Allele-specific RNA N 6-methyladenosine modifications reveal functional genetic variants in human tissues.

An intricate network of cis- and trans-elements acts on RNA N 6-methyladenosine (m6A), which in turn may affect gene expression and, ultimately, human health. A complete understanding of this network requires new approaches to accurately measure the subtle m6A differences arising from genetic variants, many of which have been associated with common diseases. To address this gap, we developed a method to accurately and sensitively detect transcriptome-wide allele-specific m6A (ASm6A) from MeRIP-seq data and applied it to uncover 12,056 high-confidence ASm6A modifications from 25 human tissues. We also identified 1184 putative functional variants for ASm6A regulation, a subset of which we experimentally validated. Importantly, we found that many of these ASm6A-associated genetic variants were enriched for common disease-associated and complex trait-associated risk loci, and verified that two disease risk variants can change m6A modification status. Together, this work provides a tool to detangle the dynamic network of RNA modifications at the allelic level and highlights the interplay of m6A and genetics in human health and disease.

Distinct roles of two myosins in C. elegans spermatid differentiation.

During spermatogenesis, interconnected haploid spermatids segregate undesired cellular contents into residual bodies (RBs) before detaching from RBs. It is unclear how this differentiation process is controlled to produce individual spermatids or motile spermatozoa. Here, we developed a live imaging system to visualize and investigate this process in C. elegans. We found that non-muscle myosin 2 (NMY-2)/myosin II drives incomplete cytokinesis to generate connected haploid spermatids, which are then polarized to segregate undesired cellular contents into RBs under the control of myosin II and myosin VI. NMY-2/myosin II extends from the pseudo-cleavage furrow formed between two haploid spermatids to the spermatid poles, thus promoting RB expansion. In the meantime, defective spermatogenesis 15 (SPE-15)/myosin VI migrates from spermatids towards the expanding RB to promote spermatid budding. Loss of myosin II or myosin VI causes distinct cytoplasm segregation defects, while loss of both myosins completely blocks RB formation. We found that the final separation of spermatids from RBs is achieved through myosin VI-mediated cytokinesis, while myosin II is dispensable at this step. SPE-15/myosin VI and F-actin form a detergent-resistant actomyosin VI ring that undergoes continuous contraction to promote membrane constriction between spermatid and RB. We further identified that RGS-GAIP-interacting protein C terminus (GIPC)-1 and GIPC-2 cooperate with myosin VI to regulate contractile ring formation and spermatid release. Our study reveals distinct roles of myosin II and myosin VI in spermatid differentiation and uncovers a novel myosin VI-mediated cytokinesis process that controls spermatid release.

Diagnosis, treatment and genetic analysis of a case of hypoglycemia caused by glucokinase gene mutation.

Congenital hyperinsulinemia (CHI) is a disease phenotype characterized by persistent or recurrent hypoglycemia due to abnormal secretion of insulin by ß cells of the pancreas. CHI induced by activation mutation of a single allele of glucokinase (GCK) is the rarest type. In this paper, the clinical data of a patient with hypoglycemia of unknown cause were collected without obvious clinical symptoms. And a heterozygous missense mutation (c.295T> C:p.W99R) was detected in exon 3 of the GCK gene. The mutation was found in both the son and daughter of the proband, and the blood glucose level was low, while the others were normal. By summarizing and analyzing the characteristics of this case and the genetic pedigree of the family, the possibility of congenital hyperinsulinemia caused by a single gene mutation should be considered for hypoglycemia whose etiology is difficult to be determined clinically. This case also provides new clinical data for subsequent genetic studies of the disease.

Association between ADAMTS7 TagSNPs and the risk of myocardialinfarction.

