Exon Recognition in Vertebrate Splicing

18/1/2019 Exon Recognition in Vertebrate Splicing
Journal of Biological Chemistry

www.jbc.org
doi: 10.1074/jbc.270.6.2411
February 10, 1995 The Journal of Biological Chemistry 270, 2411-
2414.
Exon Recognition in Vertebrate

Splicing (*)
Susan M. Berget
+ Author A liations
INTRODUCTION
The Problem
The average vertebrate gene consists of multiple small exons

(average size, 137 nucleotides) separated by introns that are
considerably larger(1). Thus, the vertebrate splicing machinery has
the task of nding small desired exons amid much longer introns.
The splice site consensus sequences that drive exon recognition are
located at the very termini of introns(2, 3). Despite the discriminatory
challenge faced during exon recognition in large multiexon
premessenger RNAs, vertebrate splice sites are short and poorly
conserved. In fact, splice site sequences in mammals are less
conserved than their yeast counterparts despite the fact that only a
minority of genes in Saccharomyces cerevisiae have introns; and those
genes that are split by introns usually have only a single intron(4, 5).
Thus, vertebrate splicing contends with a more complex speci city
problem via recognition of less precise consensus sequences. Any
mechanism for the orchestration of splicing in multiexon vertebrate
genes must provide an explanation for this puzzle.
Part of the solution of the puzzle comes from the observation that
individual splice sites are not independently recognized consensus
sequences. In both yeast and vertebrate splicing, interactions
between 5′ and 3′ splice sites and the factors that recognize them
have been observed during the earliest steps of spliceosome
assembly(4, 5, 6, 7, 8, 9, 10, 11, 12). Usually these interactions are
depicted as occurring between the 5′ and 3′ splice sites across an
intron. Experimentally, such interactions have been observed with in
vitro splicing precursor RNAs having naturally short or arti cially
shortened introns. It is di cult to extrapolate initial interactions
between the factors that recognize the 5′ and 3′ splice sites anking a
small vertebrate intron to introns that can naturally be 100 kilobases
in length, especially given the likelihood that such introns will contain
sequences that are as good a match to consensus splice sites as the
actual utilized sites.
Exon De nition
http://www.jbc.org/content/270/6/2411.long 1/25
Models that invoke pairing between the splice sites across an exon,
as contrasted with pairing across an intron, are useful perspectives of
splice site pairing for the splicing of pre-mRNAs with large introns
and small exons. Such an exonic perspective of splice site recognition
has been termed “exon de nition”(10). This review discusses exon
de nition and contrasts it with intron-oriented perspectives that are
more useful when considering splicing in lower eukaryotes with small
introns. The basic exon de nition model proposes that in pre-mRNAs
with large introns, the splicing machinery searches for a pair of
closely spaced splice sites in an exonic polarity (Fig. 1). When such a
pair is encountered, the exon is de ned by the binding of U1 and U2
snRNPs (1)and associated splicing factors, including the 3′ splice site
recognizing factors U2AF and SC35 and the 5′ splice site-recognizing
factor ASF/SF2(2, 13, 14, 15, 16). Following de nition of the exon,
neighboring exons must be juxtaposed, presumably via interactions
between the factors that recognize individual exons. Thus, from this
perspective, assembly of the active vertebrate spliceosome consists
of the sequential steps of exon de nition and exon juxtaposition.
Figure 1:
Exon De nition in pre-

mRNAs with small exons
and large introns.
snRNPs (red and green)
and SR protein (yellow)
are shown interacting
with isolated exons
View larger version: during exon de nition.
In this page In a new window U4/U5/U6 snRNPs (black)
Download as PowerPoint Slide are depicted as joining
the assembly during the
subsequent step of exon
juxtaposition.
Predictions of Exon De nition
The exon de nition model o ers predictions of pre-mRNA behavior.

Several of these predictions have been tested in the last several
years, and the results lend credence to an exonic perspective of
splice site recognition.
Exon Skipping
Exon-oriented and intron-oriented perspectives of splice site pairing

predict di erent phenotypes resulting from mutation of splice sites
bordering an internal exon (Fig. 2). Models invoking an initial pairing
of splice sites across introns predict that such mutations should
inhibit splicing of the intron in which they occur but should have
minimal impact on the splicing of neighboring introns. In contrast,
exon de nition predicts that mutation of a splice site bordering an
internal exon should depress recognition of the exon with
concomitant inhibition of splicing of the adjoining intron, i.e.
mutations in an intron will inhibit the splicing of two introns, the
intron containing the mutation and the intron on the other side of
the exon bearing the mutation. This hypothesis has been tested in
vitro, where it was observed that mutation of a 5′ splice site
depressed the removal of the upstream intron 20-fold(17). The
converse experiments have also been reported. Strengthening a
naturally weak 5′ splice site of an internal exon by making it a better
t to the consensus site increased in vitro splicing of the upstream
intron(8, 18). In vivo, mutant 5′ splice sites were genetically
suppressed by second mutations that improved the 3′ splice site
across the exon(19, 20).
Figure 2:
Predictions of the
phenotype of mutation of
the 5′ splice site
bordering an internal
exon. Exon pairing of
View larger version: splice sites predicts exon
In this page In a new window skipping or the activation
Download as PowerPoint Slide of a proximal cryptic 5′
splice site (left), whereas
intronic pairing of splice
sites predicts intron inclusion or distal cryptic site activation
(right).
Mutation of vertebrate splice sites also leads to exon skipping. A

