An exon-intron split framework to prioritize transcriptional and post-transcriptional regulatory signals and its application to study energy homeostasis in pigs

Bulk sequencing of RNA transcripts has typically been used to quantify gene expression levels in different experimental systems. However, linking differentially expressed (DE) mRNA transcripts to gene expression regulators, such as miRNAs or transcription factors (TFs), remains challenging, as in silico or experimental interactions are commonly identified post hoc after selecting differentially expressed genes of interest, thus biasing the interpretation of underlying gene regulatory mechanisms. In this study, we performed an exon-intron split analysis (EISA) to muscle and fat RNA-seq data from two Duroc pig populations subjected to fasting-feeding conditions and with divergent fatness profiles, respectively. We compared the number of reads from exonic and intronic regions for all expressed protein-coding genes and divided their expression profiles into transcriptional and post-transcriptional components, considering intronic and exonic fractions as estimates of the abundance of pre-mRNA and mature mRNA transcripts, respectively. In this way, we obtained a prioritized list of genes showing significant transcriptional and post-transcriptional regulatory signals. After running EISA analyses, protein-coding mRNA genes with downregulated exonic fractions and high post-transcriptional signals were significantly enriched for binding sites of upregulated DE miRNAs. Moreover, these genes showed an increased expression covariation for the exonic fraction compared to that of the intronic fraction. On the contrary, they did not show enrichment for binding sites of highly expressed and/or downregulated DE miRNAs. Among the set of loci displaying miRNA-driven post-transcriptional regulatory signals, we observed genes related to glucose homeostasis (PDK4, NR4A3, CHRNA1 and DKK2), cell differentiation (MYO9A, KLF5 and BACH2) or adipocytes metabolism (LEP, SERPINE2, RNF157, OSBPL10 and PRSS23). Besides, genes showing upregulated intronic fractions with a lack of exonic fractions were significantly enriched for TF-enhancer activity while depleted for miRNA targets, thus suggesting a transient transcription activation regulating skeletal muscle development. Our results highlight an efficient framework to classify mRNA genes showing transcriptional and post-transcriptional signals linked to transient transcription and miRNA-driven downregulation by using exonic and intronic fractions of RNA-seq datasets from muscle and adipose tissues in pigs.

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HIV-1 Infection Transcriptomics: Meta-Analysis of CD4+ T Cells Gene Expression Profiles

Viruses ◽

10.3390/v13020244 ◽

2021 ◽

Vol 13 (2) ◽

pp. 244 ◽

Cited By ~ 1

Author(s):

Antonio Victor Campos Coelho ◽

Rossella Gratton ◽

João Paulo Britto de Melo ◽

José Leandro Andrade-Santos ◽

Rafael Lima Guimarães ◽

...

Keyword(s):

Gene Expression ◽

T Cells ◽

Differentially Expressed Genes ◽

Cd4 T Cells ◽

Expression Profiles ◽

Meta Analysis ◽

Differentially Expressed ◽

Rna Seq ◽

Infected Cells ◽

Hiv 1

HIV-1 infection elicits a complex dynamic of the expression various host genes. High throughput sequencing added an expressive amount of information regarding HIV-1 infections and pathogenesis. RNA sequencing (RNA-Seq) is currently the tool of choice to investigate gene expression in a several range of experimental setting. This study aims at performing a meta-analysis of RNA-Seq expression profiles in samples of HIV-1 infected CD4+ T cells compared to uninfected cells to assess consistently differentially expressed genes in the context of HIV-1 infection. We selected two studies (22 samples: 15 experimentally infected and 7 mock-infected). We found 208 differentially expressed genes in infected cells when compared to uninfected/mock-infected cells. This result had moderate overlap when compared to previous studies of HIV-1 infection transcriptomics, but we identified 64 genes already known to interact with HIV-1 according to the HIV-1 Human Interaction Database. A gene ontology (GO) analysis revealed enrichment of several pathways involved in immune response, cell adhesion, cell migration, inflammation, apoptosis, Wnt, Notch and ERK/MAPK signaling.