PURPOSE OF THE STUDY: Genome-wide association studies have revealed an association of ADAMTS7 polymorphisms with the risk of cardiovascular diseases. Nonetheless, the role of ADAMTS7 polymorphisms on myocardial infarction (MI) risk remains poorly understood. Here, we aim to evaluate the effect of ADAMTS7 tag single nucleotide polymorphisms (SNPs) on individual susceptibility to MI. STUDY DESIGN: Genotyping of the four tagSNPs (rs1994016, rs3825807, rs4380028 and rs7173743) was performed in 232 MI cases and 661 control subjects using PCR-ligase detection reaction (LDR) method. The association of these four tagSNPs with MI risk was performed with SPSS software. RESULTS: Multivariate logistic regression analysis showed that ADAMTS7 tagSNP rs3825807 exhibited a significant effect on MI risk. Compared with the TT homozygotes, the CT genotype (OR1.93, 95% CI1.30to 2.85, Pc=0.004) and the combined CC/CT genotypes (OR1.70, 95% CI1.16 to 2.50, Pc=0.028) were statistically significantly associated with the increased risk for MI. Further stratified analysis revealed a more significant association with MI risk among older subjects, hypertensives, non-diabetics and patients with hyperlipidaemia. Consistently, the haplotype rs1994016T-rs3825807C containing rs3825807 C allele exhibited increased MI risk (OR1.52, 95% CI1.10 to 2.10, p=0.010). However, we did not detect any association of the other three tagSNPs with MI risk. CONCLUSIONS: Our finding suggest that ADAMTS7 tagSNP rs3825807 contributes to MI susceptibility in the Chinese Han population. Further studies are necessary to confirm the general validity of our findings and to clarify the underlying mechanism for this association.

Gcn5 determines the fate of Drosophila germline stem cells through degradation of Cyclin A.

The fluctuating CDK-CYCLIN complex plays a general role in cell-cycle control. Many types of stem cells use unique features of the cell cycle to facilitate asymmetric division. However, the manner in which these features are established remains poorly understood. The cell cycle of Drosophila female germline stem cells (GSCs) is characterized by short G1 and very long G2 phases, making it an excellent model for the study of cell cycle control in stem cell fate determination. Using a Drosophila female GSC model, we found Gcn5, the first discovered histone acetyltransferase, to maintain germline stem cells in Drosophila ovaries. Results showed that Gcn5 is dispensable for the transcriptional silencing of bam, but interacts with Cyclin A to facilitate proper turnover in GSCs. Results also showed that Gcn5 promotes Cyclin A ubiquitination, which is dependent on its acetylating activity. Finally, results showed that knockdown of Cyclin A rescued the GSC-loss phenotype caused by lack of Gcn5. Collectively, these findings support the conclusion that Gcn5 acts through acetylation to facilitate Cyclin A ubiquitination and proper turnover, thereby determining the fate of GSCs.-Liu, T., Wang, Q., Li, W., Mao, F., Yue, S., Liu, S., Liu, X., Xiao, S., Xia, L. Gcn5 determines the fate of Drosophila germline stem cells through degradation of Cyclin A.

Complete genome sequence of an isolate of a novel genotype of yellow head virus from Fenneropenaeus chinensis indigenous in China.

Genotype 8 of yellow head virus (YHV-8) was identified recently, but the complete genome sequence of this new genotype has not been reported. In this study, the complete genome of YHV-8 isolate 20120706 collected from Hebei Province of China in 2012 was sequenced. It was found to be 26,769 nucleotides (nt) in length, including a 20,060-nt open reading frame 1 (ORF1), a 435-nt ORF2, and a 4971-nt ORF3. Isolate 20120706 shared 79.7-83.9% nucleotide sequence identity with all seven of the complete genome sequences of YHV that have been reported so far. The topology of a phylogenetic tree constructed based on the ORF1b region clearly showed that strain 20120706, together with five other YHV-8 strains isolated in China, represents a new genotype of YHV. This is the first report of the complete genome sequence of a YHV-8 isolate, and the 20120706 isolate will be useful for further analysis of the epidemiology and evolution of YHV-8.

A new nodavirus is associated with covert mortality disease of shrimp.

