ZBTB40 is a telomere-associated protein and protects telomeres in human ALT cells.

Alternative lengthening of telomeres (ALTs) mechanism is activated in some somatic, germ cells, and human cancer cells. However, the key regulators and mechanisms of the ALT pathway remain elusive. Here we demonstrated that ZBTB40 is a novel telomere-associated protein and binds to telomeric dsDNA through its N-terminal BTB (BR-C, ttk and bab) or POZ (Pox virus and Zinc finger) domain in ALT cells. Notably, the knockout or knockdown of ZBTB40 resulted in the telomere dysfunction-induced foci and telomere lengthening in the ALT cells. The results also show that ZBTB40 is associated with ALT-associated promyelocytic leukemia nuclear bodies, and the loss of ZBTB40 induces the accumulation of the ALT-associated promyelocytic leukemia nuclear bodies in U2OS cells. Taken together, our results implicate that ZBTB40 is a key player of telomere protection and telomere lengthening regulation in human ALT cells.

Zbtb40 Deficiency Leads to Morphological and Phenotypic Abnormalities of Spermatocytes and Spermatozoa and Causes Male Infertility.

Studies on the gene regulation of spermatogenesis are of unusual significance for maintaining male reproduction and treating male infertility. Here, we have demonstrated, for the first time, that a loss of ZBTB40 function leads to abnormalities in the morphological and phenotypic characteristics of mouse spermatocytes and spermatids as well as male infertility. We revealed that Zbtb40 was expressed in spermatocytes of mouse testes, and it was co-localized with γH2AX in mouse secondary spermatocytes. Interestingly, spermatocytes of Zbtb40 knockout mice had longer telomeres, compromised double-strand break (DSB) repair in the sex chromosome, and a higher apoptosis ratio compared to wild-type (WT) mice. The testis weight, testicular volume, and cauda epididymis body weight of the Zbtb40+/- male mice were significantly lower than in WT mice. Mating tests indicated that Zbtb40+/- male mice were able to mate normally, but they failed to produce any pups. Notably, sperm of Zbtb40+/- mice showed flagellum deformities and abnormal acrosome biogenesis. Furthermore, a ZBTB40 mutation was associated with non-obstructive azoospermia. Our results implicate that ZBTB40 deficiency leads to morphological and phenotypic abnormalities of spermatocytes and spermatids and causes male infertility. This study thus offers a new genetic mechanism regulating mammalian spermatogenesis and provides a novel target for gene therapy in male infertility.

A Quick Method to Synthesize Extrachromosomal Circular DNA In Vitro.

Extrachromosomal circular DNA (eccDNA) is a special class of circular DNA in eukaryotes. Recent studies have suggested that eccDNA is the product of genomic instability and has important biological functions to regulate many downstream biological processes. While NGS (Next-Generation Sequencing)-based eccDNA sequencing has led to the identification of many eccDNAs in both healthy and diseased tissues, the specific biological functions of individual eccDNAs have yet to be clearly elucidated. Synthesizing eccDNAs longer than 1 kb with specific sequences remains a major challenge in the field, which has hindered our ability to fully understand their functions. Current methods for synthesizing eccDNAs primarily rely on chemical oligo synthesis, ligation, or the use of a specific gene editing and recombination systems. Therefore, these methods are often limited by the length of eccDNAs and are complex, expensive, as well as time-consuming. In this study, we introduce a novel method named QuickLAMA (Ligase-Assisted Minicircle Accumulation) for rapidly synthesizing eccDNAs up to 2.6 kb using a simple PCR and ligation approach. To validate the efficacy of our method, we synthesized three eccDNAs of varying lengths from cancer tissue and PC3 cells and confirmed successful circularization through sequencing and restriction enzyme digestion. Additional analyses have demonstrated that this method is highly efficient, cost-effective, and time-efficient, with good reproducibility. Using the method, a well-trained molecular biologist can synthesize and purify multiple eccDNAs within a single day, and it can be easily standardized and processed in a high-throughput manner, indicating the potential of the method to produce a wide range of desired eccDNAs and promote the translation of eccDNA research into clinical applications.

