Zanthoxylum bungeanum is an economically important crop worldwide due to its high content of aroma-producing monoterpenoids,and development of varieties with enhanced flavor and overall quality is a crucial research a...Zanthoxylum bungeanum is an economically important crop worldwide due to its high content of aroma-producing monoterpenoids,and development of varieties with enhanced flavor and overall quality is a crucial research area.However,the transcriptional regulatory mechanisms underlying monoterpenoid synthesis in Z.bungeanum remain unclear,hindering these breeding efforts.In this study,RNA sequencing,gas chromatography–mass spectrometry,and other molecular biology techniques were used to identify the underlying transcriptional regulation mechanisms.Two transcription factors,ZbbHLH2 and ZbERF6,were identified as key regulators of monoterpenoid synthesis in Z.bungeanum that upregulate various monoterpenoid synthesis-associated genes and are novel transcriptional activators of ZbIDI,which encodes the rate-limiting enzyme in plant monoterpenoid synthesis.Functional analysis revealed that the expression of three genes[1]modulates monoterpenoid accumulation in Z.bungeanum peel.These findings provide novel insights into the metabolic regulatory network of monoterpenoid synthesis in Z.bungeanum peel,offer potential strategies for the biofortification of specific monoterpenoids,and will promote the development of Z.bungeanum germplasm for targeted breeding and quality improvement.展开更多
Flavonoids,abundant in the fruits,are pivotal to their growth,development,and storage.In addition,they have significant beneficial effects on human health.Consequently,research is increasingly concentrating on the reg...Flavonoids,abundant in the fruits,are pivotal to their growth,development,and storage.In addition,they have significant beneficial effects on human health.Consequently,research is increasingly concentrating on the regulatory mechanisms governing flavonoid biosynthesis in fruits.Phytohormones are involved in the regulation of flavonoid biosynthesis.The abscisic acid,ethylene,jasmonic acid,cytokinins,and brassinosteroids promote flavonoid biosynthesis,while auxin negatively regulates flavonoid biosynthesis.Subsequently,transcription factors from the MYB,bHLH,WRKY,NAC,and bZIP families are pivotal in regulating flavonoid biosynthesis.In addition,non-coding RNAs(microRNA and lncRNA)also participate in the regulation of flavonoids biosynthesis.MicroRNAs are generally believed to negatively regulate flavonoid metabolism in fruits,while lncRNAs have the opposite effect.Furthermore,the interactions between plant hormones,transcription factors,and non-coding RNAs in fruit flavonoid biosynthesis were analyzed.Ultimately,a foundational regulatory network for fruit flavonoid biosynthesis was hereby established.展开更多
[Objectives]To characterize the expression pattern of Fibroblast growth factor 10(FGF10)during the differentiation of rat L6 myoblasts and to identify potential key transcription factors(TFs)regulating its expression ...[Objectives]To characterize the expression pattern of Fibroblast growth factor 10(FGF10)during the differentiation of rat L6 myoblasts and to identify potential key transcription factors(TFs)regulating its expression through bioinformatics approaches.[Methods]Rat L6 myoblasts were induced to differentiate by culturing them in DMEM supplemented with 2%donor horse serum(DHS).Morphological changes were observed using an inverted microscope.Cell samples were collected prior to induction(day 0)and on days 1,3,5,and 7 post-induction.The relative expression levels of FGF10 mRNA and protein at each time point were quantified using RT-qPCR and Western blot analysis,respectively.Furthermore,a 2000 bp sequence upstream of the transcription start site of the rat Fgf10 gene was extracted as the promoter region.Putative TF binding sites were predicted using four databases(TRANSFAC,JASPAR,HOCOMOCO,and CISBP),and high-confidence candidates were screened to construct a regulatory network.[Results]Morphological observations confirmed successful differentiation,as evidenced by the appearance of binucleated myotubes on day 3 and the formation of numerous thick,multinucleated myotubes by day 7.Both RT-qPCR and Western blot analysis demonstrated a significant dynamic expression pattern of FGF10.Expression levels were markedly upregulated during the early phase(days 1-3),reaching a peak on day 3(P<0.01),followed by a decline to basal levels during the late phase(days 5-7).Cross-validation across multiple databases identified 48 high-confidence TFs,among which Elf5,Tcf3,Nkx3-2,Zic2,Tcf7,and Egr1 were consistently predicted by all four databases.[Conclusions]FGF10 exhibits high expression levels during the early stage of differentiation,indicating its crucial role in the initiation of myogenesis.The six identified TFs serve as core candidate regulators of Fgf10 expression,offering novel insights into the molecular mechanisms underlying muscle development.展开更多
Flower color is an essential trait in ornamental plant breeding. Lycoris longituba is a popular ornamental plant native to central eastern China. The decrease in anthocyanin accumulation causes L. longituba petal colo...Flower color is an essential trait in ornamental plant breeding. Lycoris longituba is a popular ornamental plant native to central eastern China. The decrease in anthocyanin accumulation causes L. longituba petal color fading during flower development, which considerably affects the ornamental value of L. longituba. However, mechanisms underlying anthocyanin biosynthesis inhibition during L. longituba petal development remain unclear. In this study, three LlDFR genes were confirmed to be involved in anthocyanin biosynthesis and LlDFRc exerted the strongest promoting effect on anthocyanin accumulation. According to the correlation analysis results, LlbHLH12 exhibited the strongest negative correlation with LlDFRc. Quantitative real-time PCR analysis showed that LlbHLH12 was highly expressed during the medium bud and full bloom stages of flower development. LlbHLH12 was identified as a member of subgroup XII of bHLH transcription factor family. Subcellular localization and transcriptional activation ability assay revealed that LlbHLH12 was located in the nucleus without transcriptional activation activity. Overexpression of LlbHLH12 in Nicotiana tabacum and L. longituba inhibited anthocyanin accumulation by suppressing the expression of anthocyanin biosynthetic pathway genes. Furthermore, yeast one-hybrid, dual-luciferase, and β-glucuronidase activity assays showed that LlbHLH12 directly bound to the promoters of LlPAL and LlDFRc and suppressed their expression to inhibit anthocyanin biosynthesis. Overall, our study identified a novel bHLH repressor negatively regulating anthocyanin biosynthesis and provided new insights into the molecular mechanisms underlying color fading in L. longituba petals.展开更多
