Expression Profiling and Bioinformatics Analysis of CircRNA in Mice Brain Infected with Rabies Virus

Rabies virus (RABV) induces acute, fatal encephalitis in mammals including humans. The circRNAs are important in virus infection process, but whether circRNAs regulated RABV infection remains largely unknown. Here, mice brain with or without the RABV CVS-11 strain were subjected to RNA sequencing and a total of 30,985 circRNAs were obtained. Among these, 9021 candidates were shared in both groups, and 14,610 and 7354 circRNAs were expressed specifically to the control and experimental groups, indicating that certain circRNAs were specifically inhibited or induced on RABV infection. The circRNAs mainly derived from coding exons. In total, 636 circRNAs were differentially expressed in RABV infection, of which 426 significantly upregulated and 210 significantly downregulated (p < 0.05 and fold change ≥2). The expression of randomly selected 6 upregulated and 6 downregulated circRNAs was tested by RT-qPCR, and the expression trend of the 11 out of 12 circRNAs was consistent in RT- qPCR and RNA-seq analysis. Rnase R-resistant assay and Sanger sequencing were conducted to verify the circularity of circRNAs. GO analysis demonstrated that source genes of all differentially regulated circRNAs were mainly related to cell plasticity and synapse function. Both KEGG and GSEA analysis revealed that these source genes were engaged in the cGMP–PKG and MAPK signaling pathway, and HTLV-I infection. Also, pathways related to glucose metabolism and synaptic functions were enriched in KEGG analysis. The circRNA–miRNA–mRNA network was built with 25 of 636 differentially expressed circRNAs, 264 mRNAs involved in RABV infection, and 29 miRNAs. Several miRNAs and many mRNAs in the network were reported to be related to viral infection and the immune response, suggesting that circRNAs could regulate RABV infection via interacting with miRNAs and mRNAs. Taken together, this study first characterized the transcriptomic pattern of circRNAs, and signaling pathways and function that circRNAs are involved in, which may indicate directions for further research to understand mechanisms of RABV pathogenesis.

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Comparative analysis of gene expression profiles in differentiated subcutaneous adipocytes between Jiaxing Black and Large White Pigs

10.21203/rs.3.rs-19837/v1 ◽

2020 ◽

Author(s):

Dawei Zhang ◽

Wenjing Wu ◽

Xin Huang ◽

Ke Xu ◽

Cheng Zheng ◽

...

Keyword(s):

Signaling Pathway ◽

Expression Profiles ◽

Mapk Signaling ◽

Fat Deposition ◽

Mapk Signaling Pathway ◽

Differentially Expressed ◽

Rna Seq ◽

Domestic Pig ◽

Large White ◽

Pig Breeds

Abstract Background: Chinese domestic pig breeds are reputed for pork quality, but their low ratio of lean-to-fat carcass weight decreases production efficiency. A better understanding of the genetic regulation network of SC fat tissue is necessary for the rational selection of Chinese domestic pig breeds. In the present study, SC adipocytes were isolated from Jiaxing Black pigs (a Chinese indigenous pig breed with redundant SC fat deposition) and Large White pigs (a lean-type pig breed with relatively low SC fat deposition) and the expression profiles of mRNAs and lncRNAs were compared by RNA-seq analysis to identify biomarkers correlated with the differences of SC fat deposition between the two breeds.Results: A total of 3,371 differentially expressed genes (DEGs) and 1,182 differentially expressed lncRNAs (DELs) were identified in SC adipocytes between Jiaxing Black (JX) and Large White (LW) pigs, which included 797 upregulated mRNAs, 2,574 downregulated mRNAs, 461 upregulated lncRNAs and 721 downregulated lncRNAs. Gene Ontology and KEGG pathway analyses revealed that the DEGs and DELs were mainly involved in the immune response, cell fate determination, PI3K-Akt signaling pathway and MAPK signaling pathway, which are known to be related to adipogenesis and lipid metabolism. The expression levels of DEGs and DELs according to the RNA-seq data were verified by quantitative PCR, which showed 81.8% consistency. The differences in MAPK pathway activity between JX and LW pigs was confirmed by western blot analysis, with <100-fold elevated p38 phosphorylation in JX pigs.Conclusions: This study offers a detailed characterization of mRNAs and lncRNAs in fat- and lean-type pig breeds. The activity of the MAPK signaling pathway was found to be associated with subcutaneous adipogenesis. These results greatly enhance our understanding of the molecular mechanisms regulating SC fat deposition in pigs.