Deep convolutional neural networks using an active learning strategy for cervical cancer screening and diagnosis.

Cervical cancer (CC) is the fourth most common malignant tumor among women worldwide. Constructing a high-accuracy deep convolutional neural network (DCNN) for cervical cancer screening and diagnosis is important for the successful prevention of cervical cancer. In this work, we proposed a robust DCNN for cervical cancer screening using whole-slide images (WSI) of ThinPrep cytologic test (TCT) slides from 211 cervical cancer and 189 normal patients. We used an active learning strategy to improve the efficiency and accuracy of image labeling. The sensitivity, specificity, and accuracy of the best model were 96.21%, 98.95%, and 97.5% for CC patient identification respectively. Our results also demonstrated that the active learning strategy was superior to the traditional supervised learning strategy in cost reduction and improvement of image labeling quality. The related data and source code are freely available at https://github.com/hqyone/cancer_rcnn.

Machine Learning Prediction Model of Tuberculosis Incidence Based on Meteorological Factors and Air Pollutants.

BACKGROUND: Tuberculosis (TB) is a public health problem worldwide, and the influence of meteorological and air pollutants on the incidence of tuberculosis have been attracting interest from researchers. It is of great importance to use machine learning to build a prediction model of tuberculosis incidence influenced by meteorological and air pollutants for timely and applicable measures of both prevention and control. METHODS: The data of daily TB notifications, meteorological factors and air pollutants in Changde City, Hunan Province ranging from 2010 to 2021 were collected. Spearman rank correlation analysis was conducted to analyze the correlation between the daily TB notifications and the meteorological factors or air pollutants. Based on the correlation analysis results, machine learning methods, including support vector regression, random forest regression and a BP neural network model, were utilized to construct the incidence prediction model of tuberculosis. RMSE, MAE and MAPE were performed to evaluate the constructed model for selecting the best prediction model. RESULTS: (1) From the year 2010 to 2021, the overall incidence of tuberculosis in Changde City showed a downward trend. (2) The daily TB notifications was positively correlated with average temperature (r = 0.231), maximum temperature (r = 0.194), minimum temperature (r = 0.165), sunshine duration (r = 0.329), PM2.5 (r = 0.097), PM10 (r = 0.215) and O3 (r = 0.084) (p < 0.05). However, there was a significant negative correlation between the daily TB notifications and mean air pressure (r = -0.119), precipitation (r = -0.063), relative humidity (r = -0.084), CO (r = -0.038) and SO2 (r = -0.034) (p < 0.05). (3) The random forest regression model had the best fitting effect, while the BP neural network model exhibited the best prediction. (4) The validation set of the BP neural network model, including average daily temperature, sunshine hours and PM10, showed the lowest root mean square error, mean absolute error and mean absolute percentage error, followed by support vector regression. CONCLUSIONS: The prediction trend of the BP neural network model, including average daily temperature, sunshine hours and PM10, successfully mimics the actual incidence, and the peak incidence highly coincides with the actual aggregation time, with a high accuracy and a minimum error. Taken together, these data suggest that the BP neural network model can predict the incidence trend of tuberculosis in Changde City.

Association of BMAL1 clock gene polymorphisms with fasting glucose in children.

