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Review in translational hematology

MicroRNAs: regulators of gene expression and cell differentiation

Ramesh A. Shivdasani

The existence and roles of a class of
abundant regulatory RNA molecules have
recently come into sharp focus. Micro-
RNAs (miRNAs) are small (approximately
22 bases), non–protein-coding RNAs that
recognize target sequences of imperfect
complementarity in cognate mRNAs and
either destabilize them or inhibit protein
translation. Although mechanisms of
miRNA biogenesis have been elucidated
in some detail, there is limited apprecia-
tion of their biological functions. Re-
ported examples typically focus on miRNA
regulation of a single tissue-restricted
transcript, often one encoding a transcrip-
tion factor, that controls a specific aspect
of development, cell differentiation, or
physiology. However, computational algo-
rithms predict up to hundreds of putative
targets for individual miRNAs, single tran-
scripts may be regulated by multiple mi-
RNAs, and miRNAs may either eliminate
target gene expression or serve to fine-
tune transcript and protein levels. Theo-
retical considerations and early experi-
mental results hence suggest diverse
roles for miRNAs as a class. One appeal-
ing possibility, that miRNAs eliminate low-
level expression of unwanted genes and
hence refine unilineage gene expression,
may be especially amenable to evaluation
in models of hematopoiesis. This review
summarizes current understanding of
miRNA mechanisms, outlines some of
the important outstanding questions, and
describes studies that attempt to define
miRNA functions in hematopoiesis.
(Blood. 2006;108:3646-3653)
© 2006 by The American Society of Hematology

miRNAs, the sounds of (gene) silence

MicroRNAs (miRNAs) are small, often phylogenetically con-
served, non–protein-coding RNAs that mediate posttranscriptional
gene repression by inhibiting protein translation or by destabilizing
target transcripts. miRNAs recognize target sites, most commonly
found in the 3⬘-untranslated regions (UTRs) of cognate mRNAs,
through imperfect base-pairing, with 1 or more mismatches in
sequence complementarity. miRNAs are believed to fine-regulate a
diverse array of biological processes, and a convergence of genetic,
biochemical, and structural studies has led to rapid growth in
understanding of their synthesis and molecular mechanisms. In
contrast, the precise biological functions of these approximately
22-base RNA products are less clear. To date, only a handful of
studies provide definitive evidence of a role for a specific miRNA
in vertebrate biology, although such roles are probably pervasive.
The limits on current appreciation simply reflect the infancy of the
field, and it is safe to predict a vast growth in functional studies that
will refine understanding of the roles of individual miRNAs.
The history and general features of miRNAs have been
reviewed extensively in a number of different contexts.1-3 Here I
review the biogenesis and mechanisms of miRNAs briefly before
exploring the current appreciation of the role of miRNAs in cell
differentiation, with emphasis on hematopoiesis. Many of the
general and biochemical insights derive from experiments con-
ducted in worms and flies, and these studies are discussed when
appropriate. Although investigation in invertebrate species also
provides many functional insights,4 this review will focus on
miRNA functions in vertebrate animals.
The first miRNAs, lin-4 and let-7, were each identified, some 7
years apart, on the basis of their mutant phenotypes in forward
genetic screens in the worm Caenorhabditis elegans. Both entities
control developmental timing by repressing translation of their
respective targets, the protein-coding mRNA products of the lin-14
and lin-41 genes.5,6 Although posttranscriptional gene silencing by
small regulatory RNAs was initially regarded as a biological
curiosity, perhaps restricted to certain lower species, we now know
that many multicellular organisms express hundreds of miRNAs
that vary in abundance across cell and tissue types.7-10 miRNAs are
found in multicellular plant and animal species but not in unicellu-
lar organisms such as yeast. By definition, miRNAs correspond to
cloned small RNAs that, like the lin-4 and let-7 products, are
processed from stem-loop precursors transcribed from genes other
than the ones they regulate. Endogenous small RNAs that do not
meet these criteria and are known collectively as small-interfering
RNAs (siRNAs) derive from long double-stranded RNA (dsRNA)
precursors that in some species may be transcribed from repeat
elements, heterochromatin, or transposons.3 The 2 classes of short
regulatory RNAs differ mainly in their origins and not in their
functions,11 which may be grouped under the single moniker of
RNA interference (RNAi), although siRNA sequences are usually
perfectly complementary to those of their RNA targets (Figure 1).
Salient concepts in miRNA function
In zebrafish development, where miRNA expression dynamics are
the best characterized to date, most miRNAs appear relatively late
in embryogenesis and reveal tissue-specific distributions and
requirements.12-14 In certain mammalian organs, including bone
marrow, a handful of tissue-specific miRNAs tend to dominate the
miRNA expression profile,10,15 and in a limited analysis of mouse
miRNAs, expression profiles differed between fetal and adult
forms of the same tissue.16 Taken together with the original

From the Department of Medical Oncology, Dana-Farber Cancer Institute, as Blood First Edition Paper, August 1, 2006; DOI 10.1182/blood-2006-
Boston, MA; and the Departments of Medicine, Brigham & Women’s Hospital 01-030015.
and Harvard Medical School, Boston, MA.

