scholarly journals Skin transcriptome profiles associated with coat color in goat

2015 ◽  
Author(s):  
Yongdong Peng ◽  
Xiaohui Liu ◽  
Liying Geng ◽  
Chuansheng Zhang ◽  
Zhengzhu Liu ◽  
...  
Keyword(s):  
Coat Color ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Capra Hircus ◽  
Rna Seq ◽  
White Skin ◽  
Future Studies ◽  
Skin Physiology ◽  
Significant Difference ◽  
Upregulated Genes

Capra hircus, an economically important livestock, plays an indispensable role in the world animal fiber industry. To identify additional genes that may play important roles in coat color regulation, Illumina/Solexa high throughput sequencing technology was used to catalog the global gene expression profiles in the skin of three different coat colors goat (Lubei white goat (white), Jining gray goat (gray) and Jianyang big ear goat (brown)). The RNA-Seq analysis generated 83174342, 70222592 and 52091212 clean reads in white skin, gray skin and brown skin, respectively, which provided abundant data for further analysis. A total of 91 genes were differentially expressed between the gray skin and white skin libraries, with 74 upregulated and 17 genes downregulated. Between the brown skin and white skin libraries, there were 23 upregulated genes and 44 downregulated genes, while there were 33 upregulated genes and 121 downregulated genes between the brown skin and gray skin libraries. To our surprise, MC1R, MITF, TYR, KIT and KITLG showed no significant difference in the skin of three different coat colors and the expression of ASIP was only detected in white skin and not in gray and brown skins. The expression of PMEL,TRPM1, DCT, TYRP1 and ELOVL3 was validated by real-time quantitative polymerase chain reaction (qPCR) and the results of the qPCR were consistent with the RNA-seq except the expression of TYRP1 between the gray skin and white skin libraries. This study provides several candidate genes that may be associated with the development of diferent coat colors goat skin. More importantly, the fact that the ASIP gene was only detected in the white skin and not in the other dark skins and the MC1R gene showed no significant difference in expression between the three different coat colors goat is of particular interest for future studies that aim to elucidate theirs functional role in the regulation of skin color. These results will expand our understanding of the complex molecular mechanisms of skin physiology and melanogenesis in goat and provide a foundation for future studies.

Exploring differentially expressed genes associated with coat color in goat skin using RNA-seq

2019 ◽  
Vol 99 (2) ◽  
pp. 357-366
Author(s):  
Yongdong Peng ◽  
Yaqi Wang ◽  
Ruining Wang ◽  
Liying Geng ◽  
Ruxue Ma ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Quantitative Polymerase Chain Reaction ◽  
Differentially Expressed ◽  
Rna Seq ◽  
White Skin ◽  
Black And White ◽  
Goat Skin ◽  
Skin Physiology ◽  
Black Goat

Fur color in domestic goats is an important, genetically determined characteristic that is associated with economic value. This study was designed to perform a comprehensive expression profiling of genes expressed in the skin tissues from Laiwu Black goat and Lubei White goat. Comparisons of black and white goat skin transcriptomes revealed 102 differentially expressed genes (DEGs), of which 38 were upregulated and 64 downregulated in black skin compared with white skin. Among the DEGs, we identified six genes involved in pigmentation, including agouti signaling protein (ASIP), CAMP responsive element binding protein 3-like 1 (CREB3L1), dopachrome tautomerase (DCT), premelanosome protein (PMEL), transient receptor potential cation channel subfamily M member 1 (TRPM1), and tyrosinase-related protein 1 (TYRP1). Notably, there were no significant differences in the expression of melanocortin 1 receptor, microphthalmia-associated transcription factor, tyrosinase, and KIT proto-oncogene receptor tyrosine kinase between the black and white skin samples, whereas ASIP expression was detected only in white skin. PMEL, TRPM1, TYRP1, and DCT showed higher expression in black goat skin, but ASIP and CREB3L1 had higher expression in white goat skin. Quantitative polymerase chain reaction results for PMEL, TRPM1, DCT, TYRP1, and CREB3L1 expression were consistent with those for RNA-seq. These results will expand our understanding of the complex molecular mechanisms of skin physiology and melanogenesis in goats, and provide a foundation for future studies.