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248 DIESTRUS TRANSCRIPTOME DYNAMICS OF BOVINE ENDOMETRIUM IN RELATION TO PREGNANCY SUCCESS AFTER EMBRYO TRANSFER

Reproduction Fertility and Development ◽

10.1071/rdv22n1ab248 ◽

2010 ◽

Vol 22 (1) ◽

pp. 281

Author(s):

D. Salilew-Wondim ◽

N. Ghanem ◽

M. Hoelker ◽

F. Rings ◽

C. Phatsara ◽

...

Keyword(s):

Estrous Cycle ◽

Embryo Transfer ◽

System Development ◽

Mapk Signaling ◽

Nervous System Development ◽

Differentially Expressed ◽

Regulation Of Transcription ◽

Transferase Activity ◽

And Function

This experiment aimed to investigate the diestrus transcriptome dynamics of endometrium that resulted in calf delivery or no pregnancy after embryo transfer. Endometrium biopsies were collected from Simmental cyclic heifers at Days 7 and 14 of estrus cycle. On the next cycle, in vivo-produced Day 7 blastocysts were transferred to all animals at Day 7 of estrous cycle. Following pregnancy diagnosis, the endometrial biopsies collected at Day 7 and 14 were categorized based on the pregnancy success. Those endometrial biopsies collected from heifers that subsequently delivered a calf were assigned to the calf-delivery group, and those collected from heifers that did not conceive were assigned to the no-pregnancy group. The endometrial temporal transcriptome profile was compared between Days 7 and 14 in both heifer groups. Total RNA was isolated from each sample in triplicate. Two rounds of RNA amplification were performed using MEGAscript® T7 Kit (Ambion, Inc., Austin, TX, USA) and GeneChip® IVT Labeling Kit (Affymetrix, Inc., Santa Clara, CA, USA), respectively. Following fragmentation, biotin-labeled cRNA samples were hybridized to Affymetrix bovine gene chip array. The microarray data normalization and background correction were performed using GCRMA, and the differentially expressed genes (DEG) (fold change >2,P < 0.05, FDR < 0.3) were identified using LIMMA written on R package integrated with Bioconductor. The result showed that in the calf-delivery group, there were 1867 DEG, among which 1015 and 852 were up- and down-regulated, respectively, in Day 7 compared with Day 14 of the estrous cycle. Some of those genes are believed to be involved in reproductive system development and function (F3, PTGER2, PTGER4, MFGE8, PTGS2, and TDGF1), embryonic development (ALDH1A1,ALDH1A3, FGF2, TGFBR2, PDGFB, and TGFBR2), and nervous system development and function (CYP3A4, CYP3A4, HSD17B4, FOXA2, MET, TDGF, WNT11). The bioinformatic analysis using KEGG revealed that those DEG were classified into several pathways including the MAPK signaling pathway. On the other hand, in the no-pregnancy group, 254 genes were found to be differentially expressed, of which 160 and 94 were up- and down-regulated, respectively, in Day 7 compared with Day 14 of the estrous cycle. Some of these genes were found to be involved in signal transducer activity (AXIN2, AGTR1, MAPK10, NTRK2, TLR2, DMBT1, IL1RN, CDK5, CHRNE), transferase activity (DGKI, TXNDC6, RPS6KA5, RIOK3, MYLK, CDK5, MET, NTRK2), receptor activity (MET,AGTR1, NTRK2, TLR2, DMBT1, CHRNE), regulation of transcription (FOS, ELF1, BHLHB2,ATF3, HOXA11), signal transduction (TLR2, AGTR1, FCNB, DGK, NOTCH2, ADAM9, PLEK), and transcription regulator activity (BHLHB2, FOS, ELF1,ATF3, HOXA11). Those DEG were found to be involved in different pathways including the focal adhesion pathway. In conclusion, the result of the current study revealed a remarkable transcriptome dynamics between Days 7 and 14 of the estrous cycle in cows resulted in calf delivery compared with those that did not support pregnancy.

