C and G are frequently mutated into T and A in coding regions of human genes.

Nucleotide mutations in human genes have long been a hot subject for study because some of them may lead to severe human diseases. Understanding the general mutational process and evolutionary trend of human genes could help answer such questions as why certain diseases occur and what challenges we face in protecting human health. In this study, we conducted statistics on 89,895 single-nucleotide variations identified in coding regions of 18,339 human genes. The results show that C and G are frequently mutated into T and A in human genes. C/G (C or G)-to-T/A mutations lead to reduction of hydrogen bonds in double-stranded DNA because C-G and T-A base pairs are maintained by three and two hydrogen bonds respectively. C-to-T and G-to-A mutations occur predominantly in human genes because they not only reduce hydrogen bonds but also belong to transition mutation. Reduction of hydrogen bonds could reduce energy consumption not only in separating double strands of mutated DNA for transcription and replication but also in disrupting stem-loop structure of mutated mRNA for translation. It is thus considered that to reduce hydrogen bonds (and thus to reduce energy consumption in gene expression) is one of the driving forces for nucleotide mutation. Moreover, codon mutation is positively correlated to its content, suggesting that most mutations are not targeted on changing any specific codons (amino acids) but are merely for reducing hydrogen bonds. Our study provides an example of utilizing single-nucleotide variation data to infer evolutionary trend of human genes, which can be referenced to conduct similar studies in other organisms.

Growth, development, and host preference of Histiostoma feroniarum (Acaridida: Histiostomatidae): effects of temperature and types of mushroom cultivar.

One of the most common harmful mites in edible fungi is Histiostoma feroniarum Dufour (Acaridida: Histiostomatidae), a fungivorous astigmatid mite that feeds on hyphae and fruiting bodies, thereby transmitting pathogens. This study examined the effects of seven constant temperatures and 10 types of mushrooms on the growth and development of H. feroniarum, as well as its host preference. Developmental time for the total immature stages was significantly affected by the type of mushroom species, ranging from 4.3 ± 0.4 days (reared on Pleurotus eryngii var. tuoliensis Mou at 28°C) to 17.1 ± 2.3 days (reared on Auricularia polytricha Sacc. at 19°C). The temperature was a major factor in the formation of facultative heteromorphic deutonymphs (hypopi). The mite entered the hypopus stage when the temperature dropped to 16°C or rose above 31°C. The growth and development of this mite were significantly influenced by the type of species and variety of mushrooms. Moreover, the fungivorous astigmatid mite preferred to feed on the 'Wuxiang No. 1' strain of Lentinula edodes (Berk.) Pegler and the 'Gaowenxiu' strain of P. pulmonarius (Fr.) Quél., with a shorter development period compared with that of feeding on other strains. These results therefore quantify the effect of host type and temperature on fungivorous astigmatid mite growth and development rates, and provide a reference for applying mushroom cultivar resistance to biological pest control.

Identification and Validation of Common Reference Genes for Normalization of Esophageal Squamous Cell Carcinoma Gene Expression Profiles.

Esophageal squamous cell carcinoma (ESCC) is one of the subtypes of esophageal cancer with Chinese characteristics, and its five-year survival rate is less than 20%. Early diagnosis is beneficial to improving the survival rate of ESCC significantly. Quantitative Real-Time Polymerase Chain Reaction is a high-throughput technique that can quantify tumor-related genes for early diagnosis. Its accuracy largely depends on the stability of the reference gene. There is no systematic scientific basis to demonstrate which reference gene expression is stable in ESCC and no consensus on the selection of internal reference. Therefore, this research used four software programs (The comparative delta-Ct method, GeNorm, NormFinder, and BestKeeper) to evaluate the expression stability of eight candidate reference genes commonly used in other tumor tissues and generated a comprehensive analysis by RefFinder. Randomly selected transcriptome sequencing analysis confirmed the SPP1 gene is closely related to ESCC. It was found that the expression trend of SPP1 obtained by RPS18 and PPIA as internal reference genes were the same as that of sequencing. The results show that RPS18 and PPIA are stable reference genes, and PPIA + RPS18 are a suitable reference gene combination. This is a reference gene report that combines transcriptome sequencing analysis and only focuses on ESCC, which makes the quantification more precise, systematic, and standardized, and promotes gene regulation research and the early diagnosis of ESCC in the future.

