RAMPAGE: Promoter Activity Profiling by Paired-End Sequencing of 5′-Complete cDNAs

Batut, Philippe; Gingeras, T

doi:10.1002/0471142727.

Cited by 16 publications

(24 citation statements)

References 12 publications

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“…It offers unprecedented specificity and detection sensitivity for TSSs, and its multiplexing capabilities allow for the seamless acquisition of high-resolution developmental time series ( Batut et al, 2013 ). Since eukaryotic promoters often allow productive transcription initiation from multiple positions ( Batut et al, 2013 ; Carninci et al, 2006 ; Valen et al, 2009 ; Hoskins et al, 2011 ), we use a dedicated peak-calling algorithm to group neighboring TSSs into TSS clusters (TSCs) corresponding to individual promoters ( Batut et al, 2013 ; Batut and Gingeras, 2013 ).…”

Section: Resultsmentioning

confidence: 99%

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Conserved noncoding transcription and core promoter regulatory code in early Drosophila development

Batut

Gingeras

2017

eLife

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Multicellular development is driven by regulatory programs that orchestrate the transcription of protein-coding and noncoding genes. To decipher this genomic regulatory code, and to investigate the developmental relevance of noncoding transcription, we compared genome-wide promoter activity throughout embryogenesis in 5 Drosophila species. Core promoters, generally not thought to play a significant regulatory role, in fact impart restrictions on the developmental timing of gene expression on a global scale. We propose a hierarchical regulatory model in which core promoters define broad windows of opportunity for expression, by defining a range of transcription factors from which they can receive regulatory inputs. This two-tiered mechanism globally orchestrates developmental gene expression, including extremely widespread noncoding transcription. The sequence and expression specificity of noncoding RNA promoters are evolutionarily conserved, implying biological relevance. Overall, this work introduces a hierarchical model for developmental gene regulation, and reveals a major role for noncoding transcription in animal development.

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Section: Resultsmentioning

confidence: 99%

“…We systematically checked on a Bioanalyzer RNA Nano chip (Agilent) that the RNA was of very high quality. Libraries were prepared as described before ( Batut et al, 2013 ; Batut and Gingeras, 2013 ). 5’-monophosphate transcripts were depleted by TEX digest (Epicentre #TER51020).…”

Section: Methodsmentioning

confidence: 99%

Conserved noncoding transcription and core promoter regulatory code in early Drosophila development

Batut

Gingeras

2017

eLife

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“…Future study of alternative promoter usage in D. pulex would benefit from separate analysis of individual tissue types. The TSS profiling method employed by Batut et al (2012), RAMPAGE (Batut and Gingeras 2013), is wellpositioned to address alternative promoter usage in this and other species because it provides paired-end sequence information along with the 59-end of the transcript.…”

Section: Discussionmentioning

confidence: 99%

Promoter Architecture and Sex-Specific Gene Expression in Daphnia pulex

et al. 2016

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Large-scale transcription start site (TSS) profiling produces a high-resolution, quantitative picture of transcription initiation and core promoter locations within a genome. However, application of TSS profiling to date has largely been restricted to a small set of prominent model systems. We sought to characterize the cis-regulatory landscape of the water flea Daphnia pulex, an emerging model arthropod that reproduces both asexually (via parthenogenesis) and sexually (via meiosis). We performed Cap Analysis of Gene Expression (CAGE) with RNA isolated from D. pulex within three developmental states: sexual females, asexual females, and males. Identified TSSs were utilized to generate a "Daphnia Promoter Atlas," i.e., a catalog of active promoters across the surveyed states. Analysis of the distribution of promoters revealed evidence for widespread alternative promoter usage in D. pulex, in addition to a prominent fraction of compactly-arranged promoters in divergent orientations. We carried out de novo motif discovery using CAGEdefined TSSs and identified eight candidate core promoter motifs; this collection includes canonical promoter elements (e.g., TATA and Initiator) in addition to others lacking obvious orthologs. A comparison of promoter activities found evidence for considerable statespecific differential gene expression between states. Our work represents the first global definition of transcription initiation and promoter architecture in crustaceans. The Daphnia Promoter Atlas presented here provides a valuable resource for comparative study of cis-regulatory regions in metazoans, as well as for investigations into the circuitries that underpin meiosis and parthenogenesis.

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“…Recent advances in RNA sequencing technology (RNA-Seq) addressed further interrogation of the total cellular RNA, or, transcriptome, at a much higher resolution [6]. Thousands of transcripts, in addition to protein-coding mRNAs and microRNAs, have been found to be expressed in a wide range of tissues and cell types [7].…”

Section: Identification Of Lncrnasmentioning

confidence: 99%

An Emerging Role for Long Non-Coding RNA Dysregulation in Neurological Disorders

Fenoglio

Ridolfi

Galimberti

et al. 2013

IJMS

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A novel class of transcripts, long non coding RNAs (lncRNAs), has recently emerged as key players in several biological processes, including dosage compensation, genomic imprinting, chromatin regulation, embryonic development and segmentation, stem cell pluripotency, cell fate determination and potentially many other biological processes, which still are to be elucidated. LncRNAs are pervasively transcribed in the genome and several lines of evidence correlate dysregulation of different lncRNAs to human diseases including neurological disorders. Although their mechanisms of action are yet to be fully elucidated, evidence suggests lncRNA contributions to the pathogenesis of a number of diseases. In this review, the current state of knowledge linking lncRNAs to different neurological disorders is discussed and potential future directions are considered.

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RAMPAGE: Promoter Activity Profiling by Paired-End Sequencing of 5′-Complete cDNAs

Cited by 16 publications

References 12 publications

Conserved noncoding transcription and core promoter regulatory code in early Drosophila development

Conserved noncoding transcription and core promoter regulatory code in early Drosophila development

Promoter Architecture and Sex-Specific Gene Expression in Daphnia pulex

An Emerging Role for Long Non-Coding RNA Dysregulation in Neurological Disorders

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