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Abstract 128: RNA-seq Based Non-Invasive Endovascular Biopsy of Brain Arteriovenous Malformations

Stroke ◽

10.1161/str.51.suppl_1.128 ◽

2020 ◽

Vol 51 (Suppl_1) ◽

Author(s):

Ethan Winkler ◽

David McCoy ◽

Zhengda Sun ◽

Daniel Cooke

Keyword(s):

Differentially Expressed Genes ◽

Pearson Correlation ◽

Rna Extraction ◽

Correlation Coefficients ◽

Mapk Signaling ◽

Differentially Expressed ◽

Rna Seq ◽

Detachable Coil ◽

Illumina Hiseq ◽

Non Invasive

Introduction: To-date, there is no accurate means to identify which bAVMs will bleed and treatment remains controversial. Hypothesis: We developed an endovascular biopsy (EB) technique to isolate endothelial cells (ECs) from bAVMs in patients. We hypothesized this technique would allow RNA-seq analysis of relevant bAVM-related molecular pathways. Methods: EB was performed during angiography for bAVM patients undergoing resection. Cells were obtained from a bAVM juxta-nidal feeding artery and iliac artery (control) with a detachable coil and 0.035 inch wire. ECs were isolated with fluorescence assisted cell sorting (FACS). bAVM tissue was obtained from surgery, dissociated and underwent FACS sorting. Total RNA extraction and library preparation was performed, and samples sequenced on an Illumina HiSeq 4000 sequencer. Reads were aligned with Kallisto, and differentially expressed genes identified between bAVM and control with Sleuth using likelihood ratio tests. Correlations between EB and resected tissues were calculated with Pearson correlation coefficients. Principle Component Analysis (PCA) was used to assess for cell clustering. Results: EB was performed in 4 patients without complication or adverse event. PCA showed separation of bAVM ECs from controls. Analysis demonstrated 106 differentially expressed genes (FDR p ≤ 0.05). KEGG pathway analysis on these genes revealed enrichment in bAVM-related RAS/MAPK cell signaling functionally related to trophic factor, chemokine and gap junction signaling pathways. Detected genes were strongly correlated between EB and ECs isolated from resected tissues (R 2 = 0.77 for artery, nidus, and vein tissue). Results shown in Figure 1 . Conclusions: EB is a safe technique to permit non-invasive sequencing of bAVMs. These results implicate dysregulated KRAS/MAPK signaling in adult bAVMs. Whether this technique will allow for better natural history prediction or targeted medical therapies requires future study.

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Identification and Characterization of New Microrna Biomarkers and Target Genes in Drug-Insensitive CD34+ CML Stem/Progenitor Cells Using Global Comparative RNA-Seq Analyses

Blood ◽

10.1182/blood.v126.23.1567.1567 ◽

2015 ◽

Vol 126 (23) ◽

pp. 1567-1567

Author(s):

Hanyang Lin ◽

Jonathan Zeng ◽

Katharina Rothe ◽

Jens Ruschmann ◽

Oleh Petriv ◽

...

Keyword(s):

