scholarly journals Evidence Supporting the Regulatory Relationships through a Paracrine Pathway between the Sternum and Pectoral Muscles in Ducks

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 463
Author(s):  
Yanying Li ◽  
Hehe Liu ◽  
Lei Wang ◽  
Yang Xi ◽  
Jiwen Wang ◽  
...  
Keyword(s):  
Muscle Development ◽  
Regulatory Mechanism ◽  
Expression Patterns ◽  
Pectoral Muscle ◽  
Scientific Data ◽  
Secreted Proteins ◽  
Rna Seq ◽  
Genes Encoding ◽  
Key Genes ◽  
Bone Calcification

Muscles and bones are anatomically closely linked, and they can conduct communication by mechanical and chemical signals. However, the specific regulatory mechanism between the pectoral muscle and sternum in birds was largely unknown. The present study explored the potential relationship between them in ducks. The result of the sections showed that more nuclei in proliferate states were observed in the pectoral muscle fibers attached to the calcified sternum, than those attached to the un-calcified sternum. The RNA-seq identified 328 differentially expressed genes (DEGs) in the sternum between the calcified and un-calcified groups. Gene ontology (GO) showed that the DEGs were mainly enriched in pathways associated with calcification. In addition, DEGs in the muscles between the calcified and un-calcified sternum groups were mainly annotated to signal transduction receptor pathways. The expression patterns of genes encoding for secreted proteins, in bone (CXCL12, BMP7 and CTSK) and muscle (LGI1), were clustered with muscle development (MB) and bone calcification (KCNA1, OSTN, COL9A3, and DCN) related genes, respectively, indicating the regulatory relationships through a paracrine pathway existing between the sternum and pectoral muscles in ducks. Together, we demonstrated that the pectoral muscle development was affected by the sternal ossification states in ducks. The VEGFA, CXCL12, SPP1, NOG, and BMP7 were possibly the key genes to participate in the ossification of the duck sternum. We firstly listed evidence supporting the regulatory relationships through a paracrine pathway between the sternum and pectoral muscles in ducks, which provided scientific data for the study of the synergistic development of bone and skeletal muscle.

scholarly journals Expression Patterns of Convergently Overlapping Arabidopsis Thaliana Gene Pairs OHP-NDP1 and OHP2-MES14

2014 ◽  
Vol 56 (1) ◽  
pp. 80-89 ◽  
Author(s):  
Karol Stawski ◽  
Mariusz Banach ◽  
Anna Goc
Keyword(s):  
Regulatory Mechanism ◽  
Expression Patterns ◽  
Transcript Level ◽  
Abiotic And Biotic Stresses ◽  
Biotic Stresses ◽  
Gene Pairs ◽  
Etiolated Seedlings ◽  
Genes Encoding ◽  
Prolonged Heat ◽  
Prolonged Heat Treatment

Abstract The function of one-helix proteins (OHPs) in the thylakoid membrane remains poorly understood but may be linked to plant photosystem protection. In Arabidopsis, the 3'UTRs of the genes encoding OHP and OHP2 partially overlap with NDP1 and MES14 respectively. Antisense orientation of genes has the potential to form double-stranded transcript (dsRNA) molecules which can be processed to siRNA and trigger RNA interference (RNAi). Natural siRNAs are induced by abiotic and biotic stresses. We examined whether the expression of the OHP-NDP1 and OHP2-MES14 gene pairs is regulated in this way. Both OHP genes, but neither NDP1 nor MES14, were activated by light in etiolated seedlings, whereas cold and prolonged heat treatment elevated the OHP transcript level. Expression of OHP2 was down-regulated after 2 h of osmotic and heat stress, while salt and osmotic stress increased MES14 transcript levels. No inverse regulation of these overlapping gene pairs was observed, excluding RNAi as a regulatory mechanism in the tested conditions. The presence of alternatively polyadenylat-ed transcripts of the studied genes raises the possibility of another regulatory mechanism of 3'UTR overlap.