scholarly journals An integrated analysis of lncRNA and mRNA expression profiles in the kidneys of mice with lupus nephritis

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10668
Author(s):  
Juan Wang ◽  
Xiongfei Wu ◽  
Yafang Tu ◽  
Jianzhong Dang ◽  
Zhitao Cai ◽  
...  
Keyword(s):  
Lupus Nephritis ◽  
Mrna Expression ◽  
Lupus Erythematosus ◽  
Expression Profiles ◽  
Inflammatory Factors ◽  
Integrated Analysis ◽  
Limited Information ◽  
Rna Seq ◽  
And Control ◽  
Upregulated Genes

Long noncoding RNAs (lncRNAs) are persistently expressed and have been described as potential biomarkers and therapeutic targets in various diseases. However, there is limited information regarding lncRNA expression in the tissue of kidney exhibiting lupus nephritis (LN)a serious complication of systemic lupus erythematosus (SLE). In this study, RNA sequencing (RNA-seq) was performed to characterize the lncRNA and mRNA expression in kidney tissues from LN (MRL/lpr) and control mice. We identified 12,979 novel lncRNAs in mouse. The expression profiles of both mRNAs and lncRNAs were differed significantly between LN and control mice. In particular, there were more upregulated lncRNAs and mRNAs than downregulated ones in the kidney tissues of LN mice. However, GO analysis showed that more downregulated genes were enriched in immune and inflammatory response-associated pathways. KEGG analysis showed that both downregulated and upregulated genes were enriched in a number of pathways, including the SLE pathway, and approximately half of these SLE-associated genes encoded inflammatory factors. Moreover, we observed that 2,181 DElncRNAs may have targeted and regulated the expression of 778 mRNAs in LN kidney tissues. The results of this study showed that 11 DElncRNAs targeted and were co-expressed with six immune and SLE-associated genes. qPCR analysis confirmed that lncRNA Gm20513 positively regulated the expression of the SLE-associated gene H2-Aa. In conclusion, the results of our study demonstrates that lncRNAs influence the progression of LN and provide some cues for further study of lncRNAs in LN. These results regarding the lncRNA-mRNAregulatory network may have important value in LN diagnosis and therapy.

scholarly journals Identification and Analysis of Long Noncoding RNAs and mRNAs in Chicken Macrophages Infected With Coronavirus Avian Infectious Bronchitis Virus

2020 ◽  
Author(s):  
Hao Li ◽  
Pengfei Cui ◽  
Xue Fu ◽  
Lan Zhang ◽  
Wenjun Yan ◽  
...  
Keyword(s):  
Infectious Bronchitis Virus ◽  
Acid Metabolism ◽  
Expression Profiles ◽  
Nucleic Acid Metabolism ◽  
Avian Infectious Bronchitis Virus ◽  
Rna Seq ◽  
Data Bases ◽  
Infectious Bronchitis ◽  
Significant Difference ◽  
Non Coding Rnas