Moving from the most recent results on Foxg1 biology,we first summarize the available information on some special pleiotropic effectors of neurodevelopmental interest,involved in controlling both transcription and pos...Moving from the most recent results on Foxg1 biology,we first summarize the available information on some special pleiotropic effectors of neurodevelopmental interest,involved in controlling both transcription and post-transcriptional steps of gene expression.Then,after further analysis of the literature,we report evidence that,not strictly limited to neurodevelopmental effectors,such pleiotropy also applies to other transcription factors,involved in physiology and homeostasis.Furthermore,through the systematic analysis of a major public protein-protein interaction database,we gather strong evidence that the involvement of“canonical”transcription factors in post-transcriptional control of gene expression could be a pervasive phenomenon,characterizing hundreds of effectors.Finally,we discuss the biological significance of these findings and propose three evolutionary mechanisms that may have contributed to such an unexpected scenario.展开更多
Background:The regulatory mechanisms governing vasculogenic mimicry(VM)in oral squamous cell carcinoma(OSCC)remain largely undefined.This study aimed to identify critical factors and elucidate the epigenetic mechanism...Background:The regulatory mechanisms governing vasculogenic mimicry(VM)in oral squamous cell carcinoma(OSCC)remain largely undefined.This study aimed to identify critical factors and elucidate the epigenetic mechanisms underlying VM in OSCC.Methods:Bioinformatics analysis was performed utilizing single-cell RNA-seq,bulk RNA-seq,and histone H3 lysine 27 acetylation(H3K27ac)Chromatin Immunoprecipitation(ChIP)-seq data obtained from The Cancer Genome Atlas(TCGA)and Gene Expression Omnibus(GEO)databases.ChIP-qPCR was used to validate the binding of ETS transcription factor ELK4(ELK4)to the dihydrofolate reductase(DHFR)enhancer.In vitro VM formation and invasion of OSCC cells were assessed using Matrigel-based tube formation and Transwell assays,respectively.Results:Elevated expression of VM-related genes predicts unfavorable prognosis in OSCC patients.High-dimensional weighted gene co-expression network analysis(hdWGCNA)identified epithelial subcluster C4 as most strongly associated with VM and metastasis.Three co-expression modules within this subcluster exhibited significant positive correlations with both phenotypic traits.Among the 30 eigengenes from the three modules,DHFR emerged as a key regulator of VM and metastasis.Knockdown or inhibition of DHFR significantly suppressed VM formation and invasion in OSCC cells.Mechanistically,ELK4 activated DHFR transcription through direct binding to its enhancer.DHFR overexpression rescued VM and invasion impairment induced by ELK4 knockdown.Conclusion:DHFR was a pivotal enhancer-regulated gene driving VM and metastasis in OSCC.ELK4 directly binds to DHFR enhancer regions to activate its transcription,thereby promoting these malignant phenotypes.These findings identified the ELK4/DHFR axis as a promising therapeutic target for anti-angiogenic intervention in OSCC.展开更多
Heat stress reduces theanine content in tea plants,but the underlying molecular mechanism remains unclear.In this study,a temperature gradient treatment(20℃,25℃,30℃,and 35℃)was performed to unveil the effect of he...Heat stress reduces theanine content in tea plants,but the underlying molecular mechanism remains unclear.In this study,a temperature gradient treatment(20℃,25℃,30℃,and 35℃)was performed to unveil the effect of heat stress on biosynthesis and accumulation of theanine.We found that heat stress induced metabolic changes,characterized by decreased theanine content and increased catechin levels.In addition,heat stress up-regulated the expression of the class B heat shock transcription factor gene CsHSFB2c,while significantly suppressing the transcription of key theanine biosynthetic genes CsTS1 and CsGS1.Functional studies showed that silencing CsHSFB2c increased theanine content,while its overexpression significantly decreased theanine levels.Consistent with these changes,silencing CsHSFB2c upregulated the expression of CsTS1 and CsGS1,while overexpression of CsHSFB2c downregulated their expression.Yeast one-hybrid(Y1H)and dual-luciferase reporter gene(Dual-LUC)assays showed that CsHSFB2c directly binds to the promoters of CsTS1 and CsGS1 and inhibits their expression.These results demonstrate that CsHSFB2c mediates heat-induced suppression of theanine biosynthesis by directly inhibiting the expression of CsTS1 and CsGS1.This study provides a theoretical basis for improving the heat resistance and quality of tea plants via molecular breeding.展开更多
Nuclear receptor subfamily 2 group F member 1(NR2F1,also called COUP-TF1)is a transcription factor and part of the steroid/thyroid hormone receptor superfamily(Gay et al.,2002).NR2F1 is an orphan receptor that dimeriz...Nuclear receptor subfamily 2 group F member 1(NR2F1,also called COUP-TF1)is a transcription factor and part of the steroid/thyroid hormone receptor superfamily(Gay et al.,2002).NR2F1 is an orphan receptor that dimerizes to bind DNA and acts as a repressor as well as an activator of the target genes(Gay et al.,2002;Bertacchi et al.,2019;Bonzano et al.,2023).展开更多
AIM:To investigate whether vaccinia-related kinase 1(VRK1)mediates transforming growth factor-beta2(TGF-β2)-caused epithelial-mesenchymal transition(EMT)and inflammatory responses in retinal pigment epithelial(RPE)ce...AIM:To investigate whether vaccinia-related kinase 1(VRK1)mediates transforming growth factor-beta2(TGF-β2)-caused epithelial-mesenchymal transition(EMT)and inflammatory responses in retinal pigment epithelial(RPE)cells through regulating snail family transcriptional repressor 1(SNAI1),and to validate its role in a proliferative vitreoretinopathy(PVR)mouse model.METHODS:Human RPE cell line ARPE-19 cells were treated with TGF-β2 to construct an EMT model.Western blot detected VRK1 level.The effects of VRK1 on SNAI1 expression and biological behavior of ARPE-19 cells were detected by immunofluorescence,ELISA,Transwell,and scratch assay,and the interaction between VRK1 and SNAI1 was confirmed through immunoprecipitation.A PVR mouse model was constructed,and the effects of VRK1 or/and SNAI1 on retinal damage were assessed by pathologic staining.Inflammatory factors and EMT-related proteins were assessed with ELISA and Western blot.RESULTS:VRK1 was upregulated in ARPE-19 cells after TGF-β2 treatment.Overexpression of VRK1 increased cell viability,promoted cell migration and EMT,and the levels of inflammatory factors.Silencing of VRK1 reversed the above indexes.There was a direct interaction between VRK1 and SNAI1,and overexpresssion SNAI1 weakened the impacts of silencing of VRK1.In PVR mice,silencing of VRK1 ameliorated retinal structural damage,decreased proinflammatory factor levels,and suppressed SNAI1 and mesenchymal marker expression.SNAI1 overexpression antagonized the protective effects of silencing VRK1 and exacerbated EMT and inflammatory responses.CONCLUSION:VRK1 plays a key role in retinal structural and inflammatory damage in PVR mice by regulating SNAI1 and mediating TGF-β2-caused EMT and inflammatory responses in RPE cells.展开更多
