Xiu-Jie Wang
Institute of Genetics and Developmental
Biology
Chinese Academy of Sciences
Computational Identification of Natural
Antisense Transcripts in Arabidopsis
thaliana
Natural antisense transcripts
(NATs)
• Two classes of NATs
cis-NATs
trans-NATs
• Commonly seen in prokaryotes
A
• Also exist broadly in eukaryotes
B
Cis-encoded antisense transcripts
• Sense and antisense transcripts originated from
the samethe same genomic locus but in opposite directions.
senseantisens
e
dsRNAdsRNA
Trans-encoded antisense transcripts
small trans-NATs (microRNA, siRNA, etc.) long trans-NATs
• A pair of overlapping transcripts originated from differentdifferent genomic loci.
antisense
sense
dsRNAdsRNA
NATs participate in many gene expression regulatory processes
• Transcription control
• RNA processing and transport
• RNA stability and translation
- eye development of mouse
- cancer cell proliferation
- plant stress responses
- other unknown functions
A. transcription exclusion
Sense gene
Antisense gene
B. genomic imprinting (Air RNA)
Sleutels et al., Nature, 415, 810-813.
The maternal imprinting of Igf2r, Slc22a2, Slc22a3 are maintained by antisense Air RNA.
Functions of NATs at transcriptional level
C. X-chromosome inactivation (Xist)
D. DNA methylation
Functions of NATs at transcriptional level
Functions of NATs at post-transcriptional level
• RNA processing and transport
alternative splicing
RNA editing
RNA interference
• RNA stability and translation
translation regulation
Prediction and analysis of Arabidopsis NATs
- cis-NATs
- trans-NATs
Prediction of Arabidopsis cis-NATs
1340 total cis-NAT pairs were predicted957 pairs have expression evidence for both
strandsWang et al. Genome Biol. (2005)
Most Arabidopsis cis-NAT pairs overlap at 3’ end
Wang et al. Genome Biol. (2005)
Most sense and antisense transcripts of the same cis-NAT pairs were expressed in different tissues
Wang et al. Genome Biol. (2005)
Function speculation of Arabidopsis cis-NATs
11 Arabidopsis cis-NAT pairs have siRNA evidence
• gene silencing by RNAi
• genomic imprinting
three of six Arabidopsis imprinted genes have cis-antisense transcripts
FIS2, FIE and FWA Wang et al. Genome Biol. (2005)
Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK. (2005) Cell 1279-1291.
Some cis-NAT originated siRNAs are induced by stress
Conservation of Arabidopsis cis-NAT pairs in rice
Wang et al. Genome Biol. (2005)
Conclusions of cis-NATs
• Predicted 1340 putative cis-NAT pairs in Arabidopsis
• Expression evidence for both transcripts were found for 957 cis-NAT pairs
• Most cis-NAT pairs have tissue-specific expression profile
• The biological function of Arabidopsis cis-NATs includes RNA interference, genomic imprinting and gene regulation under certain conditions
- trans-NATs
Prediction and analysis of Arabidopsis NATs
- cis-NATs
Prediction of trans-NATs in Arabidopsis
High-coverage
100 nt
More than 90% of trans-NAT pairs are predicted to hybrid to each other basing on the results of RNA hybride program
Wang et al. Genome Biol. (2006)
Trans-NAT pairs tend to co-express in the same tissue
ID
LibrariesCAF INF LEF ROF SIF API AP3 AGM INS ROS SAP SO4 S52 LES GSE CAS SIS
Pair A At1g50020 0 18 6 1 0 12 22 1 17 0 0 0 0 0 73 0 0At1g04820 0 0 0 0 0 19 13 8 13 1 3 0 0 0 0 0 0
Pair B At5g02370 0 0 0 0 0 36 15 20 16 0 56 1 19 29 21 28 39At3g09390 0 0 0 0 0 60 36 27 14 0 55 8 4 28 362 0 0
Sense transcript:
At3g23260F-box protein
Antisense transcript:
At3g21580Expressed protein
Wang et al. Genome Biol. (2006)
Functional Analysis of Trans-NATs
Wang et al. Genome Biol. (2006)
Over-represented gene families in trans-NAT pairs
Wang et al. Genome Biol. (2006)
Antisense networks of UDP-glucosyl transferase family genes
Some cis- and trans-NATs form complex regulatory networks
UDP transcripts involved in trans-NAT pairs
UDP transcripts involved in cis-NAT pairs UDP transcripts involved in cis- and trans- NAT pairs Transcripts from other protein families
Wang et al. Genome Biol. (2006)
Potential roles of Arabidopsis trans-NATs
• Induce gene silencing
- generate siRNAs
148 trans-NAT associated siRNAs were found
• Regulate alternative splicing
Alternative splicing rate
All annotated genes 11.59%
Trans-NAT pairs 19.76%
Conclusions of trans-NATs
• Identified 1320 putative trans-NAT pairs
• Trans-NATs tend to co-exist in the same tissue
• Transcripts from function classes with catalytic activity, signal transducer activity and transporter activities were slightly over-represented
• Cis- and trans- NATs could form complex regulatory networks
• Potential functions of trans-NATs include inducing gene silencing and regulate alternative splicing
Xiujie WangInvestigator, Group LeaderQi Zheng
Graduate student
Guanglin LiGraduate student
Huajun WuVisiting student
Yingtao ZhaoGraduate student Xudong Wu
Graduate student
Huan WangGraduate student
Guanzheng LuoGraduate student
Jun LiuVisiting student
Ying ChenVisiting student
Zhijun ZhenResearch asistant
Acknowledgments
IGDB, CAS
Ms. Huan Wang
The Rockefeller University
Prof. Terry Gaasterland
Prof. Nam-Hai Chua
National Natural Science Foundation of China