Evolution to the rescue: using comparative genomics to understand long non-coding RNAs (Q38940313)

7 September 2017

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title

Evolution to the rescue: using comparative genomics to understand long non-coding RNAs (English)

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7 September 2017

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Igor Ulitsky

1

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7 September 2017

30 August 2016

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7 September 2017

Nature Reviews Genetics

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7 September 2017

17

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7 September 2017

601-614

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7 September 2017

10

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https://scigraph.springernature.com/pub.10.1038/nrg.2016.85

7 September 2017

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Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

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Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs

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Genome-wide characterization of long intergenic non-coding RNAs (lincRNAs) provides new insight into viral diseases in honey bees Apis cerana and Apis mellifera

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Positionally-conserved but sequence-diverged: identification of long non-coding RNAs in the Brassicaceae and Cleomaceae.

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

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Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness

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Mutations within lncRNAs are effectively selected against in fruitfly but not in human

21 January 2018

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Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice

21 January 2018

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

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Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs

21 January 2018

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Rapid turnover of long noncoding RNAs and the evolution of gene expression

21 January 2018

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Human β cell transcriptome analysis uncovers lncRNAs that are tissue-specific, dynamically regulated, and abnormally expressed in type 2 diabetes

21 January 2018

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Human long noncoding RNAs are substantially less folded than messenger RNAs

21 January 2018

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21 January 2018

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A triple helix stabilizes the 3' ends of long noncoding RNAs that lack poly(A) tails

21 January 2018

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Tandem stem-loops in roX RNAs act together to mediate X chromosome dosage compensation in Drosophila

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Regulation of histone H4 Lys16 acetylation by predicted alternative secondary structures in roX noncoding RNAs

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Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome

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RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure

21 January 2018

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

21 January 2018

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28-way vertebrate alignment and conservation track in the UCSC Genome Browser

21 January 2018

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De novo prediction of structured RNAs from genomic sequences

21 January 2018

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Noncoding RNA NORAD Regulates Genomic Stability by Sequestering PUMILIO Proteins

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

Long noncoding RNAs in C. elegans

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

Widespread purifying selection on RNA structure in mammals

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

HOTAIR forms an intricate and modular secondary structure.

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

Rapid evolutionary turnover underlies conserved lncRNA-genome interactions

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

Conservation of a triple-helix-forming RNA stability element in noncoding and genomic RNAs of diverse viruses

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

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

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

Unexpected selection to retain high GC content and splicing enhancers within exons of multiexonic lncRNA loci

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

The conservation and signatures of lincRNAs in Marek's disease of chicken.

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

The lncRNA DEANR1 facilitates human endoderm differentiation by activating FOXA2 expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons.

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

Unlinking an lncRNA from Its Associated cis Element

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Opposing Roles for the lncRNA Haunt and Its Genomic Locus in Regulating HOXA Gene Activation during Embryonic Stem Cell Differentiation

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

Genome-wide discovery and characterization of maize long non-coding RNAs.

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

Long noncoding RNAs and their proposed functions in fibre development of cotton (Gossypium spp.).

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

New gene evolution: little did we know

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

Origins, evolution, and phenotypic impact of new genes.

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Origin and evolution of the long non-coding genes in the X-inactivation center

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

The impact of retrotransposons on human genome evolution

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

Transposable elements reveal a stem cell-specific class of long noncoding RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

DUX4 binding to retroelements creates promoters that are active in FSHD muscle and testis

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Divergent transcription from active promoters

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Dealing with pervasive transcription.

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

Divergent transcription: a driving force for new gene origination?

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Bidirectional promoters as important drivers for the emergence of species-specific transcripts

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Cellular source and mechanisms of high transcriptome complexity in the mammalian testis

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

A dual origin of the Xist gene from a protein-coding gene and a set of transposable elements

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Alu elements in ANRIL non-coding RNA at chromosome 9p21 modulate atherogenic cell functions through trans-regulation of gene networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Function and evolution of local repeats in the Firre locus

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

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

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

Considerations when investigating lncRNA function in vivo.

21 January 2018

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https://api.crossref.org/works/10.1038%2FNRG.2016.85

MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

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/10.1038%2FNRG.2016.85

Structural and functional differences in the long non-coding RNA hotair in mouse and human

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Targeted disruption of Hotair leads to homeotic transformation and gene derepression

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Braveheart, a long noncoding RNA required for cardiovascular lineage commitment

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cis

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Activity-dependent human brain coding/noncoding gene regulatory networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Infernal 1.1: 100-fold faster RNA homology searches

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Full-length transcriptome assembly from RNA-Seq data without a reference genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Isoform diversity and regulation in peripheral and central neurons revealed through RNA-Seq

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Detection of nonneutral substitution rates on mammalian phylogenies

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Human pluripotent stem cell-derived neural constructs for predicting neural toxicity

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Regulation of the ESC transcriptome by nuclear long noncoding RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Human XIST yeast artificial chromosome transgenes show partial X inactivation center function in mouse embryonic stem cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Identification of novel long noncoding RNAs underlying vertebrate cardiovascular development.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

A long non-coding RNA, LncMyoD, regulates skeletal muscle differentiation by blocking IMP2-mediated mRNA translation

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Rsx is a metatherian RNA with Xist-like properties in X-chromosome inactivation

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Reverse genetic screening reveals poor correlation between morpholino-induced and mutant phenotypes in zebrafish.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Neutral evolution of ‘non-coding’ complementary DNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Evolution of the Long Non-coding RNAs MALAT1 and MENβ/ε

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Airn transcriptional overlap, but not its lncRNA products, induces imprinted Igf2r silencing

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Identification of long non-coding RNAs in insects genomes

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Functional conservation of the lncRNA NEAT1 in the ancestrally diverged marsupial lineage: Evidence for NEAT1 expression and associated paraspeckle assembly during late gestation in the opossum Monodelphis domestica

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Human X inactivation center induces random X chromosome inactivation in male transgenic mice

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.85

Regulation of X-chromosome inactivation in development in mice and humans

31 March 2020

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27573374

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Mouse transcriptome: neutral evolution of 'non-coding' complementary DNAs

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27573374

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NRG.2016.85

1 reference

PubMed ID

27573374

Dimensions Publication ID

7 September 2017

0 references

1 reference

PubMed ID

27573374