Homeotic and nonhomeotic patterns in the tetrapod vertebral formula.

Vertebrate development and phylogeny are intimately connected through the vertebral formula, the numerical distribution of vertebrae along the body axis into different categories such as neck and chest. A key window into this relationship is through the conserved gene clusters. gene expression boundaries align with vertebral boundaries, and their manipulation in model organisms often results in the transformation of one vertebral type into its neighbor, a homeotic transformation.

CWL-Based Analysis Pipeline for Hi-C Data: From FASTQ Files to Matrices.

Over a decade has passed since the development of the Hi-C method for genome-wide analysis of 3D genome organization. Hi-C utilizes next-generation sequencing (NGS) technology to generate large-scale chromatin interaction data, which has accumulated across a diverse range of species and cell types, particularly in eukaryotes. There is thus a growing need to streamline the process of Hi-C data analysis to utilize these data sets effectively.

Embryonic genome instability upon DNA replication timing program emergence.

Faithful DNA replication is essential for genome integrity. Under-replicated DNA leads to defects in chromosome segregation, which are common during embryogenesis. However, the regulation of DNA replication remains poorly understood in early mammalian embryos.

Structure and dynamics of nuclear A/B compartments and subcompartments.

Mammalian chromosomes form a hierarchical structure within the cell nucleus, from chromatin loops, megabase (Mb)-sized topologically associating domains (TADs) to larger-scale A/B compartments. The molecular basis of the structures of loops and TADs has been actively studied. However, the A and B compartments, which correspond to early-replicating euchromatin and late-replicating heterochromatin, respectively, are still relatively unexplored.

A feedback loop that drives cell death and proliferation and its defect in intestinal stem cells.

Cell death and proliferation are at a glance dichotomic events, but occasionally coupled. Caspases, traditionally known to execute apoptosis, play non-apoptotic roles, but their exact mechanism remains elusive. Here, using intestinal stem cells (ISCs), we discovered that activation of caspases induces massive cell proliferation rather than cell death.