Major cis-regulatory elements for rice bidirectional promoter activity reside in the 5′-untranslated regions

Dhadi, Surendar Reddy; Deshpande, Aparna; Driscoll, Kyle; Ramakrishna, Wusirika

doi:10.1016/j.gene.2013.05.060

Cited by 8 publications

(8 citation statements)

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“…We randomly selected five BDPs containing one DHS, four of which were experimentally verified as BDPs. When combined with 7 experimentally verified rice BDPs containing one DHS31, 10 of the 12 (83%) were BDPs and only two were UDPs (Supplementary Table S1), possibly due to the existence of an insulator or repressor blocking the promoter activity in the other direction or they actually function as UDPs.…”

Section: Resultsmentioning

confidence: 99%

“…We suspected the possible reasons as below: first the expression of gene pairs is possibly regulated by different distal cis-elements, thus the absence of related cis elements in the tested DNA fragment can affect the expression of the corresponding gene resulting in unidirectional expression. Deletion based verification demonstrates that the presence of cis-elements, like enhancers, repressors or insulators, is essential for the function of rice BDPs31. Secondly, we can not exclude the possibility that some of BDPs are misclassified and function as real UDPs.…”

Section: Discussionmentioning

confidence: 96%

“…So far, BDPs have been investigated in Arabidopsis 5282930, rice23, maize24 and Populus 23. The sequence features are well conserved between mammalian and plant genomes23283132. However, it remains unclear the epigenetic mechanisms for the bidirectional transcription and coexpression of gene pairs in plants.…”

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confidence: 99%

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Functional characterization of open chromatin in bidirectional promoters of rice

Fang

Wang

et al. 2016

Sci Rep

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Bidirectional gene pairs tend to be highly coregulated and function in similar biological processes in eukaryotic genomes. Structural features and functional consequences of bidirectional promoters (BDPs) have received considerable attention among diverse species. However, the underlying mechanisms responsible for the bidirectional transcription and coexpression of BDPs remain poorly understood in plants. In this study, we integrated DNase-seq, RNA-seq, ChIP-seq and MNase-seq data and investigated the effect of physical DNase I hypersensitive site (DHS) positions on the transcription of rice BDPs. We found that the physical position of a DHS relative to the TSS of bidirectional gene pairs can affect the expression of the corresponding genes: the closer a DHS is to the TSS, the higher is the expression level of the genes. Most importantly, we observed that the distribution of DHSs plays a significant role in the regulation of transcription and the coexpression of gene pairs, which are possibly mediated by orchestrating the positioning of histone marks and canonical nucleosomes around BDPs. Our results demonstrate that the combined actions of chromatin structures with DHSs, which contain functional cis-elements for interaction with transcriptional machinery, may play an important role in the regulation of the bidirectional transcription or coexpression in rice BDPs. Our findings may help to enhance the understanding of DHSs in the regulation of bidirectional gene pairs.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 96%

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Functional characterization of open chromatin in bidirectional promoters of rice

Fang

Wang

et al. 2016

Sci Rep

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“…Progress has been made in characterizing plant BDPs in Arabidopsis [ 6 , 24 , 25 ], rice [ 6 ], maize [ 7 ] and Populus [ 6 ] due to the recent availability of whole plant genome sequences and transcriptome data. Similar to BDPs in yeast and humans, plant BDPs have higher GC contents and fewer TATA boxes than UDPs [ 6 , 20 , 24 , 26 ]. Moreover, plant BDPs are involved in the regulation of important agricultural traits [ 27 – 31 ].…”

Section: Introductionmentioning

confidence: 99%

Histone modifications facilitate the coexpression of bidirectional promoters in rice

Fang

Wang

et al. 2016

BMC Genomics

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BackgroundBidirectional gene pairs are highly abundant and mostly co-regulated in eukaryotic genomes. The structural features of bidirectional promoters (BDPs) have been well studied in yeast, humans and plants. However, the underlying mechanisms responsible for the coexpression of BDPs remain understudied, especially in plants.ResultsHere, we characterized chromatin features associated with rice BDPs. Several unique chromatin features were present in rice BDPs but were missing from unidirectional promoters (UDPs), including overrepresented active histone marks, canonical nucleosomes and underrepresented H3K27me3. In particular, overrepresented active marks (H3K4ac, H4K12ac, H4K16ac, H3K4me2 and H3K36me3) were truly overrepresented in type I BDPs but not in the other two BDPs, based on a Kolmogorov-Smirnov test.ConclusionsOur analyses indicate that active marks (H3K4ac, H4K12ac, H4K16ac, H3K4me3, H3K9ac and H3K27ac) may coordinate with repressive marks (H3K27me3 and H3K9me1/3) to build a unique chromatin structure that favors the coregulation of bidirectional gene pairs. Thus, our findings help to enhance the understanding of unique epigenetic mechanisms that regulate bidirectional gene pairs and may improve the manipulation of gene pairs for crop bioengineering.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3125-0) contains supplementary material, which is available to authorized users.

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“…Several bidirectional promoters from other species such as melon and Capsicum annuum , have been also cloned gradually (Shin et al, 2003 ; Wang et al, 2008 ). In rice, a few promoters have been found to show bidirectional expression activities (Huang et al, 2007 ; Singh et al, 2009 ; Dhadi et al, 2013 ). So far, there has been no report about the cloning and identification of bidirectional promoters using two reporter genes simultaneously with stable transformation in rice.…”

Section: Introductionmentioning

confidence: 99%

Isolation and Functional Characterization of Bidirectional Promoters in Rice

et al. 2016

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Bidirectional promoters, which show great application potential in genetic improvement of plants, have aroused great research interest recently. However, most bidirectional promoters were cloned individually in the studies of single genes. Here, we initiatively combined RNA-seq data and cDNA microarray data to discover the potential bidirectional promoters in rice genome. Based on the expression level and correlation of each adjacent and oppositely transcribed gene pair, we selected four candidate gene pairs. Then, the intergenic region between each pair was isolated and cloned into a dual reporter vector pDX2181 for functional identification. GUS and GFP assays of the transgenic plants indicated that all the intergenic regions showed bidirectional expression activity in various tissues. Through 5′ and 3′ deletion analysis on one of the above bidirectional promoters, we identified the enhancing region which sharply increased its bidirectional expression efficiency and the essential regions respectively responsible for its 5′ and 3′ basic expression activity. The bidirectional arrangement of the four gene pairs in six gramineous plants was also analyzed, showing the conserved characteristics of the four bidirectional promoters identified in our study. In addition, two novel cis-sequences conserved in the four bidirectional promoters were discovered by bioinformatic identification. Our study proposes a feasible method for selecting, cloning, and functionally identifying bidirectional promoters as well as for discovering their bidirectional regulatory regions and conserved sequences in rice.

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Major cis-regulatory elements for rice bidirectional promoter activity reside in the 5′-untranslated regions

Cited by 8 publications

References 43 publications

Functional characterization of open chromatin in bidirectional promoters of rice

Functional characterization of open chromatin in bidirectional promoters of rice

Histone modifications facilitate the coexpression of bidirectional promoters in rice

Isolation and Functional Characterization of Bidirectional Promoters in Rice

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