Core promoters across the genome

Cvetešić, Nevena; Lenhard, Boris

doi:10.1038/nbt.3788

Cited by 9 publications

(5 citation statements)

References 9 publications

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“…Cis-acting elements in a promoter play a key role in regulating gene expression at the transcriptional level [11,13,22]. A typical promoter not only possesses CAAT and a TATA-box for initiating gene transcription, but also possesses some other cis-acting elements that respond to stimuli in vitro or in vivo, and regulate the transcription of a particular gene [23][24][25]. SaBS is a pivotal gene for synthesizing bisabolene in S. album.…”

Section: Discussionmentioning

confidence: 99%

Molecular Cloning and Functional Characterization of Bisabolene Synthetase (SaBS) Promoter from Santalum album

Yan

Xiong

Silva³

et al. 2020

Forests

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Bisabolene-type sesquiterpenoids, which have multiple bioactivities, including anticancer activity, are one of the main groups of compounds in the essential oil extracted from Santalum album L. and other Santalum species. Bisabolene synthetase (SaBS) is a key enzyme for the synthesis of bisabolene in S. album, but the regulation of the SaBS gene’s expression is poorly understood. In this study, a 1390-bp promoter sequence of the SaBS gene was isolated from the leaves of six-year-old S. album. A bioinformatics analysis showed that certain environment stresses and phytohormone-activated cis-acting elements were distributed in different regions of the SaBS promoter (PSaBS). Transgenic Arabidopsis carrying full-length PSaBS had significantly higher β-glucuronidase (GUS) activity than the untreated control after treatment with salicylic acid (SA), suggesting that PSaBS is a SA-inducible promoter. Histochemical GUS staining and GUS fluorometric assays of transgenic Arabidopsis showed that the GUS activity directed by PSaBS was mainly expressed in stem tissue, followed by leaves and flowers. Moreover, different regions of PSaBS showed significantly different GUS activity. A 171-bp fragment upstream of the transcriptional initiation codon (ATG) is the core promoter region of PSaBS. Our results provide insight into and a greater understanding of the transcriptional regulation mechanism of the SaBS gene, which could serve as an alternative inducible promoter for transgenic plant breeding.

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Section: Discussionmentioning

confidence: 99%

Molecular Cloning and Functional Characterization of Bisabolene Synthetase (SaBS) Promoter from Santalum album

Yan

Xiong

Silva³

et al. 2020

Forests

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“…Hence, in the analysis of gene expression, it is necessary to understand and to incorporate the specific components of the core promoter (Juven-Gershon and Kadonaga 2010;Kadonaga 2012). With the growing appreciation of the importance of core promoters in determining gene expression, two recent studies measured the autonomous promoter activity of random native sequences genome-wide in human and Drosophila (Arnold et al 2017;Cvetesic and Lenhard 2017;van Arensbergen et al 2017). These approaches provided a large collection of endogenous promoter sequences and uncovered that autonomous promoter activity is widely distributed across the genome.…”

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confidence: 99%

Systematic interrogation of human promoters

et al. 2019

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Despite much research, our understanding of the architecture and cis-regulatory elements of human promoters is still lacking. Here, we devised a high-throughput assay to quantify the activity of approximately 15,000 fully designed sequences that we integrated and expressed from a fixed location within the human genome. We used this method to investigate thousands of native promoters and preinitiation complex (PIC) binding regions followed by in-depth characterization of the sequence motifs underlying promoter activity, including core promoter elements and TF binding sites. We find that core promoters drive transcription mostly unidirectionally and that sequences originating from promoters exhibit stronger activity than those originating from enhancers. By testing multiple synthetic configurations of core promoter elements, we dissect the motifs that positively and negatively regulate transcription as well as the effect of their combinations and distances, including a 10-bp periodicity in the optimal distance between the TATA and the initiator. By comprehensively screening 133 TF binding sites, we find that in contrast to core promoters, TF binding sites maintain similar activity levels in both orientations, supporting a model by which divergent transcription is driven by two distinct unidirectional core promoters sharing bidirectional TF binding sites. Finally, we find a striking agreement between the effect of binding site multiplicity of individual TFs in our assay and their tendency to appear in homotypic clusters throughout the genome. Overall, our study systematically assays the elements that drive expression in core and proximal promoter regions and sheds light on organization principles of regulatory regions in the human genome.

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“…Genes [ 1 ] are the genetic code of life, which direct the synthesis of various proteins [ 2 ] through transcription [ 3 ] and translation [ 4 ] processes to maintain the normal activities of life. The promoter is a key DNA fragment for gene transcription, located in the upstream region of the gene usually [ 5 ]. The promoter is responsible for the initiation of gene transcription and under what conditions it begins [ 6 ].…”

Section: Introductionmentioning

confidence: 99%

iPro2L-DG: Hybrid network based on improved densenet and global attention mechanism for identifying promoter sequences

Lei,

Jia,

Qin

et al. 2024

Heliyon

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Core promoters across the genome

Cited by 9 publications

References 9 publications

Molecular Cloning and Functional Characterization of Bisabolene Synthetase (SaBS) Promoter from Santalum album

Molecular Cloning and Functional Characterization of Bisabolene Synthetase (SaBS) Promoter from Santalum album

Systematic interrogation of human promoters

iPro2L-DG: Hybrid network based on improved densenet and global attention mechanism for identifying promoter sequences

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