Submitted January 30, 2006; accepted July 18, 2006. Prepublished online © 2006 by The American Society of Hematology

3646 BLOOD, 1 DECEMBER 2006 䡠 VOLUME 108, NUMBER 12

 From www.bloodjournal.org by guest on March 11, 2018. For personal use only.
BLOOD, 1 DECEMBER 2006 䡠 VOLUME 108, NUMBER 12
Figure 1. miRNAs and siRNAs: differences in biogenesis and
properties. siRNAs (left) derive from long endogenous dsRNA
molecules that form either long hairpins or bimolecular duplexes.
Processing of these dsRNA precursors can generate many
different siRNAs from both strands. In contrast, processing of the
shorter hairpin structures known as pre-miRNAs (right) produces
a single miRNA molecule from one arm of the hairpin precursor.
siRNAs recognize their target transcripts with perfect sequence
complementarity (left), whereas miRNAs typically have a limited
number of mismatches with their mRNA target sequences (right).
Both classes of small regulatory RNA molecules cause posttran-
scriptional silencing of protein-coding genes.
identification of worm miRNAs as regulators of developmental
timing, such observations have led to the notion that a principal
function of miRNAs is to control cell differentiation and develop-
ment. Indeed, mouse embryonic stem cells with an engineered
inability to synthesize miRNAs are viable but fail to differentiate,
and zebrafish embryos that are unable to produce mature miRNAs
develop normally at first but display specific morphogenetic
defects during gastrulation and organogenesis.13,17 Specific and
prominent miRNA functions are illustrated in part by the roles of
miR-196 in vertebrate limb development,18 of the miR-1 cluster in
cardiomyocyte differentiation,19 and of miR-181 in maintaining a
balance between circulating T and B lymphocytes.15 However,
miRNAs are expressed widely in developing and adult tissues and
their functions are likely to be widespread, diverse, and ranging
from seminal to subtle depending on the context.
In the best-studied examples in worms and mammals, miRNAs
control key developmental processes by inhibiting just one or a few
mRNA targets. As we shall see, however, the typical miRNA can
potentially regulate dozens or scores of genes,20,21 and most targets
contain isolated miRNA recognition sites that may be inadequate
for complete gene silencing. These considerations prompted Bartel
and Chen to propose the presence of selective pressure on many
genes to avoid undesirable interference from miRNAs that are both
widespread and have limited complementarity requirements.22
Stark and colleagues recently reported that genes that seem to avoid
miRNA regulation (“antitargets”) tend to function in processes
common to all cells, whereas putative targets are more commonly
implicated in developmental processes, especially organogenesis.23
In several tested examples in Drosophila embryos, miRNAs and
some predicted targets are indeed expressed in nonoverlapping
adjacent distributions, whereas miRNAs and antitargets are coex-
pressed. Farh et al24 found similar results for targets and antitargets
of mammalian miRNAs, although in their analyses the predicted
targets were present at lower levels in tissues with the cognate
miRNAs and not excluded altogether. Furthermore, in a temporal
analysis of mouse myotube differentiation, they showed that
predicted targets of tissue-specific miR-1 and miR-133 were highly
expressed before these miRNAs accumulated and subsequently,
these targets were down-regulated. Together, these observations
raise the possibility that some transcripts are predisposed to appear
or persist in domains where they are unnecessary or potentially
harmful; miRNAs may have evolved to fine-tune gene expression
programs and to eliminate gene products more rapidly than might
miRNA REGULATION OF HEMATOPOIESIS 3647
occur by intrinsic decay. This particular role may be especially
pertinent in hematopoiesis. In a process known as multilineage
gene priming, immature blood progenitors initially activate a leaky
and promiscuous transcriptional program; as cells commit to a
restricted fate, unilineage gene expression is reinforced and tran-
scripts affiliated with alternative blood cell types disappear.25 It is
tempting to speculate that miRNAs drive the latter phase, an idea
that is as yet untested.
Animal genomes not only encode a large number of tissue-
restricted miRNAs, but these miRNAs can be expressed in high,
albeit variable, abundance, with estimates in C elegans ranging
from 800 to 50 000 molecules per cell.26 Coupled with the limited
evolutionary constraints on small non–protein-coding genes,
miRNAs may be positioned ideally to regulate tissue-specific gene
expression. As the latter function lies at the heart of cell differentia-
tion, it is fair to speculate that miRNAs as a class play a vital role in
generating and maintaining distinctive cell lineages in all multicel-
lular species. However, forward genetic screens in C elegans and
Drosophila have yielded very few miRNAs, possibly reflecting the
small size of the coding unit, subtlety in mutant phenotypes, and a
substantial degree of functional redundancy. Instead, current cata-
logs of miRNAs derive largely from the results of cDNA cloning.
In May 2006, a unified database (miRBase)27 recognized 462 and
340 individual miRNAs in the human and mouse, respectively.
Nomenclature and annotation for all species are assigned and
managed centrally, with the “miR” designation followed by a
