Developmental Biology and Gene Regulation

Decoupling Transcription from Cell Fate Preserves Germ Cell Totipotency

The paper shows that Drosophila germ cells maintain totipotency by transcribing an embryo-like program but repressing its translation through Nanos.

Parameters for stable Notch-independent Her6 oscillations across a frequency spectrum in neural stem cell populations

The paper identifies parameters for stable Her6 oscillations in zebrafish neural stem cells, showing they require equal transcript and protein degradation rates.

Regeneration can take place across Drosophila compartments or segments with different Hox gene expression

This study shows that Hox gene expression differences do not block regeneration across Drosophila segments or compartments, though some regenerative limits exist in specific genetic backgrounds.

Whole-Embryo 3D Quantification Reveals Flexible Cellular Scaling and Conserved Tissue Architecture in Xenopus Species

The paper quantifies 3D cellular organization in two Xenopus species to show how tissue architecture converges despite differences in size and cell number.

Paneth cell-derived Notch ligands DLL1 and DLL4 are crucial for intestinal crypt base stem cells.

This study shows that Paneth cell-derived Notch ligands DLL1 and DLL4 are essential for maintaining intestinal crypt base stem cells and their regeneration after injury.

Gene co-expression networks reveal differential developmental modularity in Mammalian limbs

The paper uses gene co-expression networks to analyze limb development in mice, bats, and opossums, finding increased modularity in bat forelimb development.

Extensive disruption of HoxA/D genes does not cause obvious defects in anterior vertebral patterning in zebrafish

This study shows that extensive disruption of HoxA/D genes in zebrafish does not cause visible defects in anterior vertebral patterning, suggesting HoxB/C genes play a more critical role.

From pelagic to reef: Genomic basis of morphological adaption during life-history transition in the orbicular batfish (Platax orbicularis)

The paper investigates the genomic basis of metamorphosis in orbicular batfish, identifying gene family expansions and differentially expressed genes involved in developmental reprogramming during life-history transition.

Wt1 splice isoforms bias lineage programmes during formative pluripotency

The paper identifies Wt1 splice isoforms as regulators of lineage-associated transcriptional programs during formative pluripotency, showing that alternative splicing tunes lineage bias.

Allele-Resolved Hybrid Embryos Reveal the Fates of Regulatory Divergence

The paper tracks regulatory divergence in hybrid embryos of Ciona species, showing how allelic differences are maintained or remodeled in lineage-specific ways and how GRN hierarchy influences allelic divergence.

Temporal regulation of a spatial patterning factor in Drosophila neurogenesis

The paper shows that the same selector transcription factor can be regulated by different patterning axes through distinct enhancers in Drosophila neurogenesis, revealing a cis-regulatory mechanism for neuronal diversity.

A genetically encoded redox bottleneck constrains human developmental rate

This paper identifies a genetic bottleneck in the G3P shuttle that limits human developmental rate by constraining metabolic flux and the segmentation clock.

Description of the embryonic development in the convict cichlid (Amatitlania nigrofasciata)

This paper describes the embryonic development of the convict cichlid from fertilization to hatching, providing a staging table for comparative developmental studies.

A Human Accelerated Region Drives Opposing Heterochronic Changes in Craniofacial and Limb Development

This study shows that the human-specific HAR HACNS1 drives opposing heterochronic changes in craniofacial and limb development through altered gene regulatory networks.

Cell size overrides ganglion mother cell fate specification in Drosophila

The paper shows that cell size can override fate determinants in Drosophila neuroblasts, with larger daughters retaining neuroblast-like properties despite inheriting GMC determinants.

A collagen orientation switch reshapes fin architecture

This study shows that loss of actinodin1 and actinodin2 genes in fish causes collagen fibers to orient perpendicularly to the epidermis, leading to fin reduction and thickening, and reveals similar patterns in tetrapod limbs.

Resolving cell lineages and gene functions in the developing mouse gastrointestinal tract using in utero transduction

This study uses in utero lentiviral transduction to resolve clonal relationships and gene functions in developing mouse gut lineages, revealing distinct developmental patterns in mesenchyme and enteric nervous system.

Terminal selector and subtype selector function across 200 million years of nematode evolution

The paper compares terminal and subtype selectors in two nematode species to study neuronal evolution over 200 million years, finding conservation and novelty in regulatory programs.

Spatiotemporal expression of the zebrafish pax9 gene that is essential for median fin patterning

This study investigates the spatiotemporal expression of the zebrafish pax9 gene and its role in median fin patterning using CRISPR-Cas9 knockin and knockout models.

Segmentation gene expression and function in Vanessa cardui, an emerging model for Lepidoptera

This study investigates PR-gene expression and function in Vanessa cardui, finding that lepidopterans use a subset of Drosophila PR-gene orthologs and lack hemipteran PR-orthologs for segmentation.

Abalone genomics reveals an ancient asymmetry axis and the multifunctionality of the mantle

The paper constructs a chromosome-level genome for Haliotis iris and identifies an ancient regulatory axis and a multifunctional mantle involved in body asymmetry and melanogenesis.

Distinct roles for partially redundant transcription factors in Caenorhabditis elegans mesoderm lineage development

This study investigates the distinct roles of TBX-35 and CEH-51 in C. elegans mesoderm lineage development using genetic and single-cell RNA sequencing approaches.

Developmental pleiotropy revealed by mosaic heterozygous Snrpb deletion underlies CCMS-like axial skeletal defects

This study uses a mouse model to show that Snrpb deletion causes axial skeletal defects by disrupting p53 and RA signaling, without affecting somite patterning.

Connexin-43 links Neuromesodermal progenitor states to segmentation clock robustness during vertebrate axis elongation

This study shows that connexin-43 regulates neuromesodermal progenitor states and is essential for maintaining segmentation clock robustness during vertebrate axis elongation.

Dynamic coupling of cell fate specification and cell sorting during mouse preimplantation development

This study uses agent-based modeling to show that cell fate specification and cell sorting can dynamically couple during mouse preimplantation development, with their relative contributions changing over time.

Shifts in embryonic oxygen levels cue heterochrony in limb initiation

The paper identifies differential oxygen levels as a driver of heterochrony in limb development between avian and mammalian embryos.

An ancestral pronephric contribution reveals the multilineage origin of the teleost gonad and revises the evolution of vertebrate gonadogenesis

The paper shows that the teleost gonad originates from three embryonic tissues, challenging the idea that pronephric contribution is an amniote innovation.

PRDM3 and PRDM16 define cranial neural crest cell states in zebrafish development

The paper identifies direct transcriptional targets of Prdm3 and Prdm16 in zebrafish neural crest cells using CUT&RUN and shows altered gene expression in mutants.

Pax6 homologs are required for patterning both visual systems of the daddy-longlegs Phalangium opilio

This study shows Pax6 homologs are required for patterning both visual systems in the daddy-longlegs Phalangium opilio, with double knockdown causing median eye defects and loss of vestigial eyes.

Duplicated shh genes in Xenopus laevis reveal an essential role in early limb development

This study shows that shh.L is essential for initial limb outgrowth in Xenopus laevis, revealing conserved SHH dependence for early appendage initiation across vertebrates.