4.6 Article

Non-coding RNA: what is functional and what is junk?

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article History & Philosophy Of Science

The Genomic Challenge to Adaptationism

Sahotra Sarkar

BRITISH JOURNAL FOR THE PHILOSOPHY OF SCIENCE (2015)

Article Biochemistry & Molecular Biology

lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs

Xiu Cheng Quek et al.

NUCLEIC ACIDS RESEARCH (2015)

Review Biochemistry & Molecular Biology

The Noncoding RNA Revolution-Trashing Old Rules to Forge New Ones

Thomas R. Cech et al.

Article Biochemistry & Molecular Biology

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

Ariel A. Bazzini et al.

EMBO JOURNAL (2014)

Article Evolutionary Biology

Distinguishing between Function and Effect in Genome Biology

W. Ford Doolittle et al.

GENOME BIOLOGY AND EVOLUTION (2014)

Article Biochemistry & Molecular Biology

Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes

Iakes Ezkurdia et al.

HUMAN MOLECULAR GENETICS (2014)

Article Multidisciplinary Sciences

An atlas of active enhancers across human cell types and tissues

Robin Andersson et al.

NATURE (2014)

Article Biochemistry & Molecular Biology

Alternative splicing at GYNNGY 5′ splice sites: more noise, less regulation

Meng Wang et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Multidisciplinary Sciences

Human coding RNA editing is generally nonadaptive

Guixia Xu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Review Multidisciplinary Sciences

The new frontier of genome engineering with CRISPR-Cas9

Jennifer A. Doudna et al.

SCIENCE (2014)

Editorial Material Multidisciplinary Sciences

RNA and dynamic nuclear organization

John Rinn et al.

SCIENCE (2014)

Review Genetics & Heredity

Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications

Aurelie Kapusta et al.

TRENDS IN GENETICS (2014)

Article Genetics & Heredity

The Case for Junk DNA

Alexander F. Palazzo et al.

PLOS GENETICS (2014)

Review Biochemistry & Molecular Biology

lncRNA and gene looping What's the connection?

Youtaro Shibayama et al.

TRANSCRIPTION-AUSTIN (2014)

Article Biotechnology & Applied Microbiology

Expanded identification and characterization of mammalian circular RNAs

Junjie U. Guo et al.

GENOME BIOLOGY (2014)

Review Biochemistry & Molecular Biology

Can ENCODE tell us how much junk DNA we carry in our genome?

Deng-Ke Niu et al.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2013)

Review Biochemistry & Molecular Biology

lincRNAs: Genomics, Evolution, and Mechanisms

Igor Ulitsky et al.

Article Biochemistry & Molecular Biology

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

Mitchell Guttman et al.

Editorial Material Biochemistry & Molecular Biology

The ENCODE project: Missteps overshadowing a success

Sean R. Eddy

CURRENT BIOLOGY (2013)

Article Biochemistry & Molecular Biology

Widespread and extensive lengthening of 3′ UTRs in the mammalian brain

Pedro Miura et al.

GENOME RESEARCH (2013)

Review Biochemistry & Molecular Biology

Exaptation of Transposable Elements into Novel Cis-Regulatory Elements: Is the Evidence Always Strong?

Flavio S. J. de Souza et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Multidisciplinary Sciences

Circular RNAs are a large class of animal RNAs with regulatory potency

Sebastian Memczak et al.

NATURE (2013)

Article Biochemistry & Molecular Biology

LNCipedia: a database for annotated human lncRNA transcript sequences and structures

Pieter-Jan Volders et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Multidisciplinary Sciences

Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks

Michael A. White et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Multidisciplinary Sciences

Is junk DNA bunk? A critique of ENCODE

W. Ford Doolittle

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Biochemistry & Molecular Biology

Circular RNAs are abundant, conserved, and associated with ALU repeats

William R. Jeck et al.

Editorial Material Multidisciplinary Sciences

A Circuitous Route to Noncoding RNA

Jeremy E. Wilusz et al.

SCIENCE (2013)

Article Biochemical Research Methods

The Vast, Conserved Mammalian lincRNome

David Managadze et al.

PLOS COMPUTATIONAL BIOLOGY (2013)

Review Cell Biology

ALREX-elements and introns: two identity elements that promote mRNA nuclear export

Alexander F. Palazzo et al.

WILEY INTERDISCIPLINARY REVIEWS-RNA (2013)

Review Biochemistry & Molecular Biology

Nuclear export as a key arbiter of mRNA identity in eukaryotes

Alexander F. Palazzo et al.

BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS (2012)

Editorial Material Biochemistry & Molecular Biology

The C-value paradox, junk DNA and ENCODE

Sean R. Eddy

CURRENT BIOLOGY (2012)

Article Genetics & Heredity

Why Transcription Factor Binding Sites Are Ten Nucleotides Long

Alexander J. Stewart et al.

GENETICS (2012)

Article Biochemistry & Molecular Biology

Long noncoding RNAs are rarely translated in two human cell lines

Balazs Banfai et al.

GENOME RESEARCH (2012)

Article Biochemistry & Molecular Biology

HP1Swi6 Mediates the Recognition and Destruction of Heterochromatic RNA Transcripts

Claudia Keller et al.

MOLECULAR CELL (2012)

Editorial Material Multidisciplinary Sciences

FORUM: Genomics ENCODE explained

Joseph R. Ecker

NATURE (2012)

Article Multidisciplinary Sciences

Landscape of transcription in human cells

Sarah Djebali et al.