scholarly journals Knockdown NRPC2, 3, 8, NRPABC1 and NRPABC2 Affects RNAPIII Activity and Disrupts Seed Development in Arabidopsis

2021 ◽  
Vol 22 (21) ◽  
pp. 11314
Author(s):  
Hailiang Zhao ◽  
Yao Qin ◽  
Ziyi Xiao ◽  
Kun Liang ◽  
Dianming Gong ◽  
...  
Keyword(s):  
Seed Development ◽  
Ribosome Biogenesis ◽  
Expression Patterns ◽  
Rna Polymerase Iii ◽  
5S Rrna ◽  
Rna Seq ◽  
Metabolic Processes ◽  
Control Seed ◽  
Genes Encoding ◽  
Response To Stress

RNA polymerase III (RNAPIII) contains 17 subunits forming 4 functional domains that control the different stages of RNAPIII transcription and are dedicated to the synthesis of small RNAs such as 5S rRNA and tRNAs. Here, we identified 23 genes encoding these subunits in Arabidopsis (Arabidopsis thaliana) and further analyzed 5 subunits (NRPC2, NRPC3, NRPC8, NRPABC1, and NRPABC2) encoded by 6 genes with different expression patterns and belonging to different sub-complexes. The knockdown of these genes repressed the expression of 5S rRNA and tRNAs, causing seed developmental arrest at different stages. Among these knockdown mutants, RNA-seq analysis revealed 821 common differentially expressed genes (DEGs), significantly enriched in response to stress, abscisic acid, cytokinins, and the jasmonic acid signaling pathway. Weighted gene co-expression network analysis (WGCNA) revealed several hub genes involved in embryo development, carbohydrate metabolic and lipid metabolic processes. We identified numerous unique DEGs between the mutants belonging to pathways, including cell proliferation, ribosome biogenesis, cell death, and tRNA metabolic processes. Thus, NRPC2, NRPC3, NRPC8, NRPABC1, and NRPABC2 control seed development in Arabidopsis by influencing RNAPIII activity and, thus, hormone signaling. Reduced expression of these subunit genes causes an insufficient accumulation of the total RNAPIII, leading to the phenotypes observed following the genetic knockdown of these subunits.

scholarly journals Integrated sRNAome and RNA-Seq Analysis Reveals miRNA Effects on Betalain Biosynthesis in Pitaya

2020 ◽  
Author(s):  
Canbin Chen ◽  
Fangfang Xie ◽  
Qingzhu Hua ◽  
Noemi Tel Zur ◽  
Lulu Zhang ◽  
...  
Keyword(s):  
Transient Expression ◽  
Plant Species ◽  
Negative Correlation ◽  
Target Genes ◽  
Regulatory Mechanism ◽  
Expression System ◽  
Expression Patterns ◽  
Rna Seq ◽  
Chlorophyll Accumulation ◽  
Regulatory Functions

Abstract Background: MicroRNAs (miRNAs) and their regulatory functions in anthocyanin, carotenoid, and chlorophyll accumulation have been extensively characterized in many plant species. However, the miRNA regulatory mechanism in betalain biosynthesis remains mostly unknown. Results: In this study, 126 conserved miRNAs and 41 novel miRNAs were first isolated from Hylocereus monacanthus, among which 95 conserved miRNAs belonged to 53 miRNA families. 34 candidate miRNAs related to betalain biosynthesis were found to be differentially expressed. The expression patterns of those differential expressed miRNAs were analyzed in various tissues of the pitaya by RT-qPCR. A significantly negative correlation was detected between the expression levels of half those miRNAs and corresponding target genes. Target genes of miRNAs i.e. aly-miR157d-5p_L+1_1ss4AC-comp25631_c0, aau-miR160_L-4R+ 1-comp36993_c0_seq3, nta-miR6020b-comp234190_c0, PC-5p-192_7269-comp29967_c0, PC-5p-23845_39-comp28219_c0, mdm-miR828a_1ss22AT-comp24967_c0, mdm-miR858- comp15143_c0, mdm-miR858-comp24362_c0 and mdm-miR858-comp403340_c0 were verified by 5′RACE and transient expression system in tobacco.Conclusions: aly-miR157d-5p_L+1_1ss4AC, aau-miR160_L-4R+1, nta-miR6020b PC-5p-192_7269, PC-5p-23845_39, mdm-miR828a_1ss22AT and mdm-miR858 may play important roles in pitaya fruit coloration and betalain accumulation. Our findings provide insights into the roles of miRNAs and their target genes of regulatory functions involved in betalain biosynthesis of pitaya.