unique identifying number.11,28 Identical miRNAs are given the
same number, regardless of organism, as are nearly identical
sequences that are presumed to represent orthologous miRNAs. Highly
similar miRNAs within a species also are assigned the same
number, with their genes distinguished by letter suffixes
(eg, miR-181a).
miRNA biogenesis and mechanisms of
posttranscriptional gene repression
Mature miRNAs are 18 to 26 nucleotides in length, with 5⬘-
phosphate and 3⬘-hydroxyl groups. Their immediate precursors,
called pre-miRNAs, are characteristic stem-loop structures 60 to 80
bases in length with a 2-nucleotide 3⬘ overhang. In turn, pre-
miRNAs derive from long primary miRNA transcripts (pri-
miRNAs), which can exceed 1 kb and typically are products of
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3648 SHIVDASANI
RNA polymerase II activity.29,30 Most pri-miRNAs are independent
transcriptional units, although many mammalian miRNAs are
encoded within mRNA introns and appear to share the same
primary transcripts as their protein-coding host genes. MicroRNAs
show highest evolutionary conservation in the stem, with variable
divergence within the loop.26,31 Although conservation drops sharply in
sequences flanking the miRNA hairpin,31 these regions are neverthe-
less required for nuclear processing of the primary transcript.15
Pri-miRNAs are first processed in the nucleus into 50- to
80-base pre-miRNA stem-loops by the Microprocessor complex of
nucleases and associated factors, including the RNase III Drosha
and its partner DGCR8/Pasha (Figure 2).32,33 Pre-miRNA mol-
ecules, in association with the Ran-GTP–dependent factor expor-
tin-5, are actively transported into the cytoplasm, where a second
RNase III–like nuclease, Dicer, processes them further into du-
plexes that contain the 20- to 24-nucleotide mature miRNA and an
oligonucleotide of similar size from the other arm of the hair-
pin.34-37 The nascent miRNA may be present on either arm of the
stem-loop precursor, but each pre-miRNA yields a single mature
miRNA product. Gaps, bulges, and mismatches in the secondary
structure of pre-miRNAs are predicted to reduce their stability and
to influence the efficiency by which they are processed to produce
mature miRNAs.38 The functional element in the precursor duplex
is determined when, after unwinding, one of the 2 strands is loaded
asymmetrically into the RNA-induced silencing complex (RISC);
this tends to be the strand in which the 5⬘ end is less tightly paired
to its complement.39,40
Similar thermodynamic considerations apply to the interactions
between mature miRNAs and their protein-coding RNA targets.
Thus, the ability of a miRNA to repress cognate mRNAs is
determined in large part by the free energy of binding of nucleo-
tides 2 to 8, counted from the 5⬘ end, with substantially lesser
contribution from the 3⬘ region of the miRNA.41 Nucleotides 2 to 8
are hence regarded as the “seed” for miRNA target recognition, and
evolutionary conservation of complementarity with this relatively
small region has served as a key basis for computational prediction
of target genes. Conserved adenosine residues tend to flank the
complementary region, which implies that primary sequence determi-
nants and base-pairing combine to specify target recognition.21,42
In their size and chemistry, miRNAs resemble siRNAs, which
in invertebrates recognize targets by precise complementarity and
elicit their decay. As depicted in Figure 1, these 2 classes of small,
noncoding RNAs derive from distinct classes of immediate precur-
BLOOD, 1 DECEMBER 2006 䡠 VOLUME 108, NUMBER 12
sors: long (hundreds to thousands of bases) double-stranded
molecules in the case of siRNA and, in the case of miRNA, shorter
(60- to 80-nucleotide) pre-miRNA stem-loop products. However,
both the production and functions of these diverse small RNAs
require many common factors: endonucleases such as Dicer, which
specifically cleave double-stranded RNA, and small RNA-binding
proteins of the Argonaute family, which direct target molecules into
the RISC ribonuclear complex.34 Moreover, the mRNA degrada-
tion apparatus, including RISC complexes, localizes in discrete
cytoplasmic “processing” or “P” bodies (also known as GW
bodies), where transcripts targeted by miRNAs were shown
recently to concentrate in a miRNA-dependent manner.43 Thus, like
siRNA-induced mRNA degradation, apparent repression of transla-
tion by miRNAs also involves delivery of transcripts to P-bodies,
which lack ribosomal components; this relocation could be a
consequence or, alternatively, serve as the basis for inhibiting
protein translation.
Early work suggested that siRNAs operate to eliminate their
mRNA targets, whereas miRNAs commonly preserve target tran-
script levels and were thereby inferred to block protein translation.
The distinctions between siRNAs and miRNAs continue to blur,
and miRNAs are now recognized to facilitate both translational
inhibition and mRNA degradation.44,45 Localization of the RISC
complex in P-bodies may help in understanding the apparent
differences, and miRNA-mediated transcript degradation may represent
a secondary consequence of sequestration within P-bodies.3,43 Steady-
state levels of transcripts with a high intrinsic decay rate may overtly
reveal a substantial decline, whereas inherently stable mRNAs
might persist in the cell; however, both transcript classes are
probably equally subject to translational repression.