BACKGROUND: The brain and muscle Arnt-like protein-1 (BMAL1) gene is an important circadian clock gene and previous studies have found that certain polymorphisms are associated with type 2 diabetes in adults. However, it remains unknown if such polymorphisms can affect fasting glucose in children and if other factors modify the associations. METHODS: A school-based cross-sectional study with 947 Chinese children was conducted. A multivariable linear regression model was used to analyze the association between BMAL1 gene polymorphisms and fasting glucose level. RESULTS: After adjusting for age, sex, body mass index (BMI), physical activity, and unhealthy diet, GG genotype carriers of BMAL1 rs3789327 had higher fasting glucose than AA/GA genotype carriers (b = 0.101, SE = 0.050, P = 0.045). Adjusting for the same confounders, rs3816358 was shown to be significantly associated with fasting glucose (b = 0.060, SE = 0.028, P = 0.032). Furthermore, a significant interaction between rs3789327 and nutritional status on fasting glucose was identified (Pinteraction = 0.009); rs3789327 was associated with fasting glucose in the overweight/obese subgroup (b = 0.353, SE = 0.126, P = 0.006), but not in non-overweight/non-obese children. CONCLUSIONS: BMAL1 polymorphisms were significantly associated with the fasting glucose level in children. Additionally, the observed interaction between nutritional status and BMAL1 supports promoting an optimal BMI in children genetically predisposed to higher glucose level. IMPACT: Polymorphisms in the essential circadian clock gene BMAL1 were associated with fasting blood glucose levels in children. Additionally, there was a significant interaction between nutritional status and BMAL1 affecting fasting glucose levels. BMAL1 rs3789327 was associated with fasting glucose only in overweight/obese children. This finding could bring novel insights into mechanisms by which nutritional status influences fasting glucose in children.

[Association between regional fat mass and risk of nonalcoholic fatty liver disease in overweight/obese adults].

OBJECTIVE: To explore the relationship between fat distribution and non-alcoholic fatty liver(NAFLD) in overweight/obese adults. METHODS: This cross-sectional study included 736(190 men and 546 women) 19-56 years old overweight/obese people in Beijing were selected by convenient sampling. Their age and body mass index(BMI) distribution were 36(31-46) years old and 28.0(26.2-30.7), respectively. The body fat mass and regional fat mass were measured by dual energy X-ray absorptiometry(DXA), and Logistic regression model was used to analyze the association between regional fat mass and the risk of NAFLD. RESULTS: The prevalence of NAFLD was 70.0%(515/736) in overweight/obese population. In the multivariate Logistic model, after adjusting for age, gender, BMI, hypertension and body fat mass, waist circumference(WC), thigh fat mass and android fat mass were significantly association with NAFLD risk(P<0.05), but no association was found between arms, trunk and gynoid fat mass and NAFLD risk. There were interactions between thigh fat mass and age(P_(interaction)<0.001) and BMI group(P_(interaction)=0.001). Subgroup analysis showed that thigh fat mass and NAFLD risk were significantly associated in ≤36-year-old(OR=0.62, 95%CI 0.48-0.81), male(OR=0.32, 95%CI 0.16-0.64) and overweight(OR=0.48, 95%CI 0.36-0.64) groups, but in the >36-year-old, female and the obesity group this association was not statistically significant. There was an interaction between trunk fat mass and age group(P_(interaction)=0.009). There was a positive correlation between trunk fat mass and NAFLD risk in >36-year-old group(OR=1.63, 95%CI 1.35-1.97), but no association was found in ≤36-year-old group. In addition, we also found that a significant interaction between gynoid fat mass and BMI group on NAFLD(P_(interaction)<0.001). In overweight, gynoid fat mass was negatively correlated with the risk of NAFLD(OR=0.12, 95% CI 0.06-0.25), but in the obesity group, the association was not statistically significant. There were no statistically significant interactions between WC, arms fat mass and android mass and age, sex and BMI groups. CONCLUSION: WC, android fat mass and thigh fat mass are associated with the risk of NAFLD. Thigh fat mass has a significant interaction with age and BMI group on the risk of NAFLD(only in ≤36-year-old group, male and overweight group a significant protective effect of thigh fat on NAFLD was found, but not in >36-year-old group, female and obesity group). Trunk fat mass had an interaction with age(the association between trunk fat mass and NAFLD was significant in >36-year-old group). Gynoid fat mass and BMI group also have a significant interaction on NAFLD(the detrimental effect of gynoid fat on NAFLD is much more profound in the obesity group).

The effects of the interaction between BMI and dyslipidemia on hypertension in adults.