Heterogeneity of immune control in chronic hepatitis B virus infection: Clinical implications on immunity with interferon-α treatment and retreatment.

Hepatitis B virus (HBV) infection is a global public health issue. Interferon-α (IFN-α) treatment has been used to treat hepatitis B for over 20 years, but fewer than 5% of Asians receiving IFN-α treatment achieve functional cure. Thus, IFN-α retreatment has been introduced to enhance antiviral function. In recent years, immune-related studies have found that the complex interactions between immune cells and cytokines could modulate immune response networks, in-cluding both innate and adaptive immunity, triggering immune responses that control HBV replication. However, heterogeneity of the immune system to control HBV infection, particularly HBV-specific CD8+ T cell heterogeneity, has consequ-ential effects on T cell-based immunotherapy for treating HBV infection. Altogether, the host's genetic variants, negative-feedback regulators and HBV components affecting the immune system's ability to control HBV. In this study, we reviewed the literature on potential immune mechanisms affecting the immune control of HBV and the clinical effects of IFN-α treatment and retreatment.

Metabolomics of Esophageal Squamous Cell Carcinoma Tissues: Potential Biomarkers for Diagnosis and Promising Targets for Therapy.

Background: The incidence of esophageal squamous cell carcinoma in China ranks first in the world. The early diagnosis technology is underdeveloped, and the prognosis is poor, which seriously threatens the quality of life of the Chinese people. Epidemiological findings are related to factors such as diet, living habits, and age. The specific mechanism is not clear yet. Metabolomics is a kind of omics that simultaneously and quantitatively analyzes the comprehensive profile of metabolites in living systems. It has unique advantages in the study of the diagnosis and pathogenesis of tumor-related diseases, especially in the search for biomarkers. Therefore, it is desirable to perform metabolic profiling analysis of cancer tissues through metabolomics to find potential biomarkers for the diagnosis and treatment of esophageal squamous cell carcinoma. Methods: HPLC-TOF-MS/MS technology and Illumina Hiseq Xten Sequencing was used for the analysis of 210 pairs of matched esophageal squamous cell carcinoma tissues and normal tissues in Zhenjiang City, Jiangsu Province, a high-incidence area of esophageal cancer in China. Bioinformatics analysis was also performed. Results: Through metabolomic and transcriptomic analysis, this study found that a total of 269 differential metabolites were obtained in esophageal squamous cell carcinoma and normal tissues, and 48 differential metabolic pathways were obtained through KEGG enrichment analysis. After further screening and identification, 12 metabolites with potential biomarkers to differentiate esophageal squamous cell carcinoma from normal tissues were obtained. Conclusions: From the metabolomic data, 4 unknown compounds were found to be abnormally expressed in esophageal squamous cell carcinoma for the first time, such as 9,10-epoxy-12,15-octadecadienoate; 3 metabolites were found in multiple abnormal expression in another tumor, but upregulation or downregulation was found for the first time in esophageal cancer, such as oleoyl glycine; at the same time, it was further confirmed that five metabolites were abnormally expressed in esophageal squamous cell carcinoma, which was similar to the results of other studies, such as PE.

Association of time-varying changes in physical activity with cardiac death and all-cause mortality after ICD or CRT-D implantation.

