4.7 Article

Chromatin accessibility profiling in Neurospora crassa reveals molecular features associated with accessible and inaccessible chromatin

Related references

Note: Only part of the references are listed.
Review Genetics & Heredity

Determinants of enhancer and promoter activities of regulatory elements

Robin Andersson et al.

NATURE REVIEWS GENETICS (2020)

Article Biochemistry & Molecular Biology

Protect-seq: genome-wide profiling of nuclease inaccessible domains reveals physical properties of chromatin

George Spracklin et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Biochemistry & Molecular Biology

Identification of a PRC2 Accessory Subunit Required for Subtelomeric H3K27 Methylation in Neurospora crassa

Kevin J. McNaught et al.

MOLECULAR AND CELLULAR BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Pioneer Factor-Nucleosome Binding Events during Differentiation Are Motif Encoded

Michael P. Meers et al.

MOLECULAR CELL (2019)

Article Biochemistry & Molecular Biology

Identification and dynamic quantification of regulatory elements using total RNA

Sascha H. Duttke et al.

GENOME RESEARCH (2019)

Review Genetics & Heredity

Chromatin accessibility and the regulatory epigenome

Sandy L. Klemm et al.

NATURE REVIEWS GENETICS (2019)

Article Biochemistry & Molecular Biology

Transcript-indexed ATAC-seq for precision immune profiling

Ansuman T. Satpathy et al.

NATURE MEDICINE (2018)

Article Developmental Biology

De novo recruitment of Polycomb-group proteins in Drosophila embryos

Jumana Alhaj Abed et al.

DEVELOPMENT (2018)

Article Biochemistry & Molecular Biology

Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes

Zefu Lu et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

Histone H3K36 trimethylation is essential for multiple silencing mechanisms in fission yeast

Shota Suzuki et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

deepTools2: a next generation web server for deep-sequencing data analysis

Fidel Ramirez et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Genetics & Heredity

Histone H1 Limits DNA Methylation in Neurospora crassa

Michael Seymour et al.

G3-GENES GENOMES GENETICS (2016)

Article Biochemical Research Methods

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

Guangchuang Yu et al.

BIOINFORMATICS (2015)

Article Biochemical Research Methods

HISAT: a fast spliced aligner with low memory requirements

Daehwan Kim et al.

NATURE METHODS (2015)

Article Multidisciplinary Sciences

Genome-wide redistribution of H3K27me3 is linked to genotoxic stress and defective growth

Evelina Y. Basenko et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Microbiology

Heterochromatin Controls γH2A Localization in Neurospora crassa

Takahiko Sasaki et al.

EUKARYOTIC CELL (2014)

Article Biochemistry & Molecular Biology

Evolutionary conservation of the eumetazoan gene regulatory landscape

Michaela Schwaiger et al.

GENOME RESEARCH (2014)

Article Biochemistry & Molecular Biology

Nucleosomes Are Context-Specific, H2A.Z-Modulated Barriers to RNA Polymerase

Christopher M. Weber et al.

MOLECULAR CELL (2014)

Article Multidisciplinary Sciences

An atlas of active enhancers across human cell types and tissues

Robin Andersson et al.

NATURE (2014)

Article Multidisciplinary Sciences

Comparative analysis of metazoan chromatin organization

Joshua W. K. Ho et al.

NATURE (2014)

Article Biochemical Research Methods

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

Helga Thorvaldsdottir et al.

BRIEFINGS IN BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

Spt6 Regulates Intragenic and Antisense Transcription, Nucleosome Positioning, and Histone Modifications Genome-Wide in Fission Yeast

Christine M. DeGennaro et al.

MOLECULAR AND CELLULAR BIOLOGY (2013)

Article Biochemistry & Molecular Biology

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

Yang Liao et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Multidisciplinary Sciences

Regional control of histone H3 lysine 27 methylation in Neurospora

Kirsty Jamieson et al.

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

Article Genetics & Heredity

Regulation of Gene Expression in Neurospora crassa with a Copper Responsive Promoter

Teresa M. Lamb et al.

G3-GENES GENOMES GENETICS (2013)

Article Biochemical Research Methods

Software for Computing and Annotating Genomic Ranges

Michael Lawrence et al.

PLOS COMPUTATIONAL BIOLOGY (2013)

Article Genetics & Heredity

Chromatin and Transcription in Yeast

Oliver J. Rando et al.

