Petros Kolovos

Complex transcriptional programs and signaling pathways control early hematopoietic lineage specification. Many key regulators have been identified; however, a substantial portion of the genome remains functionally uncharacterized. Here, we investigated six uncharacterized ‘Riken’ genes identified through transcriptomic profiling of Flk-1+ (also known as Kdr)/Pdgfrα− (hematoendothelial-enriched) and Flk-1+/Pdgfrα+ (cardiac mesoderm-enriched) populations at day 4 of embryoid body (EB) differentiation. We generated knockouts in mouse embryonic stem cells and performed bulk RNA-sequencing at day 4. Three of these genes (C130074G19Rik, I830077J02Rik and A530016L24Rik) were selected for further investigation by single-cell RNA-sequencing at day 7 of differentiation, which provided novel insight for two of these genes. Knockout of C130074G19Rik (hereafter G19Rik) increased the abundance of megakaryocyte progenitors and reduced endothelial populations, with differentially expressed genes enriched for hemostasis and membrane trafficking pathways. I830077J02Rik (hereafter J02Rik)-knockout cells showed subtle changes in extracellular matrix and cell adhesion genes, with a shift toward hematoendothelial lineages. Both G19Rik and J02Rik genes encode (predicted) transmembrane proteins that modulate membrane-associated processes in early hematopoietic development. This work establishes a framework for the study of uncharacterized genes with potential roles in cell fate determination.

Gene activation and coregulation have been attributed to different mechanisms, such as enhancer–promoter interactions via chromatin looping or the accumulation of transcription factors into hubs or condensates. However, genome-wide studies exploring mechanistic differences in endogenous gene regulation in primary human cells are scarce. Here we dissect the proinflammatory gene expression programme induced by tumor necrosis factor (TNF) in human endothelial cells using sequencing- and imaging-based methods. Our findings, enabled by the co-accessibility analysis of deep-coverage single-cell chromatin accessibility data with our RWireX software, identified two distinct regulatory chromatin modules: autonomous links of co-accessibility (ACs) between separated sites and domains of contiguous co-accessibility (DCs) with increased local transcription factor binding. The TNF-dependent induction timing and strength as well as changes in transcriptional bursting kinetics differed for genes in the AC and DC modules, pointing to functionally distinct regulatory mechanisms. These findings provide a framework for understanding how cells achieve rapid and precise control of gene expression.

The Thracian Sea, a semi-enclosed coastal basin in the northeastern Aegean Sea, represents a dynamic marine environment influenced by freshwater inputs, stratification, and seasonal variability. Here, we investigated the spatiotemporal dynamics of microbial and ichthyofaunal communities using environmental DNA (eDNA) and high-throughput sequencing across various stations in the vicinity of the Thracian Sea, in consecutive months (through spring and summer). Seawater samples were collected from the surface and thermocline layers, and environmental parameters were recorded to examine their influence on biodiversity patterns. Microbial communities exhibited strong seasonal and depth-related structuring. Alpha diversity was highest in spring and declined during summer, while beta diversity analyses revealed clear clustering by month and depth. Dominant taxa included Alphaproteobacteria (SAR11), Cyanobacteria (Synechococcus, Prochlorococcus), with distinct core microbiomes. Fish communities, identified via CytB metabarcoding, displayed marked temporal turnover but limited spatial segregation. While alpha diversity metrics did not differ significantly, beta diversity analyses showed seasonal shifts with dominant taxa such as Raja spp., Engraulis spp., and Diplodus sargus. Multivariate and co-structure analyses (Mantel, Procrustes) revealed moderate but significant concordance between microbial and fish communities and support the existence of similar biodiversity responses to environmental parameters across temporal and spatial variability. Co-occurrence networks further present depth-specific associations, with surface communities being more cooperative and phototrophic, while thermocline networks showed modularity and potential ecological specialization. This study highlights the value of integrated eDNA-based monitoring in revealing seasonal biodiversity dynamics and ecological interactions in coastal marine ecosystems, supporting future spatial planning and conservation strategies in the Thracian Sea.

Data sheet 3 from Single-Cell Analysis of Bone Marrow CD8+ T Cells in Myeloid Neoplasms Reveals Pathways Associated with Disease Progression and Response to Treatment with Azacitidine

Supplementary Figures and Tables

Data sheet 1 from Single-Cell Analysis of Bone Marrow CD8+ T Cells in Myeloid Neoplasms Reveals Pathways Associated with Disease Progression and Response to Treatment with Azacitidine

Data sheet 2 from Single-Cell Analysis of Bone Marrow CD8+ T Cells in Myeloid Neoplasms Reveals Pathways Associated with Disease Progression and Response to Treatment with Azacitidine

Data sheet 3 from Single-Cell Analysis of Bone Marrow CD8+ T Cells in Myeloid Neoplasms Reveals Pathways Associated with Disease Progression and Response to Treatment with Azacitidine

Data sheet 2 from Single-Cell Analysis of Bone Marrow CD8+ T Cells in Myeloid Neoplasms Reveals Pathways Associated with Disease Progression and Response to Treatment with Azacitidine

Supplementary Figures and Tables