Nature Reviews Genetics | AOP, published online 4 May 2011; doi:10.1038/nrg3001
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Transcription by RNA polymerase III:
more complex than we thought
Robert J. White
Abstract | RNA polymerase (Pol) III is highly specialized for the production of
short non-coding RNAs. Once considered to be under relatively simple controls,
recent studies using chromatin immunoprecipitation followed by sequencing
(ChIP–seq) have revealed unexpected levels of complexity for Pol III regulation,
including substantial cell-type selectivity and intriguing overlap with Pol II
transcription. Here I describe these novel insights and consider their
implications and the questions that remain.
Over 40 years ago, studies using biochemical fractionation identified three RNA
polymerases from eukaryotic nuclei:
RNA polymerase (Pol) I, which synthesizes
most ribosomal RNA (rRNA); Pol II, which
synthesizes mRNA; and Pol III, which synthesizes tRNA1. Of these, Pol II attracted by
far the most attention, initially because its
mRNA products encode proteins. It is now
clear that Pol II is also responsible for synthesizing many types of non-coding RNA
(ncRNA), such as most small nuclear RNAs
(snRNAs) and microRNAs (miRNAs).
Nevertheless, a range of essential ncRNAs
are provided by Pol III, such as the 7SK
RNA that regulates Pol II activity. Strong
evidence implicating misregulated Pol III
activity in cancer has galvanized interest in
Pol III transcription2, including the discovery that proliferative and oncogenic effects
can result from small increases in levels of
tRNAiMet, the tRNA that mediates translation
initiation3.
Most established Pol III products were
originally identified as Pol III-derived
by the sensitivity of their expression to
α‑amanitin, an inhibitor with differential
effects on RNA polymerases4. Lists of
recognized Pol III transcripts obtained
in this way grew in a random and piecemeal manner. However, genomic-scale
technologies now allow systematic evaluations of Pol III targets. Such studies were
first carried out in yeast using ChIP–chip
approaches, where DNA fragments are
crosslinked in vivo to Pol III and its
associated factors, isolated by chromatin
immunoprecipitation (ChIP) and then
hybridized to DNA microarrays5–7. Only
a few new targets were identified, implying that most Pol III-transcribed genes in
this species were already known. However,
mammals pose a far greater challenge
because of the complexity of their genomes
and the likelihood that transcriptomes vary
between cell types. Nevertheless, in early
2010, several independent genome-wide
analyses were published, which provided
comprehensive lists of loci that are occupied by Pol III and its transcription factors
in eight human cell lines8–12. These studies
used ChIP–seq, where DNA from ChIP is
analysed by massively parallel sequencing.
These analyses provided
a wealth of detailed
information, which included
some big surprises
The data were compared with what was
already known about the genomic binding
sites of Pol II, various regulatory transcription factors and the localization of an
exhaustive list of chromatin marks. These
analyses provided a wealth of detailed
information, which included some big
surprises.
NATURE REVIEWS | GENETICS
Pol III-transcribed genes
Unlike yeast, mammalian genomes contain
huge numbers of short interspersed nuclear
elements (SINEs) with Pol III promoters.
For example, human genomes are scattered
with over a million copies of Alu, a ~300 bp
SINE that arose from 7SL RNA during
primate evolution and spread throughout
the genome by retrotransposition13. Such
sequences are difficult to analyse because
they are very similar to each other and
highly repetitive. Although SINE transcriptional regulation is still poorly characterized, SINEs may nevertheless provide the
majority of sites occupied by Pol III10. Apart
from SINEs, ~80% of other loci bound
by Pol III contain tRNA genes. Other
targets include genes encoding 5S rRNA,
U6 snRNA, 7SL RNA, 7SK RNA, vault RNA,
hY RNA, H1 RNA and MRP RNA8–12. All of these
short ncRNAs were already known as Pol III
products. In addition, dozens of novel
binding sites were identified in intergenic
regions8–12, but their significance remains
to be determined. Most unexpected was the
large number of established Pol III targets
where Pol III was not detected above the
threshold. For example, half of the tRNA
genes were considered unbound by Pol III
in one analysis of HeLa cells11. Precise values
depend on the stringency of cut-off, but
these results nevertheless differ dramatically
from what was found in yeasts, in which
virtually all tRNA genes were occupied by
Pol III5–7,14. The human variation in occupancy occurs despite shared core promoter
sequences11. This strongly suggests that
additional controls influence promoter
access in human cells.