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Assessment of CircRNA Expression Profiles and Potential Functions in Brown Adipogenesis

Frontiers in Genetics ◽

10.3389/fgene.2021.769690 ◽

2021 ◽

Vol 12 ◽

Author(s):

Pengpeng Zhang ◽

Mingxuan Sheng ◽

Chunyu Du ◽

Zhe Chao ◽

Haixia Xu ◽

...

Keyword(s):

Binding Sites ◽

Expression Profiles ◽

Expression Patterns ◽

Potential Functions ◽

Rna Seq ◽

Specific Expression ◽

Protein Coding ◽

Multiple Binding Sites ◽

Brown Adipose ◽

Brown Adipogenesis

Brown adipose tissue (BAT) is specialized for energy expenditure, thus a better understanding of the regulators influencing BAT development could provide novel strategies to defense obesity. Many protein-coding genes, miRNAs, and lncRNAs have been investigated in BAT development, however, the expression patterns and functions of circRNA in brown adipogenesis have not been reported yet. This study determined the circRNA expression profiles across brown adipogenesis (proliferation, early differentiated, and fully differentiated stages) by RNA-seq. We identified 3,869 circRNAs and 36.9% of them were novel. We found the biogenesis of circRNA was significantly related to linear mRNA transcription, meanwhile, almost 70% of circRNAs were generated by alternative back-splicing. Next, we examined the cell-specific and differentiation stage-specific expression of circRNAs. Compared to white adipocytes, nearly 30% of them were specifically expressed in brown adipocytes. Further, time-series expression analysis showed circRNAs were dynamically expressed, and 117 differential expression circRNAs (DECs) in brown adipogenesis were identified, with 77 upregulated and 40 downregulated. Experimental validation showed the identified circRNAs could be successfully amplified and the expression levels detected by RNA-seq were reliable. For the potential functions of the circRNAs, GO analysis suggested that the decreased circRNAs were enriched in cell proliferation terms, while the increased circRNAs were enriched in development and thermogenic terms. Bioinformatics predictions showed that DECs contained numerous binding sites of functional miRNAs. More interestingly, most of the circRNAs contained multiple binding sites for the same miRNA, indicating that they may facilitate functions by acting as microRNA sponges. Collectively, we characterized the circRNA expression profiles during brown adipogenesis and provide numerous novel circRNAs candidates for future brown adipogenesis regulating studies.

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De novo assembly and analysis of the transcriptome of the Dermacentor marginatus genes differentially expressed after blood-feeding and long-term starvation

10.21203/rs.3.rs-57342/v4 ◽

2020 ◽

Author(s):

Ercha Hu ◽

Yuan Meng ◽

Ying Ma ◽

Ruiqi Song ◽

Zhengxiang Hu ◽

...

Keyword(s):

Gene Expression ◽

Expression Profiles ◽

Blood Feeding ◽

Differentially Expressed ◽

Whole Body ◽

Sequence Information ◽

Transcriptome Data ◽

Rna Seq ◽

Dermacentor Marginatus

Abstract Background: The ixodid tick Dermacentor marginatus is a vector of many pathogens wide spread in Eurasia. Studies of gene sequence on many tick species have greatly increased the information on tick protective antigen which might have the potential to function as effective vaccine candidates or drug targets for eco-friendly acaricide development. In the current study, RNA-seq was applied to identify D. marginatus sequences and analyze differentially expressed unigenes.Methods: To obtain a broader picture of gene sequences and changes in expression level, RNA-seq was performed to obtain the whole-body transcriptome data of D. marginatus adult female ticks after engorgement and long-term starvation. Subsequently, the real-time quantitative PCR (RT-qPCR) was applied to validate the RNA-seq data.Results: RNA-seq produced 30,251 unigenes, of which 32% were annotated. Gene expression was compared among groups that differed by status as newly molted, starved and engorged female adult ticks. Nearly one third of the unigenes in each group were differentially expressed compared to the other two groups, and the most numerous were genes encoding proteins involved in catalytic and binding activities and apoptosis. Selected up-regulated differentially expressed genes in each group were associated to protein, lipids, carbohydrate and chitin metabolism. Blood-feeding and long-term starvation also caused genes differentially expressed in the defense response and antioxidant response. RT-qPCR results indicated 6 differentially expressed transcripts showed similar trends in expression changes with RNA-seq results confirming that the gene expression profiles in transcriptome data is in consistent with RT-qPCR validation.Conclusions: Obtaining the sequence information of D. marginatus and characterizing the expression pattern of the genes involved in blood-feeding and during starvation would be helpful in understanding molecular physiology of D. marginatus and provides data for anti-tick vaccine and drug development for controlling the tick.