survey of mammalian mutations available in the data base in the
summer of 1994 indicated that over 100 splice site mutations have
been characterized in disease gene DNA(21). Four phenotypes were
observed: exon skipping, activation of a cryptic splice site, creation of
a pseudo-exon within an intron, and intron retention, in ratios of 51,
32, 11, and 6%, respectively. The most frequent phenotype was exon
skipping. Exon skipping is a predicted phenotype from an exon
perspective because mutation of the splice site at one side of an
exon should inhibit pairing of splice sites across exons and inhibit
recognition of the exon. Rejection of the exon leads directly to exon
skipping.
The observation of exon skipping strongly indicates that splice sites

are recognized as exonic pairs. It is presumably this dependence
upon a pair of sites that minimizes recognition of isolated cryptic
sites within large vertebrate introns. Occasionally, mutation of
human genes has created a strong splice site deep within an intron.
Such created sites have been observed to be utilized via the
activation of a nearby cryptic splice site of the opposite polarity to
create a pseudo-exon from within an intron. Again, the observation is
that only pairs of splice sites can be recognized and that cryptic
splices in introns can only be activated by creation of a nearby site of
the opposite type in an exonic polarity.
Occasionally, mutation of an internal splice site results in intron

retention. Exon de nition would not predict intron retention, except
perhaps for very small introns. Of the splice site mutations
mentioned above, only 6% caused intron retention. Four of the
included introns were very short, and three were terminal introns,
suggesting abrogation of exon de nition modes of recognition when
introns are very small or at the ends of pre-mRNAs (see below). Three
examples involved large internal introns and cannot be explained by
current exon perspectives.
Exon Size Maximum
In addition to exon skipping, the other major phenotype resulting

from mutation of a splice site in a human gene is activation of a
cryptic site of the same type. The activated cryptic site always lies
close to the mutated site, suggesting that splice sites are acceptable
only if they reside close to a site of the opposite polarity and that,
therefore, internal vertebrate exons may have a size maximum
imposed in part by the splicing machinery. Fig. 3 indicates the size
distribution of 1600 primate internal exons. Of these exons, only
3.5% are longer than 300 nucleotides and less than 1% are longer
than 400 nucleotides, indicating that large internal exons are rare. In
vitro, the assembly of ATP-dependent spliceosomes is inhibited if
internal exons with strong constitutive splice sites are internally
expanded to greater than 300 nucleotides(10). In vivo, expansion of
internal exons residing in vertebrate genes with moderate to large
introns has two phenotypes: activation of internal cryptic splice sites
within the expanded exon to create small exons or skipping of the
entire exon (see below). (2)These phenotypes are consistent with
splicing-imposed restriction on exon length. Presumably, such a size
limitation helps explain why cryptic splice sites located inside of long
vertebrate introns are not occasionally misrecognized to create large
internal exons when the normal sites are mutated. A few
spectacularly long vertebrate internal exons exit; the mechanism
whereby such exons bypass restrictions on exon length is unknown.
Figure 3:
Internal exon size

distribution. Length
distribution of 1600
primate internal exons
from a library normalized
to represent highly
related exons only a
View larger version:
single time (top) (library
In this page In a new window
kindly provided by D.
Download as PowerPoint Slide
Searles, University of
Pennsylvania) or 194
alternative vertebrate cassette exons (bottom) compiled by
Stamm et al.(46) or by S. Smith and T. A. Cooper (Baylor
College of Medicine).
Exon Size Minimum
Simultaneous recognition of splice sites bordering an exon also

suggests that a minimal separation between the sites might be
required to prevent steric hindrance between the factors that
recognize individual sites. When a constitutively recognized internal

exon was internally deleted below 50 nucleotides it was skipped by
the in vivo splicing machinery(23). Increasing the strength of the
splice sites alleviated problems in recognition, suggesting that exon
size and splice site strength are additive factors in exon
recognition(24). Some very small natural internal exons exist. Six and
seven nucleotide exons are frequently found in muscle protein
genes; N-CAM has a three-nucleotide exon. Although few very small
exons have been studied, those that have suggest that very small
exons require special enhancing sequences in addition to strong
splice sites for inclusion(25, 26, 27). Deletion of these elements
causes exon skipping when the exon is small but not when it has
been internally expanded to a more normal length. The small exon
enhancers are located within the neighboring introns outside of the
normal splice sites. It seems likely that such enhancers function as
binding sites for splicing factors that arti cially extend the exon
domain during exon recognition.
Terminal Exons
Exon de nition suggests that terminal exons, both rst and last
exons, will require special mechanisms for their recognition. First
exons end with a 5′ splice site but have no processing signal at their
beginning. They do, however, bear a modi cation at their beginning
via the 7-methylguanosine cap attached to all polymerase II
transcripts. The cap and nuclear proteins that bind the cap are
essential for in vitro splicing of simple one-intron pre-mRNAs(28). In
two-intron pre-mRNAs, changing the guanosine cap to an adenosine
cap depressed removal of the rst intron in vitro but had only
minimal impact on the second intron (29). These results indicate both
that pre-mRNAs are recognized segmentally in vitro and that the cap
is essential for recognition and removal of the rst intron. Or as
stated from an exon perspective, rst exons can be recognized via
interactions between the factors that recognize caps and 5′ splice
sites.
Last exons begin with a 3′ splice site and terminate with a poly(A)
site(30). They are often the largest exon in a vertebrate gene, with an
average size of approximately 600 nucleotides(1, 31). Exon
recognition predicts that factors recognizing 3′ splice sites interact
with factors recognizing poly(A) sites to recognize last exons. Indeed
mutation of 3′ splice sites inhibits the in vitro polyadenylation
cleavage reaction(32). Just as with rst exons, mutation of the signal
at the distal end of a 3-terminal exon, the poly(A) site, inhibits in vitro
removal of proximal but not distal introns(33). These results suggest
that splicing and polyadenylation factors interact across 3′-terminal
exons. The mechanism of this interaction is unclear, although recent
observations have suggested that U1 snRNPs or the U1 snRNP A
protein are involved, either positively or negatively, via recognition of
exon internal sequences upstream of the polyadenylation signal
AAUAAA(34, 35, 36).
Exon Enhancer Sequences and Di erential Splicing
Exon de nition has proven to be a useful framework for considering

