AbstractUnderstanding ribosomal protein gene regulation provides a good avenue for understanding gene regulatory networks. Even after 5 decades of research on ribosomal protein gene regulation, little is known about how higher eukaryotic ribosomal protein genes are coordinately regulated at the transcriptional level. However, a few recent papers shed some light on this complicated problem

Hu, Haiyan

Li, Xiaoman

Elsevier - Publisher Connector 

Transcriptional regulation in eukaryotic ribosomal protein genes 

Genomics 90 (2007) 421–423
www.elsevier.com/locate/ygenoMinireview
Transcriptional regulation in eukaryotic ribosomal protein genes
Haiyan Hu a, Xiaoman Li a,b,⁎
a Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, 410 W. 10th Street, HS5013, Indianapolis, IN 46202, USA
b Division of Biostatistics, School of Medicine, Indiana University, 410 W. 10th Street, HS5013, Indianapolis, IN 46202, USA
Received 12 April 2007; accepted 3 July 2007
Available online 17 August 2007
Abstract
Understanding ribosomal protein gene regulation provides a good avenue for understanding gene regulatory networks. Even after 5 decades of
research on ribosomal protein gene regulation, little is known about how higher eukaryotic ribosomal protein genes are coordinately regulated at
the transcriptional level. However, a few recent papers shed some light on this complicated problem.
© 2007 Elsevier Inc. All rights reserved.Keywords: Ribosomal protein genes; Transcription factor binding sites; Gene regulationIntroduction
In this postgenomic era, one of the most important problems
is to construct gene regulatory networks, that is, to decipher
how different genes in one organism are regulated to perform
different functions. With thousands of genes in one species,
however, constructing gene regulatory networks is extremely
difficult. In this aspect, the ribosomal protein (RP) genes may
provide a better starting point for understanding gene regulation
and for constructing gene regulatory networks.
The ribosome, the protein-synthesizing machinery in all
cells, is composed of 53 or so RPs and 3 ribosomal RNAs
(rRNA) in Escherichia coli and about 80 RPs and 4 rRNAs in
mammals [1]. It is commonly believed that RP genes in the
ribosome of one species are coordinately regulated under
various cellular states [2,3]. Therefore, RP genes in one species
form a gene regulatory network. Due to the small size of this
regulatory network and the high conservation of RP genes in
terms of sequences, expression, and functions, understanding
the basic principles behind coordinate regulation in this gene
regulatory network will greatly enhance our understanding of
other gene regulatory networks.⁎ Corresponding author. Division of Biostatistics, School of Medicine, Indiana
University, 410 W. 10th Street, HS5013, Indianapolis, IN 46202, USA. Fax: +1
317 278 9217.
E-mail address: shawnli@iupui.edu (X. Li).
0888-7543/$ - see front matter © 2007 Elsevier Inc. All rights reserved.
doi:10.1016/j.ygeno.2007.07.003Early research on RP gene regulation
How RP genes are coordinately regulated in prokaryotes was
extensively studied by the early experiments in E. coli [4]. It is
known that RP genes in prokaryotes form operons in which the
expression of multiple genes is controlled by a single promoter.
Moreover, some RPs can bind to the cistronic mRNA from
which these RPs are translated, causing the process of trans-
lation to cease, thus forming a feedback network for the regu-
lation of RP genes at the translational level.
Although the known mechanism of coordinate regulation in
prokaryotes seems simple and straightforward, the mechanism
in higher eukaryotes such as mammals is considerably more
complicated and much less understood. In higher eukaryotes,
the RP genes are scattered throughout the genome with no
operon structure [5], but surprisingly, it was still observed that
the RP genes are coordinately expressed [3].
To address why RP genes in higher eukaryotes have similar
expression patterns under various conditions, before the incept-
ion of the Human Genome Project, several experiments were
performed to identify motifs (transcription factor binding sites)
in individual eukaryotic RP genes. Some of these experiments
were performed by Perry and colleagues, who worked exten-
sively on the regulation mechanism of three RP genes (i.e.,
Rpl32, Rpl30, and Rps16) in mouse [6–10]. They found four or
five motifs associated with each of the three genes but none was
shared by all three genes. Interestingly, they have shown that the
422 H. Hu, X. Li / Genomics 90 (2007) 421–423promoters of the three genes are of equal strength by in vivo