Progenitor Cells ◽

Mirna Target ◽

Target Genes ◽

Expression Profiles ◽

Therapeutic Targets ◽

Mapk Signaling ◽

Differentially Expressed ◽

Rna Seq ◽

Cd34 Cells ◽

Differentially Expressed Mirnas

Abstract Therapeutic targeting of BCR-ABL with selective ABL tyrosine kinase inhibitors (TKIs) has led to a significant survival benefit for early phase CML. However, TKI monotherapies are rarely curative, with persistence of leukemic stem cells, emergence of resistance and relapses remaining as challenges. To identify differentially expressed and new miRNAs in CD34+ CML stem/progenitor cells that might serve as potential biomarkers and/or therapeutic targets, we have performed Illumina Deep Sequencing to obtain absolute miRNA expression profiles of highly purified CD34+ cells obtained at newly diagnosed stage from six CML patients. Three of the patients were classified retrospectively, after imatinib (IM) therapy, as IM-responders and three as IM-nonresponders. CD34+ cells isolated from five normal bone marrow (NBM) samples were similarly analyzed as controls. Bioconductor DESeq2 analysis revealed 63 differentially expressed miRNAs between CML and NBM samples (adjusted P<0.05). Most differentially expressed miRNAs identified were down-regulated in CML compared to NBM, while 17 were up-regulated. Interestingly, 12 miRNAs were found to be differentially expressed between the IM-responders and IM-nonresponders. In addition, 34 novel miRNAs were identified in the CD34+ CML stem/progenitor cells. We next validated the sequencing data in a larger cohort of samples. CD34+ cells from IM-responders (n=12), IM-nonresponders (n=10) and normal individuals (n=11) were analyzed using a high-throughput qPCR microfluidics device. These studies confirmed the differential expression in CD34+ CML cells of 32 of the 63 miRNAs (adjusted P<0.05), including an increased level of oncomirs miR-155 and miR-17-92, and a decreased level of tumor suppressors miR-145, miR-151, and miR-452. Importantly, significant changes in some of these miRNAs were detected in CD34+ cells from CML patients (n=60) after three months of nilotinib (NL) treatment compared to the same patient samples before the treatment: expression of 18 miRNAs were normalized after NL therapy, whereas 10 showed little change. To further identify potential miRNA target genes, RNA-seq analysis was performed on the same RNA samples to correlate miRNA profiles with corresponding mRNA expression changes. Bioconductor RmiR analysis was performed to match miRNA target genes whose expression was inversely correlated with the expression of deregulated miRNAs based on three of six prediction algorithms (mirBase, TargetScan, miRanda, tarBase, mirTarget2, and PicTar). We have identified 1,210 differentially expressed mRNAs that are predicted targets of the deregulated miRNAs in the comparison of CML and NBM data. Interestingly, only seven differentially expressed genes were predicted targets of the deregulated miRNAs identified in a comparison of IM-responders and IM-nonresponders. Most of the predicted target genes are involved in cell cycle regulation, MAPK signaling and TGF-beta signaling pathways according to DAVID Bioinformatics Resources analysis, which clusters predicted target genes to known KEGG pathways. To elucidate the biological significance of the differentially expressed miRNAs in TKI-insensitive CML stem/progenitor cells, a number of functional assays were performed. An initial screen of eight miRNAs, selected for their novelty and CML-related potential target genes, was performed by transiently transfecting CML cells with miRNA mimics or inhibitors, and chemically synthesized RNAs which mimic or inhibit mature endogenous miRNAs. Four of the eight miRNA mimics/inhibitors transfected cells displayed significant growth disadvantages and enhanced sensitivity to TKI treatments based on trypan-blue exclusion, thymidine incorporation, apoptosis, and colony-forming cell assays. Q-RT-PCR analysis further showed reduced expression of their predicted target genes in cells transfected with miRNA mimics. Taken together, we have identified aberrant, differentially expressed miRNAs and their target genes in TKI-insensitive CML stem/progenitor cells that may serve as useful biomarkers to predict clinical response of CML patients to TKI therapy and ultimately lead to identification of new therapeutic targets for improved treatment options in CML. Disclosures No relevant conflicts of interest to declare.

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RNA-Seq And WGCNA Analysis Identifies Salt-Responsive Genes In Pear (Pyrus Ussuriensis Maxim)

10.21203/rs.3.rs-847089/v1 ◽

2021 ◽

Author(s):

Qiming Chen ◽

Huizhen Dong ◽

Zhihua Xie ◽

Kaijie Qi ◽

Xiaosan Huang ◽

...

Keyword(s):

