(Q55059021)

16 June 2018

title

Does every transcript originate from a gene? (English)

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16 June 2018

2

Jürgen Brosius

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16 June 2018

author name string

Carsten A Raabe

series ordinal

1

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16 June 2018

language of work or name

English

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publication date

1 April 2015

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16 June 2018

Annals of the New York Academy of Sciences

published in

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16 June 2018

volume

1341

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16 June 2018

page(s)

136-148

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16 June 2018

The relationship between non-protein-coding DNA and eukaryotic complexity.

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The case for junk DNA

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Non–coding RNA genes and the modern RNA world

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Gene index analysis of the human genome estimates approximately 120,000 genes.

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A question of size: the eukaryotic proteome and the problems in defining it.

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Echoes from the past--are we still in an RNP world?

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Initial sequencing and comparative analysis of the mouse genome

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On "genomenclature": a comprehensive (and respectful) taxonomy for pseudogenes and other "junk DNA"

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Retroposons--seeds of evolution

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Exonization of transposed elements: A challenge and opportunity for evolution

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Dark matter RNA illuminates the puzzle of genome-wide association studies

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Transcribed dark matter: meaning or myth?

21 January 2018

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Large-scale transcriptional activity in chromosomes 21 and 22

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Global identification of human transcribed sequences with genome tiling arrays

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Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution

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Dark Matter RNA: Existence, Function, and Controversy

21 January 2018

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Genome-wide transcription and the implications for genomic organization

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Origin of phenotypes: genes and transcripts

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What is a gene, post-ENCODE? History and updated definition

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A genome-wide study of dual coding regions in human alternatively spliced genes

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Human tRNA synthetase catalytic nulls with diverse functions

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On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE

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An integrated encyclopedia of DNA elements in the human genome

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What does our genome encode?

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Transcriptional interference--a crash course

21 January 2018

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Deletion of the MBII-85 snoRNA gene cluster in mice results in postnatal growth retardation

21 January 2018

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Neuronal untranslated BC1 RNA: targeted gene elimination in mice.

21 January 2018

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Multiple knockout mouse models reveal lincRNAs are required for life and brain development

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

Moonlighting proteins: old proteins learning new tricks.

21 January 2018

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Alu-SINE exonization: en route to protein-coding function

21 January 2018

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Functional persistence of exonized mammalian-wide interspersed repeat elements (MIRs)

21 January 2018

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21 January 2018

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Intronic splicing enhancers, cognate splicing factors and context-dependent regulation rules

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

Introns: evolution and function

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

Retrocopy contributions to the evolution of the human genome

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

Before It Gets Started: Regulating Translation at the 5' UTR.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

Role of 5'- and 3'-untranslated regions of mRNAs in human diseases

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

Untranslated regions of mRNAs

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

The untranslated regions of eukaryotic mRNAs: structure, function, evolution and bioinformatic tools for their analysis

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

Massively parallel functional annotation of 3' untranslated regions

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

From "junk" to gene: curriculum vitae of a primate receptor isoform gene

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

Transcriptional Regulatory Elements in the Human Genome

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

Natural antisense transcripts regulate gene expression in an epigenetic manner

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

Evolution, biogenesis and function of promoter-associated RNAs

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

cis-antisense RNA, another level of gene regulation in bacteria.

21 January 2018

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Regulation of mRNA translation and stability by microRNAs

21 January 2018

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Thirty years of multiple sequence codes

21 January 2018

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21 January 2018

The small nucleolar RNAs

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lincRNAs: genomics, evolution, and mechanisms

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

Mechanisms of alternative pre-messenger RNA splicing

21 January 2018

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The multiple codes of nucleotide sequences

21 January 2018

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Function and synthesis of small nucleolar RNAs

21 January 2018

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Translational control by a small RNA: dendritic BC1 RNA targets the eukaryotic initiation factor 4A helicase mechanism

21 January 2018

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Antisense promoter of human L1 retrotransposon drives transcription of adjacent cellular genes

21 January 2018

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

21 January 2018

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Long noncoding RNAs are rarely translated in two human cell lines

21 January 2018

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Detecting non-coding selective pressure in coding regions

21 January 2018

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Multiple levels of meaning in DNA sequences, and one more

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

The persistent contributions of RNA to eukaryotic gen(om)e architecture and cellular function

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

Molecular biology. Glimpses of a tiny RNA world

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Landscape of transcription in human cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Dealing with pervasive transcription.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Transcriptional interferences in cis natural antisense transcripts of humans and mice

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Do natural antisense transcripts make sense in eukaryotes?

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Naturally occurring antisense: transcriptional leakage or real overlap?

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Long intronic noncoding RNA transcription: expression noise or expression choice?

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

MicroRNA profiling: separating signal from noise

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

Transcriptional noise as a driver of gene evolution

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

Mining diverse small RNA species in the deep transcriptome

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

Megabase deletions of gene deserts result in viable mice

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

A promoter-level mammalian expression atlas

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Promoter traps in embryonic stem cells: a genetic screen to identify and mutate developmental genes in mice

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

Gene-trap mutagenesis: past, present and beyond

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

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

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

A quantitative atlas of polyadenylation in five mammals

21 January 2018

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An efficient method for genome-wide polyadenylation site mapping and RNA quantification

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

Transcription termination by nuclear RNA polymerases

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Most "dark matter" transcripts are associated with known genes

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

Dark matter transcripts: sound and fury, signifying nothing?

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

The reality of pervasive transcription

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Binding of TBP to promoters in vivo is stimulated by activators and requires Pol II holoenzyme

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

The evolution of lncRNA repertoires and expression patterns in tetrapods

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Comparative analysis of the transcriptome across distant species

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Comparative analysis of metazoan chromatin organization

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Comparative analysis of regulatory information and circuits across distant species

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Folding and Finding RNA Secondary Structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

RNA folding during transcription

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Coupling polymerase pausing and chromatin landscapes for precise regulation of transcription.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

Genome-wide identification of miRNA targets by PAR-CLIP.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

PAR-CliP--a method to identify transcriptome-wide the binding sites of RNA binding proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Argonaute CLIP--a method to identify in vivo targets of miRNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Specific expression of long noncoding RNAs in the mouse brain

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Long non-coding RNA-mediated transcriptional interference of a permease gene confers drug tolerance in fission yeast.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Gene regulation by the act of long non-coding RNA transcription

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Transcriptional interference by RNA polymerase pausing and dislodgement of transcription factors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Potent transcriptional interference by pausing of RNA polymerases over a downstream promoter

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Sequence and genetic analysis of a dispensible 189 nucleotide snRNA from Saccharomyces cerevisiae

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12741

A snoRNA that guides the two most conserved pseudouridine modifications within rRNA confers a growth advantage in yeast.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Role of a neuronal small non-messenger RNA: behavioural alterations in BC1 RNA-deleted mice.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Noncoding RNAs and epigenetic mechanisms during X-chromosome inactivation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

What If There Are Only 30,000 Human Genes?

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

Enhancement of TBP binding by activators and general transcription factors

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12741

21 January 2018

Identifiers

DOI

10.1111/NYAS.12741

1 reference

16 June 2018

1 reference

16 June 2018