"The small introns of antisense genes are better explained by selection for rapid
transcription than by ‘genomic design’".

Jianjun Chen ^{*, @}, Miao Sun ^*, Janet D. Rowley ^*, and Laurence D. Hurst ^{1, @}

^* Section of Hematology / Oncology, Department of Medicine, University of Chicago,
Chicago, Illinois 60637, USA;
¹ Department of Biology and Biochemistry, University of Bath, Somerset, UK BA2 7AY;

^@ Correspondence should be addressed to:
J.C. ( jchen@medicine.bsd.uchicago.edu )     and L.D.H. ( l.d.hurst@bath.ac.uk )

Several models have been proposed to explain why expression parameters of a gene might
be related to the size of the gene’s introns. These include the idea that an energetic cost of
transcription should favor smaller introns in highly expressed genes (the ‘economy
selection’ argument) and that tissue-specific genes reside in genomic locations with complex
chromatin level control requiring large amounts of non-coding DNA (the ‘genomic design’
hypothesis). We recently proposed a modification of the economy model arguing that, for
some genes, the time expression takes is more important than the energetic cost, such that
some weakly but rapidly expressed genes might also have small introns. We suggested that
antisense genes might be such a class and showed that the data appears to be consistent
with this. We now re-examine this model to ask whether: (a) the effects described were solely
owing to the fact that antisense genes are often non-coding RNA and (b) whether we can
confidently reject the ‘genomic design’ model as an explanation for the facts. We show that
the effects are not specific to non-coding RNAs and that the predictions of the ‘genomic
design’ model are not for the most part upheld.

Several different models have been proposed to explain why broadly/highly expressed genes
typically have small introns. The ‘economy selection’ model argues that it reflects selection for
minimizing the costs of gene expression (Hurst et al. 1996; Castillo-Davis et al. 2002; Eisenberg
and Levanon 2003; Seoighe et al. 2005), the ‘mutational bias’ model suggests that it reflects
regional mutation biases in rates of insertion and deletion (Urrutia and Hurst 2003), while the
‘genomic design’ model postulates that it reflects selection for genomic organization to enable
control of gene expression (Vinogradov 2004, 2005). Recently, we observed that human
antisense genes have significantly shorter introns compared with other genes, including their
more broadly/highly expressed sense partners. This we argued could not be simply explained by
any of the above models. Our further analyses suggested that the short introns of antisense genes
might be related to antisense regulation that requires a rapid response time (Chen et al. 2004,
2005a). Thus, we proposed an ‘efficiency selection’ model (which can also be recognized as a
‘time-economy selection’ model) to explain the short introns of antisense genes (Chen et al.
2005a). Here, in this short note, we address two matters arising.

First, is the reduced intronic size of antisense genes true for protein-coding antisense as well as for non-coding RNA (ncRNA) or was our observation more a statement about ncRNA than about antisense per se. Note that the antisense genes are enriched for ncRNA: percentage of the genes with assigned protein-coding
region (CDS) in the antisence (A), sense (S), antisense-like (AL), sense-like (SL) and non-overlapping
bidirection (NBD) genes (see their classification in the legend of Fig. 1; see also
Chen et al. 2004, 2005a,b) is 57.5%, 94.5%, 40.2%, 91.6% and 79.1% respectively.

Second, have we been premature in our rejection of the ‘genomic design’ model?

Small introns for protein-coding antisense genes

To address the first issue we excluded all the genes without CDS. However, this leaves a
problem, namely which gene in a pair of bi-directional protein-coding genes should we consider
the sense gene and which the antisense? We defined the S and A (or SL and AL) based on the
conventional concept (e.g., Lipman 1997) that the sense (or SL) gene should exist in more tissues
and be expressed at a higher level than its antisense partner (Chen et al. 2004, 2005a,b). If the
expression levels of the paired two genes are the same, the gene pair is excluded from this
analysis. We should expect that if the ‘efficiency selection’ model is wrong and the economy
model uniquely true that the sense gene with the higher expression level should be the one with
the smaller introns. If the ‘efficiency selection’ model is correct this could in principle be
reversed. Therefore to ask if the ‘efficiency selection’ model might have merits we consider
whether antisense has smaller introns compared to its sense partner. If the more weakly
expressed antisense gene has the smaller introns, this could not be explained by economy or
regional mutational bias, but would be consistent with efficiency.