Signal Transduction ◽

Salt Stress ◽

Salt Tolerance ◽

Plant Hormone ◽

Enrichment Analysis ◽

Salt Resistance ◽

Mapk Signaling ◽

Differentially Expressed ◽

Signal Transduction Pathways ◽

Rna Seq

Abstract Background: Pear is one of the most abundant fruit crops and has been cultivated world-wide. However, the salt injury events caused by increased salinity limited the distribution and sustainable production of pear crops. Therefore, it is needed to take further efforts to understand the genetics and mechanisms of salt tolerance to improved salt resistance and productivity.Results: In this work, we analyzed the dynamic transcriptome of pear (Pyrus ussuriensis Maxim) under salt stress by using RNA-Seq and WGCNA. A total of 3540, 3831, 8374, 6267 and 5381 genes were identified that were differentially expressed after exposure to 200mM NaCl for 4, 6, 12, 24 and 48 hours, respectively, and 1163 genes were shared among the five comparisons. KEGG enrichment analysis of these DEGs (differentially expressed genes) revealed that “MAPK signaling” and “Plant hormone signal transduction” pathways were highly enriched. Meanwhile, 622 DEGs identified from WGCNA were highly correlated with these pathways, and some of them were able to indicate the salt tolerance of pear varieties. In addition, we provide a network to demonstrate the time-sequence of these co-expressed MAPK and hormone related genes.Conclusion: A comprehensive analysis about salt-responsive pear transcriptome were performed by using RNA-Seq and WGCNA. We demonstrated that “MAPK signaling” and “Plant hormone signal transduction” pathways were highly recruited during salt stress, and provided new insights into the metabolism of plant hormones related signaling at transcriptome level underlying salt resistance in pear. The dynamic transcriptome data obtained from this study and these salt-sensitive DEGs may provide potential genes as suitable targets for further biotechnological manipulation to improve pear salt tolerance.

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Using RNA-Seq to Explore the Repair Mechanism of the Three Methods and Three-Acupoint Technique on DRGs in Sciatic Nerve Injured Rats

Pain Research and Management ◽

10.1155/2020/7531409 ◽

2020 ◽

Vol 2020 ◽

pp. 1-12

Author(s):

Tao-tao Lv ◽

Yan-jun Mo ◽

Tian-yuan Yu ◽

Shuai Shao ◽

Meng-qian Lu ◽

...

Keyword(s):

Rna Sequencing ◽

Differentially Expressed Genes ◽

Sham Group ◽

Mapk Signaling ◽

Differentially Expressed ◽

Ion Binding ◽

Rna Seq ◽

Neuron Response ◽

Cell Processes ◽

Mapk Signaling Pathways

Objective. To study the effects of the three methods and three-acupoint technique on DRG gene expression in SNI model rats and to elucidate the molecular mechanism of the three methods and three-acupoint technique on promoting recovery in peripheral nerve injury. Methods. 27 male SD rats were randomly divided into three groups: a Sham group, the SNI group, and the Tuina group. The Tuina group was treated with a tuina manipulation simulator to simulate massage on points, controlling for both quality and quantity. Point-pressing, plucking, and kneading methods were administered quantitatively at Yinmen (BL37), Chengshan (BL57), and Yanglingquan (GB34) points on the affected side once a day, beginning 7 days after modeling. Intervention was applied once a day for 10 days, then 1 day of rest, followed by 10 more days of intervention, totally equaling 20 times of intervention. The effect of the three methods and three-point technique on the recovery of injured rats was evaluated using behavior analysis. RNA sequencing (RNA-Seq) analysis of differentially expressed genes in DRGs of the three groups of rats was also performed. GO and KEGG enrichment was analyzed and verified using real-time PCR. Results. RNA-Seq combined with database information showed that the number of differentially expressed genes in DRG was the largest in the Tuina group compared with the SNI group, totaling 226. GO function is enriched in the positive regulation of cell processes, ion binding, protein binding, neuron, response to pressure, response to metal ions, neuron projection, and other biological processes. GO function is also enriched in the Wnt, IL-17, and MAPK signaling pathways in the KEGG database. PCR results were consistent with those of RNA sequencing, suggesting that the results of transcriptome sequencing were reliable. Conclusion. The three methods and three-acupoint technique can promote the recovery of SNI model rats by altering the gene sequence in DRGs.

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Comparative analysis of gene expression profiles in differentiated subcutaneous adipocytes between Jiaxing Black and Large White pigs

BMC Genomics ◽

10.1186/s12864-020-07361-9 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Dawei Zhang ◽

Wenjing Wu ◽

Xin Huang ◽

Ke Xu ◽

Cheng Zheng ◽

...

