As a fundamental biological principle, genomic information is typically transmitted vertically from parent to offspring. Occasionally, however, genetic material is transferred horizontally between spe...

The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely ...

Author summary Telomeres are specialized dynamic protective structures at the ends of eukaryotic chromosomes that must be properly maintained to preserve genome stability. Telomerase extends telomeric...

Recent technological breakthroughs have transformed our understanding of how transcription initiation in eukaryotes is regulated. This Review discusses the dynamics and roles of initiation-relevant pr...

The formation of metaphase chromosomes requires the activity of condensins, DNA translocases that reduce chromosomal length through the process of loop extrusion. Reduction of length, however, does no...

RNA design has been hindered by the limited accuracy of three-dimensional (3D) structure prediction. In this study, we show that intricate RNA structures can be generated with current deep learning to...

Abstract. A virus with a circular single-stranded DNA genome, HthCRESSV1, was discovered in an oomycete, Halophytophthora thermoambigua, isolated from brac

Transposable elements (TEs) are a highly diverse group of selfish genomic elements, prevalent across the tree of life, whose uncontrolled propagati...

Inside cells, DNA is intimately associated with proteins, forming chromatin. The protein constituents of chromatin vary across the tree of life: histones are the principal building blocks of chromatin...

Ongoing project

Hammerhead ribozymes (HHRs) are small catalytic RNAs found across diverse life forms. In animals, they can occur as dispersed copies or in tandem genomic arrangements. These tandemly organized forms, ...

Complete sequencing of more than 2,000 centromeres from diverse humans reveals structures and elevated mutation rates that shape the evolution of these critically important regions.

This study introduces iChIP2, a low-input chromatin immunoprecipitation followed by sequencing method that profiles histone post-translational modifications (hPTMs) simultaneously across diverse eukar...

X-chromosome inactivation (XCI) enables gene dosage compensation in XX eutherians. Long interspersed element-1 (LINE-1 or L1) retrotransposons are unusually abundant on the human X chromosome and are ...

In S. pombe under DNA damage and replication stress, SHREC complex containing class II HDAC Clr3 is recruited to DNA breaks and stressed forks by interacting with Rad9-Rad1-Hus1 and deacetylates H2BK...

Palikyras and colleagues investigate chromatin reorganization upon senescence induction, reporting that components of nuclear speckles coordinate chromatin rewiring and a senescence-associated splicin...

In Metazoa, transposon expression is suppressed by the piRNA pathway, and disruption of this pathway leads to rampant transposon expression. However, it remains unclear whether increased transposon ex...

Abstract. Duckweeds (Lemnaceae) present a striking example of convergent genome evolution following the return from land to water. As the smallest and fast

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Aging is a complex multifactorial process that affects cellular function and tissue homeostasis over time. Despite substantial research, the molecular mechanisms driving cellular aging remain poorly understood. Many studies focused on changes in DNA methylation as an indicator of aging. In particular, methylation at polycomb CpG islands was shown to be predictive of phenotypic changes associated with aging. Since many age-related pathological processes are thought to originate from single cells, we asked whether polycomb CpG island methylation occurs preferentially in a subset of cells within a population. Using single-cell whole-genome methylation data across ages and tissues, we identify polycomb CpG methylation as a hallmark of cellular aging. This revealed that aging occurs at varying rates, with faster proliferating cells showing accelerated gain of methylation. Differential gene expression analysis identified changes in immune response, translation, tumorigenesis and neurodegener

An encyclopedia of more than 92 million enhancer–gene regulatory interactions created as part of the ENCODE4 project provides a valuable resource for future studies of gene regulation and human geneti...

Alternative lengthening of telomeres (ALT) is a specialized telomere extension mechanism associated with 5–10% of all cancers1. Although ALT has been linked to epigenetic dysregulation and genome instability, specific genomic and epigenetic rearrangements generated after ALT activation have not been identified. Here we report the insertion of centromeric α-satellite repeats and CENP-B boxes at telomeric locations specifically in ALT cancer cell lines and primary ALT paediatric neuroblastomas, indicating a pathological link for this alteration. Analysis using directed methylation with long-read sequencing (DiMeLo-seq) revealed discrete footprints of CENP-A chromatin assembled at telomeric locations on subsets of chromosomes. By modelling ALT activation, we show that epigenetic dysregulation due to ATRX loss and DNA hypomethylation facilitates the acquisition of these centromeric chromatin signatures. Functionally, interfering with HJURP-mediated CENP-A deposition compromises telomere in

Restricting or permitting H3K27me3 spreading concentrates or dilutes canonical PRC1 (cPRC1), respectively, which affects three-dimensional chromatin interactions. Disruption of cPRC1 compromises repre...