Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling
PLoS Genetics
Feb 1, 2015
Kristofer DavieStein Aerts
PMID: 25679813
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Abstract
Genomic enhancers regulate spatio-temporal gene expression by recruiting specific combinations of transcription factors (TFs). When TFs are bound to active regulatory regions, they displace canonical nucleosomes, making these regions biochemically detectable as nucleosome-depleted regio...read more
Mentioned in this Paper
Enhancer brand
Sodium Chloride
Gene Expression
Immunoprecipitation
Complex (molecular entity)
Mutant
Ligands
Phenols
JAK-STAT Cascade
JUN gene
13
1
455
Paper Details
References
- References70
- Citations23
Ectopic expression of germline genes drives malignant brain tumor growth in Drosophila
ScienceDecember 24, 2010Ana JanicCayetano Gonzalez2081
chinmo is a functional effector of the JAK/STAT pathway that regulates eye development, tumor formation, and stem cell self-renewal in Drosophila
Developmental CellApril 20, 2010Maria Sol FlahertyErika A Bach
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
Proceedings of the National Academy of Sciences of the United States of AmericaOctober 25, 2005Aravind SubramanianJill P. Mesirov511899516
A component of the transcriptional mediator complex inhibits RAS-dependent vulval fate specification in C. elegans
DevelopmentJanuary 1, 2003Nadeem Moghal, Paul W. Sternberg
PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data
BioinformaticsSeptember 15, 2014Yanxiao ZhangMaureen A. Sartor15133
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
Nucleic Acids ResearchJanuary 1, 2002Ron EdgarAlex E. Lash1119723A genetic screen in Drosophila for metastatic behavior
ScienceNovember 14, 2003Raymond A Pagliarini, Tian Xu131111The Sequence Alignment/Map format and SAMtools
BioinformaticsAugust 15, 2009H Irene Li1000 Genome Project Data Processing Subgroup31110K+6FlyBase 102--advanced approaches to interrogating FlyBase
Nucleic Acids ResearchJanuary 1, 2014Susan E St PierreFlyBase Consortium11177
Mosaic analysis with a repressible cell marker for studies of gene function in neuronal morphogenesis
NeuronMarch 1, 1999Tin Lap Lee, Liqun Luo10001
12345...
- References70
- Citations23
Identification of chromatin accessibility domains in human breast cancer stem cells
NucleusMarch 10, 2016Kristine HardySudha Narayana Rao7125
Epigenetics in Insects: Genome Regulation and the Generation of Phenotypic Diversity
Annual Review of EntomologyOctober 5, 2018Karl M GlastadMichael A. D. Goodisman24164
BTB-Zinc Finger Oncogenes Are Required for Ras and Notch-Driven Tumorigenesis in Drosophila
PloS OneJuly 24, 2015Karen DoggettAnthony M Brumby4117Identification and in silico modeling of enhancers reveals new features of the cardiac differentiation network
DevelopmentDecember 1, 2016Denis SeyresLaurent Perrin633
Selecting optimal combinations of transcription factors to promote axon regeneration: Why mechanisms matter
Neuroscience LettersDecember 28, 2016Ishwariya Venkatesh, Murray G Blackmore
Neuronal activity modifies the chromatin accessibility landscape in the adult brain
Nature NeuroscienceFebruary 7, 2017Yi-Jing SuHong-jun Song12251
Regulatory elements in molecular networks
Wiley Interdisciplinary Reviews. Systems Biology and MedicineJanuary 18, 2017Ashley Stephen Doane, Olivier Elemento6138
The origin of Metazoa: a unicellular perspective
Nature Reviews. GeneticsMay 10, 2017Arnau Sebé-PedrósIñaki Ruiz-Trillo29173131
Differential regulation of protein tyrosine kinase signalling by Dock and the PTP61F variants
The FEBS JournalMay 26, 2017Lee F WilloughbyHelena E Richardson323
Tissue growth and tumorigenesis in Drosophila: cell polarity and the Hippo pathway
Current Opinion in Cell BiologyApril 2, 2017Helena E Richardson, Marta Portela363