scholarly journals Characterization and Duodenal Transcriptome Analysis of Chinese Beef Cattle With Divergent Feed Efficiency Using RNA-Seq

2021 ◽  
Vol 12 ◽  
Author(s):  
Chaoyun Yang ◽  
Liyun Han ◽  
Peng Li ◽  
Yanling Ding ◽  
Yun Zhu ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Differentially Expressed Genes ◽  
Feed Intake ◽  
Feed Efficiency ◽  
Muscle Development ◽  
Dietary Factors ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Biological Regulation ◽  
Key Genes

Residual feed intake (RFI) is an important measure of feed efficiency for agricultural animals. Factors associated with cattle RFI include physiology, dietary factors, and the environment. However, a precise genetic mechanism underlying cattle RFI variations in duodenal tissue is currently unavailable. The present study aimed to identify the key genes and functional pathways contributing to variance in cattle RFI phenotypes using RNA sequencing (RNA-seq). Six bulls with extremely high or low RFIs were selected for detecting differentially expressed genes (DEGs) by RNA-seq, followed by conducting GO, KEGG enrichment, protein-protein interaction (PPI), and co-expression network (WGCNA, n = 10) analysis. A total of 380 differentially expressed genes was obtained from high and low RFI groups, including genes related to energy metabolism (ALDOA, HADHB, INPPL1), mitochondrial function (NDUFS1, RFN4, CUL1), and feed intake behavior (CCK). Two key sub-networks and 26 key genes were detected using GO analysis of DEGs and PPI analysis, such as TPM1 and TPM2, which are involved in mitochondrial pathways and protein synthesis. Through WGCNA, a gene network was built, and genes were sorted into 27 modules, among which the blue (r = 0.72, p = 0.03) and salmon modules (r = −0.87, p = 0.002) were most closely related with RFI. DEGs and genes from the main sub-networks and closely related modules were largely involved in metabolism; oxidative phosphorylation; glucagon, ribosome, and N-glycan biosynthesis, and the MAPK and PI3K-Akt signaling pathways. Through WGCNA, five key genes, including FN1 and TPM2, associated with the biological regulation of oxidative processes and skeletal muscle development were identified. Taken together, our data suggest that the duodenum has specific biological functions in regulating feed intake. Our findings provide broad-scale perspectives for identifying potential pathways and key genes involved in the regulation of feed efficiency in beef cattle.

scholarly journals The landscape of chromatin accessibility in skeletal muscle during embryonic development in pigs

2021 ◽  
Author(s):  
Jingwei Yue ◽  
Xinhua Hou ◽  
Xin Liu ◽  
Ligang Wang ◽  
Hongmei Gao ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Transcription Factors ◽  
Embryonic Development ◽  
Muscle Development ◽  
Expression Patterns ◽  
Chromatin Accessibility ◽  
Rna Seq ◽  
Transcription Start Sites ◽  
Embryonic Muscle ◽  
Embryonic Muscle Development