Tooth morphogenesis is orchestrated by a complex interplay of signaling pathways and transcription factors that control cell proliferation,apoptosis,and differentiation,with the Wnt/β-catenin signaling pathway playin...Tooth morphogenesis is orchestrated by a complex interplay of signaling pathways and transcription factors that control cell proliferation,apoptosis,and differentiation,with the Wnt/β-catenin signaling pathway playing a pivotal role.However,the comprehensive regulatory mechanisms of Wnt/β-catenin signaling remain largely unclear.Smad7,a key antagonist of the TGF-βsuperfamily,is essential for maintaining tissue homeostasis and ensuring proper cellular function.Our previous study has demonstrated that Smad7 knockout in mice leads to impaired proliferative property of tooth germ cells,resulting in small molars.Here,we identified SMAD7 expression in human dental papilla and dental pulp,colocalized with β-CATENIN and cell proliferationrelated proteins.RNA sequencing analysis revealed a significant reduction in Wnt signaling activity in Smad7-deficient mouse tooth germs.Using lentivirus transfection,we established SMAD7-knockdown human dental papilla stem cells,which manifested remarkably blunt proliferation rate,along with diminished Wnt signaling activity.In vivo transplantation investigations further revealed the indispensable role of SMAD7 in dentin formation.Mechanistically,we revealed that β-CATENIN interacts with P-SMAD2/3 and SMAD7 through co-immunoprecipitation and yeast two-hybrid assays.Inhibition of TGF-β pathway or disruption of SMAD7/β-CATENIN transcription factor complex formation potently impacted Wnt/β-catenin activities,indicating both direct and indirect regulatory mechanisms.These findings highlight the critical role of SMAD7 in the proliferation and diffe rentiation of human dental stem cells,which could contribute to dental tissue regeneration and engineering.展开更多
Objective:Leucine-rich alpha-2 glycoprotein 1(Lrg1)could regulate diverse cells in cerebral ischemiareperfusion.Our study seeks to uncover Lrg1’s impact on endothelial cell heterogeneity via differentiation pathways ...Objective:Leucine-rich alpha-2 glycoprotein 1(Lrg1)could regulate diverse cells in cerebral ischemiareperfusion.Our study seeks to uncover Lrg1’s impact on endothelial cell heterogeneity via differentiation pathways and transcription factors.Method:The CSOmap model measured cell-to-brain-center distances using single-cell RNA sequencing(scRNA-seq)data in middle cerebral artery occlusion reperfusion(MCAO/R).Monocle2 mapped endothelial differentiation paths.Gene set enrichment analysis(GSEA)analyzed endothelial subcluster variations.Database searches revealed a zinc finger MIZ-type containing 1 protein-frizzled 3(Zmiz1-Fzd3)promoter interaction.Endothelial cells were transfected with a Fzd3 promoter-luciferase plasmid.Polymerase chain reaction(PCR)and western blotting assessed MCAO/R or Zmiz1 overexpression effects on Fzd3-related mRNA and proteins.A retroviral vector carrying Zmiz1 was injected into the brains of mice to study its effect on Fzd3.Result:Lrg1−/−mice exhibited elevated cell adhesion proteins and decreased microvascular leakage after MCAO/R.CSOmap showed widened astrocyte spacing in thesemice.RSS revealed Zmiz1 overexpression inMCAO/R+Lrg1−/−mice.MCAO/R and pcDNA3-Zmiz1 transfection both enhanced luciferase activity with Fzd3,indicating Zmiz1 binding to Fzd3.Retroviral Zmiz1 injection or knockdown disrupted ischemic brain tight junctions,highlighting Zmiz1’s key role in blood-brain barrier protection,likely through Fzd3 pathway modulation.Conclusion:The findings indicate Lrg1 knockout induces endothelial differentiation by activating Zmiz1,which is crucial for maintaining blood-brain barrier function,possibly via modulating the Fzd3 pathway.展开更多
Aberrant RNA modification has been linked to the pathogenesis of various diseases;however,its specific molecular mechanisms in spinal cord injury remain poorly understood.The objective of this study was to explore RNA...Aberrant RNA modification has been linked to the pathogenesis of various diseases;however,its specific molecular mechanisms in spinal cord injury remain poorly understood.The objective of this study was to explore RNA modification-related biomarkers of spinal cord injury.The mRNA expression profiles of mice with spinal cord injury were retrieved from the Gene Expression Omnibus(GEO)database(GSE18179).We identified 185 differentially expressed genes using bioinformatics approaches.Functional enrichment analysis demonstrated aberrant activation or inhibition of common metabolism-related pathways,including sulfur metabolism and steroid biosynthesis,in mice with spinal cord injury.An integrated strategy comprising weighted gene co-expression network analysis,a random forest model,a support vector machine model,and a generalized linear model was employed to identify four genes whose aberrant RNA modification was linked to spinal cord injury:Elovl6,Idi1,Sqle,and Stbd1.We verified the expression levels and diagnostic performance of these four genes in the original training dataset and mouse samples via receiver operating characteristic curve analysis.Quantitative reverse transcription-polymerase chain reaction demonstrated variations in the mRNA levels of the four genes between the Sham and spinal cord injury groups at different time points following injury.We also constructed microRNA-mRNA and transcription factor-mRNA interaction networks using Cytoscape.Additionally,we evaluated the proportions of 22 types of immune cells in the spinal cords of mice using the CIBERSORT tool,revealing significant alterations in the numbers of memory B cells,resting dendritic cells,M0 macrophages,activated mast cells,resting mast cells,and CD8+T cells in spinal cord injury mice compared with Sham controls.Microglia and T cells were identified as key cell types by single-cell sequencing analysis.These findings provide new directions for the development of RNA modification-related therapeutic strategies for spinal cord injury and suggest that Elovl6,Idi1,Sqle,and Stbd1 are potential biomarkers of spinal cord injury.展开更多
