Identifying Novel Transcriptional and Epigenetic Features of Nuclear Lamina-associated Genes

DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments

(2016) Feinan Wu et al.   Jove-Journal of Visualized Experiments

Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells

(2015) Jop Kind et al.   CELL

Perinuclear Anchoring of H3K9-Methylated Chromatin Stabilizes Induced Cell Fate in C. elegans Embryos

(2015) Adriana Gonzalez-Sandoval et al.   CELL

A KAP1 phosphorylation switch controls MyoD function during skeletal muscle differentiation

(2015) Kulwant Singh et al.   GENES & DEVELOPMENT

Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins

(2015) Jennifer C. Harr et al.   JOURNAL OF CELL BIOLOGY

Identification of lamin B–regulated chromatin regions based on chromatin landscapes

(2015) Xiaobin Zheng et al.   MOLECULAR BIOLOGY OF THE CELL

PARP1- and CTCF-Mediated Interactions between Active and Repressed Chromatin at the Lamina Promote Oscillating Transcription

(2015) Honglei Zhao et al.   MOLECULAR CELL

Identification of active transcriptional regulatory elements from GRO-seq data

(2015) Charles G Danko et al.   NATURE METHODS

Three-dimensional genome architecture: players and mechanisms

(2015) Ana Pombo et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

(2014) Leighton J Core et al.   NATURE GENETICS

Chromatin decondensation is sufficient to alter nuclear organization in embryonic stem cells

(2014) Pierre Therizols et al.   SCIENCE

Spatial compartmentalization at the nuclear periphery characterized by genome-wide mapping

(2013) Feinan Wu et al.   BMC GENOMICS

Finding the active genes in deep RNA-seq gene expression studies

(2013) Traver Hart et al.   BMC GENOMICS

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Lamin A/C-promoter interactions specify chromatin state-dependent transcription outcomes

(2013) E. Lund et al.   GENOME RESEARCH

β-Globin cis-elements determine differential nuclear targeting through epigenetic modifications

(2013) Qian Bian et al.   JOURNAL OF CELL BIOLOGY

Widespread Regulation of Translation by Elongation Pausing in Heat Shock

(2013) Reut Shalgi et al.   MOLECULAR CELL

WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013

(2013) Jing Wang et al.   NUCLEIC ACIDS RESEARCH

Genome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3

(2013) Daniel C Kraushaar et al.   GENOME BIOLOGY

DNA Sequence-Dependent Compartmentalization and Silencing of Chromatin at the Nuclear Lamina

(2012) Joseph M. Zullo et al.   CELL

Step-Wise Methylation of Histone H3K9 Positions Heterochromatin at the Nuclear Periphery

(2012) Benjamin D. Towbin et al.   CELL

Genome-wide identification of enhancers in skeletal muscle: the role of MyoD1

(2012) R. Blum et al.   GENES & DEVELOPMENT

Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence

(2012) W. Meuleman et al.   GENOME RESEARCH

The Nuclear Envelope Protein Emerin Binds Directly to Histone Deacetylase 3 (HDAC3) and Activates HDAC3 Activity

(2012) Justin Demmerle et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Cell-Type-Specific Control of Enhancer Activity by H3K9 Trimethylation

(2012) Yina Zhu et al.   MOLECULAR CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

Sub-nuclear compartmentalization of core promoter factors and target genes

(2011) Jie Yao et al.   CELL CYCLE

Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells

(2011) I. M. Min et al.   GENES & DEVELOPMENT

Subnuclear segregation of genes and core promoter factors in myogenesis

(2011) Jie Yao et al.   GENES & DEVELOPMENT

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

Genome-wide remodeling of the epigenetic landscape during myogenic differentiation

(2011) P. Asp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

The uniqueome: a mappability resource for short-tag sequencing

(2010) Ryan Koehler et al.   BIOINFORMATICS

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

(2010) Guillaume J. Filion et al.   CELL

Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation

(2010) Daan Peric-Hupkes et al.   MOLECULAR CELL

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

G9a selectively represses a class of late-replicating genes at the nuclear periphery

(2009) T. Yokochi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

(2008) Lars Guelen et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE