Innovative insights into extrachromosomal circular DNAs in gynecologic tumors and reproduction

Originating but free from chromosomal DNA,extrachromosomal circular DNAs(eccDNAs)are organized in circular form and have long been found in unicellular and multicellular eukaryotes.Their biogenesis and function are poorly understood as they are characterized by sequence homology with linear DNA,for which few detection methods are available.Recent advances in high-throughput sequencing technologies have revealed that eccDNAs play crucial roles in tumor formation,evolution,and drug resistance as well as aging,genomic diversity,and other biological processes,bringing it back to the research hotspot.Several mechanisms of eccDNA formation have been proposed,including the breakage-fusion-bridge(BFB)and translocation-deletion-amplification models.Gynecologic tumors and disorders of embryonic and fetal development are major threats to human reproductive health.The roles of eccDNAs in these pathological processes have been partially elucidated since the first discovery of eccDNA in pig sperm and the double minutes in ovarian cancer ascites.The present review summarized the research history,biogenesis,and currently available detection and analytical methods for eccDNAs and clarified their functions in gynecologic tumors and reproduction.We also proposed the application of eccDNAs as drug targets and liquid biopsy markers for prenatal diagnosis and the early detection,prognosis,and treatment of gynecologic tumors.This review lays theoretical foundations for future investigations into the complex regulatory networks of eccDNAs in vital physiological and pathological processes.

Local State Capacity and Uneven Taxation across Industrial Firms

In this research we investigate the association between local state capacity(LSC)and effective tax burdens(ETBs)on industrial firms within counties between 1998 and 2013.The LSC measures a state's capacity for policy implementation and specifically its ability to acquire low-cost agricultural land for nonagricultural(industrial or commercial)purposes.Based on China's government-led development experience since the 1990s,we draw on two unique household survey datasets to capture LSC at county level.We find robust evidence that greater LSC was associated with much lower ETBs on large industrial firms.This taxation pattern implies local government's primary reliance on larger manufacturing firms,while the ETBs for small-and-medium enterprises are not as prominently addressed.This research highlights that LSC can affect both the amount of revenue a local government can generate and the methods it uses to collect these revenues.

Lysosomal cholesterol accumulation is commonly found in most peroxisomal disorders and reversed by 2-hydroxypropyl-β-cyclodextrin

Peroxisomal disorders(PDs)are a heterogenous group of diseases caused by defects in peroxisome biogenesis or functions.Xlinked adrenoleukodystrophy is the most prevalent form of PDs and results from mutations in the ABCD1 gene,which encodes a transporter mediating the uptake of very long-chain fatty acids(VLCFAs).The curative approaches for PDs are very limited.Here,we investigated whether cholesterol accumulation in the lysosomes is a biochemical feature shared by a broad spectrum of PDs.We individually knocked down fifteen PD-associated genes in cultured cells and found ten induced cholesterol accumulation in the lysosome.2-Hydroxypropyl-β-cyclodextrin(HPCD)effectively alleviated the cholesterol accumulation phenotype in PD-mimicking cells through reducing intracellular cholesterol content as well as promoting cholesterol redistribution to other cellular membranes.In ABCD1 knockdown cells,HPCD treatment lowered reactive oxygen species and VLCFA to normal levels.In Abcd1 knockout mice,HPCD injections reduced cholesterol and VLCFA sequestration in the brain and adrenal cortex.The plasma levels of adrenocortical hormones were increased and the behavioral abnormalities were greatly ameliorated upon HPCD administration.Together,our results suggest that defective cholesterol transport underlies most,if not all,PDs,and that HPCD can serve as a novel and effective strategy for the treatment of PDs.

POST1/C12ORF49 regulates the SREBP pathway by promoting site-1 protease maturation

Sterol-regulatory element binding proteins(SREBPs)are the key transcriptional regulators of lipid metabolism.The activation of SREBP requires translocation of the SREBP precursor from the endoplasmic reticulum to the Golgi,where it is sequentially cleaved by site-1 protease(S1P)and site-2 protease and releases a nuclear form to modulate gene expression.To search for new genes regulating cholesterol metabolism,we perform a genome-wide CRISPR/Cas9 knockout screen and find that partner of site-1 protease(POSH),encoded by C120RF49,is critically involved in the SREBP signaling.Ablation of POSH decreases the generation of nuclear SREBP and reduces the expression of SREBP target genes.POSH binds S1P,which is synthesized as an inactive protease(form A)and becomes fully mature via a two-step autocatalytic process involving forms B/B and C/C.POSH promotes the generation of the functional S1P-C/C from S1P-B/B(canonical cleavage)and,notably,from S1P-A directly(non-canonical cleavage)as well.This POSH-mediated S1P activation is also essential for the cleavages of other S1P substrates including ATF6,CREB3 family members and the a/p-subunit precursor of N-acetylglucosamine-1-phospho-transferase.Together,we demonstrate that POSH is a cofactor controlling S1P maturation and plays important roles in lipid homeostasis,unfolded protein response,lipoprotein metabolism and lysosome biogenesis.

Phylogenomics of non-model ciliates based on transcriptomic analyses

Ciliates are one of the oldest living eukaryotic unicellular organisms, widely distributed in the waters around the world. As a typical marine oligotrich ciliate, Strombidium sulcatum plays an important role in marine food webs and energy flow. Here we report the first deep se- quencing and analyses of RNA-Seq data from Strombidium sulcatum. We generated 42,640 unigenes with an N50 of 1,451 bp after de novo assembly and removing rRNA, mitochondrial and bacteria contaminants. We employed SPOCS to detect orthologs from S. sulcatum and 17 other ciliates, and then carried out the phyloge- nomic reconstruction using 127 single copy orthologs. In phylogenomic analyses, concatenated trees have similar topological structures with concordance tree on the class level. Together with phylogenetic networks analysis, it aroused more doubts about the placement of Protocruzia, Mesodinium and Myrionecta. While epi- plasmic proteins are known to be related to morphological characteristics, we found the potential relationship between gene expression of epiplasmic proteins and morphological characteristics. This work supports the use of high throughput approaches for phylogenomic analysis as well as correlation analysis between expression level of target genes and morphological characteristics.