Body mass index (BMI) and dyslipidemia are indicators of human health and are often associated with high blood pressure. In this study,we explored the relationship between BMI or dyslipidemia and the risk of hypertension and further verified the possible interacting influences of BMI with dyslipidemia on the risk of hypertension. The aim is to explore the possible risk factors of hypertension and to provide scientific basis for the prevention and treatment of hypertension. Eligible subjects were selected from a cross-sectional survey in Changsha City, and we collected relevant data and clinical indicators for each participant. Body mass index (BMI) was calculated as weight (kg)/height2 (m2), and divided into four categories according to the Chinese standard. Dyslipidemia is defined according to Chinese guideline. Unconditional logistic regression models were used for dichotomous variables to determine the risk or protective factors of dependent variables. Multivariate Logistic model was used to study the influence of BMI and dyslipidemia on hypertension. The following indicators were used to assess the interaction effects: (1) Relative excess risk due to interaction (RERI); (2) Attributable proportion due to interaction(AP); (3) Synergy index (SI). SPSS software was used for statistical analysis. A total of 2740 eligible participants were enrolled in the cross-sectional study, of which 765 subjects (27.9%) were diagnosed with hypertension. Multivariate Logistic model showed that overweight (OR: 1.70, 95%CI: 1.39-2.09) or obese (OR: 2.60, 95%CI: 1.84-3.66) subjects had a significantly higher risk of hypertension than normal weight people, and underweight was a protective factor for hypertension(OR: 0.52, 95%CI: 0.29-0.93). People with dyslipidemia have a higher risk of hypertension than those with normal lipids (OR: 3.05, 95%CI: 2.36-3.90). In addition,there was a significant potentiating interaction effect between overweight or obesity and dyslipidemia(overweight: RERI (1.91, 95%CI: 0.17-3.66), AP (0.40, 95%CI:0.14-0.66), SI (2.03, 95%CI:1.11-3.74) and obesity: RERI (2.20, 95%CI:1.01-3.40), AP (0.38, 95%CI:0.18-0.58), SI (1.84, 95%CI:1.18-2.89), while no interaction was found between underweight and dyslipidemia. Low body weight is an independent protective factor for hypertension, but overweight, obesity and dyslipidemia are risk factors for hypertension, and dyslipidemia significantly shared interactions with overweight and obesity that influenced the risk of hypertension.

Bend family proteins mark chromatin boundaries and synergistically promote early germ cell differentiation.

Understanding the regulatory networks for germ cell fate specification is necessary to developing strategies for improving the efficiency of germ cell production in vitro. In this study, we developed a coupled screening strategy that took advantage of an arrayed bi-molecular fluorescence complementation (BiFC) platform for protein-protein interaction screens and epiblast-like cell (EpiLC)-induction assays using reporter mouse embryonic stem cells (mESCs). Investigation of candidate interaction partners of core human pluripotent factors OCT4, NANOG, KLF4 and SOX2 in EpiLC differentiation assays identified novel primordial germ cell (PGC)-inducing factors including BEN-domain (BEND/Bend) family members. Through RNA-seq, ChIP-seq, and ATAC-seq analyses, we showed that Bend5 worked together with Bend4 and helped mark chromatin boundaries to promote EpiLC induction in vitro. Our findings suggest that BEND/Bend proteins represent a new family of transcriptional modulators and chromatin boundary factors that participate in gene expression regulation during early germline development.

Prevalence and risk factors for hyperhomocysteinemia: a population-based cross-sectional study from Hunan, China.