In analysis of the protein-coding genes only, we observed a similar pattern to the
previous observation in which both protein-coding and non-coding genes are considered (Chen et
al. 2005a), namely a reduced intronic size for the putative antisense genes: the average intron
length (nucleotides, nt) of the protein-coding A, S, AL, SL and NBD genes is 4779 (average
logarithm value: 3.3113), 5032 (3.3935), 9278 (3.4570), 12,137 (3.7340) and 4904 (3.3588)
respectively, while the values of the whole gene sets were 4995 (3.3018), 5313 (3.3759), 9049
(3.4565), 12,599 (3.7338) and 5202 (3.3558) respectively. The differences are still significant
between antisense genes and any other kind of genes (P < 0.01; both ‘independent samples t-test’
and ‘Mann-Whitney U-test’ in analyses of both the original and logarithm values), as well as
between antisense genes and their sense partners (or between AL and SL genes) in a paired
fashion (P < 0.05; ‘paired samples t-test’). Thus, the difference that we see between S (SL) and
A (AL) genes does not result exclusively from the potential difference in intron size between
protein-coding genes and ncRNA genes.

Predictions of ‘genomic design’ are not for the most part upheld

The ‘genomic design’ hypothesis (Vinogradov 2004) proposed that lowly expressed genes have
large introns as these introns may contain large suppressing control elements. The model also
proposes that the non-coding DNA in and around a gene (gene nests) affects the expression of
the gene through chromatin level regulation. It is this feature that predicts that a gene with small
introns should sit in a region with small intergenic distance and should have genes of comparable
intronic dimensions as neighbors. The model predicts, we reasoned, that in a comparison of pairs
of linked genes, the one with lower/narrower expression should be the one with the larger
introns, as it should be the one with the extra control elements. This is the opposite of what we
found in comparing antisense genes with their overlapping sense partners in a paired fashion
(Chen et al. 2005a), namely that antisense genes have significantly shorter introns (P < 0.01)
than their sense partners, although their sense partners have significantly higher expression levels
and wider expression breadths (P < 10^-4 ). We therefore rejected this as a potential explanation for
our set of observed facts. The same finding rejects biased mutation and economy selection, the
former predicting no difference between the genes in mean intron size of neighbors, the latter
predicting smaller introns for the more highly expressed gene (see also Supplementary Figs.
1a,b).

The ‘genomic design’ model makes further predictions (AE Vinogradov, personal
communication). It suggests that, although intronic sequences of the A and AL genes are shorter
than those of the S and SL genes, respectively, this may yet be consistent with the ‘genomic
design’ model were we to find that genes residing in the same genomic region have a similar
intronic to exonic length ratio (because chromatin of the gene nest condenses and decondenses as
a whole).

To test the prediction, we compared the intronic and exonic DNA lengths as well as the ratio
of intronic to exonic length in the A, S, AL, SL and NBD genes. In the following analyses, we
did not exclude non-coding genes so that it would be consistent with our previous study (Chen et
al. 2005a). Because the full lengths for both intronic and exonic sequences are necessary for the
analysis, we focus on full-length mRNA sequences that also span introns (although we observed
a similar pattern in analysis of all intron-spanning sequences; data not shown). Our findings do
not support the prediction. Although the A and AL genes are shorter (compared to the S and SL
genes) in both intron and exon (Supplementary Fig. 2), on average the A and AL genes have a
significantly lower ratio of intronic to exonic length (P < 10^-4 ) compared to the S and SL genes
respectively (Fig. 1). This is also true in a comparison of the A genes with their S partners and
the AL genes with their SL partners when considered in a paired fashion. We have collected 397
S/A and 205 SL/AL gene pairs in which both members have full-length, intron-spanning mRNA
sequences. The A and AL genes have a significantly lower ratio of intronic to exonic length (P <
10^-4 ; Paired samples t-test with the logarithm ratios) than do their S and SL partners (data not
shown). Thus, contrary to the ‘genomic design’ hypothesis, we find no evidence that the
intron/exon ratio for sense and antisense genes is a property of the genomic region (‘gene nest’)
within which they reside.