A new nodavirus, named covert mortality nodavirus (CMNV), is associated with covert mortality disease of shrimp which has caused serious loss in China since 2009. Histopathological examination of shrimp suffering the disease revealed coagulative necrosis of striated muscle similar to typical histopathology features of infectious myonecrosis virus (IMNV), Penaeus vannamei nodavirus (PvNV) and Macrobrachium rosenbergii nodavirus (MrNV). However, shrimp suffering this disease tested negative for IMNV, MrNV and PvNV by reverse transcription (RT)-PCR. Additionally, eosinophilic inclusions were found in epithelium of the tubules in the hepatopancreas and lymphoid organ, and mass karyopyknotic nuclei existed in the muscle and lymphoid organ. The tubular epithelium of the hepatopancreas showed significant atrophy. A cDNA library was constructed from total RNA of infected shrimp. Sequencing and alignment analysis showed that one clone with an 1185 bp insert (designated CMNV-7) shared 54, 53 and 39% identity with the amino acid sequences of RNA-dependent RNA polymerase from Flock House virus, black beetle virus and MrNV. The results of fluorescence in situ hybridization showed that the hepatopancreas, striated muscle and lymphoid organ were positively reacting tissues. The mean size of negative-stained virus particles was 32 nm. In addition, a nested RT-PCR assay was developed for CMNV, and the RT-PCR detection results revealed that Fenneropenaeus chinensis, Litopenaeus vannamei and Marsupenaeus japonicus suffering from this disease were CMNV-positive.

Biological responses to terahertz radiation with different power density in primary hippocampal neurons.

Terahertz (THz) radiation is a valuable imaging and sensing tool which is widely used in industry and medicine. However, it biological effects including genotoxicity and cytotoxicity are lacking of research, particularly on the nervous system. In this study, we investigated how terahertz radiation with 10mW (0.12 THz) and 50 mW (0.157 THz) would affect the morphology, cell growth and function of rat hippocampal neurons in vitro.

The Coronavirus (COVID-19) Pandemic and Mental Health of African Immigrants in the United States.

The impact of the COVID-19 pandemic on immigrants in the United States is understudied. We investigated the effect of the pandemic on the mental health of African immigrants in the United States and if subjective religiosity was a protective factor. We analyzed primary data collected using an online survey (n = 260). The study's outcome variable was incident mental health disorder associated with the pandemic, and the primary independent variable was religiosity. Chi-squared and Mann-Whitney U tests were used to compare the distribution of variables by incident mental health disorders. Logistic regression models were used to quantify the association between predictors and the outcome. There were 39 (15.0%) new cases of mental health disorders related to the pandemic. The median scores in the three domains of religiosity of those who developed a mental health disorder and those who did not were not significantly different. Significant predictors of this outcome included having a strong religious support network and loss of household employment income. African immigrants experienced an increased rate of mental health disorders during the pandemic. Implementing community-based strategies to provide social support during a disaster may be essential in promoting mental health in the African immigrant community.

The Maternal Microbiome Programs the m6A Epitranscriptome of the Mouse Fetal Brain and Intestine.

The microbiome exerts profound effects on fetal development and health, yet the mechanisms underlying remain elusive. N6-methyladenosine (m6A) plays important roles in developmental regulation. Although it has been shown that the microbiome affects the mRNA m6A modification of the host, it remains unclear whether the maternal microbiome affects m6A epitranscriptome of the fetus so as to impact fetal development. Here, we found that loss of the maternal microbiome altered the expression of m6A writers and erasers, as well as the m6A methylome of the mouse fetal brain and intestine on embryonic day 18. From the m6A profiles, we identified 2,655 and 2,252 m6A modifications regulated by the maternal microbiome in the fetal brain and intestine, respectively, and we demonstrated that these m6A-modified genes were enriched in the neuro/intestinal developmental pathways, such as the Wnt signaling pathway. Finally, we verified that antibiotic treatment mostly recapitulated changes in m6A, and we further showed that the loss of heterozygosity of Mettl3 rescued m6A levels and the expression changes of some developmental genes in the fetal intestine that resulted from antibiotic treatment. Collectively, our data revealed that the maternal microbiome programs the m6A epitranscriptome of the mouse fetal brain and intestine.