di erential splicing, especially those di erential splicing events
involving cassette exons that are di erentially included. Generally,
di erentially recognized exons have either weaker splicing signals or
a suboptimal length compared with constitutive exons (3, 37) (Fig. 3),
suggesting that the constitutive exon de nition process is so strong
as to be di cult to regulate unless the involved exon recognition
signals are weak. Exon inclusion in these cases appears to be via
recognition of special sequences by tissue or development-speci c
splicing factors(38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49). One class
of sequences commonly found associated with di erential exons,
referred to as exon enhancers, resides within the target exon. The
existence of exon internal consensus sequences was initially
surprising because of the constraints imposed upon such sequences
by coding requirements. A family of such sequences, often purine-
rich and coding for a wide variety of amino acids, has been observed
to be important for recognition of weak exons. These sequences
appear to be the binding site for a family of splicing factors known as
SR proteins because of the arginine and serine repeats that
characterize them(50). In addition to binding exon sequences via
their RNA binding domains, the SR proteins also make protein-
protein contacts via their SR domains with U2AF bound near the 3′
splice site and U1 snRNPs bound to the 5′ splice site via arginine-
serine-rich domains present in each(12, 15, 51). Such recognition
makes the SR proteins ideal candidates for exon-bridging proteins
involved in exon de nition. Bridging across exons has been
experimentally detected in that UV cross-linking of U2AF to the 3′
splice site of an isolated exon is a ected by the strength of the 5′
splice site terminating the exon(52).
Intron De nition
Interestingly, SR proteins have not yet been found in S. cerevisiae.

Even those yeast splicing proteins that are equivalent in known
function to vertebrate proteins containing SR domains lack SR
domains in their yeast forms(53, 54). From an exon de nition
viewpoint, this absence may not be surprising in that organisms with
small introns, such as S. cerevisiae, may not use exon de nition and
therefore may not need many or all of the SR proteins. In general,
evidence exists to suggest that pre-mRNAs with small introns use the
intron, rather than the exon, as the initial mode of pairing between
splice sites(4, 5, 11). In Saccharomyces pombe, pre-mRNAs have
multiple small introns of less than 100 nucleotides(55). In Drosophila,
50% of the introns are less than 100 nucleotides and are often
anked by large exons(1, 56). Expanding small introns in either
organism inhibits splicing of the intron or activates cryptic sites
within the expanded introns(57, 58). (3)Thus, in genes with small
exons, expanding the exon leads to aberrant splicing, whereas in
genes with small introns, expanding the introns leads to aberrant
splicing. These observations suggests that the pairing unit utilized is
that o ering the smallest distance between two adjacent splice sites.
Mutation of splice sites in genes with small introns has a di erent

phenotype than the same mutation in genes with large introns. In
pre-mRNAs with small introns, mutation of an internal 5′ splice site
does not lead to exon skipping. Instead the mutated intron is

included in the nal mRNA and the splicing of neighboring introns is
una ected (58). A di erence in splicing signals between the two types
of introns has also been noticed(56, 57). Small introns often lack the
pyrimidine track located between the branch point and the 3′ splice
site of vertebrate but not S. cerevisiae introns. Therefore, small
introns appear to have di erent signals and to be recognized
somewhat di erently than large introns.
Initial pairing of splice sites across an exon may be similar to initial

pairing across an intron. Except for the SR proteins, the vertebrate
factors known to be required for splicing are found in yeast and are
required there as well. Several lines of experimental evidence also
suggest that either the intron or exon can be the pairing unit during
pre-mRNA recognition. As mentioned earlier, expansion of an
internal exon in a vertebrate gene can cause exon skipping. If the
same exons and their anking splice sites, however, are placed in a
gene in which the introns anking the expanded exon are small, the
expanded exon is constitutively included(59).2 Expansion of the small
introns reverts the phenotype to exon skipping. These observations
suggest that large exons are only a problem in genes with large
introns, and more importantly, that the same splice sites can be
recognized in either intronic or exonic polarity (Fig. 4).
Figure 4:
Earliest complex
formation in vertebrates
via exon de nition versus
that in lower eukaryotes
via intron de nition.
View larger version:

In this page In a new window
Download as PowerPoint Slide
Exon/intron architecture in Drosophilamelanogaster also suggests

multiple ways of pairing splice sites within the same pre-mRNA.
Although many Drosophila genes t neatly into two categories
characterized as genes with small introns and large exons or as
genes with small exons and large introns, there are a reasonable
number of genes that have a mixed exon/intron architecture,
suggesting that over part of their length the exon is the unit of
recognition and over part of their length the intron is the unit of
recognition. Sorting out how two such recognition mechanisms can
operate within the same precursor RNA without a disruption in exon
recognition or exon ordering is one of the future challenges for exon
de nition.
Exon Juxtaposition
Although exon de nition suggests how exons and their splice sites
are initially recognized by the splicing machinery, it does not
immediately o er a solution to the second step in spliceosome
assembly (Fig. 1). Juxtaposition of exons across large vertebrate

introns is a formidable problem, especially if inadvertent exon
skipping is to be avoided. Little insight is available as to how such
juxtapositioning could occur. A likely scenario invokes interactions
between the SR proteins bound to one exon with the SR proteins
bound to an adjoining exon. In addition to the SR proteins, another
class of nuclear proteins found only in organisms with large introns is
the hnRNP proteins(60). At least one hnRNP protein a ects 5′ splice
site recognition and is likely to have a major role in di erential
splicing (22, 61). Like the SR proteins, the hnRNP proteins contain
both an RNP recognition domain and a protein-protein recognition
domain. Unlike the SR proteins, the limited information available
suggests that the hnRNP proteins recognize intronic consensus
sequences rather than exonic sequences. Given their capacity to
di erentially recognize RNA sequences and their preference for
intronic sequences, the hnRNP proteins remain potential interesting
players in both di erential splicing and exon juxtapositioning.
Footnotes
↵* This minireview will be reprinted in the 1995 Minireview

Compendium, which will be available in December, 1995.
↵1 The abbreviations used are:
snRNP small nuclear ribonucleoprotein

SR arginine- and serine-rich splicing factors
hnRNP heterogeneous nuclear ribonucleoprotein.
↵2 D. A. Sterner, T. Carlo, and S. M. Berget, unpublished data.
↵3 J. Wise, personal communication.
© 1995 by The American Society for Biochemistry and

Molecular Biology, Inc.
REFERENCES
1. Hawkins J. D. (1988 ) Nucleic Acids Res. 16, 9893–9908

Abstract/FREE Full Text
2. Green M. R. (1991 ) Annu. Rev. Cell Biol. 7, 559–599 CrossRef

Google Scholar
3. Moore M. J., Query C. C., Sharp P. A. (1993 ) The RNA World (Gestland
R., Atkins R., eds) pp. 303–357, Cold Spring Harbor Laboratory Press,
Cold Spring Harbor, NY Google Scholar
4. Guthrie C. (1991 ) Science 253, 157–163 Abstract/FREE Full Text
5. Ruby S., Abelson J. (1991 ) Trends Genet. 7, 79–85 CrossRef

Medline Google Scholar
6. Jamison S. F., Crow A., Garcia-Blanco M. A. (1992 ) Mol. Cell. Biol. 12,
4279–4287 Abstract/FREE Full Text
7. Lammond A. L., Konarska M. M., Sharp P. A. (1987 ) Genes & Dev. 1,

8. Kuo H.-C., Nasim F. H., Grabowski P. J. (1991 ) Science 251, 1045–1050
9. Michaud S., Reed R. (1993 ) Genes & Dev. 7, 1008–1020

10. Robberson B. L., Cote G. J., Berget S. M. (1990 ) Mol. Cell. Biol. 10, 84–
94 Abstract/FREE Full Text
11. Rosbash M., Seraphin B. (1991 ) Science 16, 187–190
Google Scholar
12. Wu J. Y., Maniatis T. (1993 ) Cell 75, 1061–1070 CrossRef Medline

Google Scholar
13. Eperon I. C., Ireland D. C., Smith R. A., Mayeda A., Krainer A. R. (1993 )
EMBO J. 12, 3607–3617 Medline Google Scholar
14. Fu X.-D., Maniatis T. (1992 ) Proc. Natl. Acad. Sci. U. S. A. 89, 11224–
15. Kohtz J. D., Jamison S. F., Will C. L., Zuo P., Luhrmann R.,
Garcio-Blanco M. A., Manley J. L. (1994 ) Nature 368, 119–124 CrossRef
16. Zuo P., Manley J. L. (1994 ) Proc. Natl. Acad. Sci. U. S. A. 91, 3363–
17. Talerico M., Berget S. M. (1990 ) Mol. Cell. Biol. 10, 6299–6305
18. Grabowski P. J., Nasim F. H., Kuo H.-C., Burch R. (1991 ) Mol. Cell. Biol.
11, 5919–5928 Abstract/FREE Full Text
19. Carothers A. M., Urlaub G., Grunberger D., Chasin L. (1993 ) Mol. Cell.
Biol. 13, 5085–5098 Abstract/FREE Full Text
20. Tsukahara T., Casciato C., Helfman D. M. (1994 ) Nucleic Acids Res. 22,
21. Nakai K., Sakamoto H. (1994 ) Gene (Amst.) 141, 171–177 CrossRef
22. Yang X., Bani M. R., Lu S. J., Rowan S., Ben-David Y., Chabot B. (1994 )
Proc. Natl. Acad. Sci. U. S. A. 91, 6924–6928 Abstract/FREE Full Text
23. Dominski Z., Kole R. (1991 ) Mol. Cell. Biol. 11, 6075–6083
24. Dominski Z., Kole R. (1992 ) Mol. Cell. Biol. 12, 2108–2114
25. Black D. L. (1991 ) Genes & Dev. 5, 389–402 Abstract/FREE Full Text
26. Black D. L. (1992 ) Cell 69, 795–807 CrossRef Medline