Vinogradov (personal communication) also predicts that the intronic to exonic length ratio
should be higher in the SL/AL genes (compared to the S/A genes and non-overlapping genes)
owing to the exon-intron overlap of the opposite genes in this pair (i.e., the intronic sequences of
these genes do not consist completely of noncoding DNA because they may encode exons on the
opposite strand). The evidence here is mixed. Contrary to the prediction, on average the ratio of
intronic to exonic length of the AL genes is significantly lower (P < 10^-2 ) than not only that of
the SL genes but also that of the S genes and similar to that of the NBD genes (Fig. 1). However,
in agreement with the prediction, the SL genes do have the highest ratio of all classes and the AL
genes have a higher ratio than the A genes (Fig. 1). The balance of evidence, however, suggests
that the ‘genomic design’ model cannot provide the complete explanation. Notably, the fact that
AL genes have a lower ratio than SL genes is important as, if SL genes have large introns owing
to inclusion of exons of the antisense within the SL introns, by the same logic AL genes should
have still larger introns as SL exons are larger than AL exons (Supplementary Fig 2). That the
reverse is found argues against the ‘genomic design’ model.

While the observations for the most part appear to be inconsistent with the ‘genomic design’
hypothesis, how might they be explained? Economy selection (of energy or of time) can be
realized in one of the counterpart genes of a given pair and its effect should be stronger on the
intronic than on the exonic part of the gene (because the latter is under stronger functional
constrains). As a result, the ratios of intronic to exonic length would differ between counterpart
genes, just as we observed (Fig. 1). As the A and AL genes have a significantly lower and
narrower expression compared with the S and SL genes (Supplementary Figs. 1a,b), the ‘energy-economy selection’ cannot explain the observations. Thus, only the ‘time-economy selection’
(i.e., the ‘efficiency selection’) model (Chen et al. 2005a) can provide a feasible explanation.
This notion is further bolstered by the finding that antisense genes in the co-expressed, inversely
expressed and/or evolutionarily conserved SA pairs (these classes of SA pairs being the most
likely to participate in antisense-mediated gene regulation that requires a rapid response time;
Chen et al. 2005b) have the most extremely short introns (Chen et al. 2005a). Given this, it is not
surprising that the antisense genes have a significantly lower ratio of intronic to exonic length
than do the S genes (Fig. 1).

Why do antisense-like genes have small introns?

One issue that we did not consider previously was whether ‘efficiency selection’ might
additionally explain the significant difference between the AL and SL genes in the ratio of
intronic to exonic length. Although the regulatory interactions were presumed only for the SA
pairs as they have exon overlaps (Knee and Murphy 1997; Kumar and Carmichael 1998;
Vanhee-Brossollet and Vaquero 1998; Chen et al. 2004, 2005a,b), theoretically, it is possible for
an AL gene to regulate the expression of its SL partner if their pre-mRNA molecules could form
double-strand RNAs in the nucleus. Since double-stranded secondary structures formed by base
pairing between exons and downstream intron elements in pre-mRNAs of the same genes (i.e.,
exon-intron duplex structures) have been observed in many cases (see Wang and Carmichael
2004 and references therein), it is reasonable to presume that double-strand RNAs can be formed
by base pairing between exons (and/or introns) and cognate introns (i.e., forming exon-intron
and/or intron-intron duplexes) of the counterpart genes in a given SL/AL gene pair before the
overlapped intronic regions in pre-mRNAs are spliced out. Indeed, the fact that, as with SA
pairs, human SL/AL pairs are also significantly more frequently (P < 0.05) co-expressed than are
pseudo gene pair sets with the same expression levels (Supplementary Table 3 in Chen et al.
2005b) provides indirect evidence to support the hypothesis that regulation may also exist
between AL and SL. Nevertheless, there is no direct experimental evidence yet, thus, a
systematic and genome-wide identification of all naturally occurring double-strand RNAs in the
nucleus of some cell types would be necessary to test the hypothesis.

