Genome-wide analysis of long noncoding RNA stability (Q35914857)

11 August 2017

Genome-wide analysis of long noncoding RNA stability (English)

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11 August 2017

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8

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11 August 2017

Michael B Clark

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Archa H Fox

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Archa H Fox

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Pablo Moscato

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Pablo Moscato

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Mario Inostroza-Ponta

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Mario Inostroza-Ponta

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author name string

Rebecca L Johnston

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11 August 2017

Ellen Fortini

5

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9 March 2012

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22

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5

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885-898

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describes a project that uses

11 August 2017

limma

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22 June 2022

https://europepmc.org/article/PMC/3337434

based on heuristic

inferred from PubMed Central ID database lookup

cites work

miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA

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Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

11 July 2018

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lincRNAs act in the circuitry controlling pluripotency and differentiation

11 July 2018

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PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

11 July 2018

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11 July 2018

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Global quantification of mammalian gene expression control

11 July 2018

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Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

11 July 2018

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SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer

11 July 2018

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Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice

11 July 2018

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A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

11 July 2018

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11 July 2018

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Genome-wide identification of polycomb-associated RNAs by RIP-seq

11 July 2018

1 reference

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Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs

11 July 2018

1 reference

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lncRNAdb: a reference database for long noncoding RNAs

11 July 2018

1 reference

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Expression of distinct RNAs from 3' untranslated regions

11 July 2018

1 reference

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The UCSC Genome Browser database: update 2011

11 July 2018

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Highly ordered spatial organization of the structural long noncoding NEAT1 RNAs within paraspeckle nuclear bodies

11 July 2018

1 reference

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The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

11 July 2018

1 reference

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A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

The pioneer round of translation: features and functions

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response

11 July 2018

1 reference

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Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling

11 July 2018

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Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

11 July 2018

1 reference

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Major role for mRNA stability in shaping the kinetics of gene induction

11 July 2018

1 reference

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

Paraspeckles: nuclear bodies built on long noncoding RNA

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

Conserved principles of mammalian transcriptional regulation revealed by RNA half-life

11 July 2018

1 reference

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The many pathways of RNA degradation

11 July 2018

1 reference

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Long non-coding RNAs: insights into functions

11 July 2018

1 reference

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

11 July 2018

1 reference

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

RNA exosome depletion reveals transcription upstream of active human promoters

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

Database for mRNA half-life of 19 977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

NCBI Reference Sequences: current status, policy and new initiatives

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

NRED: a database of long noncoding RNA expression

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

A cryptic unstable transcript mediates transcriptional trans-silencing of the Ty1 retrotransposon in S. cerevisiae

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

A comparison of background correction methods for two-colour microarrays

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

Beyond the 3' end: experimental validation of extended transcript isoforms

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

The imprinted Air ncRNA is an atypical RNAPII transcript that evades splicing and escapes nuclear export

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

Complex Loci in human and mouse genomes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

Linear models and empirical bayes methods for assessing differential expression in microarray experiments

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

The transcriptional landscape of the mammalian genome

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

Java Treeview--extensible visualization of microarray data

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

Open source clustering software

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

Normalization of cDNA microarray data

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

The role of deoxyribonucleic acid in ribonucleic acid synthesis. III. The inhibition of the enzymatic synthesis of ribonucleic acid and deoxyribonucleic acid by actinomycin D and proflavin

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

Directed proteomic analysis of the human nucleolus

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

ARED: human AU-rich element-containing mRNA database reveals an unexpectedly diverse functional repertoire of encoded proteins

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

UV-Induced stabilization of c-fos and other short-lived mRNAs

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

Human U19 intron-encoded snoRNA is processed from a long primary transcript that possesses little potential for protein coding

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

A transcript map for the 2.8-Mb region containing the multiple endocrine neoplasia type 1 locus

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

A mammalian gene with introns instead of exons generating stable RNA products

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

Extreme instability of myc mRNA in normal and transformed human cells.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

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

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

Genome-wide analysis of mRNA decay rates and their determinants in Arabidopsis thaliana

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

GATHER: a systems approach to interpreting genomic signatures

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

Stabilization of Xist RNA mediates initiation of X chromosome inactivation.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3337434

24 September 2018

Identifiers

DOI

10.1101/GR.131037.111

1 reference

11 August 2017

1 reference

11 August 2017

PubMed publication ID

22406755

1 reference