This study reveals that composite transposons with bivalent histone marks can serve as RNA-dependent enhancers, controlling key developmental and aging-related gene programs.

Daniel Álvarez-Villanueva et al. dissect distinct roles of the NF-κB inhibitor IκBα by generating separation-of-function mutants. Their findings reveal that chromatin-bound IκBα, independent of NF-κB ...

Yagi et al. show that, unexpectedly, H3K4 methylation is dispensable for hematopoietic stem cell maintenance but essential for progenitor cell maturation into all blood cell types by opposing H3K27 me...

Summary: This Review explores roles of the nucleolus in mammalian development, with a particular focus on genome organisation and chromatin regulation.

Blood Cancer Journal - Transposable elements as genome regulators in normal and malignant haematopoiesis

Stem cells are a promising source for cellular therapies across many diseases and tissues. Their inherent ability to differentiate into other cell types has been the focus of investigation over decade...

In vivo screening in mouse embryos provides insights into the functional interplay between chromatin and the nuclear envelope in the establishment of lamina-associated domains, the earliest feature of...

Most phenotype-associated genetic variants map to noncoding regulatory regions of the human genome, but their mechanisms remain elusive in most cases. We developed a highly efficient strategy, Perturb...

Interaction between the N6-methyladenosine (m6A) methyltransferase METTL3 and METTL14 is critical for METTL3 to deposit m6A on various types of RNAs. …

Heterochromatin plays a fundamental role in gene regulation, genome integrity, and silencing of repetitive DNA elements. Histone modifications are ess…

Sood et al. used high-throughput screening to identify regulators of gene bursting and find both gene- and cell-type-specific effectors. Acetylation alters burst size in a gene-specific manner but is ...

Once considered ‘junk DNA,’ transposons or transposable elements (TEs) are now recognized as key drivers of genome evolution, contributing to genetic diversity, gene regulation, and species diversific...

Losing parental histones during DNA replication fork passage challenges differentiation competence and cell viability.

Transcription initiation limits histone acetylation and H2AZ incorporation at promoters.

Recent sequencing-based methods, including novel ribosome profiling, ribosome affinity purification and spatial translation methods, have enabled the measurement of translation at single-cell resoluti...

Silencers play a critical role in gene transcription regulation. Here, the authors developed the Ss-STARR-seq technique to identify tens of thousands of silencers in human cells. These silencers posse...

Beyond its role as RNA m6A writer, METTL3-METTL14 can mediate 5mC deposition on DNA by recruiting the DNA methyltransferase DNMT1 to chromatin. The two marks co-orchestrate the expression of key genes...

Lentivirus-based reporter assays for 680,000 regulatory sequences from three cell lines coupled to machine-learning models lead to insights into the grammar of cis-regulatory elements.

Human gene expression is controlled from distance via enhancers, which can form longer "super-enhancer"-regions of intense regulatory activity. Whether super-enhancers constitute a separate regulatory...

Chromatin organization plays a crucial role in gene regulation [[1][1], [2][2], [3][3]], but disentangling the contributions of various epigenetic components to gene-scale chromatin structure remains ...

Gambi et al. highlight the critical role of 3D chromatin hubs for T cell leukemia progression. By integrating multi-omics data and employing CRISPR screening techniques, the researchers identify key regulatory elements controlling oncogenes expression and disease markers. The findings offer new insights into tumor heterogeneity, patient stratification, and potential therapeutic targets.

ZNF143 has been implicated in gene activation and chromatin looping. Magnitov et al. show that ZNF143 has no general looping factor activity and explain why this function has been misattributed. Instead, ZNF143 regulates transcription of nuclear-encoded mitochondrial genes, ensuring energy homeostasis, proliferation, and differentiation potential of stem cells.

Cell types are traditionally thought to be specified and stabilized by gene regulatory networks. Here, we explore how chromatin memory contributes to the specification and stabilization of cell states...

Mouse embryonic stem cells (mESCs) and other naive pluripotent stem cells can reverse typical developmental trajectories and, at low frequency, de-differentiate into 2-cell-like cells (2CLCs) that res...

Motif grammar on nucleosome fibres acts as signpost elements, directing TF combinatorial binding to enhancers.

Lou et al. engineered source-sink relations to improve carbon partitioning by targeted insertion of heat-shock cis-elements into cell-wall-invertase genes using prime editing. This delivers climate-smart crops with higher yields under normal conditions and stable yields under heat stress in tomato and rice.

In some cases, non-genetic information can be inherited across generations. Fitz-James et al. investigate the mechanism by which such epigenetic information becomes heritable in fruit flies. They show that physical contact between regions of DNA within the cell is able to trigger the histone modification H3K27me3 to become heritable.

Mahara et al. show that genome folding dynamics and the magnitude of transcriptional induction are linked during ESC differentiation. Thereby, pervasive transient interactions can contribute to full activation of connected genes, irrespective of their chromatin signature. This activity can involve temporal facilitation of promoter interactions with strong enhancers.

Thomas, Feng, et al. introduce a synthetic platform that allows the building of complex regulatory landscapes. Integrating the same enhancer at different distances from a promoter uncovered that activ...

By developing a long-read sequencing method to simultaneously map replication status and protein-DNA contacts in cells, Ostrowski, Yang, et al. show that newly replicated chromatin is enriched for unw...

All cells must fold their chromosomes. The combined action of a small set of conserved molecular and biophysical mechanisms fold chromosomes in a variety of ways across the cell cycle and tree of life...

ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...

Perturb-seq enabled the profiling of transcriptional effects of genetic perturbations in single cells but lacks the ability to examine the impact on tissue environments. We present Perturb-DBiT for si...

MultiPerturb-seq profiles gene expression and chromatin accessibility in single-cell pooled CRISPR screen.

Most of the human genome is thought to be non-functional, and includes large segments often referred to as “dark matter” DNA. The genome also encodes hundreds of putative and poorly characterized tran...

Euchromatic and heterochromatic regions of the genome tend not to interact inside the nucleus. Stutzman et al. investigate the role of HP1a binding to histone H3K9 methylation in restricting these interactions. They observe weakening, but not a complete loss, of separation between euchromatin and heterochromatin when the H3K9-HP1a interaction is disrupted.

Improved effectors for CRISPRi/CRISPRa are developed following high-throughput screening of transcriptional domains.

Abstract. SETDB1 (SET domain bifurcated histone lysine methyltransferase 1) is a major protein lysine methyltransferase trimethylating lysine 9 on histone

The pluripotency program is maintained by transcription factors from the Sox and POU families. Here they identify SOX and POU factors from unicellular relatives of animals and show that unicellular SO...