Google Scholar
27. Sterner D. A., Berget S. M. (1993 ) Mol. Cell. Biol. 13, 2677–2687
28. Izaurralde E., Lewis J., McGuigan C., Jankowska M., Darzynkiewicz E.,
Mattaj I. W. (1994 ) Cell 78, 657–668 CrossRef Medline
Google Scholar
29. Ohno M., Sakamoto H., Shimura Y. (1987 ) Proc. Natl. Acad. Sci. U. S.
A. 84, 5187–5191 Abstract/FREE Full Text
30. Manley J. L., Proudfoot N. J. (1993 ) Genes & Dev. 8, 259–264
Google Scholar
31. Brunak S., Engelbrecht J., Knudsen S. (1991 ) J. Mol. Biol. 220, 49–65
CrossRef Medline Google Scholar
32. Niwa M., Rose S. R., Berget S. M. (1990 ) Genes & Dev. 4, 1552–1559
33. Niwa M., Berget S. M. (1991 ) Genes & Dev. 5, 2086–2095

34. Boelens W. C., Jansen E. J., Ven Venrooij W. J., Stripeke R., Mattaj I. W.,
Gunderson S. I. (1993 ) Cell 72, 881–892 CrossRef Medline
Google Scholar
35. Lutz C. S., Alwine J. C. (1994 ) Genes & Dev. 8, 576–586

36. Wasserman K. M., Steitz J. A. (1993 ) Genes & Dev. 7, 647–659

37. Stamm S., Zhang M. Q., Marr T. G., Helfman D. M. (1994 ) Nucleic Acids
Res. 22, 1515–1526 Abstract/FREE Full Text
38. Cooper T. A., Ordahl C. P. (1989 ) Nucleic Acids Res. 17, 6999–7011
39. Dirksen W. P., Hampson R. K., Sun Q., Rottman F. M. (1994 ) J. Biol.
Chem. 269, 6431–6436 Abstract/FREE Full Text
40. Hedley M. L., Maniatis T. (1991 ) Cell 65, 579–586 CrossRef
41. Inoue K., Hoshijima K., Higuchi I., Sakamoto H., Shimura Y. (1992 ) Proc.
Natl. Acad. Sci. U. S. A. 88, 683–687 Google Scholar
42. Lavigueur A., La Branche H., Kornblihtt A. R., Chabot B. (1993 ) Genes &
Dev. 7, 2405–2417 Abstract/FREE Full Text
43. Mardon H. J., Sebastio G., Baralle F. E. (1987 ) Nucleic Acids Res. 15,
44. Ryner L. C., Baker B. S. (1991 ) Genes & Dev. 5, 2071–2085
45. Streuli M., Saito H. (1989 ) EMBO J. 8, 787–796 Medline

Google Scholar
46. Tian M., Maniatis T. (1994 ) Genes & Dev. 8, 1703–1712

47. Watakabe A., Tanaka K., Shimura Y. (1993 ) Genes & Dev. 7, 407–418
48. Xu R., Teng T., Cooper T. A. (1993 ) Mol. Cell. Biol. 13, 3660–3674
49. Yeakley J. M., Hedjran F., Mor n J. P., Merillat N., Rosen eld M. G.,
Emerson R. B. (1993 ) Mol. Cell. Biol. 13, 5999–6011
50. Zahler A. M., Lane W. S., Stolk J. A., Roth M. B. (1992 ) Genes & Dev. 6,
51. Staknis D., Reed R. (1994 ) Mol. Cell. Biol. 14, 7670–7682
52. Ho man B. E., Grabowski P. J. (1992 ) Genes & Dev. 6, 2554–2568

53. Abovich N., Liao X. C., Rosbash M. (1994 ) Genes & Dev. 8, 843–854
54. Liao X. C., Tang J., Rosbash M. (1993 ) Genes & Dev. 7, 419–426
55. Zhang M. Q., Marr T. G. (1994 ) Nucleic Acids Res. 22, 1750–1759
56. Mount S. M., Burks C., Hertz G., Stormo G. D., White O., Fields C. (1992 )
Nucleic Acids Res. 20, 4255–4262 Abstract/FREE Full Text
57. Guo M., Lo P. C. H., Mount S. M. (1993 ) Mol. Cell. Biol. 13, 1104–1118
58. Talerico M., Berget S. M. (1994 ) Mol. Cell. Biol. 14, 3434–3445
59. Chen I. T., Chasin L. A. (1994 ) Mol. Cell. Biol. 14, 2140–2146
60. Dreyfuss G., Matunis M. J., Pinol-Roma S., Burd C. G. (1993 ) Annu. Rev.
Biochem. 62, 289–321 CrossRef Medline Google Scholar
61. O'aceres J. F., Stamm S., Helfman D. M., Krainer A. R. (1994 ) Science
265, 1706–1709 Abstract/FREE Full Text
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EMBO Rep. 2015 16: 1640-.
Stable tri-snRNP integration is accompanied by a major

structural rearrangement of the spliceosome that is
dependent on Prp8 interaction with the 5' splice site
RNA 2015 21: 1993-.
Poly(A) Polymerase and the Nuclear Poly(A) Binding

Protein, PABPN1, Coordinate the Splicing and
Degradation of a Subset of Human Pre-mRNAs
Mol. Cell. Biol. 2015 35: 2218-.
Splicing predictions reliably classify di erent types of

alternative splicing
RNA 2015 21: 813-.
Splicing of designer exons informs a biophysical model

for exon de nition
RNA 2015 21: 213-.
RBFOX and PTBP1 proteins regulate the alternative

splicing of micro-exons in human brain transcripts
Genome Res 2015 25: 1-.
iReckon: Simultaneous isoform discovery and abundance

estimation from RNA-seq data
Genome Res 2013 23: 519-.
Implications of Widespread Covalent Modi cation of

mRNA
Circ. Res. 2012 111: 1491-.
Full Text PDF
Cotranscriptional splicing e ciency di ers dramatically

between Drosophila and mouse
RNA 2012 18: 2174-.
A U1-U2 snRNP Interaction Network during Intron

