ArticleeLife2022
Dynamic spreading of chromatin-mediated gene silencing and reactivation between neighboring genes in single cells.
Article in eLife, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
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Who cites it
27 citing papers in PubMed, 38 citations in OpenAlex.
- Single-cell chromatin state transitions during epigenetic memory formation.Science advances · 2026Article
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- Epigenetic control of PDX1 and NGN3 by a computationally designed PRC2 inhibitor enforces pancreatic endocrine differentiation from pluripotent stem cells.Research square · 2026Article
- Epigenetic editing: from concept to clinic.Nature reviews. Drug discovery · 2026Review
- DNA topological regulation in RNA polymerase II transcription.Cellular & molecular biology letters · 2026Review
- High-throughput mapping of modular regulatory domains in human RNA-binding proteins.Cell systems · 2026Article
- Optogenetic BlueGENEs engineered into a human safe harbor locus.Nucleic acids research · 2026Article
- Bifunctional transcriptional effector domains control gene expression pulses in an occupancy-dependent manner.bioRxiv : the preprint server for biology · 2025Article
- Reduced Cas9 transgene silencing by incorporation of intron sequences.Nature communications · 2025Article
- Downregulation of chalcone isomerase in Petunia hybrida: profound effects on floral morphology and transcriptional remodeling of the flavonoid biosynthetic pathway.BMC plant biology · 2025Article
- MemorySeq identifies heritable epigenetic phenotypes that initiate cell culture stress tolerance in CHO cells.iScience · 2025Article
- Human Synthetic Biology and Programmable Gene Regulation Control.Annual review of genomics and human genetics · 2025Review
- Tet Transgene Activation is Disrupted in Lipogenic Triple Negative Breast Cancer Cells.ACS synthetic biology · 2025Article
- The H3.3K36M oncohistone disrupts the establishment of epigenetic memory through loss of DNA methylation.Molecular cell · 2024Article
- Massively parallel characterization of insulator activity across the genome.Nature communications · 2024Article
- Transcriptional silencing in Saccharomyces cerevisiae: known unknowns.Epigenetics & chromatin · 2024Review
- Precision epigenetic editing: Technological advances, enduring challenges, and therapeutic applications.Cell chemical biology · 2024Review
- From enhancers to genome conformation: complex transcriptional control underlies expression of a single herpesviral gene.bioRxiv : the preprint server for biology · 2024Article
- Prediction of on-target and off-target activity of CRISPR-Cas13d guide RNAs using deep learning.Nature biotechnology · 2024Article
- Using High-Throughput Measurements to Identify Principles of Transcriptional and Epigenetic Regulators.Methods in molecular biology (Clifton, N.J.) · 2024Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
Abstract
In mammalian cells genes that are in close proximity can be transcriptionally coupled: silencing or activating one gene can affect its neighbors. Understanding these dynamics is important for natural processes, such as heterochromatin spreading during development and aging, and when designing synthetic gene regulation circuits. Here, we systematically dissect this process in single cells by recruiting and releasing repressive chromatin regulators at dual-gene synthetic reporters, and measuring how fast gene silencing and reactivation spread as a function of intergenic distance and configuration of insulator elements. We find that silencing by KRAB, associated with histone methylation, spreads between two genes within hours, with a time delay that increases with distance. This fast KRAB-mediated spreading is not blocked by the classical cHS4 insulators. Silencing by histone deacetylase HDAC4 of the upstream gene can also facilitate background silencing of the downstream gene by PRC2, but with a days-long delay that does not change with distance. This slower silencing can sometimes be stopped by insulators. Gene reactivation of neighboring genes is also coupled, with strong promoters and insulators determining the order of reactivation. Our data can be described by a model of multi-gene regulation that builds upon previous knowledge of heterochromatin spreading, where both gene silencing and gene reactivation can act at a distance, allowing for coordinated dynamics via chromatin regulator recruitment.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.