Objectives:The current treatment options and therapeutic targets for triple-negative breast cancer(TNBC),an aggressive subtype of breast cancer(BrCA),are limited.This study aimed to identify novel biomarkers and trans...Objectives:The current treatment options and therapeutic targets for triple-negative breast cancer(TNBC),an aggressive subtype of breast cancer(BrCA),are limited.This study aimed to identify novel biomarkers and transcriptional regulatory networks(TRN)inherent in TNBC samples.Methods:We analyzed pan-cancer BrCA datasets from The Cancer Genome Atlas(TCGA)to compare triple-positive breast cancer(TPBC)with TNBC.TRN algorithms and virtual inference of protein-enriched regulon(VIPER)were used to identify master regulators and their target genes.Utilizing TNBC cells(MDA-MB-231 and MDA-MB-468),we validated the relationship of nuclear factor erythroid 2-like 3(NFE2L3)and basic helix-loop-helix family member E 40(BHLHE40)by performing a luciferase assay.The expression levels of these targets were measured after transfections with plasmid and siRNA via qRT-PCR and western blots.The effect of these genes on cell proliferation and migration was studied using phenotypic assays.Results:Using computational approaches,we identified NFE2L3 as a master regulator with BHLHE40 as its target gene.NFE2L3 protein binds to the promoter region of BHLHE40 and regulates its transcriptional activity.Additionally,silencing and overexpressing NFE2L3 and BHLHE40 in TNBC cell lines MDA-MB-231 and MDA-MB-468 showed that NFE2L3 directly regulates BHLHE40 at both transcriptional and translational levels.We found that BHLHE40 requires NFE2L3 for cell proliferation and migration in TNBC.Conclusion:These findings underscore the significance of NFE2L3 and BHLHE40 in TNBC,highlighting NFE2L3’s role in regulating the oncogenic activity of BHLHE40 in TNBC cells.展开更多
AIM: To evaluate the diagnostic and prognostic value of circulating Metastasis Associated in Colon Cancer 1(MACC1) transcripts in plasma of gastric cancer patients.METHODS: We provide for the first time a blood-based ...AIM: To evaluate the diagnostic and prognostic value of circulating Metastasis Associated in Colon Cancer 1(MACC1) transcripts in plasma of gastric cancer patients.METHODS: We provide for the first time a blood-based assay for transcript quantification of the metastasis inducer MACC1 in a prospective study of gastric cancer patient plasma.MACC1 is a strong prognostic biomarker for tumor progression and metastasis in a variety of solid cancers.We conducted a study to define the diagnostic and prognostic power of MACC1 transcripts using 76 plasma samples from gastric cancer patients,either newly diagnosed with gastric cancer,newly diagnosed with metachronous metastasis of gastric cancer,as well as follow-up patients.Findings were controlled by using plasma samples from 54 tumor-free volunteers.Plasma was separated,RNA was isolated,and levels of MACC1 as well as S100A4 transcripts were determined by quantitative RT-PCR.RESULTS: Based on the levels of circulating MACC1 transcripts in plasma we significantly discriminated tumorfree volunteers and gastric cancer patients(P < 0.001).Levels of circulating MACC1 transcripts were increased in gastric cancer patients of each disease stage,compared to tumor-free volunteers: patients with tumors without metastasis(P = 0.005),with synchronous metastasis(P = 0.002),with metachronous metastasis(P = 0.005),and patients during follow-up(P = 0.021).Sensitivity was 0.68(95%CI: 0.45-0.85) and specificity was 0.89(95%CI: 0.77-0.95),respectively.Importantly,gastric cancer patients with high circulating MACC1 transcript levels in plasma demonstrated significantly shorter survival whencompared with patients demonstrating low MACC1 levels(P = 0.0015).Furthermore,gastric cancer patients with high circulating transcript levels of MACC1 as well as of S100A4 in plasma demonstrated significantly shorter survival when compared with patients demonstrating low levels of both biomarkers or with only one biomarker elevated(P = 0.001).CONCLUSION: Levels of circulating MACC1 transcripts in plasma of gastric cancer patients are of diagnostic value and are prognostic for patient survival in a prospective study.展开更多
As part of our efforts to identify novel contraceptive targets in the epididymis we performed transcriptional profiling on each of the 10 and 19 segments of the mouse and rat epididymidis, respectively, using Affymetr...As part of our efforts to identify novel contraceptive targets in the epididymis we performed transcriptional profiling on each of the 10 and 19 segments of the mouse and rat epididymidis, respectively, using Affymetrix whole genome microarrays. A total of 17 096 and 16 360 probe sets representing transcripts were identified as being expressed in the segmented mouse and rat epididymal transcriptomes, respectively. Comparison of the expressed murine transcripts against a mouse transcriptional profiling database derived from 22 other mouse tissues identified 77 transcripts that were expressed uniquely in the epididymis. The expression of these genes was further evaluated by reverse transcription polymerase chain reaction （RT-PCR） analysis of RNA from 21 mouse tissues. RT-PCR analysis confirmed epididymis-specific expression of Defensin Beta 13 and identified two additional genes with expression restricted only to the epididymis and testis. Comparison of the 16 360 expressed transcripts in the rat epididymis with data of 21 other tissues from a rat transcriptional profiling database identified 110 transcripts specific for the epididymis. Sixty-two of these transcripts were further investigated by qPCR analysis. Only Defensin 22 （E3 epididymal protein） was shown to be completely specific for the epididymis. In addition, 14 transcripts showed more than 100-fold selective expression in the epididymis. The products of these genes might play important roles in epididymal and/or sperm function and further investigation and validation as contraceptive targets are warranted. The results of the studies described in this report are available at the Mammalian Reproductive Genetics （MRG） Database （http：//mrg. genetics.washington.edu/）. （Asian J Androl 2007July; 9： 522-527）展开更多
MicroRNAs （miRNAs） are endogenous 22-nt RNAs, which play important regulatory roles by post-transcriptional gene silencing. A computational strategy has been developed for the identification of conserved miRNAs base...MicroRNAs （miRNAs） are endogenous 22-nt RNAs, which play important regulatory roles by post-transcriptional gene silencing. A computational strategy has been developed for the identification of conserved miRNAs based on features of known metazoan miRNAs in red flour beetle （Tribolium castaneum）, which is regarded as one of the major laboratory models of arthropods. Among 118 putative miRNAs, 47% and 53% of the predicted miRNAs from the red flour beetle are harbored by known protein-coding genes （intronic） and genes located outside （intergenic miRNA）, respectively. There are 31 intronic miRNAs in the same transcriptional orientation as the host genes, which may share RNA polymerase II and spliceosomal machinery with their host genes for their biogenesis. A hypothetical feed-back model has been proposed based on the analysis of the relationship between intronic miRNAs and their host genes in the development of red flour beetle.展开更多
基金supported by the National Natural Science Foundation of China(31872706)the National Key Research and Development Program of China(2019 YFD1000603).
