4.7 Article

Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Extensive Recovery of Embryonic Enhancer and Gene Memory Stored in Hypomethylated Enhancer DNA

Unmesh Jadhav et al.

MOLECULAR CELL (2019)

Article Multidisciplinary Sciences

Six6 and Six7 coordinately regulate expression of middle-wavelength opsins in zebrafish

Yohey Ogawa et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Biotechnology & Applied Microbiology

Identification of transcription factor binding sites using ATAC-seq

Zhijian Li et al.

GENOME BIOLOGY (2019)

Article Cell Biology

Widespread transcriptional pausing and elongation control at enhancers

Telmo Henriques et al.

GENES & DEVELOPMENT (2018)

Article Biochemical Research Methods

GIGGLE: a search engine for large-scale integrated genome analysis

Ryan M. Layer et al.

NATURE METHODS (2018)

Article Ophthalmology

The mechanism of cone cell death in Retinitis Pigmentosa

Peter A. Campochiaro et al.

PROGRESS IN RETINAL AND EYE RESEARCH (2018)

Article Multidisciplinary Sciences

TADs are 3D structural units of higher-order chromosome organization in Drosophila

Quentin Szabo et al.

SCIENCE ADVANCES (2018)

Article Biochemistry & Molecular Biology

A massively parallel reporter assay reveals context-dependent activity of homeodomain binding sites in vivo

Andrew E. O. Hughes et al.

GENOME RESEARCH (2018)

Article Biochemistry & Molecular Biology

Genome-wide Identification and Characterization of Enhancers Across 10 Human Tissues

Lili Xiong et al.

INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES (2018)

Article Genetics & Heredity

CRX directs photoreceptor differentiation by accelerating chromatin remodeling at specific target sites

Philip A. Ruzycki et al.

EPIGENETICS & CHROMATIN (2018)

Review Ophthalmology

Regenerative medicine in the retina: from stem cells to cell replacement therapy

Julia Oswald et al.

THERAPEUTIC ADVANCES IN OPHTHALMOLOGY (2018)

Article Biochemistry & Molecular Biology

Cis-regulatory landscapes of four cell types of the retina

Dominik Hartl et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Ophthalmology

Concepts and Strategies in Retinal Gene Therapy

Gustavo D. Aguirre

INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE (2017)

Article Ophthalmology

Regulation of Noncoding Transcriptome in Developing Photoreceptors by Rod Differentiation Factor NRL

Lina Zelinger et al.

INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE (2017)

Article Multidisciplinary Sciences

Local regulation of gene expression by lncRNA promoters, transcription and splicing

Jesse M. Engreitz et al.

NATURE (2016)

Review Genetics & Heredity

Enhancers as non-coding RNA transcription units: recent insights and future perspectives

Wenbo Li et al.

NATURE REVIEWS GENETICS (2016)

Article Cell Biology

NRL-Regulated Transcriptome Dynamics of Developing Rod Photoreceptors

Jung-Woong Kim et al.

CELL REPORTS (2016)

Article Biology

Epigenomic landscapes of retinal rods and cones

Alisa Mo et al.

ELIFE (2016)

Article Ophthalmology

Mimicking Retinal Development and Disease With Human Pluripotent Stem Cells

Divya Sinha et al.

INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE (2016)

Article Neurosciences

DNA Modification Study of Major Depressive Disorder: Beyond Locus-by-Locus Comparisons

Gabriel Oh et al.

BIOLOGICAL PSYCHIATRY (2015)

Review Biochemistry & Molecular Biology

The recruitment of chromatin modifiers by long noncoding RNAs: lessons from PRC2

Chen Davidovich et al.

Article Neurosciences

The Determination of Rod and Cone Photoreceptor Fate

Constance L. Cepko

ANNUAL REVIEW OF VISION SCIENCE, VOL 1 (2015)

Article Biochemical Research Methods

HTSeq-a Python framework to work with high-throughput sequencing data

Simon Anders et al.

BIOINFORMATICS (2015)

Article Multidisciplinary Sciences

Otx2 ChIP-seq Reveals Unique and Redundant Functions in the Mature Mouse Retina

Alexander Samuel et al.

PLOS ONE (2014)

Article Multidisciplinary Sciences

Onecut1 and Onecut2 redundantly regulate early retinal cell fates during development

Darshan Sapkota et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Genetics & Heredity

Tissue-Specific RNA Expression Marks Distant-Acting Developmental Enhancers

Han Wu et al.

PLOS GENETICS (2014)

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

Article Multidisciplinary Sciences

Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks

Michael A. White et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Multidisciplinary Sciences

Reprogramming of adult rod photoreceptors prevents retinal degeneration

Cynthia L. Montana et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Multidisciplinary Sciences

Conserved microRNA pathway regulates developmental timing of retinal neurogenesis

Anna La Torre et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Biochemical Research Methods

Software for Computing and Annotating Genomic Ranges

Michael Lawrence et al.