OBJECTIVES: Hyperhomocysteinemia is an independent risk factor for cardiovascular diseases. We aimed to investigate the prevalence and risk factors for hyperhomocysteinemia, especially modifiable lifestyle factors, such as smoking behaviour and dietary factors. DESIGN: Population-based cross-sectional study. SETTING: Hunan Province, China PARTICIPANTS: A total of 4012 participants completed the study, between July 2013 and March 2014. The median age is 55 (interquartile range: 45-63) years, with 1644 males (41%) and 2368 females (59%). MAIN OUTCOME MEASURES: Homocysteine level were measured by the microplate enzyme immunoassay method. Hyperthomocysteinemia was defined as ≥15 µmol/L. Questionnaire was used to investigate potential risk factors of hyperhomocysteinemia. Crude odd ratio (OR) or adjusted OR with 95% CI were determined by using univariable or multivariable logistic regression models. RESULTS: The prevalence of hyperhomocysteinemia is 35.4% (45.4% vs 28.5% for men, women, respectively). One-year increase in age is significantly associated with 2% higher risk of hyperhomocysteinemia (OR=1.02, 95% CI: 1.01 to 1.03). One unit increase of BMI is associated with 5% higher risk of hyperhomocysteinemia (OR=1.05, 95% CI: 1.03 to 1.07). Compared with the non-smoker, smoking participants have a 24% higher risk of hyperhomocysteinemia (OR=1.24, 95% CI: 1.006 to 1.53), while the risk for those quitting smoking are not significantly different (OR=1.14, 95% CI: 0.85 to 1.54). compared with those consuming fruit and vegetable at least once every day, those consuming less than once every day had a significantly higher risk of hyperhomocysteinemia (OR=1.29, 95% CI:1.11 to 1.50). In addition, we found there were significant sex interaction with education level or alcohol drinking on the risk of hyperhomocysteinemia (pinteraction <0.05). CONCLUSIONS: Higher BMI and older age are potential risk factors for hyperhomocysteinemia. Current smoking but not quitting smoking is associated with higher risk of hyperhomocysteinemia. Fruit and vegetable consumption may have protective effect against hyperhomocysteinemia. Alcohol consumption or education level might interact to influence the risk of hyperhomocysteinemia.

Association Between Eating Speed and Metabolic Syndrome: A Systematic Review and Meta-Analysis.

Objective: This review aimed to systematically summarize and meta-analyze the association between eating speed and metabolic syndrome (MetS). Methods: Following the Preferred Reporting Items for Systematic Reviews, and Meta Analyses (PRISMA) guidelines, four electronic databases (PubMed, Web of Science, MEDLINE, and EMBASE) were searched until March 2021 to identify eligible articles based on a series of inclusion and exclusion criteria. Heterogeneity was examined using I 2 statistics. Using random-effects models, the pooled odds ratios (ORs), and 95% CIs were calculated to evaluate the association between eating speed with MetS and its components, including central obesity, blood pressure (BP), high-density lipoprotein cholesterol (HDL), triglyceride (TG), and fasting plasma glucose (FPG). Results: Of the 8,500 original hits generated by the systematic search, 29 eligible studies with moderate-to-high quality were included, involving 465,155 subjects. The meta-analysis revealed that eating faster was significantly associated with higher risks of MetS (OR = 1.54, 95% CI: 1.27-1.86), central obesity (OR = 1.54, 95% CI: 1.37-1.73), elevated BP (OR = 1.26, 95% CI: 1.13-1.40), low HDL (OR = 1.23, 95% CI: 1.15-1.31), elevated TG (OR = 1.29, 95% CI: 1.18-1.42), and elevated FPG (OR = 1.16, 95% CI: 1.06-1.27) compared to eating slowly. Conclusions: The results of the review indicated that eating speed was significantly associated with MetS and its components. Interventions related to decreasing eating speed may be beneficial for the management of MetS. Systematic Review Registration: https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42021242213, identifier: CRD42021242213.

Prevalence of Hyperhomocysteinemia in China: An Updated Meta-Analysis.