123
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Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling
Abstract
Genomic enhancers regulate spatio-temporal gene expression by recruiting specific combinations of transcription factors (TFs). When TFs are bound to active regulatory regions, they displace canonical nucleosomes, making these regions biochemically detectable as nucleosome-depleted regio...read more
Mentioned in this Paper
Enhancer brand
Sodium Chloride
Gene Expression
Immunoprecipitation
Complex (molecular entity)
13
1
455
Related Papers
Paper Details
References
- References70
- Citations23
Ectopic expression of germline genes drives malignant brain tumor growth in Drosophila
ScienceDecember 24, 2010Ana JanicCayetano Gonzalez2081chinmo is a functional effector of the JAK/STAT pathway that regulates eye development, tumor formation, and stem cell self-renewal in Drosophila
Developmental CellApril 20, 2010Maria Sol FlahertyErika A BachGene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
Proceedings of the National Academy of Sciences of the United States of AmericaOctober 25, 2005Aravind SubramanianJill P. Mesirov511899516A component of the transcriptional mediator complex inhibits RAS-dependent vulval fate specification in C. elegans
DevelopmentJanuary 1, 2003Nadeem Moghal, Paul W. SternbergPePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data
BioinformaticsSeptember 15, 2014Yanxiao ZhangMaureen A. Sartor15133Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
Nucleic Acids ResearchJanuary 1, 2002Ron EdgarAlex E. Lash1119723A genetic screen in Drosophila for metastatic behavior
ScienceNovember 14, 2003Raymond A Pagliarini, Tian Xu131111The Sequence Alignment/Map format and SAMtools
BioinformaticsAugust 15, 2009H Irene Li1000 Genome Project Data Processing Subgroup31110K+6FlyBase 102--advanced approaches to interrogating FlyBase
Nucleic Acids ResearchJanuary 1, 2014Susan E St PierreFlyBase Consortium11177Mosaic analysis with a repressible cell marker for studies of gene function in neuronal morphogenesis
NeuronMarch 1, 1999Tin Lap Lee, Liqun Luo10001
12345...
- References70
- Citations23
Identification of chromatin accessibility domains in human breast cancer stem cells
NucleusMarch 10, 2016Kristine HardySudha Narayana Rao7125Epigenetics in Insects: Genome Regulation and the Generation of Phenotypic Diversity
Annual Review of EntomologyOctober 5, 2018Karl M GlastadMichael A. D. Goodisman24164BTB-Zinc Finger Oncogenes Are Required for Ras and Notch-Driven Tumorigenesis in Drosophila
PloS OneJuly 24, 2015Karen DoggettAnthony M Brumby4117Identification and in silico modeling of enhancers reveals new features of the cardiac differentiation network
DevelopmentDecember 1, 2016Denis SeyresLaurent Perrin633Selecting optimal combinations of transcription factors to promote axon regeneration: Why mechanisms matter
Neuroscience LettersDecember 28, 2016Ishwariya Venkatesh, Murray G BlackmoreNeuronal activity modifies the chromatin accessibility landscape in the adult brain
Nature NeuroscienceFebruary 7, 2017Yi-Jing SuHong-jun Song12251Regulatory elements in molecular networks
Wiley Interdisciplinary Reviews. Systems Biology and MedicineJanuary 18, 2017Ashley Stephen Doane, Olivier Elemento6138The origin of Metazoa: a unicellular perspective
Nature Reviews. GeneticsMay 10, 2017Arnau Sebé-PedrósIñaki Ruiz-Trillo29173131Differential regulation of protein tyrosine kinase signalling by Dock and the PTP61F variants
The FEBS JournalMay 26, 2017Lee F WilloughbyHelena E Richardson323Tissue growth and tumorigenesis in Drosophila: cell polarity and the Hippo pathway
Current Opinion in Cell BiologyApril 2, 2017Helena E Richardson, Marta Portela363
123
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