Epigenetic editing makes its mark

Researchers are rewriting the chemical tags on DNA and chromatin to tune gene expression.

nature.com

Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models

Abstract. Multiple Sequence Alignment (MSA) is a key step in phylogenetic analysis and is prone to error. Unfortunately, algorithms that remove likely alig

academic.oup.com

Conserved and divergent DNA methylation features of extraembryonic tissues between human, mouse and chicken - BMC Genomics

Background The first cell fate decisions in embryogenesis give rise to extraembryonic tissues, such as the yolk sac and placenta, which are essential for embryo survival. In mammals, extraembryonic cell types arising from these first lineage decisions show distinct DNA methylation patterning, including large partially methylated domains, gene body methylation and accumulation across developmental CpG island (CGI) promoters. Analysis of extraembryonic membranes beyond mammalian species has been limited. Using bisulphite-seq and RNA-seq, we comparatively define these epigenetic characteristics of extraembryonic tissues in both mouse and human. We then tested whether these features are conserved in the chicken extraembryonic membranes (EEMs) including the yolk sac, chorion and chorioallantoic membrane (CAM). Results Transcriptomic analysis revealed that embryonic day (E)4 yolk sac/chorion and E14 CAM express similar marker genes to the mouse chorionic trophoblast, supporting that the chicken chorionic ectoderm shares a ‘trophoblast-like’ cell identity. We find that partially methylated domains and transcription-linked gene body methylation patterning are highly conserved between mouse and human proliferative multipotent trophoblast cells but were not evident in the chicken EEMs. However, we find that methylation of CGIs associated with developmental genes was a conserved feature of mouse, human and chicken EEMs. Conclusions These findings support that features of the extraembryonic DNA methylation landscape have distinct underlying mechanisms. We find that only one feature is conserved across extant amniotes, suggesting distinct evolutionary pressures are associated with different features of EEM epigenetic landscape.

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Identifying critical lysines in mammalian histone H3 with high-throughput CRISPR prime editing - Nature Genetics

This study uses a precise and efficient clustered regularly interspaced short palindromic repeats (CRISPR) prime editing system to substitute lysine residues in histone H3, individually or in combinat...

nature.com

Genome editing of marsupial RSX reveals conserved and divergent principles in mammalian X-inactivation

X-chromosome inactivation balances X-gene dosage between the sexes in eutherians and marsupials. The lncRNA Xist mediates X-inactivation in eutherians but is absent from marsupials. An evolutionarily ...

biorxiv.org

Identifying critical lysines in mammalian histone H3 with high-throughput CRISPR prime editing - Nature Genetics

This study uses a precise and efficient clustered regularly interspaced short palindromic repeats (CRISPR) prime editing system to substitute lysine residues in histone H3, individually or in combinat...

nature.com

Remote homology and functional genetics unmask deeply preserved Scm3/HJURP orthologs in metazoans

Animals encode a rapidly evolving, essential cell cycle gene previously thought to be absent.

science.org

Unifying Repbase and Dfam: a new open foundation for transposable element research - Mobile DNA

Repbase and Dfam, the two foundational resources for transposable element annotation, are being unified into a single, fully open access framework, with Repbase released under CC-0 and its core curati...

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AI Animal Videos Are Ruining One Of The Internet's Last Good Things | Defector

Recently while picking up a banh mi in my neighborhood, I found myself transfixed by a TV in the restaurant showing what I assumed was a nature documentary. At first the footage soothed: Gentle humpba...

defector.com

Gregory J. Hannon (1964–2026)

Gregory J. Hannon passed away in April 2026 at the age of 61. A towering figure in modern molecular biology, Greg influenced remarkably diverse areas of science. His work reshaped our understanding of...

cell.com

Dual profiling of DNA modifications with enhancer features during the exit of naive pluripotency

Cis-regulatory elements, such as enhancers, play an essential role in coordinating gene expression programs during cellular transitions. As such, substantial efforts have been made to characterize enh...

biorxiv.org

A progeria syndrome links DNA hypermethylation to age-related pathology - Nature Genetics

This study investigates the consequences of hypermethylation in a progeria syndrome caused by gain-of-function DNMT3A mutations, finding effects on adult stem cell function.

nature.com

Gene body methylation suppresses intragenic transcription and permits epigenetic inheritance in a cnidarian - Nature Ecology & Evolution

Experiments in the cnidarian Nematostella vectensis show a role of gene body methylation in transposable element suppression and that epigenetic inheritance is constrained by chromatin context and tra...

nature.com

Human embryo editing against disease is unsafe and unproven — despite rosy predictions

Pitfalls of heritable genome editing undermine theoretical benefits.

nature.com

Soma-to-germline miRNA inheritance through yolk promotes stress resilience in progeny - Nature Structural & Molecular Biology

In this study, the authors use the Caenorhabditis elegans model organism to show that maternal microRNAs are delivered from the intestine to embryos by the yolk, where they regulate gene expression an...

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