NATURE (2012)

Article Multidisciplinary Sciences

An integrated encyclopedia of DNA elements in the human genome

Ian Dunham et al.

NATURE (2012)

Article Biochemistry & Molecular Biology

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

Yang Wang et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2012)

Article Multidisciplinary Sciences

Gene Loops Enhance Transcriptional Directionality

Sue Mei Tan-Wong et al.

SCIENCE (2012)

News Item Multidisciplinary Sciences

GENOMICS ENCODE Project Writes Eulogy For Junk DNA

Elizabeth Pennisi

SCIENCE (2012)

Review Biochemistry & Molecular Biology

Pervasive transcription - Lessons from yeast

Mathieu Tisseur et al.

BIOCHIMIE (2011)

Article Cell Biology

Animal Transcription Networks as Highly Connected, Quantitative Continua

Mark D. Biggin

DEVELOPMENTAL CELL (2011)

Article Evolutionary Biology

Negative Correlation between Expression Level and Evolutionary Rate of Long Intergenic Noncoding RNAs

David Managadze et al.

GENOME BIOLOGY AND EVOLUTION (2011)

Review Biochemistry & Molecular Biology

Molecular Mechanisms of Long Noncoding RNAs

Kevin C. Wang et al.

MOLECULAR CELL (2011)

Article Multidisciplinary Sciences

U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation

Daisuke Kaida et al.

NATURE (2010)

Review Genetics & Heredity

A global view of genomic information - moving beyond the gene and the master regulator

John S. Mattick et al.

TRENDS IN GENETICS (2010)

Article Biochemistry & Molecular Biology

Most Dark Matter'' Transcripts Are Associated With Known Genes

Harm van Bakel et al.

PLOS BIOLOGY (2010)

Review Biochemistry & Molecular Biology

Evolution and Functions of Long Noncoding RNAs

Chris P. Ponting et al.

Review Biochemistry & Molecular Biology

Focus on the centre: the role of chromatin on the regulation of centromere identity and function

Monica Torras-Llort et al.

EMBO JOURNAL (2009)

Review Cell Biology

Long noncoding RNAs: functional surprises from the RNA world

Jeremy E. Wilusz et al.

GENES & DEVELOPMENT (2009)

Article Multidisciplinary Sciences

Bidirectional promoters generate pervasive transcription in yeast

Zhenyu Xu et al.

NATURE (2009)

Review Multidisciplinary Sciences

Small RNAs in transcriptional gene silencing and genome defence

Danesh Moazed

NATURE (2009)

Review Genetics & Heredity

Effective population size and patterns of molecular evolution and variation

Brian Charlesworth

NATURE REVIEWS GENETICS (2009)

Article Multidisciplinary Sciences

The Peculiarities of Large Intron Splicing in Animals

Samuel Shepard et al.

PLOS ONE (2009)

Article Multidisciplinary Sciences

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

Ahmad M. Khalil et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Biochemistry & Molecular Biology

Absolute quantification of microRNAs by using a universal reference

Ute Bissels et al.

Article Biochemical Research Methods

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

Daniel Ramskold et al.

PLOS COMPUTATIONAL BIOLOGY (2009)

Article Evolutionary Biology

Evidence against the energetic cost hypothesis for the short introns in highly expressed genes

Yi-Fei Huang et al.

BMC EVOLUTIONARY BIOLOGY (2008)

Article Biochemistry & Molecular Biology

A yeast exosome cofactor, Mpp6, functions in RNA surveillance and in the degradation of noncoding RNA transcripts

Laura Milligan et al.

MOLECULAR AND CELLULAR BIOLOGY (2008)

Article Biochemical Research Methods

Mapping and quantifying mammalian transcriptomes by RNA-Seq

Ali Mortazavi et al.

NATURE METHODS (2008)

Article Multidisciplinary Sciences

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

Pascal Preker et al.

SCIENCE (2008)

Article Biochemistry & Molecular Biology

Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm

Xiao-Yong Li et al.

PLOS BIOLOGY (2008)

Article Biochemistry & Molecular Biology

The signal sequence coding region promotes nuclear export of mRNA

Alexander F. Palazzo et al.

PLOS BIOLOGY (2007)

Article Biochemistry & Molecular Biology

Transcriptional noise and the fidelity of initiation by RNA polymerase II

Kevin Struhl

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2007)

Article Genetics & Heredity

Genome-wide analysis of mammalian promoter architecture and evolution

Piero Carninci et al.

NATURE GENETICS (2006)

Article Multidisciplinary Sciences

Introns and the origin of nucleus-cytosol compartmentalization

W Martin et al.

NATURE (2006)

Article Multidisciplinary Sciences

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

CA Davis et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Multidisciplinary Sciences

The transcriptional landscape of the mammalian genome

P Carninci et al.

SCIENCE (2005)

Article Biotechnology & Applied Microbiology

Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray

MG Carter et al.

GENOME BIOLOGY (2005)

Review Cell Biology

Nonsense-mediated mRNA decay: terminating erroneous gene expression

KE Baker et al.

CURRENT OPINION IN CELL BIOLOGY (2004)

Article Biochemistry & Molecular Biology

Exonic splicing enhancers: mechanism of action, diversity and role in human genetic diseases

BJ Blencowe

TRENDS IN BIOCHEMICAL SCIENCES (2000)