OBJECTIVE: To evaluate the association of longitudinal changes in physical activity (PA) with long-term outcomes after implantable cardioverter-defibrillator (ICD) or cardiac resynchronization therapy defibrillator (CRT-D) implantation. METHODS: Patients with ICD/CRT-D implantation from SUMMIT registry were retrospectively analyzed. Accelerometer-derived PA changes over 12 months post implantation were obtained from the archived home monitoring data. The primary endpoints were cardiac death and all-cause mortality. The secondary endpoints were the first ventricular arrthymia (VA) and first appropriate ICD shock. RESULTS: In 705 patients, 446 (63.3%) patients showed improved PA over 12 months after implantation. During a mean 61.5-month follow-up duration, 99 cardiac deaths (14.0%) and 153 all-cause deaths (21.7%) occurred. Compared to reduced/unchanged PA, improved PA over 12 months could result in significantly reduced risks of cardiac death (improved PA ≤ 30 min: hazard ratio (HR) = 0.494, 95% CI: 0.288-0.848; > 30 min: HR = 0.390, 95% CI: 0.235-0.648) and all-cause mortality (improved PA ≤ 30 min: HR = 0.467, 95%CI: 0.299-0.728; > 30 min: HR = 0.451, 95% CI: 0.304-0.669). No differences in the VAs or ICD shocks were observed across different groups of PA changes. PA changes can predict the risks of cardiac death only in the low baseline PA group, but improved PA was associated with 56.7%, 57.4%, and 62.3% reduced risks of all-cause mortality in the low, moderate, and high baseline PA groups, respectively, than reduced/unchanged PA. CONCLUSIONS: Improved PA could protect aganist cardiac death and all-cause mortality, probably reflecting better clinical efficacy after ICD/CRT-D implantation. Low-intensity exercise training might be encouraged among patients with different baseline PA levels.

An Intron of Invertebrate Microphthalmia Transcription Factor Gene Is Evolved from a Longer Ancestral Sequence.

Introns are highly variable in number and size. Sequence simulation is an effective method to elucidate intron evolution patterns. Previously, we have reported that introns are more likely to evolve through mutation-and-deletion (MD) rather than through mutation-and-insertion (MI). In the present study, we further studied evolution models by allowing insertion in the MD model and by allowing deletion in the MI model at various frequencies. It was found that all deletion-biased models with proper parameter settings could generate sequences with attributes matchable to 16 invertebrate introns from the microphthalmia transcription factor gene, whereas all insertion-biased models with any parameter settings failed to generate such sequences. We conclude that the examined invertebrate introns may have evolved from a longer ancestral sequence in a deletion-biased pattern. The constructed models are useful for studying the evolution of introns from other genes and/or from other taxonomic groups. (C++ scripts of all deletion- and insertion-biased models are available upon request.).

Status of diagnosis and treatment of esophageal cancer and non-coding RNA correlation research: a narrative review.

OBJECTIVE: To describe and discuss the progression of the non-coding RNA as biomarkers in early esophageal cancer. BACKGROUND: Esophageal cancer without obvious symptoms during early stages is one of the most common cancers, the current clinical treatments offer possibilities of a cure, but the survival rates and the prognoses remain poor, it is a serious threat to human life and health. Most patients are usually diagnosed during terminal stages due to low sensitivity of esophageal cancer's early detection techniques. With the development of molecular biology, an increasing number of non-coding RNAs are found to be associated with the occurrence, development, and prognosis of esophageal cancer. Some of these have begun to be used in clinics and laboratories for diagnosis, treatment, and prognosis, with the goal of reducing mortality. METHODS: The information for this paper was collected from a variety of sources, including a search of the keynote's references, a search for texts in college libraries, and discussions with experts in the field of esophageal cancer clinical treatment. CONCLUSIONS: Non-coding RNA does play a regulatory role in the development of esophageal cancer, which can predict the occurrence or prognosis of tumors, and become a new class of tumor markers and therapeutic targets in clinical applications. In this review, we survey the recent developments in the incidence, diagnosis, and treatment of esophageal cancer, especially with new research progresses on non-coding RNA biomarkers in detail, and discuss its potential clinical applications.

Genome-wide identification and characterization of long non-coding RNAs in Tribolium castaneum.

