Natural Antisense Transcripts in Plants: A Review and Identification in Soybean Infected with Phakopsora pachyrhizi SuperSAGE Library

Abstract

Natural antisense ranscripts (NAT) are RNA molecules complementary to other endogenous RNAs. They are capable of regulating the expression of target genes at different levels (transcription, mRNA stability, translation, etc.). Such a property makes them ideal for interventions in organisms' metabolism. The present study reviewed plant NAT aspects, including features, availability and genesis, conservation and distribution, coding capacity, NAT pair expression, and functions. Besides, an in silico identification of NATs pairs was presented, using deepSuperSAGE libraries of soybean infected or not with Phakopsora pachyrhizi. Results showed that around 1/3 of the 77,903 predicted trans-NATs (by PlantsNATsDB database) detected had unitags mapped in both sequences of each pair. The same 1/3 of the 436 foreseen cis-NATs showed unitags anchored in both sequences of the related pairs. For those unitags mapped in NAT pairs, a modulation expression was assigned as upregulated, downregulated, or constitutive, based on the statistical analysis (P < 0.05). As a result, the infected treatment promoted the expression of 2,313 trans-NATs pairs comprising unitags exclusively from that library (1,326 pairs had unitags only found in the mock library). To understand the regulation of these NAT pairs could be a key aspect in the ASR plant response.

Co-expression network analysis reveals transcription factors associated to cell wall biosynthesis in sugarcane

“…We further examined metabolic and biological pathways that can be affected by natural antisense transcripts (NAT) expression by searching for NATs assigned to KEGG pathways (Kanehisa et al 2011 ). NAT expression is common among organisms (Chen et al 2012a ; Lapidot and Pilpel 2006 ), and these transcripts are able to regulate gene expression through different mechanisms (Britto-Kido et al 2013 ; Magistri et al 2012 ). In sugarcane, differential expression of NATs involved in sucrose metabolism and photosynthesis was observed under drought stress (Lembke et al 2012 ).…”

T-DNA alleles of the receptor kinase THESEUS1 with opposing effects on cell wall integrity signaling

“…The 10-fold difference in the antisense transcript abundance in the1-3 versus the1-4 is probably due to the strong activity of the bidirectional MAS promoter ( the1-3 ) and the weak read-through of the 35S promoter in the FLAG line, the1-4 . The high levels of antisense transcripts in the1-3 might act similarly to natural antisense transcripts (NATs) at different levels including mRNA processing, cellular transport, and translation ( Faghihi and Wahlestedt, 2009 ; Britto-Kido et al , 2013 ).…”

Catabolic repression in early-diverging anaerobic fungi is partially mediated by natural antisense transcripts

“…Antisense transcription, or transcription of RNA from the noncoding strand of a gene, is a key mode of gene regulation in all domains of life (Britto-Kido et al, 2013;Donaldson and Saville, 2012;Katayama et al, 2005;Wagner and Simons, 1994). The resulting RNA exhibits extended sequence complementarity to a 'sense' RNA transcript or target mRNA that it interacts with to control gene expression.…”