Gene expression enhancement mediated by the 5′ UTR intron of the rice rubi3 gene varied remarkably among tissues in transgenic rice plants

Lu, Jianjun; Sivamani, Elumalai; Azhakanandam, Kasi; Samadder, Partha; Li, Xianggan; Qu, Rongda

doi:10.1007/s00438-008-0333-6

Cited by 73 publications

(41 citation statements)

References 47 publications

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“…Also, TSSs have been found in the 3# UTR of certain protein-coding genes, which may code for transcripts that regulate downstream genes on the same or opposite strands. Moreover, regions located downstream of the TSS, such as introns (Rose, 2008;Rose et al, 2008) and 5# UTRs (Lu et al, 2008), have been shown to be involved in the regulation of transcription by acting as enhancers or through mechanisms such as intron-mediated enhancement. Noncoding regions might also be involved in replication, transcription of regulatory ncRNAs, and transposition.…”

Section: Discussionmentioning

confidence: 99%

DNA Free Energy-Based Promoter Prediction and Comparative Analysis of Arabidopsis and Rice Genomes

et al. 2011

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The cis-regulatory regions on DNA serve as binding sites for proteins such as transcription factors and RNA polymerase. The combinatorial interaction of these proteins plays a crucial role in transcription initiation, which is an important point of control in the regulation of gene expression. We present here an analysis of the performance of an in silico method for predicting cisregulatory regions in the plant genomes of Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) on the basis of free energy of DNA melting. For protein-coding genes, we achieve recall and precision of 96% and 42% for Arabidopsis and 97% and 31% for rice, respectively. For noncoding RNA genes, the program gives recall and precision of 94% and 75% for Arabidopsis and 95% and 90% for rice, respectively. Moreover, 96% of the false-positive predictions were located in noncoding regions of primary transcripts, out of which 20% were found in the first intron alone, indicating possible regulatory roles. The predictions for orthologous genes from the two genomes showed a good correlation with respect to prediction scores and promoter organization. Comparison of our results with an existing program for promoter prediction in plant genomes indicates that our method shows improved prediction capability.Sequencing and annotation of a large number of eukaryotic genomes has made available an enormous amount of information regarding genetic coding sequences (CDS). These data can be effectively utilized for studying and modifying the expression of genes if the location and contribution of cis-regulatory regions, which control spatial and temporal regulation of gene expression, are available. However, the precise annotation of regulatory regions is difficult as compared with the identification of genes, primarily because regulatory regions do not code for an identifiable product. In fact, regulatory regions are bound by proteins such as transcription factors, which bring about transcription and its regulation. Determining transcription factor-binding sites (TFBSs) from chromatin immunoprecipitation methods has limitations and requires a lot of downstream data processing (Farnham, 2009). Moreover, the mere binding of a transcription factor at a particular site does not warrant its involvement in the regulation of a gene. Development of computational approaches that enable accurate prediction of cis-regulatory sites could thus greatly aid in deciphering the regulatory mechanisms at the genome level.The preponderance of noncoding DNA in the eukaryotic genome makes it difficult to identify promoter regions. Most efforts toward the prediction of regulatory regions have traditionally focused on the detection of consensus sequences for the TATA box, Initiator elements, TFBSs, etc. Such sequence-based prediction of short motifs might be inadequate because a large number of false hits are possible by chance. Moreover, there is increasing evidence to suggest that consensus sequences vary greatly and are even absent in many cases. The TATA box, which is consi...

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Section: Discussionmentioning

confidence: 99%

DNA Free Energy-Based Promoter Prediction and Comparative Analysis of Arabidopsis and Rice Genomes

et al. 2011

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“…Intron-mediated enhancement of transgene expression has been reported in an array of plant species [30,31], and several previously reported ubiquitin promoters have shown greater transgene expression when the promoters contained the leader introns [2,12,39].…”

Section: Discussionmentioning

confidence: 98%

Truncated Ubiquitin 5′ Regulatory Region from Erianthus arundinaceus Drives Enhanced Transgene Expression in Heterologous Systems

Mohan

Philip

2015

Mol Biotechnol

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Characterization of novel plant gene promoters underpins the development of transgenic crop plants. Here, we report a novel 5' regulatory sequence (Eriubi D7) of the ubiquitin gene from Erianthus arundinaceus, a wild relative of sugarcane resistant to many biotic and abiotic stresses. A 3.2-kb regulatory sequence of ubiquitin gene was isolated through random amplification of genomic ends technique and characterized in rice, tobacco, and sugarcane. In silico analysis revealed that the regulatory sequence contained a promoter region of 1600 bp upstream to the transcription start site. Between the promoter and the coding region, two putative introns of 584 and 583 bp and two putative non-coding exons of 459 and 37 bp were spaced alternatively. To identify the active domains required for gene regulation, 12 truncations/recombinants were made in the regulatory sequence and characterized in heterologous systems. Transformation studies with the recombinant constructs revealed that Eriubi D7, a truncated fragment containing 830 bp promoter and the intron I, conferred enhanced GUS reporter gene expression in both monocots and dicots compared to other routinely used promoters such as maize ubi1 and Cauliflower Mosaic Virus 35S. Further analysis confirms that this regulatory sequence is quite distinct from the other reported ubiquitin promoters and was also found to enhance expression of the reporter gene upon wounding. This is the first report on the isolation and characterization of a promoter from a wild sugarcane germplasm and is expected to be useful for development of transgenic crop plants.

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“…Rubi3 is an abundant protein involved in protein degradation and control of the cell cycle. The 1140-bp 5′UTR of this gene enhances its promoter activity by 20-fold in transient expression assays (Sivamani and Qu 2006;Lu et al 2008). The highly expressed rice α-tubulin genes (Ostua1, Ostua2, and Ostua3) have been isolated and analyzed for expression.…”

Section: Translational Efficiency and Role Of Untranslated Regionsmentioning

confidence: 99%

Strategies to Increase Heterologous Protein Expression in Rice Grains

Nandi

Khush

2015

Recent Advancements in Gene Expression and Enabling Technologies in Crop Plants

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Gene expression enhancement mediated by the 5′ UTR intron of the rice rubi3 gene varied remarkably among tissues in transgenic rice plants

Cited by 73 publications

References 47 publications

DNA Free Energy-Based Promoter Prediction and Comparative Analysis of Arabidopsis and Rice Genomes

DNA Free Energy-Based Promoter Prediction and Comparative Analysis of Arabidopsis and Rice Genomes

Truncated Ubiquitin 5′ Regulatory Region from Erianthus arundinaceus Drives Enhanced Transgene Expression in Heterologous Systems

Strategies to Increase Heterologous Protein Expression in Rice Grains

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