De nition
Mol. Cell. Biol. 2012 32: 470-.
Changes in exon-intron structure during vertebrate

evolution a ect the splicing pattern of exons
Genome Res 2012 22: 35-.
Juxtaposition of Two Distant, Serine-Arginine-Rich

Protein-Binding Elements Is Required for Optimal
Polyadenylation in Rous Sarcoma Virus
J. Virol. 2011 85: 11351-.
Chromatin and Alternative Splicing
Cold Spring Harb Symp Quant Biol 2011 0:

sqb.2010.75.023v1-.
Abstract PDF
The Polypyrimidine Tract-Binding Protein A ects

Coronavirus RNA Accumulation Levels and Relocalizes
Viral RNAs to Novel Cytoplasmic Domains Di erent from
Replication-Transcription Sites
J. Virol. 2011 85: 5136-.
Mechanism of escape from nonsense-mediated mRNA

decay of human {beta}-globin transcripts with nonsense
mutations in the rst exon
RNA 2011 17: 843-.
Synthesis and Characterization of Pseudocantharidins,

Novel Phosphatase Modulators That Promote the
Inclusion of Exon 7 into the SMN (Survival of
Motoneuron) pre-mRNA
J Biol Chem 2011 286: 10126-.
RPL30 regulation of splicing reveals distinct roles for

Cbp80 in U1 and U2 snRNP cotranscriptional recruitment
RNA 2010 16: 2033-.
Retention of spliceosomal components along ligated

exons ensures e cient removal of multiple introns
RNA 2010 16: 1786-.
Chromatin density and splicing destiny: on the cross-talk

between chromatin structure and splicing
EMBO J. 2010 29: 1629-.
Multiple single nucleotide polymorphisms in the human

urate transporter 1 (hURAT1) gene are associated with
hyperuricaemia in Han Chinese
J. Med. Genet. 2010 47: 204-.
Splicing, cis genetic variation and disease
Nucleosomes are well positioned in exons and carry

characteristic histone modi cations
Genome Res 2009 19: 1732-.
Why there is more to protein evolution than protein

function: splicing, nucleosomes and dual-coding
sequence
Epigenetics of human T cells during the G0->G1 transition
Genome Res 2009 19: 1325-.
Polyadenylation releases mRNA from RNA polymerase II

in a process that is licensed by splicing
RNA 2009 15: 823-.
Identi cation of myo-Inositol-3-phosphate Synthase

Isoforms: CHARACTERIZATION, EXPRESSION, AND
PUTATIVE ROLE OF A 16-kDa {gamma}c ISOFORM
J Biol Chem 2009 284: 9443-.
Genome-wide evolutionary analysis of the noncoding

RNA genes and noncoding DNA of Paramecium
tetraurelia
RNA 2009 15: 503-.
Spliceosome Assembly Pathways for Di erent Types of

Alternative Splicing Converge during Commitment to
Splice Site Pairing in the A Complex
Mol. Cell. Biol. 2009 29: 1072-.
Conservation of the Protein Composition and Electron

Microscopy Structure of Drosophila melanogaster and
Human Spliceosomal Complexes
Mol. Cell. Biol. 2009 29: 281-.
The e ect of intron length on exon creation ratios during

the evolution of mammalian genomes
RNA 2008 14: 2261-.
Genome-wide analyses of alternative splicing in plants:

Opportunities and challenges
Genome Res 2008 18: 1381-.
A DNA damage signal activates and derepresses exon

inclusion in Drosophila TAF1 alternative splicing
RNA 2008 14: 1681-.
Hu Antigen R (HuR) Functions as an Alternative Pre-

mRNA Splicing Regulator of Fas Apoptosis-promoting
Receptor on Exon De nition
J Biol Chem 2008 283: 19077-.
DcpS scavenger decapping enzyme can modulate pre-

mRNA splicing
RNA 2008 14: 1132-.
Splicing regulation: From a parts list of regulatory

elements to an integrated splicing code
RNA 2008 14: 802-.
Negative and Positive mRNA Splicing Elements Act

Competitively To Regulate Human Immunode ciency
Virus Type 1 Vif Gene Expression
J. Virol. 2008 82: 3921-.
Kaposi's Sarcoma-Associated Herpesvirus ORF57

Functions as a Viral Splicing Factor and Promotes
Expression of Intron-Containing Viral Lytic Genes in
Spliceosome-Mediated RNA Splicing
J. Virol. 2008 82: 2792-.
Gag-Processing Defect of Human Immunode ciency

Virus Type 1 Integrase E246 and G247 Mutants Is Caused
by Activation of an Overlapping 5' Splice Site
J. Virol. 2008 82: 1600-.
Modulating alternative splicing by cotranscriptional

cleavage of nascent intronic RNA
RNA 2008 14: 359-.
Combinatorial Control of Exon Recognition
J Biol Chem 2008 283: 1211-.
Functional Coupling of Last-Intron Splicing and 3'-End