Case Report: A Novel Mutation Identified in CHST14 Gene in a Fetus With Structural Abnormalities.

Background: Musculocontractural Ehlers-Danlos syndrome (mcEDS) is a rare heritable connective tissue disease with various symptoms. The diagnosis of mcEDS is difficult because of the large overlap of clinical symptoms between different EDS subtypes. Methods: We performed karyotype analysis, gene copy number variation detection, whole-exome sequencing, and Sanger sequencing to reveal the underlying genetic etiology of a fetus with structural abnormalities in feet and kidneys. Results: A likely pathogenic mutation [NM_130468.3 c.958C>T (p.Arg320*)] and an uncertain significance mutation [NM_130468.3 c.896A>G (p.Tyr299Cys)] were identified in the carbohydrate sulfotransferase 14 (CHST14) gene by whole-exome sequencing and validated by Sanger sequencing. Conclusion: The two identified mutations appear highly likely to be the genetic causes of the fetal structural abnormalities.

[Mass spectrometry identification of secreted proteins from Bacillus firmus and analysis of its secretive sequences].

OBJECTIVE: Bacillus firmus was a common probiotics bacteria in nature and widely used in the shrimp aquaculture. In order to construct expression vectors for secretive proteins, we identified several major secretive proteins of Bacillus firmus by mass spectrometry and analyzed their gene sequences to find signal peptide sequences. METHODS: The secreted proteins of Bacillus firmus were extracted and separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The 3 highly expressed protein bands in the SDS-PAGE were identified by mass spectrometry Matrix Assisted Laser Desorption Ionization (MALDI)-Time of Flight (TOF)/Time of Flight (TOF) and the sequences were downloaded from National Center for Biotechnology Information (NCBI) database. Then Polymerase Chain Reaction (PCR) primers were designed according to the downloaded sequences and specific DNA bands were amplified sequenced and bioinformatics analyzed. RESULTS: The proteins were identified as the putative chitinase, enterotoxin A and protein BCG9842 of Bacillus firmus. Three signal peptides were conformed by using the online software SignaIP 3.0, namely bf-43, bf-37 and bf-16. The cellular localization of the secreted sequences were analyzed by PSORT. And we found that bf-43 located in the outer membrane of cells, bf-37 and bf-16 located in the extracellular cell. CONCLUSION: 3 major secreted proteins of Bacillus firmus have been identified. 3 possible signal peptides were obtained and will be useful for the construction of expression vectors for secretive proteins.

Interleukin-6 gene -572 G > C polymorphism and myocardial infarction risk.

INTRODUCTION: The association between interleukin-6 (IL-6) gene -572 G^C polymorphism and myocardial infarction (MI) risk has not been established. We adopted this meta-analysis for further insight into the case-control studies. MATERIALS AND METHODS: To investigate the genetic association, we searched multiple databases, including Web of Science, EMbase, CBM disc, PubMed and CNKI. Also, we manually identified the searched references. All the statistical analyses were conducted using Stata 11.0. RESULTS: A total of five studies were identified, involving 2,526 MI cases and 3,027 controls. The results revealed a significant association between IL-6 gene -572 G^C polymorphism and MI, implying that the IL-6 gene -572 C allele may be a protective factor for MI (for C allele vs K allele: OR = 0.85, 95% CI = 0.73-0.99, p = 0.041; for C/C vs G/G: OR = 0.55, 95% CI = 0.31-0.98, p = 0.044; for C/C vs G/C + G/G: OR = 0.60, 95% CI = 0.41-0.89, p = 0.011). However, in the subgroup analysis with regard to ethnicity, no significant correlation was identified between IL-6 gene -572 G^C polymorphism and MI among Europeans. CONCLUSION: The IL-6 gene -572 C allele may be a protective factor for MI. Future studies involving larger sample bases are still recommended.

N6-Methyladenosine co-transcriptionally directs the demethylation of histone H3K9me2.