Long non-coding RNAs (lncRNAs) are poorly understood in insects. In this study, we performed genome-wide analysis of lncRNAs in Tribolium castaneum by RNA-seq. In total, 4516 lncRNA transcripts corresponding to 3917 genes were identified from late embryos, early larvae, late larvae, early pupae, late pupae and early adults of T. castaneum, including 3152 novel lncRNAs and 1364 known lncRNAs. These lncRNAs have few exons and transcripts, and are short in length. During development, they exhibited nine different expression patterns. Functionally, they can act either by targeting messenger RNAs (1813 lncRNAs) and lncRNAs (45 lncRNAs) or as micro RNA (miRNA) precursors (46 lncRNAs). LncRNAs were observed to target the metabolic enzymes of glycolysis, TCA cycle and amino acids, demonstrating that lncRNAs control metabolism by regulating metabolic enzymes. Moreover, lncRNAs were shown to participate in cell differentiation and development via their targets. As miRNA precursors, lncRNAs could participate in the ecdysone signaling pathway. This study provides comprehensive information for lncRNAs of T. castaneum, and will promote functional analysis and target identification of lncRNAs in the insect.

Plasma big endothelin-1 is an effective predictor for ventricular arrythmias and end-stage events in primary prevention implantable cardioverter- defibrillator indication patients.

OBJECTIVE: To investigate whether plasma big endothelin-1 (ET-1) predicts ventricular arrythmias (VAs) and end-stage events in primary prevention implantable cardioverter-defibrillator (ICD) indication patigents. METHODS: In total, 207 patients fulfilling the inclusion criteria from Fuwai Hospital between January 2013 and December 2015 were retrospectively analyzed. The cohort was divided into three groups according to baseline plasma big ET-1 tertiles: tertile 1 (< 0.38 pmol/L, n = 68), tertile 2 (0.38-0.7 pmol/L, n = 69), and tertile 3 (> 0.7 pmol/L, n = 70). The primary endpoints were VAs. The secondary endpoints were end-stage events comprising all-cause mortality and heart transplantation. RESULTS: During a mean follow-up period of 25.6 ± 13.9 months, 38 (18.4%) VAs and 78 (37.7%) end-stage events occurred. Big ET-1 was positively correlated with NYHA class (r = 0.165, P = 0.018), serum creatinine concentration (Scr; r = 0.147, P = 0.034), high-sensitivity C-reactive protein (hs-CRP; r = 0.217, P = 0.002), Lg NT-pro BNP (r = 0.463, P < 0.001), left ventricular end diastolic diameter (LVEDD; r = 0.234, P = 0.039) and negatively correlated with left ventricular ejection fraction (LVEF; r = -0.181, P = 0.032). Kaplan-Meier analysis showed that elevated big ET-1 was associated with increased risk of VAs and end-stage events (P < 0.05). In multivariate Cox regression models, big ET-1 was an independent risk factor for VAs (hazard ratio (HR) = 3.477, 95% confidence interval (CI): 1.352-8.940, P = 0.010, tertile 2 vs. tertile 1; HR = 4.112, 95% CI: 1.604-10.540, P = 0.003, tertile 3 vs. tertile 1) and end-stage events (HR = 2.804, 95% CI: 1.354-5.806, P = 0.005, tertile 2 vs. tertile 1; HR = 4.652, 95% CI: 2.288-9.459, P < 0.001, tertile 3 vs. tertile 1). CONCLUSIONS: In primary prevention ICD indication patients, plasma big ET-1 levels can predict VAs and end-stage events and may facilitate ICD-implantation risk stratification.

Human SARS-CoV-2 has evolved to reduce CG dinucleotide in its open reading frames.

The outbreak of COVID-19 has brought great threat to human health. Its causative agent is a severe acute respiratory syndrome-related coronavirus which has been officially named SARS-CoV-2. Here we report the discovery of extremely low CG abundance in its open reading frames. We found that CG reduction in SARS-CoV-2 is achieved mainly through mutating C/G into A/T, and CG is the best target for mutation. Meanwhile, 5'-untranslated region of SARS-CoV-2 has high CG content and is capable of forming an internal ribosome entry site (IRES) to recruit host ribosome for translating its RNA. These features allow SARS-CoV-2 to reproduce efficiently in host cells, because less energy is consumed in disrupting the stem-loops formed by its genomic RNA. Notably, genomes of cellular organisms also have very low CG abundance, suggesting that mutating C/G into A/T occurs universally in all life forms. Moreover, CG is the dinucleotide related to CpG island, mutational hotspot and single nucleotide polymorphism in cellular organisms. The relationship between these features is worthy of further investigations.