We conducted a meta-analysis to systematically assess the prevalence of hyperhomocysteinemia (HHcy) in China, its change over time, and its determinants. Literature searches were conducted using English databases (PubMed, Embase, and Web of Science) and Chinese databases (CNKI, CBM, VIP, and Wanfang). The time ranges were from Jan 2014 to Mar 2021 in China. We adopted the random effects model to estimate the pooled positive rates of HHcy and corresponding 95% confidence intervals (95% CI). To find the sources of heterogeneity, we performed subgroup analysis and meta-regression. A total of 29 related articles were identified involving 338,660 participants with 128,147 HHcy cases. The estimated prevalence of HHcy in China was 37.2% (95% CI: 32.6-41.8%, I2 = 99.8%, p for heterogeneity < 0.001). The trend of HHcy prevalence was gradually upward over time, with increases during 2015-2016 (comparison to 2013-2014, p < 0.001), but steady between 2015-2016 and 2017-2018. Subgroup analysis showed that the prevalence was higher in the elderly over 55 years old, males, and residents in the north, inland, and rural China (for each comparison, p < 0.001). Meta-regression analysis revealed that age and area of study contributed to 42.3% of the heterogeneity between studies. The current meta-analysis provides strong evidence that the prevalence of HHcy is increasing in China, and varies substantially across different ages, genders, and geographic distribution. Accordingly, high-risk population groups should be focused on, and public health policies and strategies should be carried out to prevent and control HHcy in China.

Nuclear Factor Related to KappaB Binding Protein (NFRKB) Is a Telomere-Associated Protein and Involved in Liver Cancer Development.

Alternative lengthening of telomeres (ALT) is a homologous recombination-based telomere maintenance mechanism activated in 10-15% of human cancers. Although significant progress has been made, the key regulators of the ALT pathway and its role in cancer development remain elusive. Bioinformatics methods were used to predict novel telomere-associated proteins (TAPs) by analysis of large-scale ChIP-Seq data. Immunostaining and fluorescence in situ hybridization experiments were applied to detect the subcellular location of target genes and telomeres. Western blot and reverse transcription-polymerase chain reaction (RT-PCR) were used to examine the expression of targeting genes. Overall survival (OS) analyses were used to evaluate the relationship between gene expression and survival time; immunohistochemistry was used to detect the distribution of target genes in liver cancer tissues. We found that nuclear factor related to kappaB binding protein (NFRKB), a metazoan-specific subunit of the INO80 complex, can associate with telomeres in human ALT cells. Loss of NFRKB induces dysfunction of telomeres and less PML bodies in U2OS cells. In addition, NFRKB is low/moderately expressed in cytoplasm of normal hepatocytes but heavily accumulating in the nucleus of liver cancer cells. Finally, the high expression of NFRKB is associated with short OS time and poor prognosis. NFRKB is a TAP and protects telomeres from DNA damage in ALT cells. It is highly expressed in hepatocellular carcinoma (HCC) cells and predicts a poor prognosis. NFRKB may be a promising prognostic biomarker for the treatment of HCC in the future.

ATP2B1 gene polymorphisms rs2681472 and rs17249754 are associated with susceptibility to hypertension and blood pressure levels: A systematic review and meta-analysis.

OBJECTIVE: The present study aimed to conduct a systematic review and meta-analysis to evaluate the relationships between ATP2B1 gene polymorphisms with blood pressure (BP) level and susceptibility to hypertension. METHODS: PubMed, Web of Science, Embase and China National Knowledge Infrastructure (CNKI) Databases were systematically searched by 2 independent researchers to screen studies on ATP2B1 gene polymorphisms and BP related phenotypes. The records retrieval period was limited from the formation of the database to March 4, 2021. Pooled odds rations (ORs) or ß and their 95% confidence intervals (95%CI) were calculated to assess the association between ATP2B1 gene polymorphisms and the risk of hypertension or BP levels. Publication bias and sensitivity analysis were conducted to find potential bias. All the statistical analysis were conducted with Stata version 11.0 software. RESULTS: A total of 15 articles were ultimately included in the present study, including 15 polymorphisms of ATP2B1 gene. Nine articles (N = 65,362) reported the polymorphism rs17249754, and 7 articles(N = 91,997) reported rs2681472 (both loci were reported in 1 article). Meta-analysis showed that rs17249754 (G/A) and rs2681472 (A/G) were associated with the susceptibility to hypertension (rs17249754: OR = 1.19, 95%CI: 1.10-1.28; rs2681472: OR = 1.15, 95%CI: 1.12-1.17), and were positively associated with systolic BP (SBP) and diastolic blood pressure (DBP) (rs17249754: SBP, ß=1.01, 95%CI: 0.86-1.16, DBP, ß=0.48, 95%CI: 0.30-0.66; rs2681472: SBP, ß=0.92, 95%CI: 0.77-1.07, DBP, ß=0.50, 95%CI: 0.42-0.58) in the additive genetic model. Subgroup analysis stratified by race, population, sample size, and BP measurement method revealed that the association between A allele in rs2681472 polymorphism and risk of hypertension was slightly stronger in European (EUR) populations (OR = 1.16, 95%CI: 1.13-1.20) than in East Asians (OR = 1.14, 95%CI: 1.10-1.17). While in East Asians, relation between rs17249754 with risk of hypertension (OR = 1.19, 95%CI: 1.10-1.28) is stronger than rs2681472 (OR = 1.14, 95%CI: 1.10-1.17). CONCLUSIONS: Our study demonstrated that ATP2B1 gene polymorphism rs2681472 and rs17249754 were associated with BP levels and the susceptibility to hypertension.