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RNA-seq analysis of non-muscular invasive bladder cancer to reveal different gene expression profiles between smoking and non-smoking patients.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.6_suppl.478 ◽

2021 ◽

Vol 39 (6_suppl) ◽

pp. 478-478

Author(s):

Zhichao Fu ◽

Shenghua Liu ◽

Jianfei Wang ◽

Ning He ◽

Yadong Yang ◽

...

Keyword(s):

Gene Expression ◽

Bladder Cancer ◽

Tumor Progression ◽

Urothelial Carcinoma ◽

Differentially Expressed Genes ◽

Poor Prognosis ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Differentially Expressed ◽

Rna Seq

478 Background: Bladder cancer is the ninth most common malignancy in the world, approximately 75% of patients are diagnosed with non-muscle invasive bladder cancer (NMIBC). Smoking has been established to be a carcinogenic risk factor of bladder cancer. Nevertheless, the detailed relationship between smoking and progression of NMIBC are poorly understood. In this study, we revealed high expressed genes in smoking patients were significantly related to tumor progression in NMIBC patients. Methods: A total of 54 NMIBC patients including 19 never smokers and 35 smokers (current smokers and previous smokers) were enrolled in this study.The gene expression profiles were obtained by RNA-seq and the differentially expressed genes between smoking and non-smoking patients were identified using DESeq2 .The further analysis of the association between genes expression and patient survival in NMIBC cohorts(Jakob et al., 2016)and IMvigor 210 cohorts(Jonathan et al., 2016)by Kaplan-Meier survival estimate. Results: We identified 46 differentially expressed genes (p<0.05) in smoking and non-somking NMIBC patients. IDO1 and KRT14 gene, which related to bladder cancer progression and poor prognosis, was identified significantly higher expressed in somking group compared with non-smoking and they have a logFC of 2.6,3.9 with FDR 1.83E-5,3.40E-5 respectively. The expression of other genes, including KRT6A, CASP14, SERPINA1, MYO3A and IL20RB, were significantly higher in smoking patients compared to non-somking. Notably, survival data analysis from 476 NMIBC cohorts showed that IL20RB had a significant relationship with poor PFS(p = 0.021) and in the Mvigor 210 Cohort including 310 advanced or metastatic urothelial carcinoma patients treated with atezolizumab, we found that the high expression of IL20RB was significantly related to poor OS(p = 0.002). Conclusions: We identified 14 genes related to tumor progression were significantly higher in smoking NMIBC patients than in non-smoking. Among these genes, the expression of IL20RB was related to the poor prognosis of NMIBC, and it may correlates with reduced clinical benefit of immunotherapeutic in patients with urothelial carcinoma.

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Age-associated different transcriptome profiling in zebrafish and rat: insight into diversity of vertebrate aging

10.1101/478438 ◽

2018 ◽

Author(s):

Yusuke Kijima ◽

Wang Wantong ◽

Yoji Igarashi ◽

Kazutoshi Yoshitake ◽

Shuichi Asakawa ◽

...