Simulation of Chordate Intron Evolution Using Randomly Generated and Mutated Base Sequences.

Introns are well known for their high variation not only in length but also in base sequence. The evolution of intron sequences has aroused broad interest in the past decades. However, very little is known about the evolutionary pattern of introns due to the lack of efficient analytical method. In this study, we designed 2 evolutionary models, that is, mutation-and-deletion (MD) and mutation-and-insertion (MI), to simulate intron evolution using randomly generated and mutated bases by referencing to the phylogenetic tree constructed using 14 chordate introns from TF4 (transcription factor-like protein 4) gene. A comparison of attributes between model-generated sequences and chordate introns showed that the MD model with proper parameter settings could generate sequences that have attributes matchable to chordate introns, whereas the MI model with any parameter settings failed in doing so. These data suggest that the surveyed chordate introns have evolved from a long ancestral sequence through gradual reduction in length. The established methodology provides an effective measure to study the evolutionary pattern of intron sequences from organisms of various taxonomic groups. (C++ scripts of MD and MI models are available upon request.).

Phylogenetic analysis of achaete-scute complex genes in metazoans.

Achaete-scute complex (ASC) genes play essential roles in regulating neurogenesis of metazoans. Various metazoan species have greatly different numbers of genes in ASCa, ASCb and ASCc families. To explore evolutionary mechanisms of metazoan ASC genes, Blast (basic local alignment search tool) searches and phylogenetic analyses were conducted to identify ASC genes in metazoan species and to infer phylogenetic relationship between various ASC genes. As a result, 2784 ASC genes were identified in 804 metazoan species. The phylogenetic tree constructed using 1237 unique bHLH motifs shows that metazoan ASCa, ASCb and ASCc families contain six (a1-a6), five (b1-b5) and three (c1-c3) bHLH genes, respectively. Further phylogenetic analyses suggest that ASC genes in metazoans are derived from a primitive c gene, those in insects are derived from c2 gene, and those in chordates are derived from a2 and a3 genes. Data of gene linkage demonstrate that insect a6 is derived from a4 but not from a5, and chordate a2 is ancestral to b5 only, whilst a3 is ancestral to both b3 and b5. It is concluded that current ASC gene families in metazoans were established through a series of sub- and/or neo-functionalization to duplicated ancestral ASC gene(s). These results provide good references for exploring evolutionary mechanisms of other bHLH genes in metazoans. Besides, gene subtyping is considered as an efficient method for evolutionary studies on closely related homologous genes.

Heart rate-adjusted PR as a prognostic marker of long-term ventricular arrhythmias and cardiac death in ICD/CRT-D recipients.

OBJECTIVE: To evaluate the PR to RR interval ratio (PR/RR, heart rate-adjusted PR) as a prognostic marker for long-term ventricular arrhythmias and cardiac death in patients with implantable cardioverter defibrillator (ICDs) and cardiac resynchronization therapy with defibrillators (CRT-D). METHODS: We retrospectively analyzed data from 428 patients who had an ICD/CRT-D equipped with home monitoring. Baseline PR and RR interval data prior to ICD/CRT-D implantation were collected from standard 12-lead electrocardiograph, and the PR/RR was calculated. The primary endpoint was appropriate ICD/CRT-D treatment of ventricular arrhythmias (VAs), and the secondary endpoint was cardiac death. RESULTS: During a mean follow-up period of 38.8 ± 10.6 months, 197 patients (46%) experienced VAs, and 47 patients (11%) experienced cardiac death. The overall PR interval was 160 ± 40 ms, and the RR interval was 866 ± 124 ms. Based on the receiver operating characteristic curve, a cut-off value of 18.5% for the PR/RR was identified to predict VAs. A PR/RR ≥ 18.5% was associated with an increased risk of VAs [hazard ratio (HR) = 2.243, 95% confidence interval (CI) = 1.665-3.022, P < 0.001) and cardiac death (HR = 2.358, 95%CI = 1.240-4.483, P = 0.009) in an unadjusted analysis. After adjustment in a multivariate Cox model, the relationship remained significant among PR/RR ≥ 18.5%, VAs (HR = 2.230, 95%CI = 1.555-2.825, P < 0.001) and cardiac death (HR = 2.105, 95%CI = 1.101-4.025, P = 0.024. CONCLUSIONS: A PR/RR ≥ 18.5% at baseline can serve as a predictor of future VAs and cardiac death in ICD/CRT-D recipients.

