Characterization of human pseudogene-derived non-coding RNAs for functional potential (Q28660423)

April 2022 Public Data File from Crossref

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Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs

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A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?

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Pseudogenes: pseudo-functional or key regulators in health and disease?

17 March 2017

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Mammalian microRNAs predominantly act to decrease target mRNA levels

17 March 2017

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A coding-independent function of gene and pseudogene mRNAs regulates tumour biology

17 March 2017

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

17 March 2017

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Transcriptional gene silencing through epigenetic changes mediated by non-coding RNAs

17 March 2017

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Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP

17 March 2017

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Assessing the genomic evidence for conserved transcribed pseudogenes under selection

17 March 2017

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An RNA-dependent RNA polymerase formed by TERT and the RMRP RNA

17 March 2017

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Small RNAs originated from pseudogenes: cis- or trans-acting?

17 March 2017

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

17 March 2017

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TopHat: discovering splice junctions with RNA-Seq

17 March 2017

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Long non-coding RNAs: insights into functions

17 March 2017

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Biogenesis of small RNAs in animals

17 March 2017

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Small RNAs in transcriptional gene silencing and genome defence

17 March 2017

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Small silencing RNAs: an expanding universe

17 March 2017

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Pseudofam: the pseudogene families database

17 March 2017

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Most mammalian mRNAs are conserved targets of microRNAs

17 March 2017

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Widespread changes in protein synthesis induced by microRNAs

17 March 2017

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Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes

17 March 2017

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Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes

17 March 2017

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Comparative genomics search for losses of long-established genes on the human lineage

17 March 2017

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A second generation human haplotype map of over 3.1 million SNPs

17 March 2017

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Target mimicry provides a new mechanism for regulation of microRNA activity

17 March 2017

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

17 March 2017

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Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution

17 March 2017

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Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs

17 March 2017

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Argonaute-1 directs siRNA-mediated transcriptional gene silencing in human cells

17 March 2017

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Genome-wide survey for biologically functional pseudogenes

17 March 2017

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Gene losses during human origins

17 March 2017

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Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

17 March 2017

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Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Nucleotide diversity in gorillas

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

A genome-wide survey of human pseudogenes

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Pseudogenes: Are They “Junk” or Functional DNA?

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

T-Coffee: A novel method for fast and accurate multiple sequence alignment

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

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

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

lincRNAs act in the circuitry controlling pluripotency and differentiation

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Characterization of microRNA expression profiles in normal human tissues

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Non-coding RNAs in human disease

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Molecular mechanisms of long noncoding RNAs

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

7 April 2017

Vertebrate pseudogenes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Beyond transposons: the epigenetic and somatic functions of the Piwi-piRNA mechanism

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Genome-wide chromatin state transitions associated with developmental and environmental cues

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Axonal trafficking of an antisense RNA transcribed from a pseudogene is regulated by classical conditioning

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Pseudogenes: newly discovered players in human cancer

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Naturally occurring endo-siRNA silences LINE-1 retrotransposons in human cells through DNA methylation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

A noncoding RNA antisense to moesin at 5p14.1 in autism

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Small RNA in the nucleus: the RNA-chromatin ping-pong

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Transposase mediated construction of RNA-seq libraries.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Functional evidence of post-transcriptional regulation by pseudogenes.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Pseudogene-derived small interference RNAs regulate gene expression in African Trypanosoma brucei

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

A transcribed pseudogene of MYLK promotes cell proliferation.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

RNA-dependent RNA polymerases in RNA silencing

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Transcriptional regulation of Oct4 by a long non-coding RNA antisense to Oct4-pseudogene 5

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Pseudogenes as an alternative source of natural antisense transcripts

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

3 June 2018

Direct RNA sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Targets of RNA-directed DNA methylation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Promoter-associated RNA is required for RNA-directed transcriptional gene silencing in human cells

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

L1 retrotransposition is suppressed by endogenously encoded small interfering RNAs in human cultured cells

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Pseudo-messenger RNA: phantoms of the transcriptome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Post-transcriptional small RNA pathways in plants: mechanisms and regulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Short double-stranded RNA induces transcriptional gene silencing in human cancer cells in the absence of DNA methylation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Integrated pseudogene annotation for human chromosome 22: evidence for transcription

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

The profile of repeat-associated histone lysine methylation states in the mouse epigenome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Large-scale analysis of pseudogenes in the human genome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Dicer is essential for formation of the heterochromatin structure in vertebrate cells

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Tsix, a gene antisense to Xist at the X-inactivation centre

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Evolution of immunoglobulin VH pseudogenes in chickens

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3974860

Timed and targeted differential regulation of nitric oxide synthase (NOS) and anti-NOS genes by reward conditioning leading to long-term memory formation.

3 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0093972

A new role for expressed pseudogenes as ncRNA: regulation of mRNA stability of its homologous coding gene

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0093972

Genomics: protein fossils live on as RNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0093972

ceRNAs: miRNA target mimic mimics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0093972

Redefining microRNA targets

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0093972

PseudoPipe: an automated pseudogene identification pipeline

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0093972

The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0093972

Frequent emergence and functional resurrection of processed pseudogenes in the human and mouse genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0093972

Neuronal expression of neural nitric oxide synthase (nNOS) protein is suppressed by an antisense RNA transcribed from an NOS pseudogene

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24699680

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0093972

1 reference

ADS bibcode

2014PLoSO...993972G

0 references

1 reference

1 reference

PubMed publication ID

24699680

1 reference