Integrated genomic analysis reveals regulatory pathways and dynamic landscapes of the tRNA transcriptome.

tRNAs and tRNA-derived RNA fragments (tRFs) play various roles in many cellular processes outside of protein synthesis. However, comprehensive investigations of tRNA/tRF regulation are rare. In this study, we used new algorithms to extensively analyze the publicly available data from 1332 ChIP-Seq and 42 small-RNA-Seq experiments in human cell lines and tissues to investigate the transcriptional and posttranscriptional regulatory mechanisms of tRNAs. We found that histone acetylation, cAMP, and pluripotency pathways play important roles in the regulation of the tRNA gene transcription in a cell-specific manner. Analysis of RNA-Seq data identified 950 high-confidence tRFs, and the results suggested that tRNA pools are dramatically distinct across the samples in terms of expression profiles and tRF composition. The mismatch analysis identified new potential modification sites and specific modification patterns in tRNA families. The results also show that RNA library preparation technologies have a considerable impact on tRNA profiling and need to be optimized in the future.

Extrachromosomal Circular DNA (eccDNA): From Chaos to Function.

Extrachromosomal circular DNA (eccDNA) is a type of double-stranded circular DNA that is derived and free from chromosomes. It has a strong heterogeneity in sequence, length, and origin and has been identified in both normal and cancer cells. Although many studies suggested its potential roles in various physiological and pathological procedures including aging, telomere and rDNA maintenance, drug resistance, and tumorigenesis, the functional relevance of eccDNA remains to be elucidated. Recently, due to technological advancements, accumulated evidence highlighted that eccDNA plays an important role in cancers by regulating the expression of oncogenes, chromosome accessibility, genome replication, immune response, and cellular communications. Here, we review the features, biogenesis, physiological functions, potential functions in cancer, and research methods of eccDNAs with a focus on some open problems in the field and provide a perspective on how eccDNAs evolve specific functions out of the chaos in cells.

Structural and Functional Insight Into the Glycosylation Impact Upon the HGF/c-Met Signaling Pathway.

Upon interactions with its specific ligand hepatocyte growth factor (HGF), the c-Met signal is relayed to series of downstream pathways, exerting essential biological roles. Dysregulation of the HGF-c-Met signaling pathway has been implicated in the onset, progression and metastasis of various cancers, making the HGF-c-Met axis a promising therapeutic target. Both c-Met and HGF undergo glycosylation, which appears to be biologically relevant to their function and structural integrity. Different types of glycoconjugates in the local cellular environment can also regulate HGF/c-Met signaling by distinct mechanisms. However, detailed knowledge pertaining to the glycosylation machinery of the HGF-c-Met axis as well as its potential applications in oncology research is yet to be established. This mini review highlights the significance of the HGF-c-Met signaling pathway in physiological and pathological context, and discusses the molecular mechanisms by which affect the glycosylation of the HGF-c-Met axis. Owing to the crucial role played by glycosylation in the regulation of HGF/c-Met activity, better understanding of this less exploited field may contribute to the development of novel therapeutics targeting glycoepitopes.