Abstract Background: Avian infectious bronchitis virus (IBV) is a gammacoronavirus that seriously affects the world's poultry industry Long non coding RNAs (lncRNAs), a subset of non coding RNAs greater than 200 nucleotides in length, have been recently recognized as pivotal factors during the pathogenesis of viral infection. However, how lncRNAs in host cul tured cells respond to IBV infection was little known. Herein, we detected the expression profiles of the mRNAs and lncRNAs in IBV infected HD11 cells. Results: By RNA seq, 2640 novel lncRNAs were identified, and 181 lncRNAs (59 up regulated lncRNAs , 122 down regulated lncRNAs) exhibited significant difference in expression levels in IBV infected HD11 cells compared with the uninfected. Based on the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) data bases, the significant diff erentially expressed (DE) lncRNAs, such as MSTRG.25416.43, MSTRG.6458.31, MSTRG.14220.1 and MSTRG.21445.2, were mainly involved in the regulation of cellular innate immunity and amino acid, nucleic acid metabolism. In addition, 30 DE lncRNAs were screened out, and these lncRNAs may interact with gga miR 30d to regulate IBV replication. Conclusions:Our results provided novel insights into the functions of lncRNAs and the possible pathogenic mechanism following IBV infection.

scholarly journals Expression Profiles of Genes Encoded by the Supernumerary Chromosome Controlling AM-Toxin Biosynthesis and Pathogenicity in the Apple Pathotype of Alternaria alternata

2007 ◽  
Vol 20 (12) ◽  
pp. 1463-1476 ◽  
Author(s):  
Yoshiaki Harimoto ◽  
Rieko Hatta ◽  
Motoichiro Kodama ◽  
Mikihiro Yamamoto ◽  
Hiroshi Otani ◽  
...  
Keyword(s):  
Internal Control ◽  
Alternaria Alternata ◽  
Expressed Sequence Tag ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Elongation Factor ◽  
Expression Levels ◽  
Control Comparison ◽  
Alternaria Blotch ◽  
Upregulated Genes

The apple pathotype of Alternaria alternata produces host-specific AM-toxin and causes Alternaria blotch of apple. Previously, we cloned two genes, AMT1 and AMT2, required for AM-toxin biosynthesis and found that these genes are encoded by small, supernumerary chromosomes of <1.8 Mb in the apple pathotype strains. Here, we performed expressed sequence tag analysis of the 1.4-Mb chromosome encoding AMT genes in strain IFO8984. A cDNA library was constructed using RNA from AM-toxin–producing cultures. A total of 40,980 clones were screened with the 1.4-Mb chromosome probe, and 196 clones encoded by the chromosome were isolated. Sequence analyses of these clones identified 80 unigenes, including AMT1 and AMT2, and revealed that the functions of 43 (54%) genes are unknown. The expression levels of the 80 genes in AM-toxin–producing and nonproducing cultures were analyzed by real-time quantitative polymerase chain reaction (PCR). Most of the genes were found to be expressed in both cultures at markedly lower levels than the translation elongation factor 1-α gene used as an internal control. Comparison of the expression levels of these genes between two cultures showed that 21 genes, including AMT1 and AMT2, were upregulated (>10-fold) in AM-toxin–producing cultures. Two of the upregulated genes were newly identified to be involved in AM-toxin biosynthesis by the gene disruption experiments and were named AMT3 and AMT4. Thus, the genes upregulated in AM-toxin–producing cultures contain ideal candidates for novel AM-toxin biosynthetic genes.

scholarly journals High expression of RRM2 promotes the pathogenesis of malignant ovarian endometriosis.

2021 ◽  
Author(s):  
Binkai Yang ◽  
Yuanjing Hu ◽  
Tian Wang ◽  
Na Li ◽  
Wenwen Zhang
Keyword(s):  
Gene Expression ◽  
Ovarian Cancer ◽  
Malignant Transformation ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Gene Expression Profiles ◽  
High Expression ◽  
Ovarian Endometriosis ◽  
Ki 67 ◽  
Significant Difference