PLOS COMPUTATIONAL BIOLOGY (2013)

Review Genetics & Heredity

Noncoding Transcription at Enhancers: General Principles and Functional Models

Gioacchino Natoli et al.

ANNUAL REVIEW OF GENETICS, VOL 46 (2012)

Article Neurosciences

Onecut 1 and Onecut 2 are potential regulators of mouse retinal development

Fuguo Wu et al.

JOURNAL OF COMPARATIVE NEUROLOGY (2012)

Article Multidisciplinary Sciences

A map of the cis-regulatory sequences in the mouse genome

Yin Shen et al.

NATURE (2012)

Article Multidisciplinary Sciences

An integrated encyclopedia of DNA elements in the human genome

Ian Dunham et al.

NATURE (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Neurosciences

Transcriptional code and disease map for adult retinal cell types

Sandra Siegert et al.

NATURE NEUROSCIENCE (2012)

Article Biotechnology & Applied Microbiology

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

Guangchuang Yu et al.

OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY (2012)

Article Multidisciplinary Sciences

Transcription factor Olig2 defines subpopulations of retinal progenitor cells biased toward specific cell fates

Brian P. Hafler et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Biotechnology & Applied Microbiology

An encyclopedia of mouse DNA elements (Mouse ENCODE)

John A. Stamatoyannopoulos et al.

GENOME BIOLOGY (2012)

Article Developmental Biology

Identification of a retina-specific Otx2 enhancer element active in immature developing photoreceptors

Mark M. Emerson et al.

DEVELOPMENTAL BIOLOGY (2011)

Article Neurosciences

NeuroD Factors Regulate Cell Fate and Neurite Stratification in the Developing Retina

Timothy J. Cherry et al.

JOURNAL OF NEUROSCIENCE (2011)

Article Multidisciplinary Sciences

Quantifying the Activity of cis-Regulatory Elements in the Mouse Retina by Explant Electroporation

Cynthia L. Montana et al.

JOVE-JOURNAL OF VISUALIZED EXPERIMENTS (2011)

Article Biochemistry & Molecular Biology

CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors

Joseph C. Corbo et al.

GENOME RESEARCH (2010)

Review Neurosciences

Transcriptional regulation of photoreceptor development and homeostasis in the mammalian retina

Anand Swaroop et al.

NATURE REVIEWS NEUROSCIENCE (2010)

Article Multidisciplinary Sciences

Analysis of Thyroid Response Element Activity during Retinal Development

Nathan A. Billings et al.

PLOS ONE (2010)

Article Multidisciplinary Sciences

Histone H3K27ac separates active from poised enhancers and predicts developmental state

Menno P. Creyghton et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Ophthalmology

Cone Degeneration in Aging and Age-Related Macular Degeneration

Elizabeth J. Shelley et al.

ARCHIVES OF OPHTHALMOLOGY (2009)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Multidisciplinary Sciences

ChIP-seq accurately predicts tissue-specific activity of enhancers

Axel Visel et al.

NATURE (2009)

Article Biotechnology & Applied Microbiology

Model-based Analysis of ChIP-Seq (MACS)

Yong Zhang et al.

GENOME BIOLOGY (2008)

Article Biochemistry & Molecular Biology

Functional roles of Otx2 transcription factor in postnatal mouse retinal development

Chieko Koike et al.

MOLECULAR AND CELLULAR BIOLOGY (2007)

Article Multidisciplinary Sciences

The Cis-regulatory Logic of the Mammalian Photoreceptor Transcriptional Network

Timothy H. -C. Hsiau et al.

PLOS ONE (2007)

Article Multidisciplinary Sciences

A typology of photoreceptor gene expression patterns in the mouse

Joseph C. Corbo et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Multidisciplinary Sciences

Transformation of cone precursors to functional rod photoreceptors by bZIP transcription factor NRL

Edwin C. T. Oh et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Multidisciplinary Sciences

Controlled expression of transgenes introduced by in vivo electroporation

Takahiko Matsuda et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Ophthalmology

Cone photoreceptor function loss-3, a novel mouse model of achromatopsia due to a mutation in Gnat2

Bo Chang et al.

INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE (2006)

Article Multidisciplinary Sciences

The transcription factor Engrailed-2 guides retinal axons

I Brunet et al.

NATURE (2005)

Review Biochemistry & Molecular Biology

Genomic analysis of mouse retinal development

S Blackshaw et al.

PLOS BIOLOGY (2004)

Article Genetics & Heredity

Nrl is required for rod photoreceptor development

AJ Mears et al.

NATURE GENETICS (2001)

Article Biochemistry & Molecular Biology

Multiple phosphorylated isoforms of NRL are expressed in rod photoreceptors

PK Swain et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2001)

Article Biochemistry & Molecular Biology

Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx

FJ Livesey et al.

CURRENT BIOLOGY (2000)