In silico Identification of Eukaryotic Promoters

Yella, Venkata Rajesh; Bansal, Manju

doi:10.1007/978-94-017-9514-2_4

Cited by 6 publications

(6 citation statements)

References 51 publications

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“…In eukaryotes, promoters are broadly categorized into three kinds, namely, core, proximal, and distal regions . The core promoter region is a minimal segment of genomic DNA encompassing the TSS interplays with Pol-II and general transcription machinery for orchestration of the pre-initiation complex. − Recent studies indicated that core promoters occupy the [−40 to +40] nucleotide regions relative to the TSS. − They are marked by precisely positioned sequence motifs like TATA-box, Initiator element (Inr), TFIIB recognition element (BRE), DNA replication-related element (DRE), TCT motif (or polypyrimidine initiator), downstream promoter element (DPE), Pause Button, X core promoter element 1 (XCPE1), and motif-ten element (MTE). ,− ,,, TATA-box is the best-characterized ancient core promoter element that binds to the TBP subunit of the TFIID multiprotein complex . It is observed in cellular organisms varying from archaea and yeast to metazoans and plants. , The Initiator element (Inr) is regarded as the most frequent core promoter motif that is positioned across the TSS. ,, Inr may interact with several GTFs with the highest correlation for TFIID binding .…”

Section: Introductionmentioning

confidence: 99%

“…In eukaryotes, promoters are broadly categorized into three kinds, namely, core, proximal, and distal regions. 3 The core promoter region is a minimal segment of genomic DNA encompassing the TSS interplays with Pol-II and general transcription machinery for orchestration of the pre-initiation complex. 4−7 Recent studies indicated that core promoters occupy the [−40 to +40] nucleotide regions relative to the TSS.…”

Section: Introductionmentioning

confidence: 99%

“…8−10 They are marked by precisely positioned sequence motifs like TATA-box, Initiator element (Inr), TFIIB recognition element (BRE), DNA replication-related element (DRE), TCT motif (or polypyrimidine initiator), downstream promoter element (DPE), Pause Button, X core promoter element 1 (XCPE1), and motif-ten element (MTE). 3,[5][6][7]9,11,12 TATA-box is the best-characterized ancient core promoter element that binds to the TBP subunit of the TFIID multiprotein complex. 13 It is observed in cellular organisms varying from archaea 14 and yeast to metazoans and plants.…”

Section: Introductionmentioning

confidence: 99%

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Delineation of the DNA Structural Features of Eukaryotic Core Promoter Classes

Vanaja

Yella

2022

ACS Omega

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The eukaryotic transcription is orchestrated from a chunk of the DNA region stated as the core promoter. Multifarious and punctilious core promoter signals, viz., TATA-box, Inr, BREs, and Pause Button, are associated with a subset of genes and regulate their spatiotemporal expression. However, the core promoter architecture linked with these signals has not been investigated exhaustively for several species. In this study, we attempted to envisage the adaptive binding landscape of the transcription initiation machinery as a function of DNA structure. To this end, we deployed a set of k-mer based DNA structural estimates and regular expression models derived from experiments, molecular dynamic simulations, and theoretical frameworks, and high-throughout promoter data sets retrieved from the eukaryotic promoter database. We categorized protein-coding gene core promoters based on characteristic motifs at precise locations and analyzed the B-DNA structural properties and non-B-DNA structural motifs for 15 different eukaryotic genomes. We observed that Inr, BREd, and no-motif classes display common patterns of DNA sequence and structural environment. TATA-containing, BREu, and Pause Button classes show a deviant behavior with the TATA class displaying varied axial and twisting flexibility while BREu and Pause Button leaned toward G-quadruplex motif enrichment. Intriguingly, DNA meltability and shape signals are conserved irrespective of the presence or absence of distinct core promoter motifs in the majority of species. Altogether, here we delineated the conserved DNA structural signals associated with several promoter classes that may contribute to the chromatin configuration, orchestration of transcription machinery, and DNA duplex melting during the transcription process.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Delineation of the DNA Structural Features of Eukaryotic Core Promoter Classes

Vanaja

Yella

2022

ACS Omega

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“…Later advances in promoter identifi cation are sequencing methods, such as RACE 5′-tag sequencing of cDNA or mRNA sequences, which rely on reverse transcription , fragmentation, and amplifi cation of cDNAs and alignment to the genome to get information about TSS location [ 6 ]. Other high-throughput experimental procedures include hybridization methods, such as oligonucleotide tiling arrays [ 4 ].…”

Section: Introductionmentioning

confidence: 99%

“…Promoter recognition methods also benefi t from the search of evolutionarily related sequences by looking for regions of conservation upstream of annotated genes. However, such methods can only identify homologous promoters when sequence conservation is present, but might miss nonconserved promoters [ 4 ].…”

Section: Introductionmentioning

confidence: 99%

In Silico Promoter Recognition from deepCAGE Data

Yang

Marsico

2016

Methods in Molecular Biology

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The accurate identification of transcription start regions corresponding to the promoters of known genes, novel coding, and noncoding transcripts, as well as enhancer elements, is a crucial step towards a complete understanding of state-specific gene regulatory networks. Recent high-throughput techniques, such as deepCAGE or single-molecule CAGE, have made it possible to identify the genome-wide location, relative expression, and differential usage of transcription start regions across hundreds of different tissues and cell lines. Here, we describe in detail the necessary computational analysis of CAGE data, with focus on two recent in silico methodologies for CAGE peak/profile definition and promoter recognition, namely the Decomposition-based Peak Identification (DPI) and the PROmiRNA software. We apply both methodologies to the challenging task of identifying primary microRNAs transcript (pri-miRNA) start sites and compare the results.

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Identification of putative promoters in 48 eukaryotic genomes on the basis of DNA free energy

Yella

Kumar

Bansal

2018

Sci Rep

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Transcription is an intricate mechanism and is orchestrated at the promoter region. The cognate motifs in the promoters are observed in only a subset of total genes across different domains of life. Hence, sequence-motif based promoter prediction may not be a holistic approach for whole genomes. Conversely, the DNA structural property, duplex stability is a characteristic of promoters and can be used to delineate them from other genomic sequences. In this study, we have used a DNA duplex stability based algorithm ‘PromPredict’ for promoter prediction in a broad range of eukaryotes, representing various species of yeast, worm, fly, fish, and mammal. Efficiency of the software has been tested in promoter regions of 48 eukaryotic systems. PromPredict achieves recall values, which range from 68 to 92% in various eukaryotes. PromPredict performs well in mammals, although their core promoter regions are GC rich. ‘PromPredict’ has also been tested for its ability to predict promoter regions for various transcript classes (coding and non-coding), TATA-containing and TATA-less promoters as well as on promoter sequences belonging to different gene expression variability categories. The results support the idea that differential DNA duplex stability is a potential predictor of promoter regions in various genomes.

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In silico Identification of Eukaryotic Promoters

Cited by 6 publications

References 51 publications

Delineation of the DNA Structural Features of Eukaryotic Core Promoter Classes

Delineation of the DNA Structural Features of Eukaryotic Core Promoter Classes

In Silico Promoter Recognition from deepCAGE Data

Identification of putative promoters in 48 eukaryotic genomes on the basis of DNA free energy

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