Proteomics Profiling of Host Cell Response via Protein Expression and Phosphorylation upon Dengue Virus Infection

Dengue virus(DENV)infection is a worldwide public health threat.To date,the knowledge about the pathogenesis and progression of DENV infection is still limited.Combining global profiling based on proteomic analysis together with functional verification analysis is a powerful strategy to investigate the interplay between the virus and host cells.In the present study,quantitative proteomics has been applied to evaluate host responses(as indicated by altered proteins and modifications)in human cells(using K562 cell line)upon DENV-2 infection,as DENV-2 spreads most widely among all DENV serotypes.Comparative analysis was performed to define differentially expressed proteins in the infected cells compared to the mock-control,and it revealed critical pathogen-induced changes covering a broad spectrum of host cellular compartments and processes.We also discovered more dramatic changes(>20%,160 regulated phosphoproteins)in protein phosphorylation compared to protein expression(14%,321 regulated proteins).Most of these proteins/phosphoproteins were involved in transcription regulation,RNA splicing and processing,immune system,cellular response to stimulus,and macromolecule biosynthesis.Western blot analysis was also performed to confirm the proteomic data.Potential roles of these altered proteins were discussed.The present study provides valuable large-scale protein-related information for elucidating the functional emphasis of host cell proteins and their post-translational modifications in virus infection,and also provides insight and protein evidence for understanding the general pathogenesis and pathology of DENV.

Histone methyltransferase TXRl is required for both H3 and H3.3lysine 27 methylation in the well-known ciliated protist Tetrahymena thermophila

DNA replication elongation is tightly controlled by histone-modifying enzymes.Our previous studies showed that the histone methytransferase TXRl(Tetrahymena Trithorax related protein 1) specifically catalyzes H3K27 monomethylation and affects DNA replication elongation in Tetrahymena thermophila.In this study,we investigated whether TXRl has a substrate preference to the canonical H3 over the replacement variant H3.3.We demonstrated by histone mutagenesis that K27 Q mutation in H3.3further aggravated the replication stress phenotype of K27 Q mutation in canonical H3,supporting H3.3 as a physiologically relevant substrate of TXRl.This result is in apparent contrast to the strong preference for canonical H3 recently reported in Arabidopsis homologues ATXR5 and ATXR6,and further corroborates the role of TXRl in DNA replication.

Enterovirus 713C proteolytically processes the histone H3 N-terminal tail during infection

Dear Editor,Enterovirus 71(EV71)belongs to the genus Enterovirus,family Picornaviridae(Oberste et al.,1999).It was first isolated from patients with central nervous system diseases in California between 1969 and1974(Schmidt et al.,1974)and has spread worldwide(Solomon et al.,2010).EV71 infection usually causes mild,self-limiting hand,foot,and mouth disease in children.Acute EV71 infection may also cause severe polio-like neurological diseases and significant mortality.

Our recent progress in epigenetic research using the model ciliate, Tetrahymena thermophila

Epigenetic research focuses on heritable changes beyond the DNA sequence, which has led to a revolution in biologicalstudies and benefits in many other fields. The well-known model ciliate, Tetrahymena thermophila offers a unique system forepigenetic studies due to its nuclear dimorphism and special mode of sexual reproduction (conjugation), as well as abundantgenomic resources and genetic tools. In this paper, we summarize recent progress made by our research team and collaboratorsin understanding epigenetic mechanisms using Tetrahymena. This includes: (1) providing the first genome-wide basepair-resolution map of DNA N6-methyladenine (6mA) and revealed it as an integral part of the chromatin landscape;(2)dissecting the relative contribution of cis・ and trans- elements to nucleosome distribution by exploring the unique nucleardimorphism of Tetrahymena, (3) demonstrating the epigenetic controls of RNAi-dependent Polycomb repression pathwayson transposable elements, and (4) identifying a new histone monomethyltransferase, TXR1 (Tetrahymena Trithorax 1), thatfacilitates replication elongation through 让s substrate histone H3 lysine 27 monomethylation (H3K27mel).

Functional analysis of the methyltransferase SMYD in the single-cell model organism Tetrahymena thermophila

Lysine methylation of histones and non-histones plays a pivotal role in diverse cellular processes.The SMYD(SET and MYND domain)family methyltransferases can methylate various histone and non-histone substrates in mammalian systems,implicated in HSP90 methylation,myofilament organization,cancer inhibition,and gene transcription regulation.To resolve controversies concerning SMYD's substrates and functions,we studied SMYD1(TTHERM_00578660),the only homologue of SMYD in the unicellular eukaryote Tetrahymena thermophila.We epitope-tagged SMYD1,and analyzed its localization and interactome.We also characterized △SMYD1 cells,focusing on the replication and transcription phenotype.Our results show that:(1)SMYD1 is present in both cytoplasm and transcriptionally active macronucleus and shuttles between cytoplasm and macronucleus,suggesting its potential association with both histone and non-histone substrates;(2)SMYD1 is involved in DNA replication and regulates transcription of metabolism-related genes;(3)HSP90 is a potential substrate for SMYD1 and it may regulate target selection of HSP90,leading to pleiotropic effects in both the cytoplasm and the nucleus.