Abstract Objective: Our objective was to investigate the upregulated expression of ribonucleotide reductase M2 (RRM2) in the ectopic endometrium (EC) of ovarian endometriosis (OE) patients that may indicate malignant transformation. RRM2 may be used as a marker of OE, which contribute to the research of the mechanism of the malignant transformation of OE.Methods: The gene expression profiles of ovarian cancer and OE were downloaded from Gene Expression Omnibus (GEO), and a common hub gene, RRM2, was identified. The expression of RRM2 was low in OE and high in ovarian cancer. A total of 44 patients with endometriosis-associated ovarian cancers (EAOC) and 44 with OE were enrolled in this study. Immunohistochemistry (IHC) and real-time quantitative polymerase chain reaction (RT-qPCR) were used to detect the expression of RRM2, while the relationship between RRM2 and Ki-67 was analyzed by IHC co-localization. Results: There was no significant difference in the expression of RRM2 in the eutopic endometrium (EU), EC, and cancer tissues of EAOC patients. Compared with OE patients, the mRNA and protein expression levels of RRM2 were higher in the EC of EAOC patients (p＜0.01). Moreover, the high expression of RRM2 was consistent with the expression of Ki-67 in EC of EAOC patients.Conclusions: The upregulated expression of RRM2 in the EC of OE patients may indicate malignant transformation. RRM2 may be used as a marker of OE, which allows the investigation of the mechanism of the malignant transformation of OE.

scholarly journals Genome-wide sequence and expression analysis of the NAC transcription factor family in polyploid wheat

2017 ◽  
Author(s):  
Philippa Borrill ◽  
Sophie A. Harrington ◽  
Cristobal Uauy
Keyword(s):  
Transcription Factors ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Families ◽  
Rna Seq ◽  
Phylogenetic Groups ◽  
Future Studies ◽  
Nac Transcription Factors ◽  
Wide Range ◽  
Nac Family

ARTICLE SUMMARYTranscription factors are vital in plants to regulate gene expression in response to environmental stimuli and to control developmental processes. In this study, we annotated and classified transcription factors in polyploid bread wheat into gene families and explored the NAC family in detail. We combined phylogenetic analysis and transcriptome analysis, using publicly available RNA-seq data, to characterize the NAC gene family and provide hypotheses for putative functions of many NAC transcription factors. This study lays the groundwork for future studies on transcription factors in wheat which may be of great agronomic relevance.ABSTRACTMany important genes in agriculture correspond to transcription factors which regulate a wide range of pathways from flowering to responses to disease and abiotic stresses. In this study, we identified 5,776 transcription factors in hexaploid wheat (Triticum aestivum) and classified them into gene families. We further investigated the NAC family exploring the phylogeny, C-terminal domain conservation and expression profiles across 308 RNA-seq samples. Phylogenetic trees of NAC domains indicated that wheat NACs divided into eight groups similar to rice (Oryza sativa) and barley (Hordeum vulgare). C-terminal domain motifs were frequently conserved between wheat, rice and barley within phylogenetic groups, however this conservation was not maintained across phylogenetic groups. We explored gene expression patterns across a wide range of developmental stages, tissues, and abiotic stresses. We found that more phylogenetically related NACs shared more similar expression patterns compared to more distant NACs. However, within each phylogenetic group there were clades with diverse expression profiles. We carried out a co-expression analysis on all wheat genes and identified 37 modules of co-expressed genes of which 23 contained NACs. Using GO term enrichment we obtained putative functions for NACs within co-expressed modules including responses to heat and abiotic stress and responses to water: these NACs may represent targets for breeding or biotechnological applications. This study provides a framework and data for hypothesis generation for future studies on NAC transcription factors in wheat.

scholarly journals Comprehensive Expression Profiling Analysis of Pituitary Indicates that circRNA Participates in the Regulation of Sheep Estrus

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 90 ◽  
Author(s):  
Xiaoyue Li ◽  
Cunyuan Li ◽  
Junchang Wei ◽  
Wei Ni ◽  
Yueren Xu ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Circular Rna ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Endocrine Organ ◽  
Reverse Transcription Quantitative Pcr ◽  
Significant Difference ◽  
Profiling Analysis

