MEPP: more transparent motif enrichment by profiling positional correlations

Santos, Nathaniel Delos; Duttke, Sascha H.; Heinz, Sven; Benner, Chris

doi:10.1093/nargab/lqac075

Cited by 4 publications

(2 citation statements)

References 41 publications

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“…1b, Table S1). For comparison, we also performed csRNA-seq on S2 cells from fruit fly (Drosophila melanogaster) and integrated published data from fly embryos (Delos Santos et al 2022), rice (Oryza sativa, adult leaves) (Duttke et al 2019), human white blood cells (WBCs) (Lam et al 2023), human lymphocytes (Duttke et al 2019), and fungi (common mushroom, Agaricus bisporus; yeast, Saccharomyces cerevisiae) (Duttke et al 2022a) (Fig. 1b).…”

Section: A Comprehensive Atlas Of Nascent Transcripts In Plantsmentioning

confidence: 99%

Enhancers associated with unstable RNAs are rare in plants

Mcdonald,

Picard,

Brabb

et al. 2023

Preprint

Self Cite

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Unstable transcripts have emerged as markers of active enhancers in vertebrates and shown to be involved in many cellular processes and medical disorders. However, their prevalence and role in plants is largely unexplored. Here, we comprehensively captured all actively initiating (“nascent”) transcripts across diverse crops and other plants using capped small (cs)RNA-seq. We discovered that unstable transcripts are rare, unlike in vertebrates, and often originate from promoters. Additionally, many “distal” elements in plants initiate tissue-specific stable transcripts and are likelybone fidepromoters of yet-unannotated genes or non-coding RNAs, cautioning against using genome annotations to infer “enhancers” or transcript stability. To investigate enhancer function, we integrated STARR-seq data. We found that annotated promoters, and other regions that initiate stable transcripts rather than unstable transcripts, function as stronger enhancers in plants. Our findings underscore the blurred line between promoters and enhancers and suggest that cis-regulatory elements encompass diverse structures and mechanisms in eukaryotes.

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Section: A Comprehensive Atlas Of Nascent Transcripts In Plantsmentioning

confidence: 99%

Enhancers associated with unstable RNAs are rare in plants

Mcdonald,

Picard,

Brabb

et al. 2023

Preprint

Self Cite

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“…Notably, given the spatial preference of many DNA sequence motifs relative to the TSSs ( Fig. 1 ) ( Delos Santos et al 2022 ), ElemeNT 2023 also provides a unique approach to assess the quality of high-throughput TSS datasets and to confirm the existence of a core promoter region.…”

Section: Discussionmentioning

confidence: 99%

ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements

Adato,

Sloutskin,

Komemi

et al. 2024

Bioinformatics

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Motivation Prediction and identification of core promoter elements and transcription factor binding sites (TFBSs) is essential for understanding the mechanism of transcription initiation and deciphering the biological activity of a specific locus. Thus, there is a need for an up-to-date tool to detect and curate core promoter elements/motifs in any provided nucleotide sequences. Results Here, we introduce ElemeNT 2023 - a new and enhanced version of the Elements Navigation Tool, which provides novel capabilities for assessing evolutionary conservation and for readily evaluating the quality of high throughput transcription start site (TSS) datasets, leveraging preferential motif positioning. ElemeNT 2023 is accessible both as a fast web-based tool and via command line (no coding skills are required to run the tool). While this tool is focused on core promoter elements, it can also be used for searching any user defined motif, including sequence-specific DNA binding sites. Furthermore, ElemeNT’s CORE database, which contains predicted core promoter elements around annotated TSSs, is now expanded to cover 10 species, ranging from worms to human. In this applications note, we describe the new workflow and demonstrate a case study using ElemeNT 2023 for core promoter composition analysis of diverse species, revealing motif prevalence and highlighting evolutionary insights. We discuss how this tool facilitates the exploration of uncharted transcriptomic data, appraises transcription start site quality, and aids in designing synthetic promoters for gene expression optimization. Taken together, ElemeNT 2023 empowers researchers with comprehensive tools for meticulous analysis of sequence elements and gene expression strategies. Availability ElemeNT 2023 is freely available at https://www.juven-gershonlab.org/resources/element-v2023/. The source code and command line version of ElemeNT 2023 are available at https://github.com/OritAdato/ElemeNT. No coding skills are required to run the tool. Supplementary information Supplementary data are available at Bioinformatics online.

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Enhancers associated with unstable RNAs are rare in plants

McDonald,

Picard,

Brabb

et al. 2024

Nat. Plants

View full text Add to dashboard Cite

Unstable transcripts have emerged as markers of active enhancers in vertebrates and shown to be involved in many cellular processes and medical disorders. However, their prevalence and role in plants is largely unexplored. Here, we comprehensively captured all actively initiating (nascent) transcripts across diverse crops and other plants using capped small (cs)RNA sequencing. We discovered that unstable transcripts are rare in plants, unlike in vertebrates, and when present, often originate from promoters. In addition, many ‘distal’ elements in plants initiate tissue-specific stable transcripts and are likely bona fide promoters of as-yet-unannotated genes or non-coding RNAs, cautioning against using reference genome annotations to infer putative enhancer sites. To investigate enhancer function, we integrated data from self-transcribing active regulatory region (STARR) sequencing. We found that annotated promoters and other regions that initiate stable transcripts, but not those marked by unstable or bidirectional unstable transcripts, showed stronger enhancer activity in this assay. Our findings underscore the blurred line between promoters and enhancers and suggest that cis-regulatory elements can encompass diverse structures and mechanisms in eukaryotes, including humans.

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MEPP: more transparent motif enrichment by profiling positional correlations

Cited by 4 publications

References 41 publications

Enhancers associated with unstable RNAs are rare in plants

Enhancers associated with unstable RNAs are rare in plants

ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements

Enhancers associated with unstable RNAs are rare in plants

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