An insightful study recently shed light on several questions that
are pertinent to this review. After delivering miR-124 into HeLa
cells, Lim and colleagues observed a shift in the expression profile
toward that of brain, the site where endogenous miR-124 is most
abundant; similarly, transfection of miR-1 shifted the profile
toward that of muscle, where miR-1 is preferentially expressed.45
Taken at face value, even in the absence of a clear molecular
mechanism, these results implicate selected miRNAs in aspects of
gene regulation that are central to cellular identity. Notably, in each
case, the levels of dozens of transcripts declined within 12 hours,
and the 3⬘-UTRs of affected mRNAs were enriched for sequences
complementary to the 5⬘ ends of the cognate miRNAs. Thus, some
Figure 2. miRNA biogenesis and action. Most pri-mRNAs are the
products of independent genes, transcribed by RNA polymerase II.
The nuclear Microprocessor protein complex, which contains the
RNase III Drosha and its partner DGCR8/Pasha, cleaves pri-miRNAs
into 50- to 80-base pre-miRNA stem-loop moieties. The Ran-GTP–
dependent factor exportin-5 actively transports pre-miRNAs into the
cytoplasm, where the nuclease Dicer processes them further into
duplexes that contain the 20- to 24-nucleotide mature miRNA; each
pre-miRNA usually yields a single mature miRNA product. The
functional strand is determined when one of the 2 strands of the duplex
is loaded into the RISC, which contains Argonaute and related
proteins and localizes in cytoplasmic P-bodies. Recognition of target
mRNAs by partial sequence complementarity to the miRNA results in
posttranscriptional gene repression by some combination of transcript
degradation and translational inhibition.
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BLOOD, 1 DECEMBER 2006 䡠 VOLUME 108, NUMBER 12
of the down-regulated transcripts may be targets for direct miRNA-
mediated degradation, an effect distinct from the purportedly main
role of miRNAs in inhibiting protein translation. Moreover, at least
miR-1 and miR-124, but probably other tissue-specific miRNAs,
seem to regulate a large number of transcripts directly. It is thus
conceivable that establishing or maintaining cell identity depends
in part on fine regulation of lineage-specific gene expression by a
few key miRNAs.
Cardinal differentiation functions have traditionally been attrib-
uted to lineage-restricted transcription factors (TFs); either the TFs
themselves or their tissue-specific outputs, or both, are hence the
best candidates for direct miRNA regulation. In this light, it is
interesting that although current predictions of putative miRNA
targets cover a broad range of molecular functions,20,21 the early
sets are enriched for TF-coding genes,42,46 and validated examples
of miRNA function also emphasize their roles in regulating
tissue-restricted TFs such as NF-I, Hand2, and HoxB8.18,19,44,47
However, these examples reflect a certain investigation bias and
miRNA functions clearly extend beyond targeting of TF tran-
scripts, as would be expected if miRNAs as a class can affect
hundreds or thousands of genes.23,24 A well-studied counterex-
ample is offered by the evolutionarily conserved, pancreatic islet
cell–specific miR-375, which seems to inhibit glucose-induced
insulin secretion by targeting the myotrophin message and a
resultant effect on insulin exocytosis.48
Independent of the possibly widespread role of miRNAs in
suppressing TF genes, functional parallels between TFs and
miRNAs as molecular regulators are noteworthy, as articulated in a
recent review.49 Both classes of molecules exert their activity
through composite cis-regulatory elements and function in combi-
nations; single TFs or miRNAs may regulate many different genes,
as we encountered for miR-1 and miR-124. TFs and miRNAs also
may act cooperatively on their target genes, which typically harbor
multiple cis-regulatory DNA elements for transcriptional activation
and more than 1 putative miRNA recognition site for mRNA
down-regulation.20,21,50 Thus, both TFs and miRNAs may generate
combinatorial codes that dictate cellular identities and phenotypes.
Understanding the putative networks of these interactions is a
central challenge in studying miRNA functions in cell differentiation.
How many miRNAs? How many targets?
To appreciate the breadth of miRNA functions, it would be useful
to have reliable estimates of the total number of miRNA genes in a
species. After the initial cloning of more than 100 miRNAs,7-10
cloning efforts soon achieved a degree of saturation, with recurring
identification of previously cloned species. However, miRNAs that
are expressed at low abundance, restricted to a few cells in an
organ, developmentally regulated, or technically resistant to clon-
ing might elude detection in the common strategies. Likewise, even
the most sensitive algorithms to predict miRNA genes make
assumptions in order to enforce stringency in computational
searches. Nevertheless, a combination of comprehensive cloning
and computer prediction has expanded the number of animal
miRNAs greatly. Most cloned miRNAs show sequence conserva-
tion among closely related species and also across large evolution-
ary distances: among the initially identified mouse and human
miRNAs, more than half have identifiable homologs in fish, and
about half of these have homologs in flies or worms.51 It is this
evolutionary conservation, coupled with consideration of stem-
