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Promoter-intrinsic and local chromatin features determine gene repression in lamina-associated domains

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/j.cell.2012.06.051openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.cell.2012.11.018openalex-snapshot

Foxa2 and H2A.Z Mediate Nucleosome Depletion during Embryonic Stem Cell Differentiation

inferredcites →https://doi.org/10.1016/j.cell.2013.02.028openalex-snapshot

Single-Cell Dynamics of Genome-Nuclear Lamina Interactions

inferredcites →https://doi.org/10.1016/j.cell.2013.07.018openalex-snapshot

Chromatin Position Effects Assayed by Thousands of Reporters Integrated in Parallel

inferredcites →https://doi.org/10.1016/j.cell.2013.09.011openalex-snapshot

Mapping Human Epigenomes

inferredcites →https://doi.org/10.1016/j.cell.2015.08.040openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.cell.2017.04.022openalex-snapshot

Lamina-Associated Domains: Links with Chromosome Architecture, Heterochromatin, and Gene Repression

inferredcites →https://doi.org/10.1016/j.cub.2006.03.059openalex-snapshot

Long-Range Directional Movement of an Interphase Chromosome Site

inferredcites →https://doi.org/10.1016/j.molcel.2010.03.016openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.stem.2012.11.003openalex-snapshot

H2A.Z Facilitates Access of Active and Repressive Complexes to Chromatin in Embryonic Stem Cell Self-Renewal and Differentiation

inferredcites →https://doi.org/10.1016/j.tig.2016.05.004openalex-snapshot

On TADs and LADs: Spatial Control Over Gene Expression

inferredcites →https://doi.org/10.1038/nature06727openalex-snapshot

Transcriptional repression mediated by repositioning of genes to the nuclear lamina

inferredcites →https://doi.org/10.1038/nature06947openalex-snapshot

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

inferredcites →https://doi.org/10.1038/nature11247openalex-snapshot

An integrated encyclopedia of DNA elements in the human genome

inferredcites →https://doi.org/10.1038/nature13182openalex-snapshot

A promoter-level mammalian expression atlas

inferredcites →https://doi.org/10.1038/nbt.3754openalex-snapshot

Genome-wide mapping of autonomous promoter activity in human cells

inferredcites →https://doi.org/10.1038/nbt1049openalex-snapshot

Coordinate dual-gene transgenesis by lentiviral vectors carrying synthetic bidirectional promoters

inferredcites →https://doi.org/10.1038/ng.3142openalex-snapshot

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

inferredcites →https://doi.org/10.1038/ng.3550openalex-snapshot

Histone H3 globular domain acetylation identifies a new class of enhancers

inferredcites →https://doi.org/10.1038/nmeth.3542openalex-snapshot

ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors

inferredcites →https://doi.org/10.1038/nprot.2007.148openalex-snapshot

Detection of in vivo protein–DNA interactions using DamID in mammalian cells

inferredcites →https://doi.org/10.1038/nprot.2014.072openalex-snapshot

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

inferredcites →https://doi.org/10.1038/nrg.2016.138openalex-snapshot

From profiles to function in epigenomics

inferredcites →https://doi.org/10.1038/nrg3798openalex-snapshot

High-resolution digital profiling of the epigenome

inferredcites →https://doi.org/10.1038/nrm.2017.119openalex-snapshot

Ten principles of heterochromatin formation and function

inferredcites →https://doi.org/10.1038/nrm3274openalex-snapshot

Understanding the language of Lys36 methylation at histone H3

inferredcites →https://doi.org/10.1038/s41598-017-00176-xopenalex-snapshot

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

inferredcites →https://doi.org/10.1038/sdata.2017.107openalex-snapshot

FANTOM5 CAGE profiles of human and mouse reprocessed for GRCh38 and GRCm38 genome assemblies

inferredcites →https://doi.org/10.1073/pnas.0906142106openalex-snapshot

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

inferredcites →https://doi.org/10.1083/jcb.200706060openalex-snapshot

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

inferredcites →https://doi.org/10.1083/jcb.201305027openalex-snapshot

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

inferredcites →https://doi.org/10.1083/jcb.201405110openalex-snapshot

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

inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot

BEDTools: a flexible suite of utilities for comparing genomic features

inferredcites →https://doi.org/10.1093/bioinformatics/btr261openalex-snapshot

DREME: motif discovery in transcription factor ChIP-seq data

inferredcites →https://doi.org/10.1093/bioinformatics/btv053openalex-snapshot

Starcode: sequence clustering based on all-pairs search

inferredcites →https://doi.org/10.1093/nar/gkg630openalex-snapshot

REDUCE: an online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data

inferredcites →https://doi.org/10.1093/nar/gkw257openalex-snapshot

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

inferredcites →https://doi.org/10.1096/fj.12-206177openalex-snapshot

KAP1 regulates gene networks controlling T‐cell development and responsiveness

inferredcites →https://doi.org/10.1101/122226openalex-snapshot

Chromosome Conformation Paints Reveal the Role of Lamina Association in Genome Organization and Regulation