Genes encoding miRNAs were notably
absent from the lists of Pol III targets.
Although it was already clear that most cellular miRNAs are made by Pol II, there have
been reports that a subset are Pol III transcripts15,16. However, many of these miRNA
sequences contain internal Pol III terminator motifs that preclude their full-length
transcription by Pol III9,17. The ChIP–seq
studies detected Pol III at very few of the
miRNA genes that had been suggested to
be transcribed by Pol III8–12, and the exceptions in which Pol III was detected could be
explained by proximity of other genes. For
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Figure 1 | Basal transcription machinery and promoter structure at RNA polymerase III0CVWTG4GXKGYU^)GPGVKEU
transcribed genes. RNA polymerase (Pol) III-transcribed genes with internal promoters use different transcription factors from those with upstream promoters. a | Most Pol III-transcribed genes
— for example, tRNA genes — have internal promoters where the key promoter elements comprise
two sequence blocks (A and B) located within the transcribed region. The A and B blocks are recognized by transcription factor IIIC (TFIIIC). TFIIIC recruits TFIIIB, which is composed of the subunits
BRF1, BDP1 and TATA box binding protein (TBP). b | A minority of Pol III-transcribed genes — for
example, U6 small nuclear RNA (snRNA) genes — have promoters located entirely upstream of the
gene. These promoters contain TATA boxes, which are bound by TBP, and proximal sequence elements (PSEs), which are bound by a factor called small nuclear RNA activating protein complex
(SNAPc; also known as PTF). These upstream promoters use a form of TFIIIB composed of BRF2, BDP1
and TBP. Both forms of TFIIIB recruit Pol III itself.
example, the MIR886 locus is bound by
Pol III in several cell types9–12 but overlaps
completely with an established Pol III target-encoding vault RNA (VTRNA2‑1)10. The
involvement of Pol III in miRNA synthesis
appears to be minimal in the eight cell lines
examined so far by ChIP–seq. However, its
involvement might depend on cell type and
one of the studies16 that first reported Pol III
at miRNA loci used melanoma and breast
carcinoma cells that were not examined in
the more recent analyses8–12.
Basal Pol III transcription machinery
All Pol III transcription requires transcription factor IIIB (TFIIIB), which recruits
Pol III to its templates18. There are three
TFIIIB subunits, each of which is essential
for TFIIIB function in vitro: the TATA box
binding protein (TBP), which is also used by
Pol I and Pol II; BDP1, a large SANT domaincontaining polypeptide; and either of the
TFIIB-related factors BRF1 or BRF2 (REF. 18).
Previous work19 has shown that BRF1 is
used by Pol III templates with key promoter
elements located internally within the transcribed region, such as tRNA genes, whereas
BRF2 is used instead by promoters located
upstream of the initiation site, such as U6
snRNA genes (FIG. 1). Analysis by ChIP–seq
confirmed this demarcation: BRF1 was
found exclusively at genes with internal
Pol III promoters, whereas BRF2 was absent
from all these sites but found instead at
Pol III-transcribed genes with upstream promoters. There was no overlap between BRF1
and BRF2 targets, and the former were 15
times more abundant than the latter 10,11. As
predicted, the loci occupied by BRF1 are also
bound by TFIIIC, whereas BRF2 does not
colocalize with TFIIIC8,10,11. These important
data establish that the initial models, which
were based on the analysis of a few paradigm
promoters, hold true genome-wide.
Cell type specificity
Expression of tRNA is regulated under many
conditions, including during cell cycle
progression and oncogenic transformation2.
Consistent with this, ChIP–seq data showed
that fewer Pol III-transcribed genes were
occupied in untransformed fibroblasts than
in three transformed cell lines11. Most
studies of Pol III regulation have concluded
that control is mediated through TFIIIB2.
Such studies examined a few tRNA genes
that were assumed to be representative of the
entire family, an assumption based on
the high homology of tRNA promoters
and the fact that control operates on a factor
(TFIIIB) that is required by the entire family.
It was, therefore, a surprise when gene
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expression microarrays revealed that the relative proportions of individual tRNAs vary
widely between different human tissues20. It
was originally unclear whether such variations reflected differences in the rates of production or degradation of tRNA. However,
the new ChIP–seq data show that differential
promoter usage can explain much of the celltype selectivity. For example, when T cells
were compared with HeLa cells, a remarkable 26% of tRNA loci were occupied by
Pol III in one cell type but not the other 8. This
is difficult to accommodate within current
models of Pol III regulation, in which control
is exerted through shared transcription
factors at similar core promoters.
Gene-specific regulators
Established regulators of Pol III transcription
include the tumour suppressors retinoblastoma protein and p53 (REF. 21), as well as the
ancient MAF1 protein that was first discovered in yeast 22. Each of these can bind TFIIIB
and prevent Pol III recruitment to its target
genes23–25. Conversely, the proto-oncogene
product MYC binds TFIIIB and stimulates
promoter recruitment of Pol III26. Because
they all target TFIIIB, these regulators were
thought to control most, if not all, Pol IIIexpressed genes coordinately 2. Exceptional
behaviour could be readily explained by
post-transcriptional effects, such as differential RNA turnover. Evidence of unanticipated complexities in Pol III control came
from studies of MYC. Analysis by ChIP–seq
found MYC at only 74% of cellular loci occupied by Pol III12. Because the recruitment of
Pol III requires TFIIIB, it seems that the presence of TFIIIB does not ensure MYC occupancy, even though they clearly interact27.
Analysis of Epstein–Barr virus-encoded RNA
(EBER) genes suggests that DNA sequences
(E boxes) upstream of the promoter can
influence whether Pol III promoters respond
to MYC28. This contrasts with our prevailing
model29, in which protein–protein interactions with TFIIIB are sufficient to recruit
MYC to all Pol III promoters. This model
is consistent with the data from Drosophila
melanogaster, in which DNA-binding is not
required for MYC to stimulate Pol III transcription30. The situation in humans requires
clarification, but DNA motifs that are outside the consensus Pol III promoters may
allow transcription factor binding to mediate
gene-selective responses.
The ChIP–seq studies discovered several
factors colocalizing with Pol III that have not
been shown to regulate its activity, including
the proto-oncoproteins FOS, JUN and ETS1
(REFS 11,12). Although colocalization does
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not prove a functional interaction, it does
imply that these factors may influence Pol III
transcription directly. If so, they are likely to
contribute to the elevated Pol III output seen
in cancers2. Furthermore, an ability to stimulate transcription by more than one RNA
polymerase, as is the case for MYC29, may be
important for the oncogenicity of such factors. Indeed, full transformation of Rat1a rat
fibroblasts by MYC, as assayed by growth of
xenograft tumours in mice, has been shown
to require induction of Pol III transcription31.
Pol II at Pol III-transcribed genes
As well as regulators that had previously
been linked only to Pol II transcription,
the ChIP–seq analyses in human cell lines
also found Pol II itself close to many active
Pol III-transcribed genes, including tRNA,
5S and U6 genes, where its binding correlated strongly with Pol III occupancy 8,10–12.
Widespread colocalization of Pol II with
Pol III-transcribed genes had not been seen
in yeast. Pol II binding peaks at around
200 bp upstream of the Pol III initiation site
and, in most cases, does not correspond
to a known Pol II transcription unit 8,11,12.
Indeed, it is uncertain whether Pol II actually transcribes these sites. Basal Pol II initiation factors are also present, such as TFIIB8.
Pol II was also seen at Pol III-transcribed
genes in mouse and D. melanogaster cells8.
