Identification of RNA polymerase III-transcribed Alu loci by computational screening of RNA-Seq data (Q30882366)

13 October 2017

Identification of RNA polymerase III-transcribed Alu loci by computational screening of RNA-Seq data (English)

1 reference

13 October 2017

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4

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13 October 2017

6

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13 October 2017

Davide Carnevali

2

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Matteo Pellegrini

object named as

Matteo Pellegrini

series ordinal

5

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Anastasia Conti

object named as

Anastasia Conti

series ordinal

1

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language of work or name

English

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publication date

29 December 2014

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13 October 2017

19

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inferred from page(s)

published in

Nucleic Acids Research

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13 October 2017

43

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13 October 2017

817-835

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13 October 2017

2

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Creative Commons Attribution-NonCommercial 4.0 International

13 October 2017

start time

7 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

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14 July 2018

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Epigenetic regulation of transcription and possible functions of mammalian short interspersed elements, SINEs

14 July 2018

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TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

14 July 2018

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RNA polymerase III transcription - regulated by chromatin structure and regulator of nuclear chromatin organization

14 July 2018

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STAR: ultrafast universal RNA-seq aligner

14 July 2018

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Identification of RNA polymerase III-transcribed genes in eukaryotic genomes

14 July 2018

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Landscape of transcription in human cells

14 July 2018

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Alu expression in human cell lines and their retrotranspositional potential

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

Alu elements: know the SINEs

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

LINEs, SINEs and other retroelements: do birds of a feather flock together?

14 July 2018

1 reference

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Repetitive DNA and next-generation sequencing: computational challenges and solutions

14 July 2018

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Extra-transcriptional functions of RNA Polymerase III complexes: TFIIIC as a potential global chromatin bookmark.

14 July 2018

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RNA polymerase III transcription control elements: themes and variations

14 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

Transcription by RNA polymerase III: more complex than we thought

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

Widespread occurrence of non-canonical transcription termination by human RNA polymerase III

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

Dioxin receptor and SLUG transcription factors regulate the insulator activity of B1 SINE retrotransposons via an RNA polymerase switch.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

The evolution and expression of the snaR family of small non-coding RNAs

14 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

An Alu-like RNA promotes cell differentiation and reduces malignancy of human neuroblastoma cells.

14 July 2018

1 reference

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The telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae.

14 July 2018

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Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

Defining the RNA polymerase III transcriptome: Genome-wide localization of the RNA polymerase III transcription machinery in human cells

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

Close association of RNA polymerase II and many transcription factors with Pol III genes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

snaR genes: recent descendants of Alu involved in the evolution of chorionic gonadotropins

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

An overview of nested genes in eukaryotic genomes

14 July 2018

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Eukaryotic snoRNAs: a paradigm for gene expression flexibility.

14 July 2018

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The RNA polymerase dictates ORF1 requirement and timing of LINE and SINE retrotransposition

14 July 2018

1 reference

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Diverse cis factors controlling Alu retrotransposition: what causes Alu elements to die?

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

Active Alu retrotransposons in the human genome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

The Alu family repeat promoter has a tRNA-like bipartite structure

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

Novel upstream and intragenic control elements for the RNA polymerase III-dependent transcription of human 7SL RNA genes

14 July 2018

1 reference

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A composite upstream sequence motif potentiates tRNA gene transcription in yeast.

14 July 2018

1 reference

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Alu repeats and human genomic diversity

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

Upstream flanking sequences and transcription of SINEs

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

Flanking sequences of an Alu source stimulate transcription in vitro by interacting with sequence-specific transcription factors

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

BC200 RNA: a neural RNA polymerase III product encoded by a monomeric Alu element

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

Multiple dispersed loci produce small cytoplasmic Alu RNA.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

Activation of RNA polymerase III transcription of human Alu repetitive elements by adenovirus type 5: requirement for the E1b 58-kilodalton protein and the products of E4 open reading frames 3 and 6.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

Alu transcripts: cytoplasmic localisation and regulation by DNA methylation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

Transcriptional analysis of interspersed repetitive polymerase III transcription units in human DNA

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

Analysis of transcription of the human Alu family ubiquitous repeating element by eukaryotic RNA polymerase III

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

Transcriptional inactivity of Alu repeats in HeLa cells

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

Alu RNA transcripts in human embryonal carcinoma cells. Model of post-transcriptional selection of master sequences

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

cDNAs derived from primary and small cytoplasmic Alu (scAlu) transcripts.

14 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1361

Most human Alu and murine B1 repeats are unique.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1361

Alu monomer revisited: recent generation of Alu monomers

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1361

Evolution of Alu elements toward enhancers.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1361

Enrichment for Histone H3 Lysine 9 Methylation at Alu Repeats in Human Cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1361

Upstream sequences modulate the internal promoter of the human 7SL RNA gene

21 January 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4333407

25 November 2018

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1361

Multiple Roles of Alu-Related Noncoding RNAs

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25550429

12 December 2020

inferred from PubMed ID database lookup

A cellular protein binds B1 and Alu small cytoplasmic RNAs in vitro

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25550429

12 December 2020

inferred from PubMed ID database lookup

A minimal promoter for TFIIIC-dependent in vitro transcription of snoRNA and tRNA genes by RNA polymerase III

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25550429

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1093/NAR/GKU1361

1 reference

13 October 2017

1 reference

13 October 2017

1 reference

PMCID

4333407