文摘Zanthoxylum bungeanum is an economically important crop worldwide due to its high content of aroma-producing monoterpenoids,and development of varieties with enhanced flavor and overall quality is a crucial research area.However,the transcriptional regulatory mechanisms underlying monoterpenoid synthesis in Z.bungeanum remain unclear,hindering these breeding efforts.In this study,RNA sequencing,gas chromatography–mass spectrometry,and other molecular biology techniques were used to identify the underlying transcriptional regulation mechanisms.Two transcription factors,ZbbHLH2 and ZbERF6,were identified as key regulators of monoterpenoid synthesis in Z.bungeanum that upregulate various monoterpenoid synthesis-associated genes and are novel transcriptional activators of ZbIDI,which encodes the rate-limiting enzyme in plant monoterpenoid synthesis.Functional analysis revealed that the expression of three genes[1]modulates monoterpenoid accumulation in Z.bungeanum peel.These findings provide novel insights into the metabolic regulatory network of monoterpenoid synthesis in Z.bungeanum peel,offer potential strategies for the biofortification of specific monoterpenoids,and will promote the development of Z.bungeanum germplasm for targeted breeding and quality improvement.
基金supported by the China Agricultural Research System(Grant No.CARS-09)the Central Government Guiding Local Science and Technology Development Project(Grant No.YDZX2023029)the Gansu Planning Projects on Science and Technology(Grant No.23CXNJ0013).
文摘Flavonoids,abundant in the fruits,are pivotal to their growth,development,and storage.In addition,they have significant beneficial effects on human health.Consequently,research is increasingly concentrating on the regulatory mechanisms governing flavonoid biosynthesis in fruits.Phytohormones are involved in the regulation of flavonoid biosynthesis.The abscisic acid,ethylene,jasmonic acid,cytokinins,and brassinosteroids promote flavonoid biosynthesis,while auxin negatively regulates flavonoid biosynthesis.Subsequently,transcription factors from the MYB,bHLH,WRKY,NAC,and bZIP families are pivotal in regulating flavonoid biosynthesis.In addition,non-coding RNAs(microRNA and lncRNA)also participate in the regulation of flavonoids biosynthesis.MicroRNAs are generally believed to negatively regulate flavonoid metabolism in fruits,while lncRNAs have the opposite effect.Furthermore,the interactions between plant hormones,transcription factors,and non-coding RNAs in fruit flavonoid biosynthesis were analyzed.Ultimately,a foundational regulatory network for fruit flavonoid biosynthesis was hereby established.
基金Supported by Guangdong Basic and Applied Basic Research Foundation(2023A1515110973)Guangdong Provincial Young Innovative Talents Project of General Colleges and Universities(2023KQNCX089)+6 种基金Key Field Special Project of Guangdong Provincial Colleges and Universities(2025ZDZX2077)the Rural Science and Technology Commissioner Program of Guangdong Province(KTP20240673)Undergraduate Higher Education Teaching Quality and Reform Projects of Guangdong Province(Yuejiao Gao Han[2024]No.9Yuejiao Gao Han[2024]No.30)Zhaoqing Science and Technology Innovation Guidance Project(Zhaoke[2025]No.4)Scientific Research Foundation of Zhaoqing University(QN202436)College Student Innovation Training Program Project(S202510580042).
文摘[Objectives]To characterize the expression pattern of Fibroblast growth factor 10(FGF10)during the differentiation of rat L6 myoblasts and to identify potential key transcription factors(TFs)regulating its expression through bioinformatics approaches.[Methods]Rat L6 myoblasts were induced to differentiate by culturing them in DMEM supplemented with 2%donor horse serum(DHS).Morphological changes were observed using an inverted microscope.Cell samples were collected prior to induction(day 0)and on days 1,3,5,and 7 post-induction.The relative expression levels of FGF10 mRNA and protein at each time point were quantified using RT-qPCR and Western blot analysis,respectively.Furthermore,a 2000 bp sequence upstream of the transcription start site of the rat Fgf10 gene was extracted as the promoter region.Putative TF binding sites were predicted using four databases(TRANSFAC,JASPAR,HOCOMOCO,and CISBP),and high-confidence candidates were screened to construct a regulatory network.[Results]Morphological observations confirmed successful differentiation,as evidenced by the appearance of binucleated myotubes on day 3 and the formation of numerous thick,multinucleated myotubes by day 7.Both RT-qPCR and Western blot analysis demonstrated a significant dynamic expression pattern of FGF10.Expression levels were markedly upregulated during the early phase(days 1-3),reaching a peak on day 3(P<0.01),followed by a decline to basal levels during the late phase(days 5-7).Cross-validation across multiple databases identified 48 high-confidence TFs,among which Elf5,Tcf3,Nkx3-2,Zic2,Tcf7,and Egr1 were consistently predicted by all four databases.[Conclusions]FGF10 exhibits high expression levels during the early stage of differentiation,indicating its crucial role in the initiation of myogenesis.The six identified TFs serve as core candidate regulators of Fgf10 expression,offering novel insights into the molecular mechanisms underlying muscle development.
基金supported by the National Natural Science Foundation of China(Grant Nos.31870695,32071828)the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD).
文摘Flower color is an essential trait in ornamental plant breeding. Lycoris longituba is a popular ornamental plant native to central eastern China. The decrease in anthocyanin accumulation causes L. longituba petal color fading during flower development, which considerably affects the ornamental value of L. longituba. However, mechanisms underlying anthocyanin biosynthesis inhibition during L. longituba petal development remain unclear. In this study, three LlDFR genes were confirmed to be involved in anthocyanin biosynthesis and LlDFRc exerted the strongest promoting effect on anthocyanin accumulation. According to the correlation analysis results, LlbHLH12 exhibited the strongest negative correlation with LlDFRc. Quantitative real-time PCR analysis showed that LlbHLH12 was highly expressed during the medium bud and full bloom stages of flower development. LlbHLH12 was identified as a member of subgroup XII of bHLH transcription factor family. Subcellular localization and transcriptional activation ability assay revealed that LlbHLH12 was located in the nucleus without transcriptional activation activity. Overexpression of LlbHLH12 in Nicotiana tabacum and L. longituba inhibited anthocyanin accumulation by suppressing the expression of anthocyanin biosynthetic pathway genes. Furthermore, yeast one-hybrid, dual-luciferase, and β-glucuronidase activity assays showed that LlbHLH12 directly bound to the promoters of LlPAL and LlDFRc and suppressed their expression to inhibit anthocyanin biosynthesis. Overall, our study identified a novel bHLH repressor negatively regulating anthocyanin biosynthesis and provided new insights into the molecular mechanisms underlying color fading in L. longituba petals.