Human Pol II had been previously detected
upstream of U6 promoters, but this was
thought to be a peculiarity of these loci32.
Specific inhibition of Pol II using low
doses of α‑amanitin can suppress expression
of a subset of Pol III target genes8,12,32,
implying that Pol II might promote Pol III
transcription in these cases. However,
interpretation of this suppression is difficult,
as in vivo Pol II inhibition will rapidly
affect so many processes that any of Pol III’s
responses might be indirect. The strong
correlation between Pol III occupancy and
upstream Pol II colocalization8,11,12 across
the genome is highly suggestive of a regulatory interaction but is insufficient to prove a
functional relationship. Assessing the significance of these findings will be challenging
because in vivo inhibition of Pol II or Pol III
has widespread downstream effects.
Histone modifications
In budding and fission yeasts, virtually
all tRNA genes are occupied by Pol III,
including genes adjacent to regions of
heterochromatin that can silence Pol II
transcription6,7,14. Indeed, tRNA genes can
block the spread of heterochromatin in
yeast 33. Despite this resistance to chromatin-
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Figure 2 | Schematic comparison of features distinguishing many active and inactive tRNA
0CVWTG4GXKGYU^)GPGVKEU
genes. a | Active tRNA genes are occupied by transcription factor IIIC (TFIIIC), TFIIIB, RNA polymerase (Pol) III and often by MYC, which recruits the histone acetyltransferase GCN5 via the cofactor
transformation/transcription domain-associated protein (TRRAP). Histones flanking active tRNA
genes characteristically show euchromatic modifications, including trimethylation of histone H3
at lysine 4 (H3K4me3), and extensive histone acetylation — for example, acetylation of histone
H2A at lysine 5 (H2AK5Ac), H2BK5Ac, H2BK12Ac, H3K9Ac, H3K18Ac and H4K12Ac. Pol II can
often be detected ~200 bp upstream of active tRNA genes, along with basal Pol II transcription
factors that include TFIIA, TFIIB, TFIIE and TFIIH. b | By contrast, Pol II and its basal factors are not
usually associated with silent tRNA genes that are unoccupied by Pol III, TFIIIB and TFIIIC. Histones
flanking such inactive tRNA genes show minimal acetylation and instead show heterochromatic
modifications, such as H3K9me3 and H3K27me3. An example of these features is provided in
HeLa cells by two tRNA-Leu(TAA) genes on chromosome 6, one active and the other inactive8.
mediated repression in yeasts, occupancy of
human genes by Pol III correlates negatively
with heterochromatic histone modifications
and positively with euchromatic modifications8,11. This suggests that a permissive
chromatin environment may be important
for human Pol III transcription, as it is for
Pol II. For example, active — but not inactive
— tRNA genes show strong acetylation of
histone H3 (REF. 8), supporting evidence that
tRNA gene induction by MYC involves H3
acetylation by the cofactor GCN5 (REF. 26).
Pol III transcription in vitro can be stimulated by the acetyltransferase p300, which
also associates with tRNA and U6 genes in
cells34. A stimulatory role for the histone
variant H2A.Z is suggested by its enrichment at active Pol III promoters8,11. Strong
correlations were also found between tRNA
gene activity and many specific histone
methylation events8,11. For example, histone
H3 trimethylated on lysine 4 (H3K4me3) is
more prevalent at active tRNA genes than
inactive ones, whereas the converse is true
NATURE REVIEWS | GENETICS
for H3K9me3 (FIG. 2). Although it was well
established that histone methylation correlates with Pol II transcription, this had
not previously been shown for Pol III. In
fact, most of the 39 investigated epigenetic
modifications correlate with Pol III activity in
a manner that is broadly similar to what was
already known for Pol II8 (FIG. 3). However,
this fails to convey the complex details, which
can be viewed in the exhaustive supplementary data produced by Barski et al.8. In most
cases, the precise patterns of the modifications are different when Pol II and Pol III
promoters are compared. A striking example
is provided by H3K9me3, which correlates
with inactivity for both sets of promoters,
but shows dramatic peaks and troughs
around tRNA genes that are not seen at Pol II
templates8. Differences in nucleosome
positioning will contribute to the distinct
distribution patterns of modified histones, as
nucleosomes are excluded from active tRNA
promoters and enriched in flanking regions8.