Abstract Background: The development of skeletal muscle during the embryonic stage in pigs is precisely regulated by transcriptional mechanisms, which depends on chromatin accessibility. However, the landscape of chromatin accessibility in skeletal muscle during embryonic development in pigs has not been reported. To gain insight into the landscape of chromatin accessibility and the associated genome-wide transcriptome during embryonic muscle development, we performed ATAC-seq and RNA-seq on skeletal muscle of pig embryos at 45, 70 and 100 days post coitus (dpc).Results: In total, 21638, 35447 and 60181 unique regions (or peaks) were found across 45 dpc (LW45), 70 dpc (LW70) and 100 dpc (LW100) embryos, respectively. More than 91% of peaks were annotated within -1 kb to 100 bp of transcription start sites (TSSs). First, widespread increases in specific accessible chromatin regions (ACRs) from 45 to 100 dpc embryos suggested that the regulatory mechanisms became increasingly complicated during embryonic development. Second, the findings of integrated ATAC-seq and RNA-seq analyses showed that not only the numbers but also the peak intensities of ACRs could control the expression of associated genes. Finally, motif screening of stage-specific ACRs revealed some transcription factors that regulated muscle development-related genes, such as MyoD, Mef2c, and Mef2d. Motif screening of DPI of common peaks detected that a potential transcriptional repressor, namely CTCF, was identified among those genes that exhibited different change trends between the ATAC-seq and RNA-seq data.Conclusions: This work indicates that chromatin accessibility plays an important regulatory role in the embryonic muscle development of pigs and regulates the temporal and spatial expression patterns of key genes in muscle development by influencing the binding of transcription factors. Our results contribute to a better understanding of the regulatory dynamics of genes involved in pig embryonic skeletal muscle development.

scholarly journals Integrated sRNAome and RNA-Seq Analysis Reveals miRNA Effects on Betalain Biosynthesis in Pitaya

2020 ◽  
Author(s):  
Canbin Chen ◽  
Fangfang Xie ◽  
Qingzhu Hua ◽  
Noemi Tel Zur ◽  
Lulu Zhang ◽  
...  
Keyword(s):  
Transient Expression ◽  
Plant Species ◽  
Negative Correlation ◽  
Target Genes ◽  
Regulatory Mechanism ◽  
Expression System ◽  
Expression Patterns ◽  
Rna Seq ◽  
Chlorophyll Accumulation ◽  
Regulatory Functions

Abstract Background: MicroRNAs (miRNAs) and their regulatory functions in anthocyanin, carotenoid, and chlorophyll accumulation have been extensively characterized in many plant species. However, the miRNA regulatory mechanism in betalain biosynthesis remains mostly unknown. Results: In this study, 126 conserved miRNAs and 41 novel miRNAs were first isolated from Hylocereus monacanthus, among which 95 conserved miRNAs belonged to 53 miRNA families. 34 candidate miRNAs related to betalain biosynthesis were differentially expressed. The expression patterns of those differential expressed miRNAs were analyzed in various pitaya tissues by RT-qPCR. A significantly negative correlation was detected between the expression levels of half those miRNAs and corresponding target genes. Target genes of miRNAs i.e. Hmo-miR157b-HmSPL6-like, Hmo-miR160a-Hpcyt P450-like3, Hmo-miR6020-HmCYP71A8-like, Hmo-novel-2-HmCYP83B1-like, Hmo-novel-15-HmTPST-like, Hmo-miR828a-HmTT2-like, Hmo-miR858-HmMYB12-like, Hmo-miR858-HmMYBC1-like and Hmo-miR858-HmMYB2-like were verified by 5′RACE and transient expression system in tobacco.Conclusions: Hmo-miR157b, Hmo-miR160a, Hmo-miR6020 Hmo-novel-2, Hmo-novel-15, Hmo-miR828a and Hmo-miR858 play important roles in pitaya fruit coloration and betalain accumulation. Our findings provide new insights into the roles of miRNAs and their target genes of regulatory functions involved in betalain biosynthesis of pitaya.