TA, GT and AC are significantly under-represented in open reading frames of prokaryotic and eukaryotic protein-coding genes.

Genomes can be considered a combination of 16 dinucleotides. Analysing the relative abundance of different dinucleotides may reveal important features of genome evolution. In present study, we conducted extensive surveys on the relative abundances of dinucleotides in various genomic components of 28 bacterial, 20 archaean, 19 fungal, 24 plant and 29 animal species. We found that TA, GT and AC are significantly under-represented in open reading frames of all organisms and in intergenic regions and introns of most organisms. Specific dinucleotides are of greatly varied usage at different codon positions. The significantly low representations of TA, GT and AC are considered the evolutionary consequences of preventing formation of pre-mature stop codons and of reducing intron-splicing options in candidate primary mRNA sequences. These data suggest that a reduction of TA and GT occurred on both strands of the DNA sequence at an early stage of de novo gene birth. Interestingly, GT and AC are also significantly under-represented in current prokaryotic genomes, suggesting that ancient prokaryotic protein-coding genes might have contained introns. The greatly varied usages of specific dinucleotides at different codon positions are considered evolutionary accommodations to compensate the unavailability of specific codons and to avoid formation of pre-mature stop codons. This is the first report presenting data of dinucleotide relative abundance to indicate the possible existence of spliceosomal introns in ancient prokaryotic genes and to hypothesize early steps of de novo gene birth.

Identification and Phylogenetic Analysis of Basic Helix-Loop-Helix Genes in the Diamondback Moth.

Basic helix-loop-helix (bHLH) transcription factors play essential roles in regulating eukaryotic developmental and physiological processes such as neuron generation, myocyte formation, intestinal tissue development, and response to environmental stress. In this study, the diamondback moth, Plutella xylostella (L.) (Lepidoptera: Plutellidae), genome was found to encode 52 bHLH genes. All 52 P. xylostella bHLH (PxbHLH) genes were classified into correspondent bHLH families according to their orthology with bHLHs from fruit fly and other insect species. Among these 52 PxbHLH genes, 19 have been annotated consistently with our classification in GenBank database. The remaining 33 PxbHLH genes are either annotated as general bHLH genes or as hypothetical genes. Therefore, our data provide useful information for updating annotations to PxbHLH genes. P. xylostella has four stem cell leukemia (SCL) genes (one of them has three copies), two Dys genes, two copies of MyoR, Mitf, and Sima genes, and three copies of Sage genes. Further studies may be conducted to elucidate functions of these specific bHLH genes in regulating P. xylostella growth and development.

The gender difference of utilization of cardiac implantable electronic device in China: data from Arrhythmia Interventional Therapy Data Registry.