基金supported by SISSA(intramural funding to AM)International FOXG1 Research Foundation(Grant to AM)+1 种基金Italian Ministery of University and Research(Grant PRIN222022M95RC7 to AM)Fondazione Telethon(Grant GMR22T2018 to AM).
文摘Moving from the most recent results on Foxg1 biology,we first summarize the available information on some special pleiotropic effectors of neurodevelopmental interest,involved in controlling both transcription and post-transcriptional steps of gene expression.Then,after further analysis of the literature,we report evidence that,not strictly limited to neurodevelopmental effectors,such pleiotropy also applies to other transcription factors,involved in physiology and homeostasis.Furthermore,through the systematic analysis of a major public protein-protein interaction database,we gather strong evidence that the involvement of“canonical”transcription factors in post-transcriptional control of gene expression could be a pervasive phenomenon,characterizing hundreds of effectors.Finally,we discuss the biological significance of these findings and propose three evolutionary mechanisms that may have contributed to such an unexpected scenario.
基金supported by Hebei Natural Science Foundation(H2024206476)Medical Science Research Project of Hebei(20240101).
文摘Background:The regulatory mechanisms governing vasculogenic mimicry(VM)in oral squamous cell carcinoma(OSCC)remain largely undefined.This study aimed to identify critical factors and elucidate the epigenetic mechanisms underlying VM in OSCC.Methods:Bioinformatics analysis was performed utilizing single-cell RNA-seq,bulk RNA-seq,and histone H3 lysine 27 acetylation(H3K27ac)Chromatin Immunoprecipitation(ChIP)-seq data obtained from The Cancer Genome Atlas(TCGA)and Gene Expression Omnibus(GEO)databases.ChIP-qPCR was used to validate the binding of ETS transcription factor ELK4(ELK4)to the dihydrofolate reductase(DHFR)enhancer.In vitro VM formation and invasion of OSCC cells were assessed using Matrigel-based tube formation and Transwell assays,respectively.Results:Elevated expression of VM-related genes predicts unfavorable prognosis in OSCC patients.High-dimensional weighted gene co-expression network analysis(hdWGCNA)identified epithelial subcluster C4 as most strongly associated with VM and metastasis.Three co-expression modules within this subcluster exhibited significant positive correlations with both phenotypic traits.Among the 30 eigengenes from the three modules,DHFR emerged as a key regulator of VM and metastasis.Knockdown or inhibition of DHFR significantly suppressed VM formation and invasion in OSCC cells.Mechanistically,ELK4 activated DHFR transcription through direct binding to its enhancer.DHFR overexpression rescued VM and invasion impairment induced by ELK4 knockdown.Conclusion:DHFR was a pivotal enhancer-regulated gene driving VM and metastasis in OSCC.ELK4 directly binds to DHFR enhancer regions to activate its transcription,thereby promoting these malignant phenotypes.These findings identified the ELK4/DHFR axis as a promising therapeutic target for anti-angiogenic intervention in OSCC.
基金supported by the Major Project of Guizhou Provincial Science and Technology Program,China([2024]027)the High-Level Innovative Talents Project of Guizhou Province,China(GCC[2023]014)+1 种基金the Guizhou Provincial Tea Industry Technology System,China(GZCYCYJSTX-03)the Science and Technology Project of China Huaneng Group(HNKJ2022-H135)。
文摘Heat stress reduces theanine content in tea plants,but the underlying molecular mechanism remains unclear.In this study,a temperature gradient treatment(20℃,25℃,30℃,and 35℃)was performed to unveil the effect of heat stress on biosynthesis and accumulation of theanine.We found that heat stress induced metabolic changes,characterized by decreased theanine content and increased catechin levels.In addition,heat stress up-regulated the expression of the class B heat shock transcription factor gene CsHSFB2c,while significantly suppressing the transcription of key theanine biosynthetic genes CsTS1 and CsGS1.Functional studies showed that silencing CsHSFB2c increased theanine content,while its overexpression significantly decreased theanine levels.Consistent with these changes,silencing CsHSFB2c upregulated the expression of CsTS1 and CsGS1,while overexpression of CsHSFB2c downregulated their expression.Yeast one-hybrid(Y1H)and dual-luciferase reporter gene(Dual-LUC)assays showed that CsHSFB2c directly binds to the promoters of CsTS1 and CsGS1 and inhibits their expression.These results demonstrate that CsHSFB2c mediates heat-induced suppression of theanine biosynthesis by directly inhibiting the expression of CsTS1 and CsGS1.This study provides a theoretical basis for improving the heat resistance and quality of tea plants via molecular breeding.
文摘Nuclear receptor subfamily 2 group F member 1(NR2F1,also called COUP-TF1)is a transcription factor and part of the steroid/thyroid hormone receptor superfamily(Gay et al.,2002).NR2F1 is an orphan receptor that dimerizes to bind DNA and acts as a repressor as well as an activator of the target genes(Gay et al.,2002;Bertacchi et al.,2019;Bonzano et al.,2023).