measurements of polymerase loading and by the relative
efficiency of the three promoters in driving the expression of
a linked reporter gene. This shows that all RP gene promoters
may have similar regulatory ability, even though no motif is
shared by most RP genes.
After the human genome was sequenced, attempts to identify
common motifs in the regulation of RP genes in human were
made by searching the upstream sequences of 73 human RP
genes with known motifs [11]. Results showed that there was no
shared known motif except a weak oligopyrimidine tract around
the transcription start sites in every RP gene. A recent study [12]
further confirmed that no known motif is common among all RP
genes in human by carefully searching 79 pairs of human and
mouse RP gene upstream sequences. Note that these computa-
tional studies [11,12] may be affected by the current limited
knowledge of the mammalian motifs.
Thus, without the operon structure and without any shared
motifs by most RP genes, how RP genes in higher eukaryotes
such as mammals are coordinately regulated still remains a
mystery. Recently, studies of RP genes in yeast [13–21] and
mammals [3] have shed some light on this problem from
different angles. Some observed principles behind coordinate
regulation in these studies may provide insights for under-
standing RP gene regulation in higher eukaryotes.
Recent progress in RP gene transcriptional regulation
In contrast to the above-mentioned results in mammals in
which no motifs were found to be shared by most RP genes,
ChIP–chip experiments in Saccharomyces cerevisiae showed
that Rap1 [22,23] and Fhl1 [23] bind to almost all the RP gene
promoters. In fact, the upstream region of almost all RP genes in
S. cerevisiae contains one or two Rap1 binding sites, which was
originally thought to be the basis of the coordinate regulation of
RP genes in S. cerevisiae [22,24]. However, Rap1 is responsible
for the transcription of many other genes as well and Rap1 alone
cannot explain the coordinate regulation of RP genes. Thus, the
specificity of Rap1 in the regulation of RP genes presumably
lies in its recruitment of specific cofactors. Now it is known that
Fhl1 and Ifh1 are some of the key cofactors in the transcription
regulation of RP genes [14,17–21]. When the transcription of
RP genes is activated, Rap1 binds to its binding sites, and the
binding of Rap1 with DNA may recruit Fhl1, which in turn
recruits Ifh1 that interacts with Fhl1 through the forkhead-
associated domain of Fhl1 and may bind with the IFHL motif
[18–20]. When the transcription of RP genes is repressed, only
Rap1 and Fhl1 are recruited to the promoters of RP genes [19–
21]. But how is the activation and repression of the transcription
of RP genes determined? There are at least three models. First,
Crf1, a cofactor of Fhl1, can compete with Ifh1 for the binding
to Fhl1 at RP gene promoters and thereby switch the trans-
cription between repression and activation [16]. Second, Hmo1
may be the switch from activation to repression and vice versa,
since Hmo1 is required for both the assembly of transcription
factor complexes containing Fhl1 and Ifh1 at RP promoters and
the maximal transcription of rRNA genes by Pol I [14]. Third,the CURI complex is shown to contribute to the switch, because
Ifh1 is absent from the PR gene promoters and becomes part of
the CURI complex when the transcription is repressed [19].
Other proteins such as Sfp1 are also indicated to control the
switch by binding to the RP gene promoters in the nucleus and
helping promote RP gene expression under optimal growth
conditions and leaving the nucleus in response to stress and
nutrient deficiency [13,15]. In all these models, it is clear that
the RP genes in S. cerevisiae are regulated mainly at the trans-
criptional level by the combinations of many transcription
factors that have not been found in higher level species such as
the mammals. Since all these models are supported by expe-
rimental evidence, they could be the components of a more
complete regulatory network of the RP genes in S. cerevisiae.
In addition to the common motifs shared by most of the RP
genes and the combinations of motifs in S. cerevisiae, Tanay et
al. studied the evolution of the motifs regulating RP genes in
yeast [25]. By looking at the RP gene upstream sequences in 17
fungal genomes, they showed that: (i) the IFHL motif is
conserved across the 17 species, (ii) the Rap1 motif is conserved
in 11 species, and (iii) as evolutionary divergence of species
increases compared to S. cerevisiae, the Rap1 motif is replaced