Processing to Transcription In Vitro: the Poly(A) Signal
Couples to Splicing before Committing to Cleavage
Mol. Cell. Biol. 2008 28: 849-.
Coevolutionary networks of splicing cis-regulatory

elements
Proc. Natl. Acad. Sci. USA 2007 104: 18583-.
Dual-speci city splice sites function alternatively as 5'

and 3' splice sites
Concurrent splicing and transcription are not su cient

to enhance splicing e ciency
RNA 2007 13: 1546-.
Using 5'-PTMs to repair mutant beta-globin transcripts
RNA 2007 13: 1317-.
Distance-Dependent Processing of Adeno-Associated

Virus Type 5 RNA Is Controlled by 5' Exon De nition
J. Virol. 2007 81: 7974-.
Mutations in the SF1-U2AF59-U2AF23 Complex Cause

Exon Skipping in Schizosaccharomyces pombe
J Biol Chem 2007 282: 2221-.
An Exonic Splicing Silencer Is Involved in the Regulated

Splicing of Glucose 6-Phosphate Dehydrogenase mRNA
J Biol Chem 2006 281: 34146-.
An interaction between U2AF 65 and CF Im links the

splicing and 3' end processing machineries
EMBO J. 2006 25: 4854-.
Genomewide comparative analysis of alternative splicing

in plants
Arginine/Serine-rich Protein Interaction Domain-

dependent Modulation of a Tau Exon 10 Splicing
Enhancer: ALTERED INTERACTIONS AND MECHANISMS
FOR FUNCTIONALLY ANTAGONISTIC FTDP-17 MUTATIONS
{Delta}280K AND N279K
J Biol Chem 2006 281: 2460-.
p54nrb is a component of the snRNP-free U1A (SF-A)

complex that promotes pre-mRNA cleavage during
polyadenylation.
RNA 2006 12: 111-.
Turnover and Function of Noncoding RNA Polymerase II

Transcripts
Cold Spring Harb Symp Quant Biol 2006 71: 275-.
Abstract PDF
Characteristics and regulatory elements de ning

constitutive splicing and di erent modes of alternative
splicing in human and mouse
RNA 2005 11: 1777-.
Kaposi's Sarcoma-Associated Herpesvirus K8{beta} Is

Derived from a Spliced Intermediate of K8 Pre-mRNA and
Antagonizes K8{alpha} (K-bZIP) To Induce p21 and p53
and Blocks K8{alpha}-CDK2 Interaction
J. Virol. 2005 79: 14207-.
The architecture of pre-mRNAs a ects mechanisms of

splice-site pairing
A Splicing Enhancer in the E4 Coding Region of Human

Papillomavirus Type 16 Is Required for Early mRNA
Splicing and Polyadenylation as Well as Inhibition of
Premature Late Gene Expression
J. Virol. 2005 79: 12002-.
Sequence conservation, relative isoform frequencies,

and nonsense-mediated decay in evolutionarily
conserved alternative splicing
Identi cation of Splicing Silencers and Enhancers in

Sense Alus: a Role for Pseudoacceptors in Splice Site
Repression
Mol. Cell. Biol. 2005 25: 6912-.
A Duplication in the Canine {beta}-Galactosidase Gene

GLB1 Causes Exon Skipping and GM1-Gangliosidosis in
Alaskan Huskies
Genetics 2005 170: 1857-.
Role for PSF in Mediating Transcriptional Activator-

Dependent Stimulation of Pre-mRNA Processing In Vivo
Mol. Cell. Biol. 2005 25: 6734-.
Spectrum of splicing errors caused by CHRNE mutations

a ecting introns and intron/exon boundaries
J. Med. Genet. 2005 42: e53.
Dichotomous splicing signals in exon anks
Genome Res 2005 15: 768-.
Subdivision of Large Introns in Drosophila by Recursive

Splicing at Nonexonic Elements
Genetics 2005 170: 661-.
A simple answer for a splicing conundrum
Full Text PDF
Serine/arginine-rich protein-dependent suppression of

exon skipping by exonic splicing enhancers
Post-entrapment genome engineering: First exon size

does not a ect the expression of fusion transcripts
generated by gene entrapment
Genome Res 2005 15: 428-.
Exonic splicing enhancers in ssion yeast: functional

conservation demonstrates an early evolutionary origin
Genes Dev. 2005 19: 242-.
A Novel Intronic cis Element, ISE/ISS-3, Regulates Rat

Fibroblast Growth Factor Receptor 2 Splicing through
Activation of an Upstream Exon and Repression of a
Downstream Exon Containing a Noncanonical Branch
Point Sequence
Mol. Cell. Biol. 2005 25: 250-.
Variation in sequence and organization of splicing

regulatory elements in vertebrate genes
SF2/ASF Binds the Human Papillomavirus Type 16 Late

RNA Control Element and Is Regulated during
Di erentiation of Virus-Infected Epithelial Cells
J. Virol. 2004 78: 10598-.
A Non-EST-Based Method for Exon-Skipping Prediction
Genome Res 2004 14: 1617-.
Ser/Arg-rich Protein-mediated Communication between

U1 and U2 Small Nuclear Ribonucleoprotein Particles
J Biol Chem 2004 279: 29647-.
A Bidirectional SF2/ASF- and SRp40-Dependent Splicing