loop structures, that provides an important basis for computational
miRNA REGULATION OF HEMATOPOIESIS 3649
prediction of hundreds of miRNAs.52,53 In an especially thorough
approach that integrated bioinformatic prediction, microarray anal-
ysis, and sequence-directed cloning, Bentwich and coworkers
identified nearly 100 new miRNAs and predicted the presence of at
least 800 miRNAs in aggregate.54 However, the scope of potential
miRNA regulation remains uncertain, and predicted miRNAs should be
regarded cautiously until they are confirmed by experiments.
To add further complexity, miRNAs share limited sequence
complementarity with their mRNA targets, so that each miRNA
could possibly interact with scores of genes; conversely, a single
gene can harbor multiple miRNA recognition sites within 1 or more
potential 3⬘-UTRs. Published studies in vertebrate species center
on the results of bioinformatic predictions, and no mammalian
miRNA target has yet been identified prospectively without the
benefit of computationally derived clues. The algorithms used to
predict miRNA targets typically develop scoring schemes based on
sequence complementarity, free energy calculations of RNA duplex
formation, and phylogenetic conservation. In a 4-genome analysis
of 3⬘-UTRs, Lewis et al used the TargetScanS algorithm to identify
13 000 putative regulatory relationships conserved among the 4
species, thereby implicating more than 5 000 human genes (30% of
the tested gene set) as candidate miRNA targets.42 Using the
independent PicTar algorithm, Krek et al reached similar conclu-
sions on the scope of conserved miRNA targeting in mammals,
with a set of predictions that largely overlaps that of the Tar-
getScanS analysis.20 By contrast, John et al have predicted about
2 000 human gene targets, which currently have little overlap with
those of TargetScanS and PicTar.46 Lewis et al detected additional
targeting in open reading frames and concluded that more than
one-third of human genes are under selective pressure to maintain
pairing to miRNAs.42 Furthermore, there is increasing experimen-
tal and computational evidence for a large number of nonconserved
targets.23,24,45 However, individual predictions of miRNA targets
should be regarded as provisional, and attempts at biological
investigation should be preceded by careful experimental valida-
tion of putative miRNA-target combinations.
The possibility that a single miRNA may target multiple
transcripts and that individual transcripts may be subject to
regulation by multiple miRNAs amplifies the scope of putative
miRNA regulation in potentially unfathomable terms. The concep-
tual and bioinformatic problems presented by these considerations
are formidable and may be compared with those that follow from
genome-scale identification of protein-protein interactions. In the
latter example, however, mapping the domains of gene expression
reduces the magnitude of the challenge as proteins can legitimately
interact only when they are coexpressed. In contrast, miRNAs may
be coexpressed with their targets to dampen gene expression, or the
2 may appear in complementary distributions when the miRNA
serves to eliminate target gene expression. Resolution of the
underlying questions will require rigorous experimentation and
confident assessment of low levels of miRNA and mRNA products.
In addition, it is likely that not all miRNAs function similarly: some
may indeed regulate a single gene tightly, whereas others may have
a wider influence over gene expression programs associated with
selected developmental or physiologic states (Figure 3).
Before reviewing what little is known about miRNA influences
in hematopoiesis, it is worthwhile to explore the general lessons we
might learn from the few reported examples of mammalian miRNA
functions. Mouse miR-196, which is encoded at 3 paralogous
locations in the mammalian A, B, and C Hox gene clusters,
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3650 SHIVDASANI
represses HoxB8 mRNA and downstream Sonic hedgehog signal-
ing, factors that distinguish developing forelimbs from hind-
limbs.18,44 In a different scenario, the miR-1 genes are direct
transcriptional targets of muscle differentiation TFs such as serum
response factor, MyoD, and Mef2, and their miRNA products
appear to regulate levels of Hand2, a TF that promotes cardiomyo-
cyte expansion in the cardiac ventricles; overexpression of miR-1
in the developing heart reduces the pool size of proliferating
ventricular cardiomyocytes.19 In addition to a third instance that is
described in the next section, “miRNA expression and functions in
hematopoiesis,”47 these examples share certain common themes
that may be instructive. First, in each case, the miRNA under
detailed investigation shows significant differential expression in a
manner that permitted generation of cogent and testable hypoth-
eses. miR-1 is highly enriched in cardiac and skeletal muscle
precursors, whereas miR-196 expression is at least 20-fold higher
in hindlimb buds than in the forelimbs. A second, related point is
that in each case there was already considerable information about
the tissue under study so that the investigators could test for
consistency and rely on experimental systems that are well
validated. Third, identification of miRNA targets remains heavily
reliant on computational prediction, again coupled with prior
knowledge that helped focus on plausible candidates. These themes