文摘AIM:To investigate whether vaccinia-related kinase 1(VRK1)mediates transforming growth factor-beta2(TGF-β2)-caused epithelial-mesenchymal transition(EMT)and inflammatory responses in retinal pigment epithelial(RPE)cells through regulating snail family transcriptional repressor 1(SNAI1),and to validate its role in a proliferative vitreoretinopathy(PVR)mouse model.METHODS:Human RPE cell line ARPE-19 cells were treated with TGF-β2 to construct an EMT model.Western blot detected VRK1 level.The effects of VRK1 on SNAI1 expression and biological behavior of ARPE-19 cells were detected by immunofluorescence,ELISA,Transwell,and scratch assay,and the interaction between VRK1 and SNAI1 was confirmed through immunoprecipitation.A PVR mouse model was constructed,and the effects of VRK1 or/and SNAI1 on retinal damage were assessed by pathologic staining.Inflammatory factors and EMT-related proteins were assessed with ELISA and Western blot.RESULTS:VRK1 was upregulated in ARPE-19 cells after TGF-β2 treatment.Overexpression of VRK1 increased cell viability,promoted cell migration and EMT,and the levels of inflammatory factors.Silencing of VRK1 reversed the above indexes.There was a direct interaction between VRK1 and SNAI1,and overexpresssion SNAI1 weakened the impacts of silencing of VRK1.In PVR mice,silencing of VRK1 ameliorated retinal structural damage,decreased proinflammatory factor levels,and suppressed SNAI1 and mesenchymal marker expression.SNAI1 overexpression antagonized the protective effects of silencing VRK1 and exacerbated EMT and inflammatory responses.CONCLUSION:VRK1 plays a key role in retinal structural and inflammatory damage in PVR mice by regulating SNAI1 and mediating TGF-β2-caused EMT and inflammatory responses in RPE cells.
基金supported by the National Key Research and Development Program of China to W.Tian (2022YFA1104400)the National Natural Science Foundation of China to T.Chen (82100959)a grant from the Sichuan Science and Technology Program to Z.Liu (2024YFFK0068)。
文摘Tooth morphogenesis is orchestrated by a complex interplay of signaling pathways and transcription factors that control cell proliferation,apoptosis,and differentiation,with the Wnt/β-catenin signaling pathway playing a pivotal role.However,the comprehensive regulatory mechanisms of Wnt/β-catenin signaling remain largely unclear.Smad7,a key antagonist of the TGF-βsuperfamily,is essential for maintaining tissue homeostasis and ensuring proper cellular function.Our previous study has demonstrated that Smad7 knockout in mice leads to impaired proliferative property of tooth germ cells,resulting in small molars.Here,we identified SMAD7 expression in human dental papilla and dental pulp,colocalized with β-CATENIN and cell proliferationrelated proteins.RNA sequencing analysis revealed a significant reduction in Wnt signaling activity in Smad7-deficient mouse tooth germs.Using lentivirus transfection,we established SMAD7-knockdown human dental papilla stem cells,which manifested remarkably blunt proliferation rate,along with diminished Wnt signaling activity.In vivo transplantation investigations further revealed the indispensable role of SMAD7 in dentin formation.Mechanistically,we revealed that β-CATENIN interacts with P-SMAD2/3 and SMAD7 through co-immunoprecipitation and yeast two-hybrid assays.Inhibition of TGF-β pathway or disruption of SMAD7/β-CATENIN transcription factor complex formation potently impacted Wnt/β-catenin activities,indicating both direct and indirect regulatory mechanisms.These findings highlight the critical role of SMAD7 in the proliferation and diffe rentiation of human dental stem cells,which could contribute to dental tissue regeneration and engineering.
基金supported by the Foundation Project:National Natural Science.Foundation of China(Nos.:82460249,82100417,81760094)The Foundation of Jiangxi Provincial Department of Science and Technology Outstanding Youth Fund Project(20212BAB206022,20242BAB23080).
文摘Objective:Leucine-rich alpha-2 glycoprotein 1(Lrg1)could regulate diverse cells in cerebral ischemiareperfusion.Our study seeks to uncover Lrg1’s impact on endothelial cell heterogeneity via differentiation pathways and transcription factors.Method:The CSOmap model measured cell-to-brain-center distances using single-cell RNA sequencing(scRNA-seq)data in middle cerebral artery occlusion reperfusion(MCAO/R).Monocle2 mapped endothelial differentiation paths.Gene set enrichment analysis(GSEA)analyzed endothelial subcluster variations.Database searches revealed a zinc finger MIZ-type containing 1 protein-frizzled 3(Zmiz1-Fzd3)promoter interaction.Endothelial cells were transfected with a Fzd3 promoter-luciferase plasmid.Polymerase chain reaction(PCR)and western blotting assessed MCAO/R or Zmiz1 overexpression effects on Fzd3-related mRNA and proteins.A retroviral vector carrying Zmiz1 was injected into the brains of mice to study its effect on Fzd3.Result:Lrg1−/−mice exhibited elevated cell adhesion proteins and decreased microvascular leakage after MCAO/R.CSOmap showed widened astrocyte spacing in thesemice.RSS revealed Zmiz1 overexpression inMCAO/R+Lrg1−/−mice.MCAO/R and pcDNA3-Zmiz1 transfection both enhanced luciferase activity with Fzd3,indicating Zmiz1 binding to Fzd3.Retroviral Zmiz1 injection or knockdown disrupted ischemic brain tight junctions,highlighting Zmiz1’s key role in blood-brain barrier protection,likely through Fzd3 pathway modulation.Conclusion:The findings indicate Lrg1 knockout induces endothelial differentiation by activating Zmiz1,which is crucial for maintaining blood-brain barrier function,possibly via modulating the Fzd3 pathway.
文摘Aberrant RNA modification has been linked to the pathogenesis of various diseases;however,its specific molecular mechanisms in spinal cord injury remain poorly understood.The objective of this study was to explore RNA modification-related biomarkers of spinal cord injury.The mRNA expression profiles of mice with spinal cord injury were retrieved from the Gene Expression Omnibus(GEO)database(GSE18179).We identified 185 differentially expressed genes using bioinformatics approaches.Functional enrichment analysis demonstrated aberrant activation or inhibition of common metabolism-related pathways,including sulfur metabolism and steroid biosynthesis,in mice with spinal cord injury.An integrated strategy comprising weighted gene co-expression network analysis,a random forest model,a support vector machine model,and a generalized linear model was employed to identify four genes whose aberrant RNA modification was linked to spinal cord injury:Elovl6,Idi1,Sqle,and Stbd1.We verified the expression levels and diagnostic performance of these four genes in the original training dataset and mouse samples via receiver operating characteristic curve analysis.Quantitative reverse transcription-polymerase chain reaction demonstrated variations in the mRNA levels of the four genes between the Sham and spinal cord injury groups at different time points following injury.We also constructed microRNA-mRNA and transcription factor-mRNA interaction networks using Cytoscape.Additionally,we evaluated the proportions of 22 types of immune cells in the spinal cords of mice using the CIBERSORT tool,revealing significant alterations in the numbers of memory B cells,resting dendritic cells,M0 macrophages,activated mast cells,resting mast cells,and CD8+T cells in spinal cord injury mice compared with Sham controls.Microglia and T cells were identified as key cell types by single-cell sequencing analysis.These findings provide new directions for the development of RNA modification-related therapeutic strategies for spinal cord injury and suggest that Elovl6,Idi1,Sqle,and Stbd1 are potential biomarkers of spinal cord injury.
