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co-expression network analysis predicts a key role of microRNAs in the adaptation of the porcine skeletal muscle to nutrient supply

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Journal of Animal Science and Biotechnology 2020年第2期11卷 327-347页

作者： Emilio Mármol-Sánchez Yuliaxis Ramayo-Caldas Raquel Quintanilla TainãFigueiredo Cardoso Rayner González-Prendes Joan Tibau Marcel Amills Centre for Research in Agricultural Genomics(CRAG) CSIC-IRTA-UAB-UBUniversitat Autònoma de Barcelona08193 BellaterraSpain Animal Breeding and Genetics Program Institute for Research and Technology in Food and Agriculture(IRTA)Torre Marimon08140 Caldes de MontbuiSpain Present address:Embrapa Pecuária Sudeste Empresa Brasileira de Pesquisa Agropecuária(EMBRAPA)São CarlosSP 13560-970Brazil Department of Animal Science Universitat de Lleida-Agrotecnio Center25198 LleidaSpain Departament de Ciència Animal i dels Aliments Universitat Autònoma de Barcelona08193 BellaterraBarcelonaSpain

Background:The role of non-coding RNAs in the porcine muscle metabolism is poorly understood,with few studies investigating their expression patterns in response to nutrient supply.Therefore,we aimed to investigate the changes in microRNAs(miRNAs),long intergenic non-coding RNAs(lincRNAs)and mRNAs muscle expression before and after food intake.Results:We measured the miRNA,lincRNA and mRNA expression levels in the gluteus medius muscle of 12 gilts in a fasting condition(AL-T0)and 24 gilts fed ad libitum during either 5 h.(AL-T1,N=12)or 7 h.(AL-T2,N=12)prior to slaughter.The small RNA fraction was extracted from muscle samples retrieved from the 36 gilts and sequenced,whereas lincRNA and mRNA expression data were already available.In terms of mean and variance,the expression profiles of miRNAs and lincRNAs in the porcine muscle were quite different than those of mRNAs.Food intake induced the differential expression of 149(AL-T0/AL-T1)and 435(AL-T0/AL-T2)mRNAs,6(AL-T0/AL-T1)and 28(AL-T0/AL-T2)miRNAs and none lincRNAs,while the number of differentially dispersed genes was much lower.Among the set of differentially expressed miRNAs,we identified ssc-miR-148a-3p,ssc-miR-22-3p and ssc-miR-1,which play key roles in the regulation of glucose and lipid metabolism.Besides,co-expression network analyses revealed several miRNAs that putatively interact with mRNAs playing key metabolic roles and that also showed differential expression before and after feeding.One case example was represented by seven miRNAs(ssc-miR-148a-3p,ssc-miR-151-3p,ssc-miR-30a-3p,ssc-miR-30e-3p,ssc-miR-421-5p,ssc-miR-493-5p and ssc-miR-503)which putatively interact with the PDK4 mRNA,one of the master regulators of glucose utilization and fatty acid oxidation.conclusions:As a whole,our results evidence that microRNAs are likely to play an important role in the porcine skeletal muscle metabolic adaptation to nutrient availability.

关键词： co-expression analysis lincRNAs microRNAs Pig Regulatory impact factor Skeletal muscle

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Single-cell analysis of transcription factor regulatory networks reveals molecular basis for subtype-specific dysregulation in acute myeloid leukemia

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Blood Science 2022年第2期4卷 65-75页

作者： Ruixia Sun Lina Sun Xiaowei Xie Xuan Li Peng Wu Lu Wang Ping Zhu State Key Laboratory of Experimental Hematology National Clinical Research Center for Blood DiseasesHaihe Laboratory of Cell EcosystemInstitute of Hematology&Blood Diseases HospitalChinese Academy of Medical Sciences&Peking Union Medical CollegeTianjinChina Center for Stem Cell Medicine and Department of Stem Cell&Regenerative Medicine Chinese Academy of Medical Sciences&Peking Union Medical CollegeTianjinChina

Highly heterogeneous acute myeloid leukemia(AML)exhibits dysregulated transcriptional programs.Transcription factor(TF)regulatory networks underlying AML subtypes have not been elucidated at single-cell resolution.Here,we comprehensively mapped malignancy-related TFs activated in different AML subtypes by analyzing single-cell RNA sequencing data from AMLs and healthy donors.We first identified six modules of regulatory networks which were prevalently dysregulated in all AML patients.AML subtypes featured with different malignant cellular composition possessed subtype-specific regulatory TFs associated with differentiation suppression or immune modulation.At last,we validated that ERF was crucial for the development of hematopoietic stem/progenitor cells by performing loss-and gain-of-function experiments in zebrafish embryos.collectively,our work thoroughly documents an abnormal spectrum of transcriptional regulatory networks in AML and reveals subtype-specific dysregulation basis,which provides a prospective view to AML pathogenesis and potential targets for both diagnosis and therapy.