scholarly journals Discovering sparse transcription factor codes for cell states and state transitions during development

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Leon A Furchtgott ◽  
Samuel Melton ◽  
Vilas Menon ◽  
Sharad Ramanathan
Keyword(s):  
Expression Patterns ◽  
Cell Types ◽  
State Transitions ◽  
Rna Seq ◽  
Statistical Framework ◽  
Multipotent Cells ◽  
Lineage Decision ◽  
Small Set ◽  
Key Genes ◽  
Early Human

Computational analysis of gene expression to determine both the sequence of lineage choices made by multipotent cells and to identify the genes influencing these decisions is challenging. Here we discover a pattern in the expression levels of a sparse subset of genes among cell types in B- and T-cell developmental lineages that correlates with developmental topologies. We develop a statistical framework using this pattern to simultaneously infer lineage transitions and the genes that determine these relationships. We use this technique to reconstruct the early hematopoietic and intestinal developmental trees. We extend this framework to analyze single-cell RNA-seq data from early human cortical development, inferring a neocortical-hindbrain split in early progenitor cells and the key genes that could control this lineage decision. Our work allows us to simultaneously infer both the identity and lineage of cell types as well as a small set of key genes whose expression patterns reflect these relationships.

scholarly journals De novo transcriptome sequence of Senna tora provides insights into anthraquinone biosynthesis

2019 ◽  
Author(s):  
Sang-Ho Kang ◽  
Woo-Haeng Lee ◽  
Chang-Muk Lee ◽  
Joon-Soo Sim ◽  
So Youn Won ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
Regulatory Mechanism ◽  
De Novo ◽  
Differential Expression Analysis ◽  
Rna Seq ◽  
De Novo Transcriptome ◽  
Secondary Metabolite Biosynthesis ◽  
Long Read ◽  
Annual Herb ◽  
Key Genes

AbstractSenna tora is an annual herb with rich source of anthraquinones that have tremendous pharmacological properties. However, there is little mention of genetic information for this species, especially regarding the biosynthetic pathways of anthraquinones. To understand the key genes and regulatory mechanism of anthraquinone biosynthesis pathways, we performed spatial and temporal transcriptome sequencing of S. tora using short RNA sequencing (RNA-Seq) and long-read isoform sequencing (Iso-Seq) technologies, and generated two unigene sets composed of 118,635 and 39,364, respectively. A comprehensive functional annotation and classification with multiple public databases identified array of genes involved in major secondary metabolite biosynthesis pathways and important transcription factor (TF) families (MYB, MYB-related, AP2/ERF, C2C2-YABBY, and bHLH). Differential expression analysis indicated that the expression level of genes involved in anthraquinone biosynthetic pathway regulates differently depending on the degree of tissues and seeds development. Furthermore, we identified that the amount of anthraquinone compounds were greater in late seeds than early ones. In conclusion, these results provide a rich resource for understanding the anthraquinone metabolism in S. tora.

scholarly journals Integrated sRNAome and RNA-Seq Analysis Reveals miRNA Effects on Betalain Biosynthesis in Pitaya

2020 ◽  
Author(s):  
Canbin Chen ◽  
Fangfang Xie ◽  
Qingzhu Hua ◽  
Noemi Tel Zur ◽  
Lulu Zhang ◽  
...  
Keyword(s):  
Transient Expression ◽  
Plant Species ◽  
Negative Correlation ◽  
Target Genes ◽  
Regulatory Mechanism ◽  
Expression System ◽  
Expression Patterns ◽  
Rna Seq ◽  
Chlorophyll Accumulation ◽  
Regulatory Functions

