Genomic gems: SINE RNAs regulate mRNA production (Q24632289)

Current Opinion in Genetics & Development

Europe PubMed Central

title

Genomic gems: SINE RNAs regulate mRNA production (English)

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author name string

Steven L Ponicsan

series ordinal

1

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Jennifer F Kugel

series ordinal

2

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James A Goodrich

series ordinal

3

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language of work or name

English

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publication date

April 2010

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published in

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volume

20

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issue

2

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page(s)

149-55

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cites work

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7 April 2017

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Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome

7 April 2017

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Editing of glutamate receptor B subunit ion channel RNAs by four alternatively spliced DRADA2 double-stranded RNA adenosine deaminases

7 April 2017

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Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts

7 April 2017

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Initial sequencing and comparative analysis of the mouse genome

7 April 2017

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The role of chromatin during transcription

7 April 2017

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Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays

7 April 2017

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Transcriptional coactivator complexes

7 April 2017

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Alternative splicing of Alu exons--two arms are better than one

7 April 2017

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Thousands of human mobile element fragments undergo strong purifying selection near developmental genes

7 April 2017

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Functional noncoding sequences derived from SINEs in the mammalian genome

7 April 2017

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A large family of ancient repeat elements in the human genome is under strong selection

7 April 2017

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Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors

7 April 2017

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Regulation of alternative splicing by RNA editing

7 April 2017

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Pre-mRNA processing reaches back to transcription and ahead to translation

7 April 2017

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A distal enhancer and an ultraconserved exon are derived from a novel retroposon

7 April 2017

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Systematic identification of abundant A-to-I editing sites in the human transcriptome

7 April 2017

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Alu repeats and human disease

7 April 2017

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TFIIF facilitates dissociation of RNA polymerase II from noncoding RNAs that lack a repression domain

7 April 2017

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B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes

27 September 2017

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Alu exonization events reveal features required for precise recognition of exons by the splicing machinery

27 September 2017

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Diverse splicing patterns of exonized Alu elements in human tissues

27 September 2017

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Intronic Alus influence alternative splicing

27 September 2017

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The take and give between retrotransposable elements and their hosts

27 September 2017

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Boundaries. Boundaries...Boundaries???

27 September 2017

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Alu element-mediated gene silencing

27 September 2017

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Multifactorial interplay controls the splicing profile of Alu-derived exons

27 September 2017

1 reference

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Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock

27 September 2017

1 reference

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Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome.

27 September 2017

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Repetitive sequences in complex genomes: structure and evolution

27 September 2017

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The general transcription machinery and general cofactors

27 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

Non-coding-RNA regulators of RNA polymerase II transcription

27 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

Short retroposons in eukaryotic genomes

27 September 2017

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Widespread RNA editing of embedded alu elements in the human transcriptome

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

B2 RNA binds directly to RNA polymerase II to repress transcript synthesis

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

How prevalent is functional alternative splicing in the human genome?

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

AluGene: a database of Alu elements incorporated within protein-coding genes

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

A slow RNA polymerase II affects alternative splicing in vivo

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

Alu-containing exons are alternatively spliced

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

Transcriptional activation of short interspersed elements by DNA-damaging agents

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

Cis-acting influences on Alu RNA levels

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

Functions and mechanisms of RNA editing

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

Physiological stresses increase mouse short interspersed element (SINE) RNA expression in vivo

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

Silk worm Bm1 SINE RNA increases following cellular insults

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

Does SINE evolution preclude Alu function?

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

Determination of the phylogenetic relationships among Pacific salmonids by using short interspersed elements (SINEs) as temporal landmarks of evolution.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

Repeat sequence families derived from mammalian tRNA genes

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

Induction of specific transcription by RNA polymerase III in transformed cells

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

The subset of mouse B1 (Alu-equivalent) sequences expressed as small processed cytoplasmic transcripts

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

A swine SINE (PRE-1 sequence) distribution in swine-related animal species and its phylogenetic analysis in swine genome

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

Alu sequences in the coding regions of mRNA: a source of protein variability

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

The herpes simplex virus immediate-early protein ICP27 stimulates the transcription of cellular Alu repeated sequences by increasing the activity of transcription factor TFIIIC

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

Beyond DNA: RNA editing and steps toward Alu exonization in primates

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

Developmentally regulated activation of a SINE B2 repeat as a domain boundary in organogenesis

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

Bov-tA short interspersed nucleotide element sequences in circulating nucleic acids from sera of cattle with bovine spongiform encephalopathy (BSE) and sera of cattle exposed to BSE.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

Alu repeat analysis in the complete human genome: trends and variations with respect to genomic composition

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2859989

Transposable B2 SINE elements can provide mobile RNA polymerase II promoters

28 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20176473

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Alu RNA secondary structure consists of two independent 7 SL RNA-like folding units

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20176473

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Genetic relationships among hippopotamus, whales, and bovine based on SINE insertion analysis

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20176473