Keyword(s):

Gene Expression ◽

Muscle Development ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Model Organisms ◽

Human Beings ◽

Rna Seq ◽

Down Regulation ◽

Circadian Genes ◽

Age Related

AbstractBackgroundAging and death are inevitable for most species and are of intense interest for human beings. Most mammals, including humans, show obvious aging phenotypes, for example, loss of tissue plasticity and sarcopenia. In this regard, fish provide attractive models because of their unique aging characteristics. First, the lifespan of fish is highly varied and some long-lived fish can live for over 200 years. Second, some fish show anti-aging features and indeterminate growth throughout their life. Because these characteristics are not found in mammalian model organisms, exploring mechanisms of senescence in fish is expected to provide new insights into vertebrate aging. Therefore, we conducted transcriptome analysis for brain, gill, heart, liver and muscle from 2-month-, 7-month-, 16month- and 39-month-old zebrafish. In addition, we downloaded RNA-seq data for sequential age related gene expression in brain, heart, liver and muscle of rat (1). These RNA-seq data from two species were compared, and common and species-specific features of senescence were analyzed.ResultsScreening of differentially expressed genes (DEGs) in all zebrafish tissues examined revealed up-regulation of circadian genes and down-regulation of hmgb3a. Comparative analysis of DEG profiles associated with aging between zebrafish and rat showed both conserved and clearly different aging phenomena. Furthermore, up-regulation of circadian genes with aging and down-regulation of collagen genes were observed in both species. On the other hand, in zebrafish, up-regulation of autophagy related genes in muscle and atf3 in various tissues suggested fish-specific anti- aging characteristics. Consistent with our knowledge of mammalian aging, a tissue deterioration-related DEG profile was observed in rat. We also detected aging-associated down-regulation of muscle development and ATP metabolism-related genes in zebrafish gill. Correspondingly, hypoxia-related genes were systemically up-regulated in aged zebrafish, suggesting age-related hypoxia as a senescence modulator in fish.ConclusionsOur results indicate both common and different aging profiles between fish and mammals. Gene expression profiles specific to fish will provide new insight for future translational research.

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Different gene expression profiles in iPSC-derived motor neurons from ALS8 patients with variable clinical courses suggest mitigating pathways for neurodegeneration

Human Molecular Genetics ◽

10.1093/hmg/ddaa069 ◽

2020 ◽

Vol 29 (9) ◽

pp. 1465-1475 ◽

Cited By ~ 1

Author(s):

Danyllo Oliveira ◽

David A Morales-Vicente ◽

Murilo S Amaral ◽

Livia Luz ◽

Andrea L Sertié ◽

...

Keyword(s):

Gene Expression ◽

Cell Death ◽

Differentially Expressed Genes ◽

Motor Neurons ◽

Oxidative Metabolism ◽

Protein Targeting ◽

Expression Profiles ◽

Protein Translation ◽

Differentially Expressed ◽

Rna Seq

Abstract Amyotrophic lateral sclerosis type 8 (ALS8) is an autosomal dominant form of ALS, which is caused by pathogenic variants in the VAPB gene. Here we investigated five ALS8 patients, classified as ‘severe’ and ‘mild’ from a gigantic Brazilian kindred, carrying the same VAPB mutation but displaying different clinical courses. Copy number variation and whole exome sequencing analyses in such individuals ruled out previously described genetic modifiers of pathogenicity. After deriving induced pluripotent stem cells (iPSCs) for each patient (N = 5) and controls (N = 3), motor neurons were differentiated, and high-throughput RNA-Seq gene expression measurements were performed. Functional cell death and oxidative metabolism assays were also carried out in patients’ iPSC-derived motor neurons. The degree of cell death and mitochondrial oxidative metabolism were similar in iPSC-derived motor neurons from mild patients and controls and were distinct from those of severe patients. Similar findings were obtained when RNA-Seq from such cells was performed. Overall, 43 genes were upregulated and 66 downregulated in the two mild ALS8 patients when compared with severe ALS8 individuals and controls. Interestingly, significantly enriched pathways found among differentially expressed genes, such as protein translation and protein targeting to the endoplasmic reticulum (ER), are known to be associated with neurodegenerative processes. Taken together, the mitigating mechanisms here presented appear to maintain motor neuron survival by keeping translational activity and protein targeting to the ER in such cells. As ALS8 physiopathology has been associated with proteostasis mechanisms in ER–mitochondria contact sites, such differentially expressed genes appear to relate to the bypass of VAPB deficiency.