Nevertheless, the data suggest at least some
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determined whether basal Pol III transcription factors can directly recognize specific
histone modifications, which might allow
chromatin features to help dictate whether
genes become active. The BDP1 subunit of
TFIIIB has a SANT domain, which, in the
context of certain chromatin-remodelling
complexes, provides a histone tail-binding
module35. It is possible that the SANT
domain of BDP1 allows TFIIIB to respond
to histone modifications.
acetylation at tRNA and 5S rRNA genes
coincides with MYC-dependent recruitment of the histone acetyltransferase GCN5
and precedes elevated transcription26.
Furthermore, transcriptional induction can
be blocked by depletion of GCN5 or by a
specific inhibitor of its activity 26. These data
clearly implicate GCN5‑mediated acetylation in the activation process, although
targets other than histones remain possible. In the same context, histone H4
acetylation does not change in response
to MYC, GCN5 or elevated transcription26. Clearly, the situation is complex and
much work will be necessary to establish
the significance of chromatin marks at
Pol III-transcribed genes. It remains to be
Barriers
In yeasts, tRNA genes can serve as barriers
to heterochromatin spreading. This barrier
function depends on the Pol III machinery,
histone acetylation and discontinuity in the
regular spacing of nucleosomal arrays14,36–38.
The chromatin landscapes of active human
Pol III-transcribed genes are consistent
with similar activities in higher organisms;
indeed, Pol III-mediated barrier activity has
been demonstrated for mouse SINEs39,40. It
is, therefore, exciting that the most active
10% of human tRNA genes were found to
be occupied by CCCTC-binding factor
(CTCF), a protein that is heavily involved
in barrier function11. CTCF was also found
at many human loci that are not recognizable genes and appear not to be transcribed
but are bound by TFIIIC in the absence of
TFIIIB or Pol III10. Sites like this were first
identified in budding yeast, where they were
dubbed ‘extra TFIIIC’ (ETC) loci7. Similar
loci in fission yeast have been implicated in
higher-order chromosome organization14.
There may be several thousand human ETC
sites, many of which are near to Pol II promoters, particularly between genes that are
close together and divergently transcribed10.
Such positioning might allow them to act
as barriers to separate chromatin domains,
thereby allowing independent regulation of
proximal genes. Active Pol III transcription
5S rRNA
hY RNA
SANT domain
(5S ribosomal RNA). The smallest of the rRNAs.
It is found in the large subunit of ribosomes.
Human Y RNA, which has putative roles
in DNA replication and quality control of
non-coding RNAs.
A motif of ~50 amino acid residues that is found in
transcription cofactors, chromatin-remodelling proteins
and BDP1.
MRP RNA
U6 snRNA
Mitochondrial RNA processing (MRP) RNA is
part of a ribonucleoprotein particle that processes
precursor ribosomal RNA and mitochondrial
DNA replication primers. MRP RNA (encoded by
the RMRP gene) also associates with the
catalytic subunit of human telomerase reverse
transcriptase (TERT) to form an RNAdependent RNA polymerase which generates
RNAs that are processed by DICER into small
interfering RNAs.
(U6 small nuclear RNA). A component of splicesomes,
which are required for splicing precursor mRNAs.
Figure 3 | How specific histone modifications correlate with expression
of RNA polymerase
0CVWTG4GXKGYU^)GPGVKEU
III- and RNA polymerase II‑transcribed genes. Histone modifications that correlate with RNA
polymerase (Pol) II transcription positively (black text) or negatively (white text in red boxes) are
listed within the pink oval; those that correlate with Pol III transcription are listed within the blue
oval. It is evident that most modifications correlate with the same transcriptional response (active
versus inactive) for Pol II and Pol III, including all acetylation events examined and the presence of
the H2A.Z variant of histone H2A. Ac, acetylation; H, histone; K, lysine; me1, monomethylation; me2,
dimethylation; me3, trimethylation; R, arginine.
differential usage of histone-modifying
enzymes by Pol II and Pol III. This is consistent with the apparent absence from tRNA
and 5S rRNA genes of TIP60 (also known as
KAT5), a histone acetyltransferase that
regulates many Pol II promoters26.
