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Computational Identification of Natural Antisense Transcripts in Arabidopsis thaliana. Xiu-Jie Wang Institute of Genetics and Developmental Biology Chinese Academy of Sciences. A. Commonly seen in prokaryotes . Also exist broadly in eukaryotes. B.

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computational identification of natural antisense transcripts in arabidopsis thaliana

Computational Identification of Natural Antisense Transcripts in Arabidopsisthaliana

Xiu-Jie Wang

Institute of Genetics and Developmental Biology

Chinese Academy of Sciences

slide2

A

  • Commonly seen in
  • prokaryotes
  • Also exist broadly in
  • eukaryotes

B

Natural antisense transcripts (NATs)

  • Two classes of NATs
  •  cis-NATs
  •  trans-NATs
cis encoded antisense transcripts

sense

antisense

dsRNA

Cis-encoded antisense transcripts
  • Sense and antisense transcripts originated from

the same genomic locus but in opposite directions.

trans encoded antisense transcripts

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
nats participate in many gene expression regulatory processes
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
slide6

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

slide7

C. X-chromosome inactivation (Xist)

D. DNA methylation

Functions of NATs at transcriptional level

slide8

Functions of NATs at post-transcriptional level

  • RNA processing and transport
  •  alternative splicing
  •  RNA editing
  •  RNA interference
  • RNA stability and translation
  •  translation regulation
prediction of arabidopsis cis nats
Prediction of Arabidopsiscis-NATs

1340 total cis-NAT pairs were predicted

957 pairs have expression evidence for both strands

Wang etal. Genome Biol. (2005)

most sense and antisense transcripts of the same cis nat pairs were expressed in different tissues
Most sense and antisense transcripts of the same cis-NAT pairs were expressed in different tissues

Wang etal. Genome Biol. (2005)

slide13

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)

slide14

Some cis-NAT originated siRNAs are induced by stress

Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK. (2005) Cell 1279-1291.

conclusions of cis nats
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
prediction of trans nats in arabidopsis

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)

slide19

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)

functional analysis of trans nats
Functional Analysis of Trans-NATs

Wang etal. Genome Biol. (2006)

some cis and trans nats form complex regulatory networks
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)

potential roles of arabidopsis trans nats
Potential roles of Arabidopsistrans-NATs
  • Induce gene silencing

- generate siRNAs

148 trans-NAT associated siRNAs were found

  • Regulate alternative splicing
conclusions of trans nats
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
slide25

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

acknowledgments
Acknowledgments

IGDB, CAS

Ms. Huan Wang

The Rockefeller University

Prof. Terry Gaasterland

Prof. Nam-Hai Chua

National Natural Science Foundation of China