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Morphological changes and functional circRNAs screening of rabbit skeletal muscle development

BMC Genomics ◽

10.1186/s12864-021-07706-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Qi Zheng ◽

Cuiyun Zhu ◽

Jing Jing ◽

Yinghui Ling ◽

Shuaiqi Qin ◽

...

Keyword(s):

Skeletal Muscle ◽

Muscle Development ◽

Expression Profiles ◽

Paraffin Section ◽

Rabbit Skeletal Muscle ◽

Differentially Expressed ◽

Adult Rabbit ◽

Rna Seq ◽

Skeletal Muscle Development ◽

Host Genes

Abstract Background The temporal expression pattern of circular RNAs (circRNAs) across developmental stages is essential for skeletal muscle growth and functional analysis. However, there are few analyses on the potential functions of circRNAs in rabbit skeletal muscle development. Results Initially, the paraffin sections showed extremely significant differences in the diameter, number, area and density of skeletal muscle fibers of the fetus, child, adult rabbit hind legs (P < 0.01). Then, RNA-seq libraries of these three stages were constructed. A total of 481 differentially expressed circRNAs (DE-circRNAs) and 5,658 differentially expressed genes (DEGs) were identified. Subsequently, DE-circRNAs, whose host genes were DEGs or non-DEGs, were analyzed by GO respectively. In the fetus vs. child group, up-regulated DE-circRNAs (whose host genes were DEGs) were related to muscle fiber structure, and down-regulated ones were related to mitosis. The up-regulated DE-circRNAs (whose host genes were non-DEGs) were involved in enzyme activity, methylation and glycosylation, and the down-regulated ones were involved in mitosis and catabolism. In the fetus vs. adult group, the up-regulated DE-circRNAs (whose host genes were DEGs) were related to skeletal muscle basic structure, and the down-regulated ones were also associated with cell proliferation. But the up-regulated DE-circRNAs (whose host genes were non-DEGs) were connected with regulation of histone ubiquitination, chromatin and organelles. The down-regulated DE-circRNAs were connected with the catabolism processes. In addition, novel_circ_0022663 and novel_circ_0005489, which might have coding potential, and novel_circ_0004210 and novel_circ_0001669, which might have miRNA sponge capability, were screened out. Conclusions In this study, hind leg muscles of fetus, child and adult rabbits were collected for paraffin section and RNA-seq to observe the structural changes of skeletal muscle and obtain circRNA expression profiles at different stages. These data provided a catalog of circRNAs related to muscle development in New Zealand rabbits, allowing us to better understand the functional transitions in mammalian muscle development.

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Transcriptome Analysis Reveals the Profile of Long Non-coding RNAs During Chicken Muscle Development

Frontiers in Physiology ◽

10.3389/fphys.2021.660370 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jie Liu ◽

Yan Zhou ◽

Xin Hu ◽

Jingchao Yang ◽

Qiuxia Lei ◽

...

Keyword(s):

Gene Expression ◽

Muscle Development ◽

Differentially Expressed ◽

Chicken Breast ◽

Regulation Of Transcription ◽

Rna Seq ◽

Regulatory Interactions ◽

Chicken Muscle ◽

Non Coding Rnas

The developmental complexity of muscle arises from elaborate gene regulation. Long non-coding RNAs (lncRNAs) play critical roles in muscle development through the regulation of transcription and post-transcriptional gene expression. In chickens, previous studies have focused on the lncRNA profile during the embryonic periods, but there are no studies that explore the profile from the embryonic to post-hatching period. Here, we reconstructed 14,793 lncRNA transcripts and identified 2,858 differentially expressed lncRNA transcripts and 4,282 mRNAs from 12-day embryos (E12), 17-day embryos (E17), 1-day post-hatch chicks (D1), 14-day post-hatch chicks (D14), 56-day post-hatch chicks (D56), and 98-day post-hatch chicks (D98), based on our published RNA-seq datasets. We performed co-expression analysis for the differentially expressed lncRNAs and mRNAs, using STEM, and identified two profiles with opposite expression trends: profile 4 with a downregulated pattern and profile 21 with an upregulated pattern. The cis- and trans-regulatory interactions between the lncRNAs and mRNAs were predicted within each profile. Functional analysis of the lncRNA targets showed that lncRNAs in profile 4 contributed to the cell proliferation process, while lncRNAs in profile 21 were mainly involved in metabolism. Our work highlights the lncRNA profiles involved in the development of chicken breast muscle and provides a foundation for further experiments on the role of lncRNAs in the regulation of muscle development.