A dynamic epigenome is critical for appropriate gene expression in development and health1-5. Central to this is the intricate process of transcription6-11, which integrates cellular signaling with chromatin changes, transcriptional machinery and modifications to messenger RNA, such as N6-methyladenosine (m6A), which is co-transcriptionally incorporated. The integration of these aspects of the dynamic epigenome, however, is not well understood mechanistically. Here we show that the repressive histone mark H3K9me2 is specifically removed by the induction of m6A-modified transcripts. We demonstrate that the methyltransferase METTL3/METTL14 regulates H3K9me2 modification. We observe a genome-wide correlation between m6A and occupancy by the H3K9me2 demethylase KDM3B, and we find that the m6A reader YTHDC1 physically interacts with and recruits KDM3B to m6A-associated chromatin regions, promoting H3K9me2 demethylation and gene expression. This study establishes a direct link between m6A and dynamic chromatin modification and provides mechanistic insight into the co-transcriptional interplay between RNA modifications and histone modifications.

Risk factors in metabolic syndrome predict the progression of diabetic nephropathy in patients with type 2 diabetes.

BACKGROUND: While metabolic syndrome can independently predict the development of diabetic kidney disease (DKD) in patients with type 2 diabetes, the risk factors for DKD progression have rarely been discussed. The purpose of this study is to evaluate the association between metabolic syndrome and the progression of DKD in patients with type 2 diabetes. MATERIAL AND METHODS: This retrospective observational cohort study lasted approximately five years. We defined metabolic syndrome using the criteria of the National Cholesterol Education Program Adult Treatment Panel III with the Asian definition of obesity. The progression of DKD was demonstrated by either the progression of albuminuria or worsening renal function. Progression of albuminuria was defined by the transition from normoalbuminuria (<30 mg/g) to microalbuminuria (30-300 mg/g) or from micro- to macroalbuminuria (>300 mg/g). Worsening renal function was defined by a reduction of eGFR to 50% of the baseline or the doubling of serum creatinine. We adopted multivariate Cox-regression analysis to determine the risk factors associated with DKD progression. RESULTS: This study consisted of 935 type 2 diabetic patients with a mean age of 64.62 years. We found progression of albuminuria in 172 patients (18.4%) and worsened renal function in 41 patients (4.4%). After Cox regression analysis, the multivariable-adjusted HR for the progression of albuminuria and worsened renal function was 1.65 (95% C.I.:1.07-2.53 P = 0.022) and 2.62 (95% C.I.:1.01-6.79 P = 0.047) respectively, for those with metabolic syndrome compared to those without metabolic syndrome. CONCLUSION: The presence of metabolic syndrome independently predicts DKD progression in patients with type 2 diabetes.

The RNA N6-methyladenosine modification landscape of human fetal tissues.

A single genome gives rise to diverse tissues through complex epigenomic mechanisms, including N6-methyladenosine (m6A), a widespread RNA modification that is implicated in many biological processes. Here, to explore the global landscape of m6A in human tissues, we generated 21 whole-transcriptome m6A methylomes across major fetal tissues using m6A sequencing. These data reveal dynamic m6A methylation, identify large numbers of tissue differential m6A modifications and indicate that m6A is positively correlated with gene expression homeostasis. We also report m6A methylomes of long intergenic non-coding RNA (lincRNA), finding that enhancer lincRNAs are enriched for m6A. Tissue m6A regions are often enriched for single nucleotide polymorphisms that are associated with the expression of quantitative traits and complex traits including common diseases, which may potentially affect m6A modifications. Finally, we find that m6A modifications preferentially occupy genes with CpG-rich promoters, features of which regulate RNA transcript m6A. Our data indicate that m6A is widely regulated by human genetic variation and promoters, suggesting a broad involvement of m6A in human development and disease.

Progressive Indosinian N-S deformation of the Jiaochang structure in the Songpan-Ganzi fold-belt, Western China.