will likely continue to guide further work in biological miRNA
functions into the foreseeable future. Of course, these examples
illustrate the seminal role of selected factors that may have a
limited repertoire of TF targets. This scenario is quite possibly the
exception rather than the rule for general miRNA functions. It will
require new experimental paradigms to gain better insights into
cases where a few or many miRNAs operate in combination with
innumerable targets to fine-regulate biological processes.
miRNA expression and functions
in hematopoiesis
Hematopoietic cells were not included in the earliest reported
efforts to identify tissue-restricted miRNAs.10 Subsequently, Chen
and colleagues15 cloned about 100 unique miRNAs from mouse
bone marrow. Whereas many had been identified previously from
nonhematopoietic tissues, a select few, including miR-142, miR-
181a, and miR-223, are expressed preferentially in blood cells and
BLOOD, 1 DECEMBER 2006 䡠 VOLUME 108, NUMBER 12
Figure 3. Models for the biological significance of
miRNA functions. Three nonmutually exclusive models
are presented, and the truth is likely to incorporate
elements from each. Different modes may also operate in
different cells or at different stages in development.
Computational predictions form the basis for much of the
current thinking and experimental evidence favoring each
of the models remains limited.
a limited number of other sites. miR-223 and miR-142 showed the
most restricted distribution, virtually confined to bone marrow and
spleen; some miR-142 expression is also seen in thymus, where
miR-181a is especially abundant.15 Other results from miRNA
microarray and Northern analysis of assorted blood cell (mainly
lymphocyte) populations suggest that few miRNAs are truly
restricted in distribution.55 Indeed, tissue specificities reported for
miRNA expression in general probably reflect enrichment, which
can even be considerable, in certain cells and not necessarily
exclusion from all other sites. Nevertheless, some miRNAs are
remarkably responsive to cellular manipulations: miR-150 is
rapidly down-regulated upon T-cell stimulation under T helper 1
(Th1) or Th2 conditions, whereas miR-146 is selectively increased
in Th1 lymphocytes.55 In a recent expression analysis of megakaryo-
cyte cultures derived from CD34⫹ bone marrow cells, Garzon and
colleagues identified 19 miRNAs that were reduced by 2- to
50-fold and none that increased with megakaryocytic differentia-
tion.56 Although 2 of these miRNAs, miR-10a and miR-130a, are
thought to target the transcription factor genes HOXA1 and MAFB,
respectively,56 the true significance of most miRNA differential
expression or of changes induced in hematopoiesis is not known.
To interrogate miRNA functions in hematopoiesis, Chen et al15
introduced the blood cell–specific miRNAs they identified into
murine Lin⫺ hematopoietic progenitor cells, followed by in vitro
differentiation or transplantation into lethally irradiated hosts.
Overexpression of miR-181a induced a 2-fold increase in B
lymphocyte numbers without affecting the T-cell lineage in vitro,
although the mouse transplantation studies yielded a nearly 2-fold
reduction in the number of circulating T lymphocytes and about a
90% decrease in the CD8⫹ subpopulation. In contrast, miR-142s
and miR-223, both evaluated only in vitro, modestly increased
T-cell and not B-cell numbers; miR-30, which is not preferentially
expressed in blood cells, did not affect hematopoiesis as judged by
flow cytometry for lineage markers. Whereas miR-181a hence
seems capable of modulating lymphoid cell lineages, it is important
to note that these conclusions rely exclusively on studies of
overexpressed miRNAs. Indeed, experimental constraints limit the
ability to assess miRNA functions rapidly through loss of function,
and in any event, it is likely that regulation by miRNAs encom-
passes considerable redundancy.
In contrast to the specific requirement of selected miRNAs, the
general requirement for miRNAs in a hematopoietic organ has been
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BLOOD, 1 DECEMBER 2006 䡠 VOLUME 108, NUMBER 12
evaluated in mice with selective deletion of the dcr-1 (Dicer) gene
in the thymus.57 These mice displayed a severe block in develop-
ment of peripheral CD8⫹ T cells and reduced numbers of CD4⫹ T
lymphocytes, which also proliferated poorly or died by apoptosis
quickly after agonist stimulation. Dicer-deficient CD4⫹ T cells
preferentially expressed interferon-␥, a cytokine affiliated with the
Th1 lineage. These observations represent the net effect of miRNA
deficiency and perhaps other unknown Dicer functions, possibly
including processing of siRNA. Accordingly, it remains unclear
whether they reflect tissue-specific absence of a single critical
miRNA, of a few regulators that control a limited number of
mRNA targets, or the functional output of a complex pathway
consisting of many miRNAs, each with a defined individual role.
Indeed, the fundamental limitation of both the miR-181 overexpres-
sion and Dicer gene deletion studies is that the identity and
activities of the primary mRNA targets are unknown. Target
prediction algorithms identify no fewer than 340 conserved candi-
date targets for miR-181a, with equivalent degrees of confidence
for dozens of them. Thus, dissecting the regulatory circuit poses an
enormous challenge. By contrast, the miRanda algorithm,46 whose