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De novo assembly and analysis of the transcriptome of the Dermacentor marginatus genes differentially expressed after blood feeding and long-term starvation

10.21203/rs.3.rs-57342/v2 ◽

2020 ◽

Author(s):

Ercha Hu ◽

Yuan Meng ◽

Ying Ma ◽

Ruiqi Song ◽

Zhengxiang Hu ◽

...

Keyword(s):

Gene Expression ◽

Expression Profiles ◽

Blood Feeding ◽

Differentially Expressed ◽

Whole Body ◽

Sequence Information ◽

Transcriptome Data ◽

Rna Seq ◽

Dermacentor Marginatus

Abstract Background: The ixodid tick Dermacentor marginatus is a vector of many pathogens wide spread in Eurasia. Studies of gene sequence on many tick species have greatly increased the information on tick protective antigen which might have the potential to function as effective vaccine candidates or drug targets for eco-friendly acaricide development. In the current study, RNA-seq was applied to identify D. marginatus sequences and analyze differentially expressed unigenes.Methods: To obtain a broader picture of gene sequences and changes in expression level, RNA-seq was performed to obtain the whole-body transcriptome data of D. marginatus adult female ticks after engorgement and long-term starvation. Subsequently, the real-time quantitative PCR (RT-qPCR) was applied to validate the RNA-seq data.Results: RNA-seq produced 30,251 unigenes, of which 32% were annotated. Gene expression was compared among groups that differed by status as newly molted, starved and engorged female adult ticks. Nearly 1/3 of the unigenes in each group were differentially expressed compared to the other two groups, and the most numerous were genes encoding proteins involved in catalytic and binding activities and apoptosis. Selected up-regulated differentially expressed genes in each group were associated to protein, lipids, carbohydrate and chitin metabolism. Blood-feeding and long-term starvation also caused genes differentially expressed in the defense response and antioxidant response. RT-qPCR results indicated 6 differentially expressed transcripts showed similar trends in expression changes with RNA-seq results confirming that the gene expression profiles in transcriptome data is in consistent with RT-qPCR validation.Conclusions: Obtaining the sequence information of D. marginatus and characterizing the expression pattern of the genes involved in blood feeding and during starvation would be helpful in understanding molecular physiology of D. marginatus and provides data for anti-tick vaccine and drug development for controlling the tick.

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Identification and characteristic analysis of enhancers across 13 major cancer types

Precision Clinical Medicine ◽

10.1093/pcmedi/pbab019 ◽

2021 ◽

Author(s):

Mingming Qian ◽

Wenzhu Wang ◽

Yana Zhang ◽

Yi Zhao ◽

Huige Quan ◽

...

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

Binding Sites ◽

Expression Profiles ◽

Differentially Expressed ◽

Rna Seq ◽

Characteristic Analysis ◽

Cancer Types ◽

Highly Correlated ◽

Functional Transcription Factor

Abstract Enhancers are often mutated and dysregulated in various diseases such as cancer. By integrating the FANTOM enhancers expression profiles and RNA-seq data from TCGA of 13 cancers and their corresponding para-cancerous tissues, we systematically identified a total of 4702 significantly differentially expressed enhancers (DE enhancers). Furthermore, a total of 1036 differentially expressed genes (DE genes) regulated by differentially expressed enhancers (DE enhancers) were identified. It was found that in these 13 cancers, most (61.13%) enhancers were ubiquitously expressed, whereas DE enhancers were more likely to be tissue-specific expressed, and the DE genes regulated by DE enhancers were significantly enriched in cancer-related pathways. Finally, it was manifested that 74 SNPs located in 37 DE enhancers, and these SNPs affected the gain and loss of functional transcription factor binding sites (TFBS) of 758 transcription factors, which had been shown to be highly correlated with tumorigenesis and development.

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