Keyword(s):

Signaling Pathway ◽

Differentially Expressed Genes ◽

Expression Profiles ◽

Subcutaneous Fat ◽

Mapk Signaling ◽

Fat Deposition ◽

Differentially Expressed ◽

Rna Seq ◽

Large White ◽

Pig Breeds

Abstract Background Chinese domestic pig breeds are reputed for pork quality, but their low ratio of lean-to-fat carcass weight decreases production efficiency. A better understanding of the genetic regulation network of subcutaneous fat tissue is necessary for the rational selection of Chinese domestic pig breeds. In the present study, subcutaneous adipocytes were isolated from Jiaxing Black pigs a Chinese indigenous pig breed with redundant subcutaneous fat deposition and Large White pigs a lean-type pig breed with relatively low subcutaneous fat deposition. The expression profiles of mRNAs and lncRNAs were compared by RNA-seq analysis to identify biomarkers correlated with the differences of subcutaneous fat deposition between the two breeds. Results A total of 1058 differentially expressed genes and 221 differentially expressed lncRNAs were identified in subcutaneous adipocytes between Jiaxing Black and Large White pigs, which included 275 up-regulated mRNAs, 783 down-regulated mRNAs, 118 up-regulated lncRNAs and 103 down-regulated lncRNAs. Gene Ontology and KEGG pathway enrichment analyses revealed that the differentially expressed genes and differentially expressed lncRNAs were mainly involved in the immune response, cell fate determination, PI3K-Akt signaling pathway and MAPK signaling pathway, which are known to be related to adipogenesis and lipid metabolism. The expression levels of differentially expressed genes and differentially expressed lncRNAs according to the RNA-seq data were verified by quantitative PCR, which showed 81.8% consistency. The differences in MAPK pathway activity between Jiaxing Black and Large White pigs was confirmed by western blot analysis, which revealed elevated p38 phosphorylation in Jiaxing Black pigs. Conclusions This study offers a detailed characterization of mRNAs and lncRNAs in fat- and lean-type pig breeds. The activity of the MAPK signaling pathway was found to be associated with subcutaneous adipogenesis. These results provide new targets for further investigation of the molecular mechanisms regulating subcutaneous fat deposition in pigs.

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RNA-Seq based exploration of differentially expressed genes (DEGs) in cotton(Gossypium hirsutum. L) upon infection with Aspergillus tubingensis

10.21203/rs.3.rs-770815/v1 ◽

2021 ◽

Author(s):

Maria Khizar ◽

Jianxin Shi ◽

Urooj Haroon ◽

Musrat Ali ◽

Fiza Liaquat ◽

...

Keyword(s):

Gossypium Hirsutum ◽

Differentially Expressed Genes ◽

Defense Responses ◽

Mapk Signaling ◽

Differentially Expressed ◽

Ascorbate Oxidase ◽

Resistant Variety ◽

Potential Candidate ◽

Aspergillus Tubingensis ◽

Rna Seq

Abstract Differentially expressed genes help in exploring plant defense mechanism under variable stress conditions. In current investigation, RNA sequencing was executed to explore the differential gene expression in resistant and susceptible varieties of Cotton (Gossypium hirsutum), upon infection with Aspergillus tubingensis. Comparative RNA-Seq of control and infected plants was performed using Illumina HiSeq 2,500. Overall 79.84 G clean data was generated and 6,558 DEGs were identified in both varieties, in response to pathogen inoculation. Differentially expressed genes were found to be involved in defense, antifungal response, signaling pathways, oxidative burst and transcription. Genes involved in defense responses, MAPK signaling, cell wall fortification and signal transduction were highly induced in resistant variety. Real time PCR also revealed the up regulation of MAPKKK YODA like, L-ascorbate oxidase, late embryogenesis abundant protein (At1g64065) and flavonoid 3',5'-hydroxylase-like, in resistant variety. Elevated accumulation of such DEGs in resistant variety could function as the source for identifying biomarkers for breeding and these can be used as potential candidate genes for transgenic manipulation. Their study also helped in understanding complex plant-fungal interaction and advanced the understanding of plant-microbe interaction. Inclusively, our findings provide an indispensable foundation for advanced understanding of the plant resistance mechanisms of cotton.

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Transcriptome Analysis Reveals Key Genes and Pathways Associated with Egg Production in Nandan-Yao Domestic Chicken

10.21203/rs.3.rs-29025/v1 ◽

2020 ◽

Author(s):

Tiantian Sun ◽

Cong Xiao ◽

Jixian Deng ◽

Zhuliang Yang ◽

Wenwen Xu ◽

...