Hsa-miR-1908-3p Mediates the Self-Renewal and Apoptosis of Human Spermatogonial Stem Cells via Targeting KLF2.

Spermatogenesis depends on precise epigenetic and genetic regulation of spermatogonial stem cells (SSCs). However, it remains largely unknown about the roles and mechanisms of small noncoding RNA in regulating the self-renewal and apoptosis of human SSCs. Notably, we have found that Homo sapiens-microRNA (hsa-miR)-1908-3p is expressed at a higher level in human spermatogonia than pachytene spermatocytes. MiR-1908-3p stimulated cell proliferation and DNA synthesis of the human SSC line. Allophycocyanin (APC) Annexin V and propidium iodide staining, determined by flow cytometric analysis and TUNEL assays, showed that miR-1908-3p inhibited early and late apoptosis of the human SSC line. Furthermore, Kruppel-like factor 2 (KLF2) was predicted and verified as the target of miR-1908-3p, and, significantly, KLF2 silencing resulted in the increase of proliferation and DNA synthesis, as well as reduction of apoptosis of the human SSC line. Moreover, KLF2 silencing ameliorated the decrease in the proliferation and DNA synthesis and the enhancement in the apoptosis of the human SSC line caused by miR-1908-3p inhibition. Collectively, these results implicate that miR-1908-3p stimulates the self-renewal and suppresses the apoptosis of human SSCs by targeting KLF2. This study thus provides a novel epigenetic regulatory mechanism underlying the fate determinations of human SSCs, and it offers new endogenous targets for treating male infertility.

BCREval: a computational method to estimate the bisulfite conversion ratio in WGBS.

BACKGROUND: Whole genome bisulfite sequencing (WGBS) also known as BS-seq has been widely used to measure the methylation of whole genome at single-base resolution. One of the key steps in the assay is converting unmethylated cytosines into thymines (BS conversion). Incomplete conversion of unmethylated cytosines can introduce false positive methylation call. Developing a quick method to evaluate bisulfite conversion ratio (BCR) is benefit for both quality control and data analysis of WGBS. RESULTS: Here we provide a computational method named "BCREval" to estimate the unconverted rate (UCR) by using telomeric repetitive DNA as native spike-in control. We tested the method by using public WGBS data and found that it is very stable and most of BS conversion assays can achieve> 99.5% efficiency. The non-CpG DNA methylation at telomere fits a binomial model and may result from a random process with very low possibility (the ratio < 0.4%). And the comparison between BCREval and Bismark (Krueger and Andrews, Bioinformatics 27:1571-1572, 2011), a widely used BCR evaluator, suggests that our algorithm is much faster and more efficient than the latter. CONCLUSION: Our method is a simple but robust method to QC and speculates BCR for WGBS experiments to make sure it achieves acceptable level. It is faster and more efficient than current tools and can be easily integrated into presented WGBS pipelines.

The roles and mechanisms of Leydig cells and myoid cells in regulating spermatogenesis.

Spermatogenesis is fundamental to the establishment and maintenance of male reproduction, whereas its abnormality results in male infertility. Somatic cells, including Leydig cells, myoid cells, and Sertoli cells, constitute the microenvironment or the niche of testis, which is essential for regulating normal spermatogenesis. Leydig cells are an important component of the testicular stroma, while peritubular myoid cells are one of the major cell types of seminiferous tubules. Here we addressed the roles and mechanisms of Leydig cells and myoid cells in the regulation of spermatogenesis. Specifically, we summarized the biological features of Leydig cells and peritubular myoid cells, and we introduced the process of testosterone production and its major regulation. We also discussed other hormones, cytokines, growth factors, transcription factors and receptors associated with Leydig cells and myoid cells in mediating spermatogenesis. Furthermore, we highlighted the issues that are worthy of further studies in the regulation of spermatogenesis by Leydig cells and peritubular myoid cells. This review would provide novel insights into molecular mechanisms of the somatic cells in controlling spermatogenesis, and it could offer new targets for developing therapeutic approaches of male infertility.