BACKGROUND: Cardiac implantable electronic devices (CIEDs) greatly improve survival and life quality of patients. However, there are gender differences regarding both the utilization and benefit of these devices. In this prospective CIED registry, we aim to appraise the gender differences in CIED utilization in China. METHODS: Twenty centers from 14 provinces in China were included in our registry study. All patients who underwent a CIED implantation in these twenty centers between Jan 2015 and Dec 2016 were included. RESULTS: A total of 8570 patients were enrolled in the baseline cohort, including 7203 pacemaker, 664 implantable cardiac defibrillators (ICD) implants and 703 cardiac resynchronization therapy device (CRT/D). Totally, 4117 (48.0%) CIED patients were female, and more than 59% pacemaker patients were female, but women account only one third of ICD or CRT/D implantation in this registry. There were significant differences between genders at pacemaker and ICD indications. Female was more likely received a pacemaker due to sick sinus syndrome (SSS) (63.9% vs. 51.0%, P < 0.001). Female patients receiving an ICD were more likely due to cardiac ion channel disease (29.2% vs. 4.2%, P < 0.001). The percentage of utilization of dual-chamber pacemaker in female patients was significantly higher than male (85.3% vs. 81.1%, P < 0.001). But male patients were more likely received a cardiac resynchronization therapy devices with defibrillator than female (56.5% vs. 41.9%, P = 0.001). In pacemaker patient, male was more likely to have structure heart disease (31.3% vs. 28.0%, P = 0.002). In ICD patient, male patients were more likely to have ischemic heart disease (48.2% vs. 29.2%, P < 0.001). The mean age of women at the time of CRT/D implantation was older than men (P = 0.014). Nonischemic cardiomyopathy (70.9%) was the most common etiology in the patients who underwent the treatment of CRT/D, no matter male or female. CONCLUSIONS: In real-world setting, female do have different epidemiology, pathophysiology and clinical presentation of many cardiac rhythm disorders when compared with male, and all these factors may affect the utilization of CIED implantation. But it also possibility that cultural and socioeconomic features may play a role in this apparent discrimination.

The Emerging Role of Circular RNAs in Hepatocellular Carcinoma.

Hepatocellular carcinoma (HCC) ranks the third leading cause of cancer death in the world and has a notably low survival rate. Circular RNAs (circRNAs) are newly classed non-coding RNA (ncRNA) members that are capable of regulating gene expression at transcription or post-transcription levels. Recent studies demonstrate that some circRNAs are differentially expressed in HCC, and the deregulation of these circRNAs is associated with the clinical pathological and prognostic significance. They also play essential roles in HCC progression, and contribute to cell proliferation, migration, invasion and metastasis by targeting different microRNAs (miRNAs) and protein-coding genes. In this review, we concentrate on recent progress of some important circRNAs in HCC, with an emphasis on their deregulation, functions and regulatory mechanisms, and discuss their potential utility as diagnostic and/or prognostic biomarkers or therapeutic targets for HCC.

Current Bacterial Gene Encoding Capsule Biosynthesis Protein CapI Contains Nucleotides Derived from Exonization.

Since the proposition of introns-early hypothesis, although many studies have shown that most eukaryotic ancestors possessed intron-rich genomes, evidence of intron existence in genomes of ancestral bacteria has still been absent. While not a single intron has been found in all protein-coding genes of current bacteria, analyses on bacterial genes horizontally transferred into eukaryotes at ancient time may provide evidence of intron existence in bacterial ancestors. In this study, a bacterial gene encoding capsule biosynthesis protein CapI was found in the genome of sea anemone, Nematostella vectensis. This horizontally transferred gene contains a phase 1 intron of 40 base pairs. The nucleotides of this intron have high sequence identity with those encoding amino acids in current bacterial CapI gene, indicating that the intron and the amino acid-coding nucleotides are originated from the same ancestor sequence. Moreover, 5'-splice site of this intron is located in a GT-poor region associated with a closely following AG-rich region, suggesting that deletion mutation at 5'-splice site has been employed to remove this intron and the intron-like amino acid-coding nucleotides in current bacterial CapI gene are derived from exonization. These data suggest that bacterial CapI gene contained intron(s) at ancient time. This is the first report providing the result of sequence analysis to suggest possible existence of spliceosomal introns in ancestral bacterial genes. The methodology employed in this study may be used to identify more such evidence that would aid in settlement of the dispute between introns-early and introns-late theories.