Zhang, Y. (2005). miRU: an automated plant
miRNA target prediction server. Nucleic Acids Res.
33,W701
-W704.
Zhao, Y., Samal, E. and Srivastava, D. (2005). Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 436,214 -220.[CrossRef][Medline]