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 same the same genomic locus but in opposite directions. sense antisense dsRNA

Trans-encoded antisense transcripts  small trans-NATs (microRNA, siRNA, etc.)  long trans-NATs differentA pair of overlapping transcripts originated from different genomic loci. antisens e sensedsRNA

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, 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 predicted 957 pairs have expression evidence for both strands Wang 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 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 Libraries CAF INF LEF ROF SIF API AP3 AGM INS ROS SAP SO4 S52 LES GSE CAS SIS Pair A At1g At1g Pair B At5g At3g Sense transcript: At3g23260 F-box protein Antisense transcript: At3g21580 Expressed 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 Wang Investigator, Group Leader Qi Zheng Graduate student Guanglin Li Graduate student Huajun Wu Visiting student Yingtao Zhao Graduate student Xudong Wu Graduate student Huan Wang Graduate student Guanzheng Luo Graduate student Jun Liu Visiting student Ying Chen Visiting student Zhijun Zhen Research asistant

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