Integrated field data, microstructural and three-dimensional strain analyses are used to document coaxial N-S shortening and southward increase in deformation intensity and metamorphism at the Jiaochang structure. Two episodes of deformation (D1,D2) with localized post-D2 deformation have been identified in the area. The first deformation (D1) episode is defined by a main axial-plane of parallel folds observable on a micro- to kilometer-scale, while the second episode of deformation (D2) is defined by micro-scale metamorphic folds, associated with E-W oriented stretching lineation. These processes are the result of Indosinian tectonism (Late Triassic to Early Jurassic) characterized by nearly coaxial N-S compression and deformation. This is indicated by E-W trending, sub-parallel to parallel foliation (S1, e.g. axial-plane of folds, and S2, i.e. axial-plane of metamorphic folds, crenulation cleavage) and lineation (L1, e.g. axis of folds, and L2, i.e. stretching lineation, axis of metamorphic folds and B-axis of echelon lens). Most of the porphyroblasts and minerals (e.g. pyrite, biotite) show two growth phases with localized growth in the third phase (muscovite). The progressive D1-D2 structure is widespread in the south of the Jiaochang area, but only D1 structure crops out at the north. The strain intensity (γ), compression ratios (c%) and octahedral strain intensity (εs) are similar across the Jiaochang structure (i.e., γ ≈ 1.8, c ≈ 27%, εs = 0.9), showing a broad range of Flinn values (K = 0.77 to 7.57). The long-axis orientations are roughly symmetric between two limbs of the structure. Therefore, we suggest that the architecture of the Jiaochang structure has been controlled by coaxial N-S shortening and deformation (D1-D2) during the Indosinian tectonic epoch, with insignificant post-D2 deformation.

Overexpression of the insulin-like growth factor I receptor in human colon carcinomas.

BACKGROUND: High concentrations of insulin-like growth factor (IGF)-I and IGF-II have been demonstrated in human colonic adenocarcinomas and exert mitogenic effects through paracrine/autocrine interactions with the IGF-I receptor (IGF-IR). However, definitive studies of IGF-IR expression in these tissues have not been performed. METHODS: To study changes in the levels of the IGF-IR in colorectal carcinoma, we analyzed the expression of IGF-IR in 40 paired samples of normal and carcinomatous colonic tissue by quantitative reverse-transcription-polymerase chain reaction (RT-PCR), immunohistochemistry, and ligand binding. RESULTS: As measured by RT-PCR, the IGF-IR mRNA ratio in paired tumor and adjacent normal mucosa was higher than 2.0 in 32 of 40 (80%) samples. The overall mean IGF-IR mRNA level was five-fold higher in tumor versus adjacent normal mucosa (P < 0.0001). Overexpression of IGF-IR in colon carcinomas was confirmed at the protein level by immunohistochemistry and receptor-binding studies. Colon carcinoma cells exhibited a positive staining for IGF-IR in 91% of all tumors (30 of 33) whereas the adjacent normal colonic epithelial cells showed only a very faint or no significant IGF-IR immunoreactivity. Radioligand assays and Scatchard analysis in both tissue types revealed a single class of high-affinity IGF-IR-binding sites with a similar dissociation constant (K(d;) 0.14 +/- 0.02 nmol/L, n = 18). However, specific (125)IGF-I-binding and receptor concentrations were elevated in tumor membranes compared with normal mucosa (33.6 +/- 5.6 vs. 22.7 +/- 3.4 fmol/mg protein, P < 0.05). IGF-I affinity crosslinking and sodium dodecyl sulfate-polyacrylamide gel electrophoresis displayed specific bands corresponding to the size of the normal alpha-subunit of the IGF-IR that were more intense in carcinomatous samples. IGF-II mRNA levels were significantly elevated in colorectal carcinomas (P < 0.0001). The IGF-II mRNA ratio in tumor versus normal tissue was elevated more than twofold in 28 of 40 paired samples and a positive correlation was observed between the overexpression of IGF-II and IGF-IR in the tumors. CONCLUSIONS: Our results demonstrate that, in addition to IGF-II, a strong overexpression of IGF-IR is found in the majority of colorectal carcinomas, supporting the hypothesis of an important role of the IGF system in the pathogenesis of colorectal carcinoma.