Local rewiring of genome–nuclear lamina interactions by transcription

Lamina Associated Domains and Gene Regulation in Development and Cancer

(2019) Silke J.A. Lochs et al.   Cells

Role of lamins in 3D genome organization and global gene expression

(2019) Youngjo Kim et al.   Nucleus

The role of transcription in shaping the spatial organization of the genome

(2019) Bas van Steensel et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Promoter-Intrinsic and Local Chromatin Features Determine Gene Repression in LADs

(2019) Christ Leemans et al.   CELL

Active chromatin marks drive spatial sequestration of heterochromatin in C. elegans nuclei

(2019) Daphne S. Cabianca et al.   NATURE

Selective Loss of PARG Restores PARylation and Counteracts PARP Inhibitor-Mediated Synthetic Lethality

(2018) Ewa Gogola et al.   CANCER CELL

Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq

(2018) Claire Marchal et al.   Nature Protocols

Nuclear Lamins: Thin Filaments with Major Functions

(2018) Rebecca de Leeuw et al.   TRENDS IN CELL BIOLOGY

Transcription Elongation Can Affect Genome 3D Structure

(2018) Sven Heinz et al.   CELL

Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication

(2018) Jiao Sima et al.   CELL

The interdependence of gene-regulatory elements and the 3D genome

(2018) Marit W. Vermunt et al.   JOURNAL OF CELL BIOLOGY

Constrained release of lamina-associated enhancers and genes from the nuclear envelope during T-cell activation facilitates their association in chromosome compartments

(2017) Michael I. Robson et al.   GENOME RESEARCH

TUBB3 overexpression has a negligible effect on the sensitivity to taxol in cultured cell lines

(2017) Mihoko A. Tame et al.   Oncotarget

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

(2017) Feinan Wu et al.   Scientific Reports

Tissue-Specific Gene Repositioning by Muscle Nuclear Membrane Proteins Enhances Repression of Critical Developmental Genes during Myogenesis

(2016) Michael I. Robson et al.   MOLECULAR CELL

Deletion ofDXZ4on the human inactive X chromosome alters higher-order genome architecture

(2016) Emily M. Darrow et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On TADs and LADs: Spatial Control Over Gene Expression

(2016) Adriana Gonzalez-Sandoval et al.   TRENDS IN GENETICS

High-throughput assessment of context-dependent effects of chromatin proteins

(2016) Laura Brueckner et al.   Epigenetics & Chromatin

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

Starcode: sequence clustering based on all-pairs search

(2015) Eduard Zorita et al.   BIOINFORMATICS

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

(2015) Jop Kind et al.   CELL

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

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

WASP: allele-specific software for robust molecular quantitative trait locus discovery

(2015) Bryce van de Geijn et al.   NATURE METHODS

A generic strategy for CRISPR-Cas9-mediated gene tagging

(2015) Daniel H. Lackner et al.   Nature Communications

Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures

(2014) D. H. Phanstiel et al.   BIOINFORMATICS

Age-Associated Loss of Lamin-B Leads to Systemic Inflammation and Gut Hyperplasia

(2014) Haiyang Chen et al.   CELL

A Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging

(2014) Marvin E. Tanenbaum et al.   CELL

Topologically associating domains are stable units of replication-timing regulation

(2014) Benjamin D. Pope et al.   NATURE

Using TRIP for genome-wide position effect analysis in cultured cells

(2014) Waseem Akhtar et al.   Nature Protocols

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

(2014) Pierre Therizols et al.   SCIENCE

Developmentally Regulated Subnuclear Genome Reorganization Restricts Neural Progenitor Competence in Drosophila

(2013) Minoree Kohwi et al.   CELL

Single-Cell Dynamics of Genome-Nuclear Lamina Interactions

(2013) Jop Kind et al.   CELL

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

(2013) E. Lund et al.   GENOME RESEARCH

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

Interactions among Polycomb Domains Are Guided by Chromosome Architecture

(2011) Bas Tolhuis et al.   PLoS Genetics

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

(2010) Guillaume J. Filion et al.   CELL

The role of Drosophila Lamin C in muscle function and gene expression

(2010) G. Dialynas et al.   DEVELOPMENT

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

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The B-type lamin is required for somatic repression of testis-specific gene clusters

(2009) Y. Y. Shevelyov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A genetic locus targeted to the nuclear periphery in living cells maintains its transcriptional competence

(2008) R. Ileng Kumaran et al.   JOURNAL OF CELL BIOLOGY

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

(2008) Lars Guelen et al.   NATURE

Transcriptional repression mediated by repositioning of genes to the nuclear lamina

(2008) K. L. Reddy et al.   NATURE

Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation

(2008) Ichiro Hiratani et al.   PLOS BIOLOGY

Global Chromatin Domain Organization of the Drosophila Genome

(2008) Elzo de Wit et al.   PLoS Genetics

Recruitment to the Nuclear Periphery Can Alter Expression of Genes in Human Cells

(2008) Lee E. Finlan et al.   PLoS Genetics