Fork coupling directs DNA replication elongation and termination.

DNA replication is initiated at multiple loci to ensure timely duplication of eukaryotic genomes. Sister replication forks progress bidirectionally, and replication terminates when two convergent forks encounter one another. To investigate the coordination of replication forks, we developed a replication-associated in situ HiC method to capture chromatin interactions involving nascent DNA. We identify more than 2000 fountain-like structures of chromatin contacts in human and mouse genomes, indicative of coupling of DNA replication forks. Replication fork interaction not only occurs between sister forks but also involves forks from two distinct origins to predetermine replication termination. Termination-associated chromatin fountains are sensitive to replication stress and lead to coupled forks-associated genomic deletions in cancers. These findings reveal the spatial organization of DNA replication forks within the chromatin context.

Cohesin maintains replication timing to suppress DNA damage on cancer genes.

Cohesin loss-of-function mutations are frequently observed in tumors, but the mechanism underlying its role in tumorigenesis is unclear. Here, we found that depletion of RAD21, a core subunit of cohesin, leads to massive genome-wide DNA breaks and 147 translocation hotspot genes, co-mutated with cohesin in multiple cancers. Increased DNA damages are independent of RAD21-loss-induced transcription alteration and loop anchor disruption. However, damage-induced chromosomal translocations coincide with the asymmetrically distributed Okazaki fragments of DNA replication, suggesting that RAD21 depletion causes replication stresses evidenced by the slower replication speed and increased stalled forks. Mechanistically, approximately 30% of the human genome exhibits an earlier replication timing after RAD21 depletion, caused by the early initiation of >900 extra dormant origins. Correspondingly, most translocation hotspot genes lie in timing-altered regions. Therefore, we conclude that cohesin dysfunction causes replication stresses induced by excessive DNA replication initiation, resulting in gross DNA damages that may promote tumorigenesis.

Effects of different soil types on gas exhange parameters and fruits of Hippophae rhamnoides ssp. mongolica "Ulanshalin" plants.

Background: This study aims to explore the growth and production potential of Hippophae rhamnoides ssp. mongolica "Ulanshalin," a pioneer species of soil and water conservation, after being planted in the Yellow River Basin area with serious soil erosion. An analysis of the differences in photosynthesis and fruit yield of H. rhamnoides plants grown in two typical soils in the watershed is key to understanding whether local conditions are suitable for the growth and yield of H. rhamnoides, as well as the impact of the plants on soil and water conservation. Methods: During the growing season, diurnal changes in the gas exchange parameters of Hippophae rhamnoides-like plants growing in Loess soil and Aeolian soil were continuously monitored, and the effects of total nitrogen (TN) and other elements on the net photosynthetic rate (P N) of the plants were analyzed and compared in the two different soil types. The morphological and quality differences of Hippophae rhamnoides fruits were also compared after reaching the ripening stage. Results: (1) There was a significant difference in the composition of Loess soil and of Aeolian soil. The organic matter content and AK content of the Loess soil was significantly higher than in the Aeolian soil, and the pH was closer to neutral. However, the TK content, TP content, and AP content of the Aeolian soil were slightly higher than in the Loess soil, the pH was higher, and it was alkaline. (2) After controlling the light and temperature, with all other external factors consistent, the daily variation trend of P N, T r, and G s in the leaves of H. rhamnoides plants growing in the two different soils were basically the same. There were differences, however, in when these factors reached their peaks. Soil composition had an impact on the photosynthetic characteristics of H. rhamnoides, with TN, TP, AP, and SOM being the main factors promoting the photosynthetic rate of H. rhamnoides P N. The peaks of P N, T r, and G s of H. rhamnoides plants growing in Aeolian soil were higher than those growing in Loess soil. (3) The average stem length of H. rhamnoides plants growing in Aeolian soil was higher than the plants growing in Loess soil. The number of thorns in the branches of plants in the Aeolian soil was relatively low, and the weight of 100 fruits (28.28 g) was significantly higher than the weight of 100 fruits of the H. rhamnoides plants grown in Loess soil (11.14 g). Conclusions: The results of this study show that in the Yellow River Basin area, Aeolian soil is more conducive to the growth of H. rhamnoides plants than Loess soil. H. rhamnoides plants growing in Aeolian soil had good adaptability and stress resistance, and a larger potential for fruit production. These findings provide insights for ecological restoration and the creation of economic value in the Yellow River Basin area.

Extracellular ATP and cAMP signaling promote Piezo2-dependent mechanical allodynia after trigeminal nerve compression injury.

Trigeminal neuralgia (TN) is a type of severe paroxysmal neuropathic pain commonly triggered by mild mechanical stimulation in the orofacial area. Piezo2, a mechanically gated ion channel that mediates tactile allodynia in neuropathic pain, can be potentiated by a cyclic adenosine monophosphate (cAMP)-dependent signaling pathway that involves the exchange protein directly activated by cAMP 1 (Epac1). To study whether Piezo2-mediated mechanotransduction contributes to peripheral sensitization in a rat model of TN after trigeminal nerve compression injury, the expression of Piezo2 and activation of cAMP signal-related molecules in the trigeminal ganglion (TG) were detected. Changes in purinergic P2 receptors in the TG were also studied by RNA-seq. The expression of Piezo2, cAMP, and Epac1 in the TG of the TN animals increased after chronic compression of the trigeminal nerve root (CCT) for 21 days, but Piezo2 knockdown by shRNA in the TG attenuated orofacial mechanical allodynia. Purinergic P2 receptors P2X4, P2X7, P2Y1, and P2Y2 were significantly up-regulated after CCT injury. In vitro, Piezo2 expression in TG neurons was significantly increased by exogenous adenosine 5'-triphosphate (ATP) and Ca2+ ionophore ionomycin. ATP pre-treated TG neurons displayed elevated [Ca2+ ]i and faster increase in responding to blockage of Na+ /Ca2+ exchanger by KB-R7943. Furthermore, mechanical stimulation of cultured TG neurons led to sustained elevation in [Ca2+ ]i in ATP pre-treated TG neurons, which is much less in naïve TG neurons, or is significantly reduced by Piezo2 inhibitor GsMTx4. These results indicated a pivotal role of Piezo2 in peripheral mechanical allodynia in the rat CCT model. Extracellular ATP, Ca2+ influx, and the cAMP-to-Epac1 signaling pathway synergistically contribute to the pathogenesis and the persistence of mechanical allodynia.

Single-cell analyses identify distinct and intermediate states of zebrafish pancreatic islet development.

Pancreatic endocrine islets are vital for glucose homeostasis. However, the islet developmental trajectory and its regulatory network are not well understood. To define the features of these specification and differentiation processes, we isolated individual islet cells from TgBAC(neurod1:EGFP) transgenic zebrafish and analyzed islet developmental dynamics across four different embryonic stages using a single-cell RNA-seq strategy. We identified proliferative endocrine progenitors, which could be further categorized by different cell cycle phases with the G1/S subpopulation displaying a distinct differentiation potential. We identified endocrine precursors, a heterogeneous intermediate-state population consisting of lineage-primed alpha, beta and delta cells that were characterized by the expression of lineage-specific transcription factors and relatively low expression of terminally differentiation markers. The terminally differentiated alpha, beta, and delta cells displayed stage-dependent differentiation states, which were related to their functional maturation. Our data unveiled distinct states, events and molecular features during the islet developmental transition, and provided resources to comprehensively understand the lineage hierarchy of islet development at the single-cell level.