by the Homol-D motif, which is conserved in 8 species. This
study of motif evolution indicates that the transcription factors
regulating RP genes evolve, although RP genes and their func-
tions are highly conserved. Thus, the common transcription
factors that regulate RP genes in higher eukaryotes, if there are
any, should be different from those of yeast.
To determine whether some phenomena discovered in yeast
also occur in other species, Li et al. recently attempted to
identify novel motifs in RP genes of 13 eukaryotic species and
found unknown but frequently shared motifs in RP genes of
species other than yeast [3]. In every species they considered,
except for the 2 worm species, they found at least one motif
appearing in almost all RP gene promoters (the two most
frequent motifs identified in worms occur in about half of the
RP gene promoters under consideration). Moreover, these
motifs are conserved across species. For instance, the motifs
found in human are conserved in mouse and rat, the motifs
found in Drosophila melanogaster are conserved in Anopheles
gambiae, and the motifs found in Caenorhabditis elegans are
conserved in Caenorhabditis briggsae. Furthermore, the motifs
do not look similar across distant species. For example, the
mammalian motifs are not similar to the insect motifs and the
insect motifs are not similar to those of the worm. One of the
most surprising findings is that the most frequent motif found in
mammals is located in the intronic region of mammalian RP
genes—most of them being in the first intron—while motifs
found in other species are within 1000 bp upstream of the
transcription start sites of the RP genes. The middle part of the
predicted binding site of the most frequent motif in the mouse
RP gene RPL30 has been experimentally verified to be critical
for RPL30 promoter function [6]. However, the authors did not
find that this motif is actually shared by the three RP genes they
did experiments on [6], because they treated the middle part of
this motif predicted by Li et al. as the motif, while the middle
part of this motif is very degenerate and the two ends of this
423H. Hu, X. Li / Genomics 90 (2007) 421–423motif are more conserved [3]. These frequent motifs in the re-
gulatory regions of RP genes of human, mouse, and rat together
with those in fly and mosquito suggest that the RP genes in
higher eukaryotes may be coordinately regulated at the trans-
criptional level as well, instead of only at the translational level.
These results also further confirm the notion that motifs
regulating RP genes are evolving although RP gene sequences
and functions are extremely conserved across species. Together
with the experimental results in mouse [6] and many studies in
yeast [13–21], it is likely that the most frequent motifs in the
individual species may have roles in RP gene regulation similar
to that of the Rap1 motif in S. cerevisiae, and there should be
other undiscovered motifs that are important for RP gene
regulation.
Concluding remarks
Given the aforementioned motifs in every species identified
by Li et al. [3], together with the results of yeast RP gene motif
studies [13–21,24,25], it is clear that there are motifs shared by
almost all RP genes in most eukaryotic species. Moreover, RP
genes are more likely to be controlled by multiple transcription
factors instead of only a single one. Furthermore, the control
mechanism behind RP gene regulation evolves. However, many
unanswered questions remain. For instance, what transcription
factors will bind to these most frequent motifs? How did these
transcription factors and motifs coevolve? What are the other
transcription factors and motifs that are also important in
regulating RP genes? How were the most frequent motifs
transferred from the upstream to the downstream region of the
transcription start sites of RP genes in mammals? How different
is the mechanism of RP gene regulation between yeast and
higher eukaryotes? We anticipate additional research to address
these issues and further uncover the secrets of RP gene coor-
dinate transcription in higher eukaryotes, especially mammals.
Acknowledgments
We thank Drs. Robert Perry, Marc Cortese, Arthur Berg,
Patrick Monahan, and Peru Narayanan for their valuable com-
ments. This work was supported by the Showalter Trust Award
(X.L.) and the Indiana Genomics Initiative (X.L. and H.H.),
which is funded in part by the Lilly Endowment.References
[1] I.G. Wool, The structure and function of eukaryotic ribosomes, Annu. Rev.
Biochem. 48 (1979) 719–754.
[2] O. Meyuhas, R.P. Perry, Construction and identification of cDNA clones