The ChIP–seq analyses have provided
a wealth of information concerning epigenetic marks at Pol III-transcribed genes, but
making sense of this information remains
a challenge. Cause and effect between transcription and histone modification can be
difficult to separate, with active chromatin
marks sometimes appearing as a consequence of transcription. The Pol III case
that is best analysed for chromatin changes
in vivo is induction by MYC, where H3
Glossary
7SK RNA
Binds and represses P-TEFb, a factor that stimulates
transcript elongation by RNA polymerase II.
7SL RNA
Acts as a scaffold within the signal recognition
particle (SRP), which inserts nascent polypeptides
into membranes.
H1 RNA
The RNA component of RNase P, which processes
the 5′ end of tRNAs.
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Vault RNA
Part of a very large ribonucleoprotein particle that is
implicated in multidrug resistance and intracellular
transport. Although 20% of vault RNA is found in vault
particles, ~80% is free in the cytosol, where it is processed
by DICER to generate small intefering RNAs that
downregulate CYP3A4, a key enzyme in drug metabolism.
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Robert J. White is at the Beatson Institute for
Cancer Research, Garscube Estate,
Switchback Road, Bearsden,
Glasgow G61 1BD, UK.
e‑mail: r.white@beatson.gla.ac.uk
units are also significantly enriched within
2 kb of Pol II promoters11. These observations support the possibility that TFIIIC is
involved in organizing human chromosomal
domains when bound at some tRNA genes,
SINEs and ETC loci.
Perspective
The recent studies have added considerable
detail to our view of Pol III activity, as well
as raising some intriguing possibilities. The
variations in usage of individual tRNA genes
between different cell types came as a
surprise; they contrast with models in which
the family is regulated coordinately through
changes in shared transcription factors,
acting at promoters that are highly related.
Is Pol III transcription micro-managed
to ensure that relative levels of individual
tRNAs are optimal for translating each cell’s
mRNA content according to their codon
usage? If so, how is this achieved? Pol III
occupancy does not correlate well with the
quality of the internal promoter elements
that are recognized by TFIIIC10,11. The
answer may involve additional transcription
factors such as MYC, FOS and STAT1
(REFS 11,12), which seem to target subsets
of tRNA genes, but the molecular basis of
this selectivity has yet to be established.
Chromatin environment seems to be important in dictating which Pol III templates are
transcribed in human cells, in apparent contrast to the situation in yeasts. Ultimately, the
sets of tRNA genes expressed in a given cell
type are likely to reflect the specific
repertoire of regulatory factors.
There is also the intriguing finding of
Pol II and its basal machinery upstream
of active Pol III promoters in the apparent
absence of protein-coding or transcribed
sequence. What brings it there and what is
its significance at these locations? Its recruitment might result from the presence at Pol III
promoters of regulatory factors such as
MYC, which are able to attract basal apparatus of more than one RNA polymerase.
The Pol II machinery, when upstream of
active Pol III-transcribed genes, may often
have minimal impact, but there are likely to
be cases in which its serendipitous presence
does have functional consequences. If so,
this may have been exploited during evolution to provide new regulatory networks.
Cancers might also use Pol II recruitment to
raise the expression of key Pol III products
during tumorigenesis.
doi:10.1038/nrg3001
Published online 4 May 2011
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.
20.
Roeder, R. G. & Rutter, W. J. Multiple forms of
DNA-dependent RNA polymerase in eukaryotic
organisms. Nature 224, 234–237 (1969).