inferredcites →https://doi.org/10.1101/cshperspect.a020990openalex-snapshot

MYC and Transcription Elongation

inferredcites →https://doi.org/10.1101/gad.176826.111openalex-snapshot

Pioneer transcription factors: establishing competence for gene expression

inferredcites →https://doi.org/10.1101/gad.265439.115openalex-snapshot

Transcriptional repression by PRC1 in the absence of H2A monoubiquitylation

inferredcites →https://doi.org/10.1101/gad.286278.116openalex-snapshot

Direct interrogation of the role of H3K9 in metazoan heterochromatin function

inferredcites →https://doi.org/10.1101/gad.310367.117openalex-snapshot

Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation

inferredcites →https://doi.org/10.1101/gr.135350.111openalex-snapshot

GENCODE: The reference human genome annotation for The ENCODE Project

inferredcites →https://doi.org/10.1101/gr.211433.116openalex-snapshot

Clustering of Drosophila housekeeping promoters facilitates their expression

inferredcites →https://doi.org/10.1101/gr.237180.118openalex-snapshot

Polycomb repressive complex 1 shapes the nucleosome landscape but not accessibility at target genes

inferredcites →https://doi.org/10.1126/science.1259587openalex-snapshot

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

inferredcites →https://doi.org/10.1126/science.aad9841openalex-snapshot

TT-seq maps the human transient transcriptome

inferredcites →https://doi.org/10.1126/science.aan6826openalex-snapshot

Single-cell epigenomics: Recording the past and predicting the future

inferredcites →https://doi.org/10.1186/gb-2012-13-10-r85openalex-snapshot

H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions

inferredcites →https://doi.org/10.1186/s12859-016-1349-2openalex-snapshot

Feature-based classification of human transcription factors into hypothetical sub-classes related to regulatory function

inferredcites →https://doi.org/10.1186/s13148-016-0284-4openalex-snapshot

Genome-wide epigenomic profiling for biomarker discovery

inferredcites →https://doi.org/10.1242/dev.048231openalex-snapshot

The role ofDrosophilaLamin C in muscle function and gene expression

inferredcites →https://doi.org/10.1371/journal.pcbi.1003419openalex-snapshot

Combinatorial Modeling of Chromatin Features Quantitatively Predicts DNA Replication Timing in Drosophila

inferredcites →https://doi.org/10.1371/journal.pgen.1000039openalex-snapshot

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

inferredcites →https://doi.org/10.1371/journal.pgen.1004250openalex-snapshot

Chromatin Landscapes of Retroviral and Transposon Integration Profiles

inferredcites →https://doi.org/10.1371/journal.pone.0173723openalex-snapshot

Genome-wide mapping of histone H3K9me2 in acute myeloid leukemia reveals large chromosomal domains associated with massive gene silencing and sites of genome instability

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1038/s41556-025-01822-7openalex-snapshot

LBR and LAP2 mediate heterochromatin tethering to the nuclear periphery to preserve genome homeostasis

inferred← citeshttps://doi.org/10.1093/nar/gkz220openalex-snapshot

Replication dynamics of individual loci in single living cells reveal changes in the degree of replication stochasticity through S phase

inferred← citeshttps://doi.org/10.1101/2022.01.28.478236openalex-snapshot

Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin

inferred← citeshttps://doi.org/10.1101/481598openalex-snapshot

The repressive genome compartment is established early in the cell cycle before forming the lamina associated domains

inferred← citeshttps://doi.org/10.1101/gr.238279.118openalex-snapshot

Identification of regulatory elements from nascent transcription using dREG

inferred← citeshttps://doi.org/10.1186/s13072-023-00492-9openalex-snapshot

Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin

inferred← citeshttps://doi.org/10.3390/cells8030271openalex-snapshot

Lamina Associated Domains and Gene Regulation in Development and Cancer

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