for mouse ribosomal proteins: application for the study of r-protein gene
expression, Gene 10 (1980) 113–129.
[3] X. Li, S. Zhong, W.H. Wong, Reliable prediction of transcription factor
binding sites by phylogenetic verification, Proc. Natl. Acad. Sci. USA 102
(2005) 16945–16950.
[4] M. Nomura, R. Gourse, G. Baughman, Regulation of the synthesis ofribosomes and ribosomal components, Annu. Rev. Biochem. 53 (1984)
75–117.
[5] N. Kenmochi, T. Kawaguchi, S. Rozen, E. Davis, N. Goodman, T.J.
Hudson, T. Tanaka, D.C. Page, A map of 75 human ribosomal protein
genes, Genome Res. 8 (1998) 509–523.
[6] N. Hariharan, D.E. Kelley, R.P. Perry, Equipotent mouse ribosomal protein
promoters have a similar architecture that includes internal sequence
elements, Genes Dev. 3 (1989) 1789–1800.
[7] N. Hariharan, R.P. Perry, A characterization of the elements comprising the
promoter of the mouse ribosomal protein gene RPS16, Nucleic Acids Res.
17 (1989) 5323–5337.
[8] M.L. Atchison, O. Meyuhas, R.P. Perry, Localization of transcriptional
regulatory elements and nuclear factor binding sites in mouse ribosomal
protein gene rpL32, Mol. Cell. Biol. 9 (1989) 2067–2074.
[9] S. Chung, R.P. Perry, Importance of introns for expression of mouse
ribosomal protein gene rpL32, Mol. Cell. Biol. 9 (1989) 2075–2082.
[10] R. Moura-Neto, K.P. Dudov, R.P. Perry, An element downstream of the cap
site is required for transcription of the gene encoding mouse ribosomal
protein L32, Proc. Natl. Acad. Sci. USA 86 (1989) 3997–4001.
[11] M. Yoshihama, T. Uechi, S. Asakawa, K. Kawasaki, S. Kato, S. Higa, N.
Maeda, S. Minoshima, T. Tanaka, N. Shimizu, N. Kenmochi, The human
ribosomal protein genes: sequencing and comparative analysis of 73 genes,
Genome Res. 12 (2002) 379–390.
[12] R. Perry, The architecture of mammalian ribosomal protein promoters,
BMC Evol. Biol. 5 (2005) 15.
[13] P. Jorgensen, I. Rupes, J.R. Sharom, L. Schneper, J.R. Broach, M. Tyers, A
dynamic transcriptional network communicates growth potential to
ribosome synthesis and critical cell size, Genes Dev. 18 (2004) 2491–2505.
[14] D.B. Hall, J.T. Wade, K. Struhl, An HMG protein, Hmo1, associates with
promoters of many ribosomal protein genes and throughout the rRNA
gene locus in Saccharomyces cerevisiae, Mol. Cell. Biol. 26 (2006)
3672–3679.
[15] R.M. Marion, A. Regev, E. Segal, Y. Barash, D. Koller, N. Friedman, et al.,
Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene
expression, Proc. Natl. Acad. Sci. USA 101 (2004) 14315–14322.
[16] D.E. Martin, A. Soulard, M.N. Hall, TOR regulates ribosomal protein gene
expression via PKA and the Forkhead transcription factor FHL1, Cell 119
(2004) 969–979.
[17] S.B. Schawalder, M. Kabani, I. Howald, U. Choudhury, M. Werner, D.
Shore, Growth-regulated recruitment of the essential yeast ribosomal
protein gene activator Ifh1, Nature 432 (2004) 1058–1061.
[18] J.T. Wade, D.B. Hall, K. Struhl, The transcription factor Ifh1 is a key
regulator of yeast ribosomal protein genes, Nature 432 (2004) 1054–1058.
[19] D. Rudra, J. Mallick, Y. Zhao, J.R. Warner, Potential interface between
ribosomal protein production and pre-rRNA processing, Mol. Cell. Biol.
27 (2007) 4815–4824.
[20] D. Rudra, Y. Zhao, J.R. Warner, Central role of Ifh1p–Fhl1p interaction in
the synthesis of yeast ribosomal proteins, EMBO J. 24 (2005) 533–542.
[21] Y. Zhao, K.B. McIntosh, D. Rudra, S. Schawalder, D. Shore, J.R. Warner,
Fine-structure analysis of ribosomal protein gene transcription, Mol. Cell.
Biol. 26 (2006) 4853–4862.
[22] J.D. Lieb, X. Liu, D. Botstein, P.O. Brown, Promoter-specific binding of
Rap1 revealed by genome-wide maps of protein–DNA association, Nat.
Genet. 28 (2001) 327–334.
[23] T.I. Lee, N.J. Rinaldi, F. Robert, D.T. Odom, Z. Bar-Joseph, G.K. Gerber, N.
M. Hannett, C.R. Harbison, C.M. Thompson, I. Simon, J. Zeitlinger, E.G.
Jennings, H.L. Murray, D.B. Gordon, B. Ren, J.J. Wyrick, J. Tagne, T.L.
Volkert, E. Fraenkel, D.K. Gifford, R.A. Young, Transcriptional regulatory
networks in Saccharomyces cerevisiae, Science 298 (2002) 799–804.
[24] R.F. Lascaris, W.H. Mager, R.J. Planta, DNA-binding requirements of the
yeast protein Rap1p as selected in silico from ribosomal protein gene
promoter sequences, Bioinformatics 15 (1999) 267–277.
[25] A. Tanay, A. Regev, R. Shamir, Conservation and evolvability in regulatory
networks: the evolution of ribosomal regulation in yeast, Proc. Natl. Acad.
Sci. USA 102 (2005) 7203–7208.


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Transcriptional regulation in eukaryotic ribosomal protein genes

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