Enhancer Regulates Human Immunode ciency Virus
Type 1 rev, env, vpu, and nef Gene Expression
J. Virol. 2004 78: 6517-.
Computational de nition of sequence motifs governing

constitutive exon splicing
Genes Dev. 2004 18: 1241-.
Prp5 bridges U1 and U2 snRNPs and enables stable U2

snRNP association with intron RNA
EMBO J. 2004 23: 376-.
Sequence Information for the Splicing of Human Pre-

mRNA Identi ed by Support Vector Machine
Classi cation
Genome Res 2003 13: 2637-.
Association of polyadenylation cleavage factor I with U1

snRNP
RNA 2003 9: 1400-.
5' Exon replacement and repair by spliceosome-

mediated RNA trans-splicing
RNA 2003 9: 1290-.
Perturbation of transcription elongation in uences the

delity of internal exon inclusion in Saccharomyces
cerevisiae
RNA 2003 9: 993-.
Multiple exon skipping and RNA circularisation

contribute to the severe phenotypic expression of exon 5
dystrophin deletion
J. Med. Genet. 2003 40: e100-.
Full Text PDF
The Porcine Ig {delta} Gene: Unique Chimeric Splicing of

the First Constant Region Domain in its Heavy Chain
Transcripts
J. Immunol. 2003 171: 1312-.
Inhibiting expression of speci c genes in mammalian

cells with 5' end-mutated U1 small nuclear RNAs
targeted to terminal exons of pre-mRNA
Nova Regulates GABAA Receptor {gamma}2 Alternative

Splicing via a Distal Downstream UCAU-Rich Intronic
Splicing Enhancer
Mol. Cell. Biol. 2003 23: 4687-.
Impact of Alternative Initiation, Splicing, and

Termination on the Diversity of the mRNA Transcripts
Encoded by the Mouse Transcriptome
Genome Res 2003 13: 1290-.
Computational Discovery of Internal Micro-Exons
Genome Res 2003 13: 1216-.
Re ned Annotation of the Arabidopsis Genome by

Complete Expressed Sequence Tag Mapping
Plant Physiol. 2003 132: 469-.
Phosphorylation-dependent and -independent Nuclear

Import of RS Domain-containing Splicing Factors and
Regulators
J Biol Chem 2003 278: 18050-.
Analysis of Germ Cell Nuclear Factor Transcripts and

Protein Expression During Spermatogenesis
Biol. Reprod. 2003 68: 1620-.
E cient use of a 'dead-end GA 5' splice site in the human

broblast growth factor receptor genes
EMBO J. 2003 22: 1620-.
Splicing of a Myosin Phosphatase Targeting Subunit 1

Alternative Exon Is Regulated by Intronic Cis-elements
and a Novel Bipartite Exonic Enhancer/Silencer Element
J Biol Chem 2003 278: 9722-.
Pre-mRNA splicing and human disease
Genes Dev. 2003 17: 419-.
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Exon Recognition in Vertebrate Splicing

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18/1/2019 Exon Recognition in Vertebrate Splicing

Journal of Biological Chemistry

Exon Recognition in Vertebrate

The average vertebrate gene consists of multiple small exons

Exon De nition in pre-

Predictions of Exon De nition

The exon de nition model o ers predictions of pre-mRNA behavior.

Exon-oriented and intron-oriented perspectives of splice site pairing

Mutation of vertebrate splice sites also leads to exon skipping. A

The observation of exon skipping strongly indicates that splice sites

Occasionally, mutation of an internal splice site results in intron

Exon Size Maximum

In addition to exon skipping, the other major phenotype resulting

Internal exon size

Exon Size Minimum

Simultaneous recognition of splice sites bordering an exon also

recognize individual sites. When a constitutively recognized internal

Exon Enhancer Sequences and Di erential Splicing

Exon de nition has proven to be a useful framework for considering

Interestingly, SR proteins have not yet been found in S. cerevisiae.

Mutation of splice sites in genes with small introns has a di erent

does not lead to exon skipping. Instead the mutated intron is

Initial pairing of splice sites across an exon may be similar to initial

View larger version:

Exon/intron architecture in Drosophilamelanogaster also suggests

assembly (Fig. 1). Juxtaposition of exons across large vertebrate

↵* This minireview will be reprinted in the 1995 Minireview

↵1 The abbreviations used are:

snRNP small nuclear ribonucleoprotein

↵2 D. A. Sterner, T. Carlo, and S. M. Berget, unpublished data.

↵3 J. Wise, personal communication.

© 1995 by The American Society for Biochemistry and

1. Hawkins J. D. (1988 ) Nucleic Acids Res. 16, 9893–9908

2. Green M. R. (1991 ) Annu. Rev. Cell Biol. 7, 559–599 CrossRef

5. Ruby S., Abelson J. (1991 ) Trends Genet. 7, 79–85 CrossRef

7. Lammond A. L., Konarska M. M., Sharp P. A. (1987 ) Genes & Dev. 1,

9. Michaud S., Reed R. (1993 ) Genes & Dev. 7, 1008–1020

12. Wu J. Y., Maniatis T. (1993 ) Cell 75, 1061–1070 CrossRef Medline

26. Black D. L. (1992 ) Cell 69, 795–807 CrossRef Medline

33. Niwa M., Berget S. M. (1991 ) Genes & Dev. 5, 2086–2095

35. Lutz C. S., Alwine J. C. (1994 ) Genes & Dev. 8, 576–586

36. Wasserman K. M., Steitz J. A. (1993 ) Genes & Dev. 7, 647–659

45. Streuli M., Saito H. (1989 ) EMBO J. 8, 787–796 Medline

46. Tian M., Maniatis T. (1994 ) Genes & Dev. 8, 1703–1712

52. Ho man B. E., Grabowski P. J. (1992 ) Genes & Dev. 6, 2554–2568

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