predicted targets overlap minimally with others’, hints at the
human HOXA5 gene as a candidate miR-181 target. This putative
target gene is expressed in hematopoietic cells, where it has
previously been implicated in regulating the balance between
myeloid and erythroid cell precursors.58,59 The latter studies did
not, however, report lymphocyte ratios; miR-181a overexpression
does not influence erythroid cell differentiation;15 and interaction
between miR-181a and HOXA5 remains speculative at best.
miR-223 is another blood cell–restricted miRNA, which achieves
highest levels in CD34⫺ bone marrow cells, is not present in T or B
lymphocytes, and is induced by retinoic acid treatment of myeloid
precursors through the transcriptional activator C/EBP␣.47 C/EBP␣
is known to be important in myelopoiesis as it regulates many
myeloid cell–specific genes and promotes granulocyte-specific
genes at the expense of the monocytic differentiation program in
bipotential precursors60; C/EBP␣ knockout mice show selective
failure of neutrophil and eosinophil differentiation.61 Overexpres-
sion of miR-223 in the undifferentiated NB4 cell line induced
morphologic changes consistent with maturation and expression of
CD11b and the granulocyte colony-stimulating factor receptor.
Conversely, in one of the few examples where a vertebrate miRNA
function has been evaluated through experimental reduction in its
levels, miR-223–complementary locked nucleic acid oligonucleo-
tides induced modest reductions in the amounts of both miR-223
and CD11b.47 These miR-223 effects are mediated in part through
translational inhibition of mRNA for the TF NFI-A. In a particu-
larly provocative twist, NFI-A and C/EBP␣ compete for binding to
partially overlapping DNA sequences in the miR-223 gene pro-
Figure 4. Working model for the regulatory circuit involving
miR-223, C/EBP␣, and NFI-A in neutrophil differentiation. Experi-
mental results47 are consistent with the idea that NFI-A and C/EBP␣
compete for binding to partially overlapping DNA sequences in the
miR-223 gene promoter, and as long as NFI-A is present, this miR
gene is inactive. Cells committed to granulocytic differentiation ex-
press C/EBP␣, which activates miR-223 expression, resulting in
repression of its NFI-A mRNA target. Thus, miR-223 appears to
participate in a simple regulatory circuit of TFs that control granulopoi-
esis and may help stabilize the neutrophil phenotype induced by
C/EBP␣. Reprinted from Fazi et al47 with permission.
miRNA REGULATION OF HEMATOPOIESIS 3651
moter, and as long as NFI-A is present, this miR gene is inactive.
With the appearance of C/EBP␣, which occurs upon retinoic
acid–induced commitment to granulocytic differentiation, miR-223
expression is activated, resulting in repression of its NFI-A mRNA
target. Thus, miR-223 appears to be a key player in a simple
regulatory circuit of TFs that control granulopoiesis and may help
stabilize the neutrophil phenotype induced by C/EBP␣ (Figure 4).
As NFI-A mRNA is just one among literally hundreds of possible
miR-223 targets, the particular circuit described here may represent
only a facet of its full molecular effects. In principle, miR-223
could serve to down-regulate many genes that would ordinarily be
expressed in multipotential progenitors or nongranulocytic cells
and thus help refine the neutrophil-specific gene expression program.
Although this hypothesis remains to be tested, it is consistent both
with emerging concepts in the field and with the demonstration that
particular miRNAs can influence discrete aspects of hematopoiesis.
In a similar vein, Felli and colleagues62 found high expression
of miR-221 and miR-222 in human cord blood–derived CD34⫹
hematopoietic progenitor cells; unilineage erythroid differentiation
of these cells in culture caused reduction in the levels of these 2
miRNAs, which have virtually identical sequence in the seed
region of target pairing. Bioinformatic analysis suggested c-kit as a
possible target transcript, and c-kit mRNA levels correlate in-
versely with those of miR-221 and miR-222 in cultured cells.
Forced expression of these miRNAs in TF-1 erythroleukemia cells
or in erythroid culture of CD34⫹ cord blood cells slowed cell
growth concomitant with reduced c-kit protein levels. Although
these results do not address the true functions of the X-linked
miR-221/miR-222 cluster in vivo, the authors’ approach and the
internal consistency of the findings highlight current experimental
paradigms to link specific, tissue-restricted miRNAs with candi-
date mRNA targets. In the future, such studies will need to be
extended in 2 complementary ways: targeted disruption of indi-
vidual miRNA genes and targeted mutation of putative miRNA-
binding sites in the 3⬘-UTRs of candidate targets. While redun-
dancy among miRNA regulators may limit the force of such
experiments, a thorough understanding of miRNA functions will
only emerge from integrated consideration of complementary
results. miRNAs implicated to date in specific hematopoietic
functions are summarized in Table 1.
miRNA expression and functions in leukemia
Naturally, there has been considerable interest in any connection
between miRNAs and cancer, including leukemias. The miR-15a/
miR-16 locus lies within a region of human chromosome 13 that is
also the site of the most common structural abnormality in B-cell
 From www.bloodjournal.org by guest on March 11, 2018. For personal use only.

