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Introduction
Evolution of RNA polyadenylation Sites
Xiu-Qing Li
Agriculture and Agri-Food Canada
Fredericton, NB, Canada
[email protected];
• Polyadenylation of RNA is at the centre of gene
expression.
• Knowledge about RNA poly(A) site may be valuable for
designing new genes, distinguishing gene alleles, and
regulating gene expression.
• However, the characteristics and evolution of poly(A) site
selection, poly(A) site region base composition, signal
motifs, and base abundance patterns around mRNA
poly(A) sites are still largely uncharacterized in most
species.
(Plant and Animal Genome XXII, San Diego January 10-14, 2015, Abstract W744)
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Approaches
• After comparing the sequence quality between mRNA
database and Sequence Read Archive (SRA) datasets,
we analyzed the poly(A) site regions of 31 species or
phyla by mapping NCBI mRNA sequences to their
reference genomes.
• Redundant mRNA sequences or poly(A) sites were
eliminated.
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The poly(A) site region
5’
CDS
UTR
Site
COR
DNA:
____________________UC_________
Pre-RNA:
____________________UC_________
3’
Attachment↕↕Starting position
RNA (cleaved):
____________________U
RNA (polyA tailed):____________________UAAAAAAAAAA…
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Results
The alignment of 3′ end sequences of potato Kunitz-type
protease inhibitor mRNAs. Note that each polyadenylation
[poly(A)] tail likely starts from an adenosine.
(Li and Du 2013)
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Adenosine content for the first six bases of 3’COR
(Li, 2014, PloS ONE)
(Li and Du, 2014)
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Base U contents of the poly(A) tail regions (3’COR) in
different subkingdoms
C/G ratios at the poly(A) tail attachment position of non-A-type poly(A)
transcripts can clearly separate the three groups: animals < dicots <
monocots.
In order: dog, rabbit, rat, zebrafish, mouse, cattle, zebra finch, orangutan, chicken,
human, pig, and fruit fly. The three dicot plants are, in order, M. truncatula, A.
thaliana, and poplar. The three monocot plants are, in order, rice, maize, and
sorghum.
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Region and subkingdom
3′UTR_Dicots
3′COR_Dicots
3′UTR_Monocots
3′UTR_Non-mammals
3′COR_Monocots
3′COR_Non-mammals
Genome_Dicots
3′UTR_Mammals
3′COR_Mammals
Genome_Non-mammals
Genome_Mammals
Genome_Monocots
Duncan
testa
A
B
BC
C
C
CD
CDE
DEF
DEF
EF
FG
G
a:Means
with the same letter are not significantly different (P < 0.05).
ANOVA-Duncan’s multiple range tests
(Li, 2014, PloS ONE)
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3′UTR base composition and the 3′UTR/genome ratio
No. of Mean of uracil (U)
species contents (%)
4
39.88
4
37.45
3
35.34
6
34.93
3
34.47
6
33.92
4
32.84
5
31.87
5
31.46
6
30.78
5
29.48
3
27.63
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3′COR base composition and the 3′COR/genome ratio
(Li, 2014, PloS ONE)
(Li, 2014, PloS ONE)
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Average base abundance at each position of the 45-nucleotide
polyadenylation [poly(A)] site regions in protists.
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Protist and potato polyA site seqlogs.
Potato
(Li and Du 2014).
(Li and Du 2014 BMC Evol Biol)
Average base abundance at each position of the
201-nucleotide polyadenylation site region, showing
the U-A-U-SiteA-U base abundance pattern in plants
and animals
Type and location of the predominant motif in the
poly(A) site region in different species
(Li and Du 2014 BMC Evol Biol)
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(Li and Du 2014 BMC Evol Biol)
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Most frequent 20 motifs in the poly(A) site region in 30,499
unique poly(A) sites mapped to the human genome
Poly(A) site
A maize mRNA showing that both the AAUAAA motif
and the poly(A) sites are on loops.
(Li and Du 2014 BMC Evol Biol)
(Li, unpublished)
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Conclusions
• The poly(A) site is usually an A in most (30/31) species or phyla
• The base composition on the poly(A) tail attachment position can
separate animals, dicots, and monocots.
• Lower species (protists) placed the polyadenylation motif
upstream of, on, or downstream of the poly(A) site, but fungi,
animals, and most plants, place the signal motif upstream.
• There is a mechanism operating in both animals and plants
which is biased toward U and against C in the 3′COR and 3′UTR.
• The 3′UTR and 3′COR, as functional units, minimized the
difference between dicotyledonous and monocotyledonous
plants, while the dicotyledonous and monocotyledonous
genomes evolved into two extreme groups in terms of base
composition.
• Poly(A) site essayed several options during evolution prior to
establishing the U-A-U-A-U pattern of the poly(A) site region.
RNA poly(A) sites in microorganisms, plants
and animals: Characteristics and evolution
Xiu-Qing Li 李 修 庆
Agriculture and Agri-Food Canada
Fredericton, NB, Canada
[email protected];
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