Composite transposons with bivalent histone marks function as RNA-dependent enhancers in cell fate regulation

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

cell.com

kwnsfk27.r.eu-west-1.awstrack.me

Separation-of-function mutants reveal the NF-κB-independent involvement of IκBα in the regulation of intestinal stemness

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 ...

cell.com

Bivalent chromatin instructs lineage specification during hematopoiesis

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...

cell.com

Emerging roles for the nucleolus in development and stem cells

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

journals.biologists.com

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

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

nature.com

Stem cells as role models for reprogramming and repair

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...

science.org

The establishment of nuclear organization in mouse embryos is orchestrated by multiple epigenetic pathways

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...

cell.com

Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes

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...

science.org

Spatial control of m6A deposition on enhancer and promoter RNAs through co-acetylation of METTL3 and H3K27 on chromatin

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

sciencedirect.com

The molecular basis of heterochromatin assembly and epigenetic inheritance

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

sciencedirect.com

Predictable Engineering of Signal-Dependent Cis-Regulatory Elements

biorxiv.org

Identification of molecular determinants of gene-specific bursting patterns by high-throughput imaging screens

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 ...

cell.com

Transposon–host arms race: a saga of genome evolution

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...

cell.com

Disabling leading and lagging strand histone transmission results in parental histones loss and reduced cell plasticity and viability

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

tinyurl.com

RNA polymerase II coordinates histone deacetylation at active promoters

Transcription initiation limits histone acetylation and H2AZ incorporation at promoters.

science.org

Sequencing technologies to measure translation in single cells - Nature Reviews Molecular Cell Biology

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...

nature.com

Uncovering the whole genome silencers of human cells via Ss-STARR-seq - Nature Communications

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...

nature.com

Fine-tuning of gene expression through the Mettl3-Mettl14-Dnmt1 axis controls ESC differentiation

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...

cell.com

Massively parallel characterization of transcriptional regulatory elements - Nature

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.

nature.com

Resolution of a human super-enhancer by targeted genome randomisation

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...

biorxiv.org

Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture

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 ...

biorxiv.org

3D chromatin hubs as regulatory units of identity and survival in human acute leukemia

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.

cell.com

ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF

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.com

Chromatin-based memory as a self-stabilizing influence on cell identity - Genome Biology

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...

genomebiology.biomedcentral.com