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Article
Open AccessSystematic assessment of ISWI subunits shows that NURF creates local accessibility for CTCF
Catalytic activity of the imitation switch (ISWI) family of remodelers is critical for nucleosomal organization and DNA binding of certain transcription factors, including the insulator protein CTCF. Here we d...
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Article
Open AccessCancer lineage-specific regulation of YAP responsive elements revealed through large-scale functional epigenomic screens
YAP is a key transcriptional co-activator of TEADs, it regulates cell growth and is frequently activated in cancer. In Malignant Pleural Mesothelioma (MPM), YAP is activated by loss-of-function mutations in up...
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Article
Open AccessCooperation between bHLH transcription factors and histones for DNA access
The basic helix–loop–helix (bHLH) family of transcription factors recognizes DNA motifs known as E-boxes (CANNTG) and includes 108 members1. Here we investigate how chromatinized E-boxes are engaged by two struct...
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Article
Open AccessReadout of histone methylation by Trim24 locally restricts chromatin opening by p53
The genomic binding sites of the transcription factor (TF) and tumor suppressor p53 are unusually diverse with regard to their chromatin features, including histone modifications, raising the possibility that ...
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Article
ZFP462 safeguards neural lineage specification by targeting G9A/GLP-mediated heterochromatin to silence enhancers
ZNF462 haploinsufficiency is linked to Weiss–Kruszka syndrome, a genetic disorder characterized by neurodevelopmental defects, including autism. Though conserved in vertebrates and essential for embryonic develop...
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Article
Generating specificity in genome regulation through transcription factor sensitivity to chromatin
Cell type-specific gene expression relies on transcription factors (TFs) binding DNA sequence motifs embedded in chromatin. Understanding how motifs are accessed in chromatin is crucial to comprehend different...
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Article
Open AccessEvidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation
Cytosine methylation efficiently silences CpG-rich regulatory regions of genes and repeats in mammalian genomes. To what extent this entails direct inhibition of transcription factor (TF) binding versus indire...
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Article
Open AccessDNA sequence and chromatin modifiers cooperate to confer epigenetic bistability at imprinting control regions
Genomic imprinting is regulated by parental-specific DNA methylation of imprinting control regions (ICRs). Despite an identical DNA sequence, ICRs can exist in two distinct epigenetic states that are memorized...
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Article
BANP opens chromatin and activates CpG-island-regulated genes
The majority of gene transcripts generated by RNA polymerase II in mammalian genomes initiate at CpG island (CGI) promoters1,2, yet our understanding of their regulation remains limited. This is in part due to th...
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Article
Open AccessPAX8 and MECOM are interaction partners driving ovarian cancer
The transcription factor PAX8 is critical for the development of the thyroid and urogenital system. Comprehensive genomic screens furthermore indicate an additional oncogenic role for PAX8 in renal and ovarian...
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Article
Mammalian SWI/SNF continuously restores local accessibility to chromatin
Chromatin accessibility is a hallmark of regulatory regions, entails transcription factor (TF) binding and requires nucleosomal reorganization. However, it remains unclear how dynamic this process is. In the p...
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Article
Open AccessA genome-scale map of DNA methylation turnover identifies site-specific dependencies of DNMT and TET activity
DNA methylation is considered a stable epigenetic mark, yet methylation patterns can vary during differentiation and in diseases such as cancer. Local levels of DNA methylation result from opposing enzymatic a...
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Article
Targeting neuronal and glial cell types with synthetic promoter AAVs in mice, non-human primates and humans
Targeting genes to specific neuronal or glial cell types is valuable for both understanding and repairing brain circuits. Adeno-associated viruses (AAVs) are frequently used for gene delivery, but targeting ex...
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Publisher Correction: DNA damage detection in nucleosomes involves DNA register shifting
In this Article, in Fig. 1a, the 5′ and 3′ labels were reversed in the DNA sequence, and Fig. 4 was missing panel labels a–e. These errors have been corrected online.
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DNA damage detection in nucleosomes involves DNA register shifting
Access to DNA packaged in nucleosomes is critical for gene regulation, DNA replication and DNA repair. In humans, the UV-damaged DNA-binding protein (UV-DDB) complex detects UV-light-induced pyrimidine dimers ...
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Article
Mammalian ISWI and SWI/SNF selectively mediate binding of distinct transcription factors
Chromatin remodelling complexes evict, slide, insert or replace nucleosomes, which represent an intrinsic barrier for access to DNA. These remodellers function in most aspects of genome utilization including t...
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Article
Open AccessCell cycle-resolved chromatin proteomics reveals the extent of mitotic preservation of the genomic regulatory landscape
Regulation of transcription, replication, and cell division relies on differential protein binding to DNA and chromatin, yet it is unclear which regulatory components remain bound to compacted mitotic chromoso...
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Article
Author Correction: H3K64 trimethylation marks heterochromatin and is dynamically remodeled during developmental reprogramming
In this article, the Ponceau staining presented in Fig. 1b (right, bottom) does not follow best practices for figure preparation since itinadvertently included duplications from the Ponceau staining presented ...
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Article
Competition between DNA methylation and transcription factors determines binding of NRF1
The relationship between DNA methylation and transcription factor binding was studied across the genome in mouse embryonic stem cells-the study reveals that the transcription factor NRF1 is methylation-sensiti...
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Article
Open AccessLoss of Ezh2 promotes a midbrain-to-forebrain identity switch by direct gene derepression and Wnt-dependent regulation
Precise spatiotemporal control of gene expression is essential for the establishment of correct cell numbers and identities during brain development. This process involves epigenetic control mechanisms, such a...