Keyword(s):

Egg Production ◽

Physiological Function ◽

Genetic Selection ◽

Enrichment Analysis ◽

Mapk Signaling ◽

Receptor Interaction ◽

Rna Seq ◽

Native Breed ◽

Key Genes ◽

And Function

Abstract Background Egg production is a very important economic trait in chicken breeding, but its molecular mechanism is unclear until now. Nandan-Yao chicken (Gallus gallus domesticus) is a native breed in Guangxi province, China, which is famous for good meet quality, but low egg production. To explore the molecular regulation related egg production, high egg production (HEP) and low egg production (LEP) were divided according to the total egg number at 50 weeks, and the concentration of serum sex hormones was tested to evaluate the physiological function of ovary and uterus. RNA sequencing (RNA-Seq) was used to explore the transcriptome from the ovary and uterus of Nandan-Yao chicken. Results The levels of serum sex hormone were showed that concentrations of estradiol (E2), follicle-stimulating hormone (FSH), and luteotropic hormone (LH) were very significantly higher in HEP compared with LEP respectively (P < 0.01), and concentrations of testosterone (T) were very significantly lower in HEP compared with LEP (P < 0.01), which indicated there were better physiological function in HEP compared with LEP. Analysis results of RNA-Seq showed that 901 and 2763 differentially expressed genes (DEGs) in ovary and uterus between HEP and LEP chicken, respectively. Enrichment analysis of DEGs showed that DEGs were involved significantly in the regulation of tight junction in the ovary (P < 0.05), while in uterus DEGs were mainly enriched significantly in the phagosome, ECM-receptor interaction, cell adhesion molecules (CAMs), focal adhesion, cardiac muscle contraction, cytokine-cytokine receptor interaction, and the regulation of MAPK signaling pathway (P < 0.05). Protein network interaction and function analyses revealed FN1, FGF7, SOX2,ALDOB, HSPA2 in the ovary, and UQCRH, COX5A, FN1, TGFB, ACTN1 in the uterus were key candidate genes for egg production in Nandan-Yao chicken. Conclusions The current study identified key genes and pathway contribute to improving our understanding of reproductive biology of chicken and isolating effective molecular markers that can be used for genetic selection in Nandan-Yao chicken.

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Differential expression, distribution, and function of PPAR-γ in the proximal and distal colon

Physiological Genomics ◽

10.1152/physiolgenomics.00042.2007 ◽

2007 ◽

Vol 30 (3) ◽

pp. 342-353 ◽

Cited By ~ 41

Author(s):

Weidong Su ◽

Craig R. Bush ◽

Brian M. Necela ◽

Shelly R. Calcagno ◽

Nicole R. Murray ◽

...

Keyword(s):

Epithelial Cells ◽

Target Genes ◽

Distal Colon ◽

Mapk Signaling ◽

Cellular Adhesion ◽

Differentially Expressed ◽

Colonic Epithelial Cells ◽

Tissue Specific ◽

Ppar Γ ◽

And Function

Suppression of colon carcinogenesis by peroxisome proliferator-activated receptor (PPAR)-γ is likely due to some effect of PPAR-γ on normal colonic epithelial cells. However, our understanding of the effects of PPAR-γ in such cells is limited. We analyzed the abundance, distribution, and function of PPAR-γ in epithelial cells isolated from the murine proximal and distal colon. Marked differences in PPAR-γ abundance and distribution were observed, suggesting tissue-specific responses. Analysis of PPAR-γ effects on DNA synthesis, formation of preneoplastic lesions, and activation of MAPK signaling in proximal and distal colonic epithelial cells in vivo indicates that PPAR-γ regulates both tissue-specific and common responses within the proximal and distal colon. Three major functional cohorts of PPAR-γ target genes were identified by genomic profiling of isolated colonic epithelial cells: genes that are involved in metabolism, in signaling, and in cellular adhesion and motility. Two subsets of PPAR-γ target genes were differentially expressed in the proximal and distal epithelium. Proximal target genes were primarily involved in metabolic activities, whereas signal transduction, adhesion, and motility targets were more pronounced in the distal colon. Remarkably, those target genes that are differentially expressed in the proximal colon were all induced on activation of PPAR-γ, whereas all target genes that are preferentially expressed in the distal colon were repressed. Our data indicate that PPAR-γ exerts both common and tissue-specific effects in the colon and challenge the general conclusions that PPAR-γ is induced on differentiation of colonic epithelial cells and that this receptor stimulates differentiated function in epithelial cells throughout the colon.

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