(Q34845153)

4 August 2017

Genetic selection for context-dependent stochastic phenotypes: Sp1 and TATA mutations increase phenotypic noise in HIV-1 gene expression (English)

1 reference

4 August 2017

4

0 references

author name string

Kathryn Miller-Jensen

1

1 reference

4 August 2017

Ron Skupsky

2

1 reference

4 August 2017

Priya S Shah

3

1 reference

4 August 2017

David V Schaffer

5

1 reference

4 August 2017

11 July 2013

1 reference

PLOS Computational Biology

4 August 2017

1 reference

4 August 2017

9

1 reference

4 August 2017

7

1 reference

4 August 2017

e1003135

1 reference

Creative Commons Attribution 4.0 International

4 August 2017

start time

11 July 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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RNA-mediated displacement of an inhibitory snRNP complex activates transcription elongation

8 July 2018

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8 July 2018

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Transcriptional bursting from the HIV-1 promoter is a significant source of stochastic noise in HIV-1 gene expression.

8 July 2018

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A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations

8 July 2018

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Variability in gene expression underlies incomplete penetrance

8 July 2018

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8 July 2018

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Latently-infected CD4+ T cells are enriched for HIV-1 Tat variants with impaired transactivation activity

8 July 2018

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The challenge of finding a cure for HIV infection

8 July 2018

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The impact of genomic neighborhood on the evolution of human and chimpanzee transcriptome

8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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HIV rebounds from latently infected cells, rather than from continuing low-level replication

8 July 2018

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Phenotypic consequences of promoter-mediated transcriptional noise

8 July 2018

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8 July 2018

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Stochastic mRNA synthesis in mammalian cells

8 July 2018

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Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise

8 July 2018

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Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity

8 July 2018

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8 July 2018

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8 July 2018

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Diversity in times of adversity: probabilistic strategies in microbial survival games

8 July 2018

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Ultrasensitivity and noise propagation in a synthetic transcriptional cascade.

8 July 2018

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HIV-1 Tat stimulates transcription complex assembly through recruitment of TBP in the absence of TAFs

8 July 2018

1 reference

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Kinetics of human immunodeficiency virus type 1 decay following entry into resting CD4+ T cells

8 July 2018

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Specific sequence configurations of HIV-1 LTR G/C box array result in altered recruitment of Sp isoforms and correlate with disease progression.

8 July 2018

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The multifactorial nature of HIV-1 latency

8 July 2018

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Bacterial persistence as a phenotypic switch

8 July 2018

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The human immunodeficiency virus type 1 promoter contains a CATA box instead of a TATA box for optimal transcription and replication.

8 July 2018

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Control of stochasticity in eukaryotic gene expression

8 July 2018

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T-cell subsets that harbor human immunodeficiency virus (HIV) in vivo: implications for HIV pathogenesis

8 July 2018

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Tat and trans-activation-responsive (TAR) RNA-independent induction of HIV-1 long terminal repeat by human and murine cyclin T1 requires Sp1.

8 July 2018

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HIV-1 integration in the human genome favors active genes and local hotspots

8 July 2018

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Stochastic gene expression in a single cell

8 July 2018

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Intrinsic noise in gene regulatory networks

8 July 2018

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The site of HIV-1 integration in the human genome determines basal transcriptional activity and response to Tat transactivation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3708878

Tat modifies the activity of CDK9 to phosphorylate serine 5 of the RNA polymerase II carboxyl-terminal domain during human immunodeficiency virus type 1 transcription

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3708878

A compilation of cellular transcription factor interactions with the HIV-1 LTR promoter

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3708878

Directed evolution converts subtilisin E into a functional equivalent of thermitase

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3708878

Transcription reinitiation rate: a potential role for TATA box stabilization of the TFIID:TFIIA:DNA complex

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3708878

A third-generation lentivirus vector with a conditional packaging system

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3708878

Identification of a reservoir for HIV-1 in patients on highly active antiretroviral therapy

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3708878

Transcription reinitiation rate: a special role for the TATA box.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3708878

Quantification of latent tissue reservoirs and total body viral load in HIV-1 infection

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3708878

Stochastic mechanisms in gene expression

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3708878

Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3708878

HIV-1 tat trans-activation requires the loop sequence within tar.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3708878

Activation of the AIDS retrovirus promoter by the cellular transcription factor, Sp1.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3708878

Role of SP1-binding domains in in vivo transcriptional regulation of the human immunodeficiency virus type 1 long terminal repeat

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3708878

The accuracy of reverse transcriptase from HIV-1.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3708878

HIV-1 entry into quiescent primary lymphocytes: molecular analysis reveals a labile, latent viral structure

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3708878

Yeast and human TATA-binding proteins have nearly identical DNA sequence requirements for transcription in vitro

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3708878

The role of Tat in the human immunodeficiency virus life cycle indicates a primary effect on transcriptional elongation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3708878

Characterization of a human TAR RNA-binding protein that activates the HIV-1 LTR

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3708878

Sp1-dependent activation of a synthetic promoter by human immunodeficiency virus type 1 Tat protein

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3708878

Functional roles for the TATA promoter and enhancers in basal and Tat-induced expression of the human immunodeficiency virus type 1 long terminal repeat

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3708878

Contribution of the TATA motif to Tat-mediated transcriptional activation of human immunodeficiency virus gene expression

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3708878

Non-genetic individuality: chance in the single cell

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3708878

Evolution of chromosome organization driven by selection for reduced gene expression noise

8 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003135

Stochastic switching as a survival strategy in fluctuating environments

21 January 2018

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Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003135

Fidelity of HIV-1 reverse transcriptase

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3708878

Promoter influences transcription elongation: TATA-box element mediates the assembly of processive transcription complexes responsive to cyclin-dependent kinase 9

26 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23874178

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Derivation of infectious HIV-1 molecular clones with LTR mutations: sensitivity to the CD8+ cell noncytotoxic anti-HIV response

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23874178

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Contributions of the TATA box sequence to rate-limiting steps in transcription initiation by RNA polymerase II

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23874178

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1003135

1 reference

journals/ploscb/Miller-JensenSSAS13

4 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

4 August 2017

1 reference