Transcriptome analysis based on high-throughput sequencing of a cDNA library has been widely applied to functional genomic studies. However, the cDNA dependence of most RNA sequencing techniques constrains their ability to detect base modifications on RNA, which is an important element for the post-transcriptional regulation of gene expression. To comprehensively profile the N⁶-methyladenosine (m⁶A) and N⁵-methylcytosine (m⁵C) modifications on RNA, direct RNA sequencing (DRS) using the latest Oxford Nanopore Technology was applied to analyze the transcriptome of six tissues in rice. Approximately 94 million reads were generated, with an average length ranging from 619 nt to 1013 nt, and a total of 45,707 transcripts across 34,763 genes were detected. Expression profiles of transcripts at the isoform level were quantified among tissues. Transcriptome-wide mapping of m⁶A and m⁵C demonstrated that both modifications exhibited tissue-specific characteristics. The transcripts with m⁶A modifications tended to be modified by m⁵C, and the transcripts with modifications presented higher expression levels along with shorter poly(A) tails than transcripts without modifications, suggesting the complexity of gene expression regulation. Gene Ontology analysis demonstrated that m⁶A- and m⁵C-modified transcripts were involved in central metabolic pathways related to the life cycle, with modifications on the target genes selected in a tissue-specific manner. Furthermore, most modified sites were located within quantitative trait loci that control important agronomic traits, highlighting the value of cloning functional loci. The results provide new insights into the expression regulation complexity and data resource of the transcriptome and epitranscriptome, improving our understanding of the rice genome.
RNA ; Oryza/genetics* ; RNA, Messenger ; Gene Expression Profiling ; Transcriptome ; Sequence Analysis, RNA ; High-Throughput Nucleotide Sequencing/methods* ; RNA Processing, Post-Transcriptional

Objective:To summarize the case data of endometrial cancer (EC), analyze the related factors of lymph node metastasis, and establish the prediction model, so as to provide reference for clinical practice.Methods:191 patients with endometrial cancer who were diagnosed and treated in department of gynecology of Baoding Maternal and Child Health Hospital from January 2010 to December 2019 were selected as the research objects. The demographic and surgical pathological information of the patients were analyzed retrospectively. The risk factors of lymph node metastasis were analyzed by univariate and logistic regression analysis, and the predictive model was established.Results:A total of 191 patients with EC, aged 26-76(53.1±9.5)years old, body mass index (BMI)18.70-40.20(25.84±3.94)kg/m 2, 13 cases (6. 81%) had lymph node metastasis. Univariate analysis showed that lymph node metastasis was associated with obesity (BMI≥28 kg/m 2), pathological type (non endometrioid adenocarcinoma), degree of differentiation, depth of myometrial invasion (>1/2) and vascular invasion ( P<0.05). Logistic multivariate analysis showed that low differentiation ( OR=9.475, 95% CI: 1.840-48.799), vascular invasion ( OR=6.614, 95% CI: 1.457-30.024) and deep muscle invasion ( OR=4.997, 95% CI: 1.342-18.600) were independent risk factors ( P<0.05). The regression equation: Logit P=-4.488+ 1.609× myometrial infiltration depth+ 1.889×vascular infiltration+ 2.249×degree of tissue differentiation. The area under the receiver operating characteristic (ROC) curve (AUC) of EC lymph node metastasis probability P was 0.813 (95% CI: 0.688-0.938). The cut off value of 0.56 was ideal. At this time, the prediction sensitivity was 76.9% and the specificity was 79.2%. Conclusions:In clinical practice, gynecologists should consider the condition of EC patients and make operation plan to avoid over treatment or under treatment.