关键词： Acute myeloid leukaemia co-expression analysis Single-cell RNA-sequencing Transcription factor Transcriptional regulatory network

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analysis of long noncoding RNA-associated competing endogenous RNA network in glucagon-like peptide-1 receptor agonist-mediated protection inβcells

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World Journal of Diabetes 2020年第9期11卷 374-390页

作者： Li-Juan Cui Tao Bai Lin-Ping Zhi Zhi-Hong Liu Tao Liu Huan Xue Huan-Huan Yang Xiao-Hua Yang Min Zhang Ya-Ru Niu Yun-Feng Liu Yi Zhang Department of Pharmacology Basic Medical CollegeShanxi Medical UniversityTaiyuan 030001Shanxi ProvinceChina Department of Endocrinology The First Clinical Hospital of Shanxi Medical UniversityTaiyuan 030001Shanxi ProvinceChina Department of Respiratory Medicine The First Clinical Hospital of Shanxi Medical UniversityTaiyuan 030001Shanxi ProvinceChina Department of General Surgery Shanxi Bethune HospitalTaiyuan 030006Shanxi ProvinceChina college of Pharmacy Shanxi Medical UniversityTaiyuan 030001Shanxi ProvinceChina Second Clinical Medical college Shanxi Medical UniversityTaiyuan 030001Shanxi ProvinceChina

BACKGROUND Long noncoding RNAs(lncRNAs)and mRNAs are widely involved in various physiological and pathological processes.The use of glucagon-like peptide-1 receptor agonists(GLP-1RAs)is a novel therapeutic strategy that could promote insulin secretion and decrease the rate ofβ-cell apoptosis in type 2 diabetes mellitus(T2DM)patients.However,the specific lncRNAs and mRNAs and their functions in these processes have not been fully identified and elucidated.AIM To identify the lncRNAs and mRNAs that are involved in the protective effect of GLP-1RA inβcells,and their roles.METHODS Rat gene microarray was used to screen differentially expressed(DE)lncRNAs and mRNAs inβcells treated with geniposide,a GLP-1RA.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analyses were performed to assess the underlying functions of DE mRNAs.Hub mRNAs were filtered using the STRING database and the Cytoscape plugin,CytoHubba.In order to reveal the regulatory relationship between lncRNAs and hub mRNAs,their co-expression network was constructed based on the Pearson coefficient of DE lncRNAs and mRNAs,and competing endogenous RNA(ceRNA)mechanism was explored through miRanda and TargetScan databases.RESULTS We identified 308 DE lncRNAs and 128 DE mRNAs with a fold change filter of≥1.5 and P valuecoupled receptor signaling pathway,inflammatory response,calcium signaling pathway,positive regulation of cell proliferation,and ERK1 and ERK2 cascade.Pomc,Htr2a,and Agtr1a were screened as hub mRNAs using the STRING database and the Cytoscape plugin,CytoHubba.This result was further verified using SwissTargetPrediction tool.Through the co-expression network and competing endogenous(ceRNA)mechanism,we identified seven lncRNAs(NONRATT027738,NONRATT027888,NONRATT030038,etc.)co-expressed with the three hub mRNAs(Pomc,Htr2a,and Agtr1a)based on the Pearson coefficient of the expression levels.These lncRNAs regulated h

关键词： Type 2 diabetes βcell Long noncoding RNA competing endogenous RNA co-expression analysis Glucagon-like peptide-1 receptor agonist

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Identification and characterization of MeERF genes and their targets in pathogen response by cassava(Manihot esculenta)

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The Crop Journal 2021年第5期9卷 1145-1153页

作者： Yuhui Hong Yong Xiao Na Song Shousong Zhu Rui Zhao Ke Li Mengting Geng Xiaohui Yu Honggang Wang Wei Xia Yinhua Chen Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource College of Tropical CropsHainan UniversityHaikou 570228HainanChina coconut Research Institute Chinese Academy of Tropical Agricultural SciencesWenchang 571339HainanChina School of Bioengineering Dalian University of TechnologyDalian 116024LiaoningChina

Cassava,Manihot esculenta Crantz (Me),is a major dietary source of calories for over 700 million people in tropical regions.The production of cassava is constantly threatened by cassava bacterial blight (CBB),caused by Xanthomonas axonopodis pv.manihotis (Xam).The gene resources for CBB-resistant breeding of cassava are limited.In model plant species,ethylene response factors play important roles in response to pathogen infection.In this study,cassava ethylene response factors (MeERFs) were identified and characterized as the first step in studying their potential for CBB-resistant breeding of cassava.In the cassava genome 155 MeERFs were identified,of which 23 were induced by Xam infection.The promoter regions of204 genes harbored GCC-box that had the potential to interact with MeERFs.Using 37 transcriptomes derived from Xam infection treatment,four gene co-expression modules for the MeERFs and GCC-box containing genes were constructed.Six MeERFs were associated with two GCC-box containing genes:transcription initiation factor TFIIE subunit beta (MeTFIIE),and histone-lysine N-methyltransferase ASHR1 (MeASHR1).Dual-luciferase reporter assays showed that MeERF10 and MeERF58 positively regulated Me TFIIE;MeERF137 negatively regulated Me TFIIE;MeERF10 and MeERF137 positively regulated Me ASHR1;and MeERF35 negatively regulated Me ASHR1.The four MeERFs may mediate pathogen response by regulating the expression of the two GCC-box containing genes.

关键词： Cassava Ethylene response factor expression profile co-expression analysis Pathogen

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