Discussion

In sum, predictions of the ‘genomic design’ model regarding the ratios of intronic to exonic
length between antisense (antisense-like) genes and sense (sense-like) genes are for the most part
not upheld and hence the above results argue against this model as a means to account for the
unusually small introns of antisense genes. Both protein-coding and non-coding antisense genes
show the same reduced intronic dimensions. More generally, the results strengthen our previous
conclusion (Chen et al. 2005a) that the findings are inconsistent with prior models but are
consistent with ‘efficiency selection’. We should, however, reiterate that we do not propose that
the ‘efficiency selection’ model explains all variation in intronic sizes. We still consider the
‘genomic design’ model as one of several models that need to be considered in the more general
context of understanding inter-gene variation in intronic dimensions, not least because it is one
of the few models that attempts to account for the correlation between intron size and intergenic
distance (Vinogradov 2004, 2005). Indeed, it is worth noting that the SL genes have much longer
introns (Chen et al. 2005a; Supplementary Fig. 2) and much higher ratio of intronic to exonic
length (Fig. 1) than do the NBD genes although the SL genes have significantly higher
expression levels and wider expression breadths than do the NBD genes (Supplementary Fig. 1).
This observation could not be explained by either our model or the ‘economy selection’ model,
but can be explained by the ‘genomic design’ model. The ‘genomic design’ model proposed that
the phenomenon that SL genes have much longer introns than do the NBD genes is owing to the
fact that the intronic sequences of the SL genes do not consist completely of noncoding DNA
because they may encode exons on the opposite strand for the AL genes (AE Vinogradov,
personal communication).

ACKNOWLEDGEMENTS

We thank Dr. Alexander E. Vinogradov for allowing us to cite his thoughtful prediction and
hypothesis as personal communication, and Dr. Laurent Duret for his constructive discussions.
This work was supported by the G. Harold and Leila Y. Mathers Charitable Foundation (J.C.),
National Institutes of Health grant CA84405 (J.D.R.), the Spastic Paralysis Foundation of the
Illinois, Eastern Iowa Branch of Kiwanis International (J.D.R.), and the UK Biotechnology and
Biological Sciences Research Council (L.D.H.).

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Chen, J., M. Sun, W. J. Kent, X. Huang, H. Xie, et al., 2004 Over 20% of human transcripts
might form sense–antisense pairs. Nucleic Acids Res. 32: 4812–4820

Chen, J., M. Sun, L. D. Hurst, G. G. Carmichael and J. D. Rowley, 2005a Human antisense
genes have unusually short introns: evidence for selection for rapid transcription. Trends
Genet. 21: 203-207.

Chen, J., M. Sun, L. D. Hurst, G. G. Carmichael and J. D. Rowley, 2005b Genome-wide analysis
of coordinate expression and evolution of human cis-encoded sense-antisense transcripts.
Trends Genet. 21: 326-329.

Eisenberg, E., and E. Y. Levanon, 2003 Human housekeeping genes are compact. Trends Genet.
19: 362-365

Hurst, L.D., G. McVean and T. Moore, 1996 Imprinted genes have few and small introns. Nat
Genet. 12: 234-237.

Knee, R., and P. R. Murphy, 1997 Regulation of gene expression by natural antisense RNA
transcripts. Neurochem Int. 31: 379-392.

Kumar, M., and G. G. Carmichael, 1998 Antisense RNA: function and fate of duplex RNA in
cells of higher eukaryotes. Microbiol Mol Biol Rev. 62: 1415-1434.

Lipman, D. J., 1997 Making (anti)sense of non-coding sequence conservation. Nucleic Acids
Res. 25: 3580-3583.

Seoighe, C., C. Gehring and L. D. Hurst, 2005 Gametophytic selection in Arabidopsis thaliana
supports the selective model of intron length reduction. PLoS Genetics 1: e13.

Urrutia, A. O., and L. D. Hurst, 2003 The signature of selection mediated by expression on
human genes. Genome Res. 13: 2260-2264.

Vanhee-Brossollet, C., and C. Vaquero, 1998 Do natural antisense transcripts make sense in
eukaryotes? Gene 211: 1-9.

Vinogradov, A. E., 2004 Compactness of human housekeeping genes: selection for economy or
genomic design? Trends Genet. 20: 248-253.