The pituitary gland is the most important endocrine organ that mainly regulates animal estrus by controlling the hormones synthesis. There is a significant difference between the estrus state and anestrus state of sheep pituitary system. Here, we studied the circular RNA (circRNA) expression profiles of the anterior pituitary of estrus and anestrus sheep using RNA-seq technology. Through this study, we identified a total of 12,468 circRNAs and 9,231 differentially expressed circRNAs in the estrus and anestrus pituitary system of sheep. We analyzed some differentially expressed circRNAs by reverse transcription quantitative-PCR (RT-qPCR), and some circRNAs were demonstrated using RNase-R+ resistance experiments. CircRNAs involving the regulation of estrus-related terms and pathways are enriched by using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. In addition, we also predicted partial microRNA-circRNA interaction network for circRNAs that regulate sheep estrus. Overall, this study explored a potential substantial role played by circRNAs involved in pituitary regulation on sheep estrus and proposed new questions for further study.

scholarly journals Transcriptomic Analysis of Coding Genes and Non-Coding RNAs Reveals Complex Regulatory Networks Underlying the Black Back and White Belly Coat Phenotype in Chinese Wuzhishan Pigs

Genes ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 201
Author(s):  
Qiao Xu ◽  
Ximing Liu ◽  
Zhe Chao ◽  
Kejun Wang ◽  
Jue Wang ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Coat Color ◽  
Mirna Gene ◽  
White Skin ◽  
Melanin Biosynthesis ◽  
Black Skin ◽  
Skin Physiology ◽  
Non Coding Rnas ◽  
Different Levels ◽  
White Belly

Coat color is one of the most important characteristics for distinguishing Chinese indigenous pig breeds. In Wuzhishan pigs, the animals have black on the back and white on the abdomen. However, the molecular genetic basis of this phenotype is unclear. In this study, we used high-throughput RNA sequencing to compare expression profiles of coding and non-coding RNAs from white and black skin samples obtained from individual Wuzhishan pigs. The expression profiling revealed that 194 lncRNAs (long non-coding RNAs), 189 mRNAs (messenger RNAs), and 162 miRNAs (microRNAs) had significantly different levels of expression (|log2 fold change| > 1, p-value < 0.05) in white and black skin. Compared to RNA levels in black skin, white skin had higher levels of expression of 185 lncRNAs, 181 mRNAs, and 23 miRNAs and lower levels of expression of 9 lncRNAs, 8 mRNAs, and 139 miRNAs. Functional analysis suggested that the differentially expressed transcripts are involved in biological processes such as melanin biosynthesis, pigmentation and tyrosine metabolism. Several key genes involved in melanogenesis, including MLANA, PMEL, TYR, TYRP1, DTC, TRPM1 and CAMK2A, had significantly different levels of expression in the two skin tissues. Potential lncRNA–miRNA–gene interactions were also examined. A total of 15 lncRNAs, 11 miRNAs and 7 genes formed 23 lncRNA–miRNA–gene pairs, suggesting that complex regulatory networks of coding and non-coding genes underlie the coat color trait in Wuzhishan pigs. Our study provides a foundation for understanding how lncRNA, miRNA and genes interact to regulate coat color in black-back/white-belly pigs. We also constructed lncRNA–miRNA–gene interaction networks to elucidate the complex molecular mechanisms underlying skin physiology and melanogenesis. The results extend our knowledge about the diversity of coat color among different domestic animals and provide a foundation for studying novel mechanisms that control coat color in Chinese indigenous pigs.

scholarly journals Transcriptomal dissection of soybean circadian rhythmicity in two geographically, phenotypically and genetically distinct cultivars

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yanlei Yue ◽  
Ze Jiang ◽  
Enoch Sapey ◽  
Tingting Wu ◽  
Shi Sun ◽  
...  
Keyword(s):  
Gene Expression ◽  
Circadian Clock ◽  
Chromosome Structure ◽  
Clock Genes ◽  
Expression Profiles ◽  
Circadian Rhythmicity ◽  
Rna Seq ◽  
Night Time ◽  
Time Points ◽  
Circadian Clock Genes