Marshall, L. & White, R. J. Non-coding RNA
production by RNA polymerase III is implicated in
cancer. Nature Rev. Cancer 8, 911–914 (2008).
Marshall, L., Kenneth, N. S. & White, R. J.
Elevated tRNAiMet synthesis can drive cell proliferation
and oncogenic transformation. Cell 133, 78–89
(2008).
Kedinger, C., Gniazdowski, M., Mandel, J. L.,
Gissinger, F. & Chambon, P. α‑Amanitin: a specific
inhibitor of one of two DNA-dependent RNA
polymerase activities from calf thymus. Biochem.
Biophys. Res. Commun. 38, 165–171 (1970).
Harismendy, O. et al. Genome-wide location of yeast
RNA polymerase III transcription machinery. EMBO J.
22, 4738–4747 (2003).
Roberts, D. N., Stewart, A. J., Huff, J. T. & Cairns, B. R.
The RNA polymerase III transcriptome revealed by
genome-wide localization and activity-occupancy
relationships. Proc. Natl Acad. Sci. USA 100,
14695–14700 (2003).
Moqtaderi, Z. & Struhl, K. Genome-wide occupancy
profile of the RNA polymerase III machinery in
Saccharomyces cerevisiae reveals loci with incomplete
transcription complexes. Mol. Cell. Biol. 24,
4118–4127 (2004).
Barski, A. et al. Pol II and its associated epigenetic
marks are present at Pol III-transcribed noncoding
RNA genes. Nature Struct. Mol. Biol. 17, 629–634
(2010).
Canella, D., Praz, V., Reina, J. H., Cousin, P. &
Hernandez, N. Defining the RNA polymerase III
transcriptome: genome-wide localization of the RNA
polymerase III transcription machinery in human cells.
Genome Res. 20, 710–721 (2010).
Moqtaderi, Z. et al. Genomic binding profiles of
functionally distinct RNA polymerase III transcription
complexes in human cells. Nature Struct. Mol. Biol.
17, 635–640 (2010).
Oler, A. J. et al. Human RNA polymerase III
transcriptomes and relationships to Pol II promoter
chromatin and enhancer-binding factors. Nature
Struct. Mol. Biol. 17, 620–628 (2010).
Raha, D. et al. Close association of RNA
polymerase II and many transcription factors
with Pol III genes. Proc. Natl Acad. Sci. USA 107,
3639–3644 (2010).
Batzer, M. A. & Deininger, P. L. Alu repeats and
human genomic diversity. Nature Rev. Genet. 3,
370–379 (2002).
Noma, K., Cam, H. P., Maraia, R. & Grewal, S. I.
A role for TFIIIC transcription factor complex in
genome organization. Cell 125, 859–872 (2006).
Borchert, G. M., Lanier, W. & Davidson, B. L.
RNA polymerase III transcribes human microRNAs.
Nature Struct. Mol. Biol. 13, 1097–1101 (2006).
Ozsolak, F. et al. Chromatin structure analyses identify
miRNA promoters. Genes Dev. 22, 3172–3183 (2008).
Bortolin-Cavaille, M., Dance, M., Weber, M. &
Cavaille, J. C19MC microRNAs are processed from
introns of large Pol-II, non‑protein‑coding transcripts.
Nucleic Acids Res. 37, 3464–3473 (2009).
Schramm, L. & Hernandez, N. Recruitment of RNA
polymerase III to its target promoters. Genes Dev. 16,
2593–2620 (2002).
Schramm, L., Pendergrast, P. S., Sun, Y. &
Hernandez, N. Different human TFIIIB activities direct
RNA polymerase III transcription from TATA-containing
and TATA-less promoters. Genes Dev. 14, 2650–2663
(2000).
Dittmar, K. A., Goodenbour, J. M. & Pan, T.
Tissue-specific differences in human transfer RNA
expression. PLoS Genet. 2, 2107–2115 (2006).
NATURE REVIEWS | GENETICS
21. White, R. J. RNA polymerases I and III, growth control
and cancer. Nature Rev. Mol. Cell Biol. 6, 69–78
(2005).