Vinogradov, A. E., 2005 Noncoding DNA, isochores and gene expression: nucleosome
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Comparison of the ratios of intronic to exonic length among the five gene categories.
The S (sense) and A (antisense) genes form SA (sense-antisense) gene pairs with exon overlaps,
while the SL (sense-like) and AL (antisense-like) genes form NOB (non-exon-overlapping bi-directional)
gene pairs without exon overlaps; both SA and NOB pairs are bi-directional (BD)
gene pairs. NBD (non-bi-directional) genes contain only single-direction transcribed sequences.
We classified the S and A or SL and AL genes in each BD (bi-directional) gene pair mainly
based on the conventional concept (e.g., Lipman 1997) that the S (or SL) gene should exist in
more tissues and/or be expressed at a higher level than its A (or AL) partner gene (Chen et al.
2004, 2005a,b). The mean and median values with their 95% confidence intervals of the
logarithm (log) values of the ratios of intronic to exonic DNA length are shown in the plot. Note
that, the original values are not normally distributed, but the logarithm values are almost
normally distributed.

Thus, we use ‘independent samples t-test’ and ‘Mann-Whitney U-test’ to
determine significance (P-value) in their mean-value and median-value differences in the
logarithm ratio data, respectively. The A and AL genes have significantly lower ratios of intronic
to exonic DNA length (P < 10^-4 ) compared with the S and SL genes, respectively. In addition,
the mean and median values of the logarithm ratios in the AL genes are significantly lower (P <
0.001) than in the S genes and similar to in the NBD genes. The A genes have the lowest ratios
among the five gene categories, which is in accord with the ‘efficiency selection’ model (Chen et
al. 2005a). The detailed values of the original and log-transformed data as well as the
significance (P-values) of the comparisons based on the logarithm values are shown in the
embedded table. In fact, we observed a similar pattern in analysis of the original data. Although
the mean value of the original ratios is higher in the AL genes than in the S and NBD genes, the
median value of the original ratios as well as the mean and median values of the logarithm ratios
in the AL genes is significantly lower (P < 0.001) than in the S genes and similar to in the NBD
genes. Indeed, we observed that the high mean value of the original ratios in the AL genes was
caused by a very small group of extreme big ratios (data not shown).

Figure 1.

Comparison of expression level and expression breadth among the five gene categories. The mean and median values of the logarithm data with their 95% confidence intervals are shown.

(a) The A and AL genes have a significantly lower expression level (P < 10^-4 ; both ‘independent samples t-test’ and ‘Mann-Whitney U-test’) than do the S and SL genes. The expression level of the NBD genes is significantly lower (P < 10^-2 ) than those of the S and SL genes, but significantly higher (P < 10^-4 ) than those of the A and AL genes.

(b) The average expression breadths of the A and AL genes are significantly narrower (P < 10^-4 ) than those of the S and SL genes. The expression breadth of the NBD genes is significantly narrower (P < 10^-2 ) than those of the S and SL genes, but significantly wider ( P < 10^-4 ) than those of the A and AL genes.

Supplementary Figure 1a.

Comparison of the intronic and exonic DNA lengths among the five gene categories. The mean and median values with their 95% confidence intervals of the logarithm (log) values of the intronic and exonic DNA lengths are shown. Both intronic and exonic DNA lengths of the A and AL genes are significantly shorter (P < 10^-4 ; both ‘independent samples t-test’ and ‘Mann-Whitney U-test’) than those of the S and SL genes. The A genes have the shortest intronic DNA length while the AL genes have the shortest exonic DNA length among the five gene categories. A similar pattern was observed in analysis of the average length per intron and per exon (data not shown). Note that, although the average length per intron of the AL genes is significantly longer than that of the A genes (Fig. 2 in Chen et al. 2005a), their full intronic DNA lengths are roughly similar due to the fact that the AL genes have a smaller intron number (in average, the A, S, AL, SL and NBD genes have 5.3, 9.1, 4.2, 9.6 and 6.6 introns, respectively).

Supplementary Figure 2.

Additional References:

1. Hovsepian JA, and Frenster JH, "Sense and Antisense during RNA Initiation of the DNA Transcription Bubble".

2. Cho DH, Thienes CP, Mahoney SE, Analau E, Filippova GN, and Tapscott SJ,
"Antisense Transcription and Heterochromatin at the DM1 CTG Repeats Are Constrained by CTCF".

3. Navarro P, Pichard S, Ciaudo C, Avner P, and Rougeulle C, "Tsix transcription across the Xist gene alters chromatin conformation without affecting Xist transcription: implications for X-chromosome inactivation".

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