Summary: Proper nucleosome positioning is essential for gene regulation and genomic integrity. Current models posit that chromatin regulators override histones’ intrinsic sequence preferences to establish nucleosome landscapes observed in vivo , implying a minimal role for DNA sequence in guiding nucleosomal structure. In contrast, we show that DNA sequence intrinsically guides nucleosome structure and remodeling from yeast to mammals. Nucleosomes with weak translational settings in vitro , in yeast, and in mammalian cells display strong rotational positioning that favors inward-facing A/T and outward-facing G/C dinucleotides at 10 bp spacings. Foreign DNA sequences heterologously inserted into the yeast genome obey the same rules, indicating that DNA sequence itself is causal. Remodelers and transcription elongation shift the preference among translational positions 10 bp apart, which maintains the same rotational setting. We propose that DNA sequence creates an energy landscape with preferred rotational settings, and that chromatin regulators navigate within, rather than override, these preferences.
Diffuse gastric cancer is highly metastatic and lacks effective therapeutic targets. Using membrane proteomics, gastric cancer cell models, biophysical measurements, and in vivo metastasis assays, we identify EpCAM as a regulator of membrane-cytoskeletal mechanics. EpCAM overexpression was associated with reduced apparent plasma membrane tension, ERM-actin remodeling, increased traction forces, and nuclear deformation. Functional perturbation of ezrin and lamin A/C supported the involvement of membrane-cytoskeleton-nucleus mechanical coupling in confined migration. EpCAM knockout or monoclonal antibody blockade reduced tumor invasion and lymph node dissemination in vivo. These findings establish a mechanobiological framework linking EpCAM-dependent membrane mechanics to metastatic behavior and highlight EpCAM-associated mechanical regulation as a potential therapeutic vulnerability in diffuse gastric cancer.
High-risk neuroblastoma remains a leading cause of pediatric cancer mortality, underscoring the need for novel therapeutics. MYCN amplification drives transcriptional addiction, creating vulnerabilities for therapeutic intervention. Inhibition of CDK12, a key regulator of transcription elongation, downregulates DNA damage response (DDR) genes. CDK12 inactivation using protein degraders and small molecules, including the orally bioavailable, selective CDK12/13 inhibitor OKI-1546, induced BRCAness and apoptosis in neuroblastoma cells. High-throughput compound screening combined with CDK12 inhibition/degradation revealed synergistic interactions encompassing multiple biological pathways. Merestinib, a multi-kinase inhibitor, emerged as the top synergistic agent across a panel of neuroblastoma in vitro models. Combining OKI-1546 with merestinib amplified DDR downregulation and diminished MYCN-driven signaling. OKI-1546 treatment reduced tumor growth and extended survival in vivo, which was enhanced when combined with merestinib. Whilst further in vivo validation is warranted, our findings nominate CDK12 as a promising therapeutic target in high-risk neuroblastoma, which can be exploited through combinatorial treatments.
Recursive splice sites are rare motifs postulated to facilitate splicing across massive introns and shape isoform diversity. The necessity of recursive splicing (RS) and its role in human disease are unsubstantiated. Here, we use CRISPR to model intronic deletions eliminating an RS site (RS1) in CADM2 and conferring risk for attention deficit hyperactivity disorder and other neurobehavioral traits. Ablating RS1 in human induced neurons alters the gradient of RNA abundance across CADM2’s first intron, decreases CADM2 expression, and impacts transcript usage. Decreased CADM2 expression is reflected in reduced exon usage downstream of RS1 and global alteration to genes involved in neuronal processes. In vivo rodent models harboring Cadm2 RS1 deletions exhibit an attenuated effect on Cadm2 expression and modest changes in behavior and functional brain connectivity. This study demonstrates RS as a noncoding regulatory mechanism in a gene associated with a spectrum of neuropsychiatric and behavioral traits.
Summary: The middle and lower Yellow River regions were crucial for early agricultural development and the emergence of complex societies in East Asia, yet their fine-scale population history from the Neolithic to historical periods remains incompletely resolved. Here, we present genome-wide data from 61 ancient individuals (∼4,500–200 before present [BP]) from Henan and Shandong. Our analyses show that middle-to-late Neolithic populations at Dahecun in Henan are genetically homogeneous and closely related to contemporaneous Yellow River millet-farming populations. By ∼3,000 BP, Shandong populations shift toward a late Neolithic middle Yellow River-related ancestry profile, consistent with the eastward expansion of middle Yellow River agricultural populations. This ancestry profile persists into historical periods, indicating long-term genetic continuity in Shandong. Two Tang-Song-period individuals from western Shandong carry ∼15% West Eurasian-related ancestry, indicating limited cross-regional genetic interaction. These findings refine the population history of the middle and lower Yellow River regions.