3652 SHIVDASANI BLOOD, 1 DECEMBER 2006 䡠 VOLUME 108, NUMBER 12

Table 1. miRNAs implicated to date in hematopoietic functions

miRNA Candidate target genes Function Source

miR-181a None identified Lymphopoiesis Chen et al15

miR-223 NFI-A Granulopoiesis Fazi et al47
miR-221, miR-222 c-kit Erythropoiesis Felli et al62
miR-130a MafB Megakaryopoiesis (assumed) Garzon et al56
miR-10a HoxA1 Megakaryopoiesis (assumed) Garzon et al56

chronic lymphocytic leukemia (CLL) and mantle cell lymphoma;
both miRNAs are deleted or down-regulated in nearly two-thirds of
CLL samples.63 Other miRNA genes also are frequently located at
fragile sites, minimal regions of loss of heterozygosity or amplifica-
tion, and common breakpoint regions previously identified in a
range of human malignancies.64 Calin and colleagues65 identified
germline or somatic mutations in 5 of 42 sequenced miRNAs in 11
of 75 patients with CLL and no such mutations in 160 subjects
without cancer. Whereas these observations provoke speculation
about direct miRNA functions in leukemogenesis, other advances
center on more general features of miRNA expression in the
disease context. The mixed-lineage leukemia (MLL) 1 transcrip-
tional regulator binds to transcription-start sites of innumerable
genes, including 30% of all tested miRNA loci,66 which suggests
that broad dysregulation of both mRNA and miRNA expression
may underlie leukemic phenotypes. Lu and coworkers67 report
widespread down-regulation of miRNAs in tumors compared with
their normal tissue counterparts, much as others found reduced
levels of specific miRNAs in colon cancer specimens.68 In one
study, miRNA expression profiles were more successful than
mRNA expression in classifying poorly differentiated tumors.67
Furthermore, a unique expression profile consisting of 13 miRNA
genes could distinguish cases of CLL with distinct molecular
markers and clinical outcomes.65 The broader role of miRNAs in
classifying tumors or contributing to disease progression remains
to be defined and is likely to be an area of intense investigation.
Concluding remarks
Progress in the area of miRNAs seems to have occurred faster than
in any major biological discipline in recent memory. The field has
moved from virtual ignorance about an abundant class of regula-
tory molecules to a reasonably advanced understanding of the
mechanisms of miRNA biogenesis and an emerging consensus
about the numbers of miRNAs and their targets in several species,
including humans. The next series of challenges is already becom-
ing evident: how is transcription of miRNA genes controlled? Do
miRNAs operate more commonly through single, critical target
transcripts, as the examples reported to date would imply, or do
they regulate broad programs of unique gene expression through
minor effects on multiple targets, as suggested by evolutionary
considerations and some experimental results? What is the larger
role of miRNAs in human disease and do they provide novel
therapeutic opportunities? As these questions begin to capture
investigators’ attention, it is worth recalling the seminal contribu-
tions of hematologists and their particular models in solving
problems in genetics, cell differentiation, and biochemistry. Inas-
much as miRNAs may control molecular aspects of cell specializa-
tion, hematopoiesis offers an ideal model system in which ideas
about their mechanisms and functions can be tested incisively.
Meanwhile, the apparent scope of miRNA regulation has disturbed
simple and conventional views about the classes of candidate
regulators in hematopoiesis and hematologic disorders. No doubt
the field will rapidly embrace the new biology and endeavor to
understand how and to what degree miRNAs influence different
aspects of blood cell renewal and specialization. By the time these
problems are solved, we can look forward to other discoveries that
might inform us about the functions of the vast majority of the
genome that encodes neither proteins nor other known regulatory
molecules like miRNAs.
Acknowledgments
I am grateful to Jochen Hartner, David Nathan, and Stuart Orkin for
critical review of the manuscript and to Alice Chen for help in
preparing figures. As Blood guidelines limit the number of cited
references, I regret the highly selective (and sometimes arbitrary)
citation process I needed to adopt in writing a succinct review.
This work was supported in part by grants from the National
Institutes of Health.
Authorship
The author declares no competing financial interests.
Correspondence: Ramesh A. Shivdasani, Dana-Farber Cancer
Institute, 44 Binney St, Boston, MA 02115; e-mail:
ramesh_shivdasani@dfci.harvard.edu.

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2006 108: 3646-3653

doi:10.1182/blood-2006-01-030015 originally published
online August 1, 2006

MicroRNAs: regulators of gene expression and cell differentiation

Ramesh A. Shivdasani

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