ObjectiveTo observe the effect of parathyroid hormone on expression of matrix GLA protein (MGP) in ovariectomized SD rats and primary osteoblast,and to study the role of MGP on the possible mechanism of postmenopausal osteoporosis.MethodsThirty-six Sprague-Dawley female rats were allocated into 3 groups,12 in each:sham operation group,ovariectomized group( OVX group),ovariectomized and parathyroid hormone treatment group.Animals in the parathyroid hormone group were injected parathyroid hormone (20 μg/kg,three times a week for 12 weeks) three weeks after ovariectomy.All rats were sacrificed after 18 weeks.Urine and serum were collected every three weeks.Lumbar vertebral bones were observed by immunohistochemistry.Bone mineral density (BMD) of lumbar vertebra of rats was determined.The content of MGP in serum and urine was determined by enzyme-linked immunosorbent assay (ELISA).Expression of undercarboxylated Matrix GLA Protein (ucMGP) was detected by immunochistochemistry.Relative quantification of MGP mRNA expression in lumbar vertebra bone was detected by Fluorescent real-time quantitative polymerause chain reaction.Results ( 1 ) 18 weeks after ovariectomy,BMD of lumbar vertebra in OVX group was lower than those in sham group and parathyroid hormone group significantly ( P＜0.05 ).(2) The content of MGP in serum and urine was dynamic variation after treatment hy parathyroid hormone,and it was significant compared with OVX group ( P＜0.05 ).( 3 ) Immunohistochemical localization of ucMGP was seen in lumbar vertebra in OVX group.(4) Relative quantification of MGP mRNA expression in lumbar vertebra in OVX group was increased significantly compared with other groups ( P＜0.01 ).( 5 ) parathyroid hormone ( 1-34 ) in 10-7mol/L,10-8mol/L,10-9 mol/L up-regulated MGP mRNA expression in primary osteoblasts about 6.78,5.31,and 2.23 times than control respectively.It was in a dose-dependent manner.ConclusionThe effect of parathyroid hormone on the expression of matrix gla protein may play an important role in mechanism of postmenopausal osteoporosis

Objective To observe the expression of matrix gla protein(MGP) mRNA in primary osteoblasts of Sprague-Dawley (SD) rat in vitro after treatment with anti-osteoporosis agents [vitamin K2,PTH,1,25 (OH)2D3,and alendronate],and to investigate the potential role of MGP in the pathogenesis of osteoporosis.Methods Primary osteoblasts(OBs) were derived from sequential trypsin/collagenase-digested calvaria isolated from newborn SD rat (postnastal day 1-3).OBs of the second generation were identified by Van Gieson collagen staining,alkaline phosphatase(ALP) staining and calcified nodules staining.OBs of the fourth generation were selected to interfere with vitamin K2,PTH,1,25 (OH)2D3,and alendronate,then cultured for 24 h in mediums which contained various concentrations of vitamin K2 (10-7,10-6,and 10-5 mol/L),PTH (10-9,10-8,and 10-7 mol/L),1,25 (OH) 2D3(10-10,10-9,and 10-8mol/L),alendronate(10-6,10-5,and 10-4mol/L).After being cultured for 24 h,total RNA was extracted and examined by real-time quantitative RT-PCR.Results The primary cultured cells had typical morphological characters of osteoblast.van Gieson collagen staining,ALP staining,and calcified nodules staining were all positive.Vitamin K2,PTH,1,25 (OH)2D3,and alendronate could modulate the expression of MGP mRNA in osteoblasts in a dose-dependent fashion.MGP mRNA expressions were 2.56-fold,2.12-fold,and 1.57-fold with 10-5,10-6,and 10-7 mol/L of vitamin K2 treatment,respectively.The expressions were 6.78-fold,5.31-fold,and 2.23-fold with 10-7,10-8,and 10-9mol/L of PTH(1-34) treatment,8.93-fold,6.95-fold,and 3.47-fold with 10-8 10-9,and 10-10mol/L of 1,25 (OH)2D3 treatment,and 3.47-fold,2.49-fold,and 1.98-fold with 10-4,10-5,and 10-6mol/L of alendronate treatment.Conclusion Vitamin K2,PTH,1,25 (OH)2D3,and alendronate all canregulate MGP mRNA expression in calvarial osteoblasts in a dose-dependent manner.MGP seems to be a potent target of anti-osteoporosis agents,and involved in the pathogenesis of osteoporosis.