Abstract Background In soybean, some circadian clock genes have been identified as loci for maturity traits. However, the effects of these genes on soybean circadian rhythmicity and their impacts on maturity are unclear. Results We used two geographically, phenotypically and genetically distinct cultivars, conventional juvenile Zhonghuang 24 (with functional J/GmELF3a, a homolog of the circadian clock indispensable component EARLY FLOWERING 3) and long juvenile Huaxia 3 (with dysfunctional j/Gmelf3a) to dissect the soybean circadian clock with time-series transcriptomal RNA-Seq analysis of unifoliate leaves on a day scale. The results showed that several known circadian clock components, including RVE1, GI, LUX and TOC1, phase differently in soybean than in Arabidopsis, demonstrating that the soybean circadian clock is obviously different from the canonical model in Arabidopsis. In contrast to the observation that ELF3 dysfunction results in clock arrhythmia in Arabidopsis, the circadian clock is conserved in soybean regardless of the functional status of J/GmELF3a. Soybean exhibits a circadian rhythmicity in both gene expression and alternative splicing. Genes can be grouped into six clusters, C1-C6, with different expression profiles. Many more genes are grouped into the night clusters (C4-C6) than in the day cluster (C2), showing that night is essential for gene expression and regulation. Moreover, soybean chromosomes are activated with a circadian rhythmicity, indicating that high-order chromosome structure might impact circadian rhythmicity. Interestingly, night time points were clustered in one group, while day time points were separated into two groups, morning and afternoon, demonstrating that morning and afternoon are representative of different environments for soybean growth and development. However, no genes were consistently differentially expressed over different time-points, indicating that it is necessary to perform a circadian rhythmicity analysis to more thoroughly dissect the function of a gene. Moreover, the analysis of the circadian rhythmicity of the GmFT family showed that GmELF3a might phase- and amplitude-modulate the GmFT family to regulate the juvenility and maturity traits of soybean. Conclusions These results and the resultant RNA-seq data should be helpful in understanding the soybean circadian clock and elucidating the connection between the circadian clock and soybean maturity.

scholarly journals Genetic Mapping and Identification of the Candidate Gene for White Seed Coat in Cucurbita maxima

2021 ◽  
Vol 22 (6) ◽  
pp. 2972
Author(s):  
Yuzi Shi ◽  
Meng Zhang ◽  
Qin Shu ◽  
Wei Ma ◽  
Tingzhen Sun ◽  
...  
Keyword(s):  
Seed Coat ◽  
Molecular Breeding ◽  
Coat Color ◽  
Recessive Gene ◽  
Myb Transcription Factor ◽  
Cucurbita Maxima ◽  
Seed Coat Color ◽  
Rna Seq ◽  
Edible Seed ◽  
Segregating Population

Seed coat color is an important agronomic trait of edible seed pumpkin in Cucurbita maxima. In this study, the development pattern of seed coat was detected in yellow and white seed coat accessions Wuminglv and Agol. Genetic analysis suggested that a single recessive gene white seed coat (wsc) is involved in seed coat color regulation in Cucurbita maxima. An F2 segregating population including 2798 plants was used for fine mapping and a candidate region containing nine genes was identified. Analysis of 54 inbred accessions revealed four main Insertion/Deletion sites in the promoter of CmaCh15G005270 encoding an MYB transcription factor were co-segregated with the phenotype of seed coat color. RNA-seq analysis and qRT-PCR revealed that some genes involved in phenylpropanoid/flavonoid metabolism pathway displayed remarkable distinction in Wuminglv and Agol during the seed coat development. The flanking InDel marker S1548 was developed to predict the seed coat color in the MAS breeding with an accuracy of 100%. The results may provide valuable information for further studies in seed coat color formation and structure development in Cucurbitaceae crops and help the molecular breeding of Cucurbita maxima.

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