文摘Objectives:The current treatment options and therapeutic targets for triple-negative breast cancer(TNBC),an aggressive subtype of breast cancer(BrCA),are limited.This study aimed to identify novel biomarkers and transcriptional regulatory networks(TRN)inherent in TNBC samples.Methods:We analyzed pan-cancer BrCA datasets from The Cancer Genome Atlas(TCGA)to compare triple-positive breast cancer(TPBC)with TNBC.TRN algorithms and virtual inference of protein-enriched regulon(VIPER)were used to identify master regulators and their target genes.Utilizing TNBC cells(MDA-MB-231 and MDA-MB-468),we validated the relationship of nuclear factor erythroid 2-like 3(NFE2L3)and basic helix-loop-helix family member E 40(BHLHE40)by performing a luciferase assay.The expression levels of these targets were measured after transfections with plasmid and siRNA via qRT-PCR and western blots.The effect of these genes on cell proliferation and migration was studied using phenotypic assays.Results:Using computational approaches,we identified NFE2L3 as a master regulator with BHLHE40 as its target gene.NFE2L3 protein binds to the promoter region of BHLHE40 and regulates its transcriptional activity.Additionally,silencing and overexpressing NFE2L3 and BHLHE40 in TNBC cell lines MDA-MB-231 and MDA-MB-468 showed that NFE2L3 directly regulates BHLHE40 at both transcriptional and translational levels.We found that BHLHE40 requires NFE2L3 for cell proliferation and migration in TNBC.Conclusion:These findings underscore the significance of NFE2L3 and BHLHE40 in TNBC,highlighting NFE2L3’s role in regulating the oncogenic activity of BHLHE40 in TNBC cells.
文摘AIM: To evaluate the diagnostic and prognostic value of circulating Metastasis Associated in Colon Cancer 1(MACC1) transcripts in plasma of gastric cancer patients.METHODS: We provide for the first time a blood-based assay for transcript quantification of the metastasis inducer MACC1 in a prospective study of gastric cancer patient plasma.MACC1 is a strong prognostic biomarker for tumor progression and metastasis in a variety of solid cancers.We conducted a study to define the diagnostic and prognostic power of MACC1 transcripts using 76 plasma samples from gastric cancer patients,either newly diagnosed with gastric cancer,newly diagnosed with metachronous metastasis of gastric cancer,as well as follow-up patients.Findings were controlled by using plasma samples from 54 tumor-free volunteers.Plasma was separated,RNA was isolated,and levels of MACC1 as well as S100A4 transcripts were determined by quantitative RT-PCR.RESULTS: Based on the levels of circulating MACC1 transcripts in plasma we significantly discriminated tumorfree volunteers and gastric cancer patients(P < 0.001).Levels of circulating MACC1 transcripts were increased in gastric cancer patients of each disease stage,compared to tumor-free volunteers: patients with tumors without metastasis(P = 0.005),with synchronous metastasis(P = 0.002),with metachronous metastasis(P = 0.005),and patients during follow-up(P = 0.021).Sensitivity was 0.68(95%CI: 0.45-0.85) and specificity was 0.89(95%CI: 0.77-0.95),respectively.Importantly,gastric cancer patients with high circulating MACC1 transcript levels in plasma demonstrated significantly shorter survival whencompared with patients demonstrating low MACC1 levels(P = 0.0015).Furthermore,gastric cancer patients with high circulating transcript levels of MACC1 as well as of S100A4 in plasma demonstrated significantly shorter survival when compared with patients demonstrating low levels of both biomarkers or with only one biomarker elevated(P = 0.001).CONCLUSION: Levels of circulating MACC1 transcripts in plasma of gastric cancer patients are of diagnostic value and are prognostic for patient survival in a prospective study.
文摘As part of our efforts to identify novel contraceptive targets in the epididymis we performed transcriptional profiling on each of the 10 and 19 segments of the mouse and rat epididymidis, respectively, using Affymetrix whole genome microarrays. A total of 17 096 and 16 360 probe sets representing transcripts were identified as being expressed in the segmented mouse and rat epididymal transcriptomes, respectively. Comparison of the expressed murine transcripts against a mouse transcriptional profiling database derived from 22 other mouse tissues identified 77 transcripts that were expressed uniquely in the epididymis. The expression of these genes was further evaluated by reverse transcription polymerase chain reaction （RT-PCR） analysis of RNA from 21 mouse tissues. RT-PCR analysis confirmed epididymis-specific expression of Defensin Beta 13 and identified two additional genes with expression restricted only to the epididymis and testis. Comparison of the 16 360 expressed transcripts in the rat epididymis with data of 21 other tissues from a rat transcriptional profiling database identified 110 transcripts specific for the epididymis. Sixty-two of these transcripts were further investigated by qPCR analysis. Only Defensin 22 （E3 epididymal protein） was shown to be completely specific for the epididymis. In addition, 14 transcripts showed more than 100-fold selective expression in the epididymis. The products of these genes might play important roles in epididymal and/or sperm function and further investigation and validation as contraceptive targets are warranted. The results of the studies described in this report are available at the Mammalian Reproductive Genetics （MRG） Database （http：//mrg. genetics.washington.edu/）. （Asian J Androl 2007July; 9： 522-527）
文摘MicroRNAs （miRNAs） are endogenous 22-nt RNAs, which play important regulatory roles by post-transcriptional gene silencing. A computational strategy has been developed for the identification of conserved miRNAs based on features of known metazoan miRNAs in red flour beetle （Tribolium castaneum）, which is regarded as one of the major laboratory models of arthropods. Among 118 putative miRNAs, 47% and 53% of the predicted miRNAs from the red flour beetle are harbored by known protein-coding genes （intronic） and genes located outside （intergenic miRNA）, respectively. There are 31 intronic miRNAs in the same transcriptional orientation as the host genes, which may share RNA polymerase II and spliceosomal machinery with their host genes for their biogenesis. A hypothetical feed-back model has been proposed based on the analysis of the relationship between intronic miRNAs and their host genes in the development of red flour beetle.
