Establishing legitimacy and function in the new transcriptome (Q37615737)

21 August 2017

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title

Establishing legitimacy and function in the new transcriptome (English)

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21 August 2017

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21 August 2017

Timothy R Hughes

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21 August 2017

publication date

1 November 2009

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Briefings in functional genomics & proteomics

21 August 2017

published in

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21 August 2017

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21 August 2017

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21 August 2017

page(s)

424-436

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The genetic signatures of noncoding RNAs

21 August 2017

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Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments

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Genome-wide transcription and the implications for genomic organization

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Non-coding RNAs: hope or hype?

21 January 2018

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Empirical analysis of transcriptional activity in the Arabidopsis genome

21 January 2018

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The transcriptional landscape of the mammalian genome

21 January 2018

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Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

21 January 2018

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Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays

21 January 2018

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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

21 January 2018

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Tandem chimerism as a means to increase protein complexity in the human genome

21 January 2018

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Transcription-mediated gene fusion in the human genome

21 January 2018

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Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection

21 January 2018

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Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome

21 January 2018

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Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

21 January 2018

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Large-scale transcriptional activity in chromosomes 21 and 22

21 January 2018

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A comprehensive transcript index of the human genome generated using microarrays and computational approaches

21 January 2018

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The transcriptional activity of human Chromosome 22

21 January 2018

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Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution

21 January 2018

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Functionality of intergenic transcription: an evolutionary comparison

21 January 2018

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Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22

21 January 2018

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Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping

21 January 2018

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RNA-Seq: a revolutionary tool for transcriptomics

21 January 2018

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Stem cell transcriptome profiling via massive-scale mRNA sequencing

21 January 2018

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Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

21 January 2018

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Mapping and quantifying mammalian transcriptomes by RNA-Seq

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Integrative annotation of 21,037 human genes validated by full-length cDNA clones

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Highly integrated single-base resolution maps of the epigenome in Arabidopsis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Alternative trans-splicing: a novel mode of pre-mRNA processing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Small silencing RNAs: an expanding universe

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Identification of hundreds of conserved and nonconserved human microRNAs

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

miRBase: tools for microRNA genomics

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Biogenesis and germline functions of piRNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Characterization of the piRNA Complex from Rat Testes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

qiRNA is a new type of small interfering RNA induced by DNA damage.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

MicroRNA-mediated gene silencing modulates the UV-induced DNA-damage response

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Modulation of microRNA processing by p53

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

The mir-34 microRNA is required for the DNA damage response in vivo in C. elegans and in vitro in human breast cancer cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

RNA maps reveal new RNA classes and a possible function for pervasive transcription

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

RNA exosome depletion reveals transcription upstream of active human promoters

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Tiny RNAs associated with transcription start sites in animals.

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Divergent transcription from active promoters

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Bidirectional promoters generate pervasive transcription in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Widespread bidirectional promoters are the major source of cryptic transcripts in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Genome-wide analysis of mammalian promoter architecture and evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

A high-resolution map of active promoters in the human genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

A chromatin landmark and transcription initiation at most promoters in human cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

RNA polymerase is poised for activation across the genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Genome-scale identification of nucleosome positions in S. cerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Nucleosome organization in the Drosophila genome.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

High-throughput mapping of the chromatin structure of human promoters.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Fundamentally different logic of gene regulation in eukaryotes and prokaryotes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Chromatin- and transcription-related factors repress transcription from within coding regions throughout the Saccharomyces cerevisiae genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Transcriptional noise and the fidelity of initiation by RNA polymerase II.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Waste not, want not--transcript excess in multicellular eukaryotes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Analysis of transcriptional activation at a distance in Saccharomyces cerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Footprinting analysis of mammalian RNA polymerase II along its transcript: an alternative view of transcription elongation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Breaking barriers to transcription elongation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Poised RNA polymerase II gives pause for thought

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Transcription regulation through promoter-proximal pausing of RNA polymerase II.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Antisense transcription in the mammalian transcriptome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Complex Loci in human and mouse genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Overlapping antisense transcription in the human genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Antisense transcripts in the human genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Widespread occurrence of antisense transcription in the human genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Antisense transcripts with FANTOM2 clone set and their implications for gene regulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

The antisense transcriptomes of human cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

The DNA-encoded nucleosome organization of a eukaryotic genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Clusters of internally primed transcripts reveal novel long noncoding RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

A strategy for probing the function of noncoding RNAs finds a repressor of NFAT

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

RNA-mediated response to heat shock in mammalian cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Missing lincs in the transcriptome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Global identification of human transcribed sequences with genome tiling arrays

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Sense-antisense pairs in mammals: functional and evolutionary considerations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

A computational screen for methylation guide snoRNAs in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

RNA sequence analysis using covariance models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Noncoding RNA gene detection using comparative sequence analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Regulation of a eukaryotic gene by GTP-dependent start site selection and transcription attenuation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Futile cycle of transcription initiation and termination modulates the response to nucleotide shortage in S. cerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Chromatin decouples promoter threshold from dynamic range

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

LIT1, an imprinted antisense RNA in the human KvLQT1 locus identified by screening for differentially expressed transcripts using monochromosomal hybrids

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Post-transcriptional regulation of endothelial nitric-oxide synthase by an overlapping antisense mRNA transcript

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Antisense transcription controls cell fate in Saccharomyces cerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Specific expression of long noncoding RNAs in the mouse brain

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Specific and potent RNAi in the nucleus of human cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Elongator interactions with nascent mRNA revealed by RNA immunoprecipitation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Megabase deletions of gene deserts result in viable mice

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

A gene expression map for the euchromatic genome of Drosophila melanogaster.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Alternative isoform regulation in human tissue transcriptomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELP037

21 January 2018

Identifiers

DOI

10.1093/BFGP/ELP037

1 reference

release_jzkq5she6zbcxbgrv4daoygony

21 August 2017

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/jzkq5she6zbcxbgrv4daoygony

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference