Genome Biology

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Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana

Xiu-Jie Wang, Terry Gaasterland and Nam-Hai Chua*

Genome Biology 2005, 6:R30 doi:10.1186/gb-2005-6-4-r30

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BioMed Central: 13 citations

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Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function

Xiaoming Zhang, Jing Xia, Yifan E Lii, Blanca E Barrera-Figueroa, Xuefeng Zhou, Shang Gao, Lu Lu, Dongdong Niu, Zheng Chen, Christy Leung, Timothy Wong, Huiming Zhang, Jianhua Guo, Yi Li, Renyi Liu, Wanqi Liang, Jian-Kang Zhu, Weixiong Zhang, Hailing Jin Genome Biology 2012, 13:R20 (22 March 2012)

In Arabidopsis and rice, natural antisense transcripts are processed into siRNAs by DCL1 and DCL3

Research article   Open Access

Functional and evolutionary correlates of gene constellations in the Drosophila melanogaster genome that deviate from the stereotypical gene architecture

Shuwei Li, Ching-Hua Shih, Michael H Kohn BMC Genomics 2010, 11:322 (24 May 2010)

Research article   Open Access

Natural antisense transcript of natriuretic peptide precursor A (NPPA): structural organization and modulation of NPPA expression

Tarmo Annilo, Katrin Kepp, Maris Laan BMC Molecular Biology 2009, 10:81 (11 August 2009)

Research article   Open Access

Gene expression profiling via LongSAGE in a non-model plant species: a case study in seeds of Brassica napus

Christian Obermeier, Bashir Hosseini, Wolfgang Friedt, Rod Snowdon BMC Genomics 2009, 10:295 (3 July 2009)

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Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays

Samuel P Hazen, Felix Naef, Tom Quisel, Joshua M Gendron, Huaming Chen, Joseph R Ecker, Justin O Borevitz, Steve A Kay Genome Biology 2009, 10:R17 (11 February 2009)

Whole genome tiling array analysis reveals the extent of transcriptional oscillation for both coding and non-coding genes in regulating Arabidopsis thaliana circadian rhythms

Research article   Open Access

Sense and antisense OsDof12 transcripts in rice

Dejun Li, Chunhua Yang, Xiaobing Li, Guobiao Ji, Lihuang Zhu BMC Molecular Biology 2008, 9:80 (17 September 2008)

Methodology article   Open Access Highly Accessed

Genome-wide analysis of antisense transcription with Affymetrix exon array

Xijin Ge, Wendy S Rubinstein, Yong-chul Jung, Qingfa Wu BMC Genomics 2008, 9:27 (22 January 2008)

Database   Open Access

antiCODE: a natural sense-antisense transcripts database

Yifei Yin, Yi Zhao, Jie Wang, Changning Liu, Shuguang Chen, Runsheng Chen, Haitao Zhao BMC Bioinformatics 2007, 8:319 (30 August 2007)

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Sense-antisense pairs in mammals: functional and evolutionary considerations

Pedro AF Galante, Daniel O Vidal, Jorge E de Souza, Anamaria A Camargo, Sandro J de Souza Genome Biology 2007, 8:R40 (19 March 2007)

Analysis of a catalog of S-AS pairs in the human and mouse genomes revealed several putative roles for natural antisense transcripts and showed that some are artifacts of cDNA library construction.

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Prediction of trans-antisense transcripts in Arabidopsis thaliana

Huan Wang, Nam-Hai Chua, Xiu-Jie Wang Genome Biology 2006, 7:R92 (13 October 2006)

A genome-wide screen for trans-natural antisense transcripts in Arabidopsis thaliana suggests that antisense transcripts could be involved in complex regulatory networks in eukaryotes.

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RNA interference is not involved in natural antisense mediated regulation of gene expression in mammals

Mohammad Faghihi, Claes Wahlestedt Genome Biology 2006, 7:R38 (9 May 2006)

The study of two examples of endogenous genes with coding or non-coding natural antisense transcript partners provides evidence against the involvement of RNAi in the natural antisense-mediated regulation of mammalian gene expression.

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Comparative profiling of the sense and antisense transcriptome of maize lines

Jiong Ma, Darren J Morrow, John Fernandes, Virginia Walbot Genome Biology 2006, 7:R22 (13 March 2006)

Comparative transcriptome profiling of inbred maize lines demonstrates remarkable similarities and a large number of antisense transcripts.

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Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation

Chih-Hung Jen, Ioannis Michalopoulos, David R Westhead, Peter Meyer Genome Biology 2005, 6:R51 (1 June 2005)

Transcription data analysis of overlapping gene pairs in Arabidopsis thaliana argues against a predominant RNA degradation effect induced by dsRNA formation. Instead, it suggests alternative roles for dsRNAs such as regulation of alternative splicing in polyadenylation.