Identification of novel transcripts in annotated genomes using RNA-Seq

Roberts, Anjeanette; Pimentel, Harold; Trapnell, Cole; Pachter, Lior

doi:10.1093/bioinformatics/btr355

Cited by 902 publications

(771 citation statements)

References 21 publications

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“…Reads were aligned to the human genome using the split-read mapper TopHat (Trapnell et al 2009), generating between 100 3 10 6 and 110 3 10 6 mapped reads per condition. Reads were then assembled using reference annotationbased transcriptome assembly (Roberts et al 2011) from the Cufflinks suite using RefSeq predicted genes as a reference. Significantly expressed transcripts were categorized based on this assembly into three groups: annotated proteincoding, annotated noncoding, and unannotated novel intergenic RNAs.…”

Section: Resultsmentioning

confidence: 99%

Suppression of progenitor differentiation requires the long noncoding RNA ANCR

Kretz¹,

Webster²,

Flockhart³

et al. 2012

Genes Dev.

402

355

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Long noncoding RNAs (lncRNAs) regulate diverse processes, yet a potential role for lncRNAs in maintaining the undifferentiated state in somatic tissue progenitor cells remains uncharacterized. We used transcriptome sequencing and tiling arrays to compare lncRNA expression in epidermal progenitor populations versus differentiating cells. We identified ANCR (anti-differentiation ncRNA) as an 855-base-pair lncRNA down-regulated during differentiation. Depleting ANCR in progenitor-containing populations, without any other stimuli, led to rapid differentiation gene induction. In epidermis, ANCR loss abolished the normal exclusion of differentiation from the progenitor-containing compartment. The ANCR lncRNA is thus required to enforce the undifferentiated cell state within epidermis.

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Section: Resultsmentioning

confidence: 99%

Suppression of progenitor differentiation requires the long noncoding RNA ANCR

Kretz¹,

Webster²,

Flockhart³

et al. 2012

Genes Dev.

402

355

View full text Add to dashboard Cite

show abstract

“…Transcripts were annotated using the RefSeq Hg19 annotation (version 09/2013, UCSC). In addition, a novel annotation guide was created following alignment of Bam file reads to the hg19 Refseq annotation guide using Cuffmerge (part of the Cufflinks suite) 16, 17. The resultant .gtf annotation file merges the Hg19 Refseq database with the novel, un‐annotated RNAs we discovered using whole transcriptome analysis (see Fig.…”

Section: Subjects/materials and Methodsmentioning

confidence: 99%

Blood transcriptome changes after stroke in an African American population

Meller

Pearson

Hardy

et al. 2016

Ann Clin Transl Neurol

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ObjectiveMolecular diagnostic medicine holds much promise to change point of care treatment. An area where additional diagnostic tools are needed is in acute stroke care, to assist in diagnosis and prognosis. Previous studies using microarray‐based gene expression analysis of peripheral blood following stroke suggests this approach may be effective. Next‐generation sequencing (NGS) approaches have expanded genomic analysis and are not limited to previously identified genes on a microarray chip. Here, we report on a pilot NGS study to identify gene expression and exon expression patterns for the prediction of stroke diagnosis and prognosis.MethodsWe recruited 28 stroke patients and 28 age‐ and sex‐matched hypertensive controls. RNA was extracted from 3 mL blood samples, and RNA‐Seq libraries were assembled and sequenced.ResultsBioinformatical analysis of the aligned RNA data reveal exonic (30%), intronic (36%), and novel RNA components (not currently annotated: 33%). We focused our study on patients with confirmed middle cerebral artery occlusion ischemic stroke (n = 17). On the basis of our observation of differential splicing of gene transcripts, we used all exonic RNA expression rather than gene expression (combined exons) to build prediction models using support vector machine algorithms. Based on model building, these models have a high predicted accuracy rate >90% (spec. 88% sen. 92%). We further stratified outcome based on the improvement in NIHss scores at discharge; based on model building we observe a predicted 100% accuracy rate.Interpretation NGS‐based exon expression analysis approaches have a high potential for patient diagnosis and outcome prediction, with clear utility to aid in clinical patient care.

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“…Reads were trimmed with cutadapt and aligned to the maize B73 reference genome (ZmB73 AGPv3) with TopHat (Trapnell et al, 2009). The directional RNA-seq libraries were used to obtain a reassembly of the maize transcriptome with Cufflinks (RABT mode; Roberts et al, 2011).…”

Section: Total Rna Sequencing and Maize Transcriptome Reassemblymentioning

confidence: 99%

Genome-Wide Characterization of Maize Small RNA Loci and Their Regulation in the required to maintain repression6-1 (rmr6-1) Mutant and Long-Term Abiotic Stresses

et al. 2016

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(A.L., M.J.A.) Endogenous small RNAs (sRNAs) contribute to gene regulation and genome homeostasis, but their activities and functions are incompletely known. The maize genome has a high number of transposable elements (TEs; almost 85%), some of which spawn abundant sRNAs. We performed sRNA and total RNA sequencing from control and abiotically stressed B73 wild-type plants and rmr6-1 mutants. RMR6 encodes the largest subunit of the RNA polymerase IV complex and is responsible for accumulation of most 24-nucleotide (nt) small interfering RNAs (siRNAs). We identified novel MIRNA loci and verified miR399 target conservation in maize. RMR6-dependent 23-24 nt siRNA loci were specifically enriched in the upstream region of the most highly expressed genes. Most genes misregulated in rmr6-1 did not show a significant correlation with loss of flanking siRNAs, but we identified one gene supporting existing models of direct gene regulation by TE-derived siRNAs. Long-term drought correlated with changes of miRNA and sRNA accumulation, in particular inducing down-regulation of a set of sRNA loci in the wild-typeleaf.

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Identification of novel transcripts in annotated genomes using RNA-Seq

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 902 publications

References 21 publications

Suppression of progenitor differentiation requires the long noncoding RNA ANCR

Suppression of progenitor differentiation requires the long noncoding RNA ANCR

Blood transcriptome changes after stroke in an African American population

Genome-Wide Characterization of Maize Small RNA Loci and Their Regulation in the required to maintain repression6-1 (rmr6-1) Mutant and Long-Term Abiotic Stresses

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