GENETICS (2012)

Article Biochemistry & Molecular Biology

Histone H3 Lysine 36 Methylation Targets the Isw1b Remodeling Complex to Chromatin

Vicki E. Maltby et al.

MOLECULAR AND CELLULAR BIOLOGY (2012)

Article Multidisciplinary Sciences

Set2 methylation of histone H3 lysine 36 suppresses histone exchange on transcribed genes

Swaminathan Venkatesh et al.

NATURE (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Biochemistry & Molecular Biology

Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange

Michaela Smolle et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2012)

Review Cell Biology

Pioneer transcription factors: establishing competence for gene expression

Kenneth S. Zaret et al.

GENES & DEVELOPMENT (2011)

Review Multidisciplinary Sciences

The Polycomb complex PRC2 and its mark in life

Raphael Margueron et al.

NATURE (2011)

Review Genetics & Heredity

Pioneer factors: directing transcriptional regulators within the chromatin environment

Luca Magnani et al.

TRENDS IN GENETICS (2011)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

Lihua J. Zhu et al.

BMC BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

Heterochromatic marks are associated with the repression of secondary metabolism clusters in Aspergillus nidulans

Yazmid Reyes-Dominguez et al.

MOLECULAR MICROBIOLOGY (2010)

Article Multidisciplinary Sciences

Widespread transcription at neuronal activity-regulated enhancers

Tae-Kyung Kim et al.

NATURE (2010)

Article Biochemistry & Molecular Biology

Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa

Zachary A. Lewis et al.

GENOME RESEARCH (2009)

Article Biotechnology & Applied Microbiology

Model-based Analysis of ChIP-Seq (MACS)

Yong Zhang et al.

GENOME BIOLOGY (2008)

Article Multidisciplinary Sciences

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

Tarjei S. Mikkelsen et al.

NATURE (2007)

Article Multidisciplinary Sciences

RNA maps reveal new RNA classes and a possible function for pervasive transcription

Philipp Kapranov et al.

SCIENCE (2007)

Article Biochemistry & Molecular Biology

High-resolution profiling of histone methylations in the human genome

Artern Barski et al.

Article Biochemistry & Molecular Biology

Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis

Xiaoyu Zhang et al.

PLOS BIOLOGY (2007)

Article Genetics & Heredity

Cyclosporin A-resistance based gene placement system for Neurospora crassa

Nirmala Bardiya et al.

FUNGAL GENETICS AND BIOLOGY (2007)

Article Multidisciplinary Sciences

Dynamics of replication-independent histone turnover in budding yeast

Michael F. Dion et al.

SCIENCE (2007)

Article Biochemistry & Molecular Biology

Polycomb complexes and the propagation of the methylation mark at the Drosophila Ubx gene

Tatyana G. Kahn et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2006)

Article Multidisciplinary Sciences

A genomic code for nucleosome positioning

Eran Segal et al.

NATURE (2006)

Article Multidisciplinary Sciences

A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors

Hildur V. Colot et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Biochemistry & Molecular Biology

Single-nucleosome mapping of histone modifications in S-cerevisiae

CL Liu et al.

PLOS BIOLOGY (2005)

Article Biochemistry & Molecular Biology

Genome-wide map of nucleosorne acetylation and methylation in yeast

DK Pokholok et al.

Article Biochemistry & Molecular Biology

Dynamic regulation of replication independent deposition of histone H3 in fission yeast

ES Choi et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Multidisciplinary Sciences

Role of transposable elements in heterochromatin and epigenetic control

Z Lippman et al.

NATURE (2004)

Article Biochemistry & Molecular Biology

The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes

A Ruepp et al.

NUCLEIC ACIDS RESEARCH (2004)

Article Biochemistry & Molecular Biology

Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II

NJ Krogan et al.

MOLECULAR AND CELLULAR BIOLOGY (2003)

Article Biochemistry & Molecular Biology

The histone 3 lysine 36 methyltransferase, SET2, is involved in transcriptional elongation

D Schaft et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Biochemistry & Molecular Biology

The Set2 histone methyltransferase functions through the phosphorylated carboxyl-terminal domain of RNA polymerase II

B Li et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2003)

Article Biochemistry & Molecular Biology

Association of the histone methyltransferase Set2 with RNA polymerase II plays a role in transcription elongation

JX Li et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2002)