22. Ciesla, M. & Boguta, M. Regulation of RNA
polymerase III transcription by Maf1 protein.
Acta Biochim. Pol. 55, 215–225 (2008).
23. Sutcliffe, J. E., Brown, T. R. P., Allison, S. J.,
Scott, P. H. & White, R. J. Retinoblastoma protein
disrupts interactions required for RNA polymerase III
transcription. Mol. Cell. Biol. 20, 9192–9202
(2000).
24. Crighton, D. et al. p53 represses RNA polymerase III
transcription by targeting TBP and inhibiting promoter
occupancy by TFIIIB. EMBO J. 22, 2810–2820 (2003).
25. Desai, N. et al. Two steps in Maf1‑dependent
repression of transcription by RNA polymerase III.
J. Biol. Chem. 280, 6455–6462 (2005).
26. Kenneth, N. S. et al. TRRAP and GCN5 are used by
c‑Myc to activate RNA polymerase III transcription.
Proc. Natl Acad. Sci. USA 104, 14917–14922 (2007).
27. Gomez-Roman, N., Grandori, C., Eisenman, R. N. &
White, R. J. Direct activation of RNA polymerase III
transcription by c‑Myc. Nature 421, 290–294 (2003).
28. Owen, T. J. et al. Epstein-Barr virus-encoded EBNA1
enhances RNA polymerase III-dependent EBER
expression through induction of EBER-associated
cellular transcription factors. Mol. Cancer 9, 241
(2010).
29. Kenneth, N. S. & White, R. J. Regulation by c‑Myc of
ncRNA expression. Curr. Opin. Genet. Dev. 19, 38–43
(2009).
30. Steiger, D., Furrer, M., Schwinkendorf, D. & Gallant, P.
Max-independent functions of Myc in Drosophila
melanogaster. Nature Genet. 40, 1084–1091 (2008).
31. Johnson, S. A. S., Dubeau, L. & Johnson, D. L.
Enhanced RNA polymerase III-dependent transcription
is required for oncogenic transformation. J. Biol. Chem.
283, 19184–19191 (2008).
32. Listerman, I., Bledau, A. S., Grishina, I. &
Neugebauer, K. M. Extragenic accumulation of
RNA polymerase II enhances transcription by RNA
polymerase III. PLoS Genet. 3, e212 (2007).
33. Haldar, D. & Kamakaka, R. T. tRNA genes as
chromatin barriers. Nature Struct. Mol. Biol. 13,
192–193 (2006).
34. Mertens, C. & Roeder, R. G. Different functional
modes of p300 in activation of RNA polymerase III
transcription from chromatin templates. Mol. Cell.
Biol. 28, 5764–5776 (2008).
35. Boyer, L. A., Latek, R. R. & Peterson, C. L.
The SANT domain: a unique histone‑tail‑binding
module? Nature Rev. Mol. Cell Biol. 5, 158–163
(2004).
36. Donze, D. & Kamakaka, R. T. RNA polymerase III and
RNA polymerase II promoter complexes are
heterochromatin barriers in Saccharomyces
cerevisiae. EMBO J. 20, 281–287 (2001).
37. Oki, M. & Kamakaka, R. T. Barrier function at HMR.
Mol. Cell 19, 707–716 (2005).
38. Scott, K. C., Merrett, S. L. & Willard, H. F.
A heterochromatin barrier partitions the fission
yeast centromere into discrete chromatin domains.
Curr. Biol. 16, 119–129 (2006).
39. Lunyak, V. V. et al. Developmentally regulated
activation of a SINE B2 repeat as a domain boundary
in organogenesis. Science 317, 248–251 (2007).
40. Roman, A. C. et al. Dioxin receptor and slug
transcription factors regulate the insulator activity of
B1 SINE retrotransposons via an RNA polymerase
switch. Genome Res. 21, 422–432 (2011).
Acknowledgements
The author gratefully acknowledges funding from Cancer
Research UK.
Competing interests statement
The author declares no competing financial interests.
FURTHER INFORMATION
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