Computational Identification of Natural Antisense Transcripts in Arabidopsis thaliana

1. Computational Identification of Natural Antisense Transcripts in Arabidopsisthaliana Xiu-Jie Wang Institute of Genetics and Developmental Biology Chinese Academy of Sciences

2. A • Commonly seen in • prokaryotes • Also exist broadly in • eukaryotes B Natural antisense transcripts (NATs) • Two classes of NATs •  cis-NATs •  trans-NATs

3. sense antisense dsRNA Cis-encoded antisense transcripts • Sense and antisense transcripts originated from the same genomic locus but in opposite directions.

4. sense antisense dsRNA Trans-encoded antisense transcripts • A pair of overlapping transcripts originated from different genomic loci. • small trans-NATs (microRNA, siRNA, etc.) • long trans-NATs

5. NATs participate in many gene expression regulatory processes - cancer cell proliferation - eye development of mouse - plant stress responses - other unknown functions • Transcription control • RNA processing and transport • RNA stability and translation

6. 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

7. C. X-chromosome inactivation (Xist) D. DNA methylation Functions of NATs at transcriptional level

8. Functions of NATs at post-transcriptional level • RNA processing and transport •  alternative splicing •  RNA editing •  RNA interference • RNA stability and translation •  translation regulation

9. Prediction and analysis of Arabidopsis NATs - cis-NATs - trans-NATs

10. Prediction of Arabidopsiscis-NATs 1340 total cis-NAT pairs were predicted 957 pairs have expression evidence for both strands Wang etal. Genome Biol. (2005)

11. Most Arabidopsiscis-NAT pairs overlap at 3’ end Wang etal. Genome Biol. (2005)

12. Most sense and antisense transcripts of the same cis-NAT pairs were expressed in different tissues Wang etal. Genome Biol. (2005)

13. Function speculation of Arabidopsiscis-NATs • gene silencing by RNAi 11 Arabidopsiscis-NAT pairs have siRNA evidence • genomic imprinting • three of six Arabidopsis imprinted genes have • cis-antisense transcripts • FIS2, FIE and FWA Wang etal. Genome Biol. (2005)

14. Some cis-NAT originated siRNAs are induced by stress Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK. (2005) Cell 1279-1291.

15. Conservation of Arabidopsiscis-NAT pairs in rice Wang etal. Genome Biol. (2005)

16. 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 Arabidopsiscis-NATs • includes RNA interference, genomic imprinting and • gene regulation under certain conditions

17. Prediction and analysis of Arabidopsis NATs - cis-NATs - trans-NATs

18. High-coverage 100 nt Prediction of trans-NATs in Arabidopsis More than 90% of trans-NAT pairs are predicted to hybrid to each other basing on the results of RNA hybride program Wang etal. Genome Biol. (2006)

19. ID Libraries CAF 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 0 At1g04820 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 1520 16 0 56 1 19 29 21 28 39 At3g09390 0 0 0 0 0 60 36 27 14 0 55 8 4 28 362 0 0 Trans-NAT pairs tend to co-express in the same tissue Sense transcript: At3g23260 F-box protein Antisense transcript: At3g21580 Expressed protein Wang etal. Genome Biol. (2006)

20. Functional Analysis of Trans-NATs Wang etal. Genome Biol. (2006)

21. Over-represented gene families in trans-NAT pairs Wang etal. Genome Biol. (2006)

22. Some cis- and trans-NATs form complex regulatory networks Antisense networks of UDP-glucosyl transferase family genes 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 etal. Genome Biol. (2006)

23. Potential roles of Arabidopsistrans-NATs • Induce gene silencing - generate siRNAs 148 trans-NAT associated siRNAs were found • Regulate alternative splicing

24. 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

25. Xiujie Wang Investigator, Group Leader Qi Zheng Graduate student Huan Wang Graduate student Guanglin Li Graduate student Guanzheng Luo Graduate student Jun Liu Visiting student Huajun Wu Visiting student Zhijun Zhen Research asistant Ying Chen Visiting student Yingtao Zhao Graduate student Xudong Wu Graduate student

26. Acknowledgments IGDB, CAS Ms. Huan Wang The Rockefeller University Prof. Terry Gaasterland Prof. Nam-Hai Chua National Natural Science Foundation of China

27. Thank you !