Abstract Background MicroRNAs (miRNAs) and their regulatory functions in anthocyanin, carotenoid, and chlorophyll accumulation have been extensively characterized in many plant species. However, the miRNA regulatory mechanism in betalain biosynthesis remains mostly unknown. Results In this study, 126 conserved miRNAs and 41 novel miRNAs were first isolated from Hylocereus monacanthus , among which 95 conserved miRNAs belonged to 53 miRNA families. 34 candidate miRNAs related to betalain biosynthesis were differentially expressed. The expression patterns of those differential expressed miRNAs were analyzed in various pitaya tissues by RT-qPCR. A significantly negative correlation was detected between the expression levels of half those miRNAs and corresponding target genes. Target genes of miRNAs i.e. Hmo-miR157b- HmSPL6-like , Hmo-miR160a- Hpcyt P450-like3 , Hmo-miR6020- HmCYP71A8-like , Hmo-novel-2- HmCYP83B1-like , Hmo-novel-15- HmTPST-like , Hmo-miR828a- HmTT2-like , Hmo-miR858- HmMYB12-like , Hmo-miR858- HmMYBC1-like and Hmo-miR858- HmMYB2-like were verified by 5′RACE and transient expression system in tobacco. Conclusions Hmo-miR157b, Hmo-miR160a, Hmo-miR6020 Hmo-novel-2, Hmo-novel-15, Hmo-miR828a and Hmo-miR858 play important roles in pitaya fruit coloration and betalain accumulation. Our findings provide new insights into the roles of miRNAs and their target genes of regulatory functions involved in betalain biosynthesis of pitaya.

scholarly journals De novo transcriptome analysis and comparative expression profiling of genes associated with the taste-modifying protein neoculin in Curculigo latifolia and Curculigo capitulata fruits

2020 ◽  
Author(s):  
Satoshi Okubo ◽  
Kaede Terauchi ◽  
Shinji Okada ◽  
Takao Yamaura ◽  
Keiko Abe ◽  
...  
Keyword(s):  
De Novo ◽  
Expression Profiles ◽  
Expression Patterns ◽  
3D Structure ◽  
Rna Seq ◽  
High Similarity ◽  
Perennial Plant ◽  
Mannose Binding ◽  
Genes Encoding ◽  
Galanthus Nivalis

Abstract Background Curculigo latifolia is a perennial plant found in Southeast Asia whose fruits contain the taste-modifying protein neoculin, which binds to sweet receptors to make sour fruits taste sweet. Although neoculin is similar to Galanthus nivalis agglutinin (GNA), which contains mannose-binding sites in its sequence and 3D structure, neoculin lacks such sites and has no lectin activity. Whether the fruits of C. latifolia and other Curculigo plants contain neoculin and/or GNA family genes is unclear. Results We performed de novo RNA-seq assembly of the fruits of C. latifolia and the related C. capitulata and analyzed the expression patterns of neoculin and neoculin-like genes in both species in detail. We assembled 85,697 transcripts from C. latifolia and 76,775 from C. capitulata using Trinity and annotated them using public databases. We identified 70,371 unigenes in C. latifolia and 63,704 in C. capitulata. In total, 38.6% of unigenes from C. latifolia and 42.6% from C. capitulata shared high similarity between the two species. We identified ten neoculin-related transcripts in C. latifolia and 15 in C. capitulata. Genes encoding both the basic and acidic subunits of neoculin were present in both plants. We aligned these 25 transcripts and generated a phylogenetic tree. Many orthologs in both species shared high similarity, despite the low number of common genes, suggesting that these genes likely existed before the two species diverged. The relative expression levels of these genes, as indicated by their transcript per million (TPM) values, differed considerably between the two species: the TPM values of neoculin genes were 60 times higher in C. latifolia than in C. capitulata, whereas those of GNA family members were 15,000 times lower in C. latifolia than in C. capitulata. Conclusions The genetic diversity of the neoculin-related genes strongly suggests that neoculin genes underwent duplication during evolution. The marked differences in the expression profiles of neoculin-related genes between C. latifolia and C. capitulata could be due to mutations in regions involved in transcriptional regulation. Comprehensive analysis of the genes expressed in the fruits of these two Curculigo species helped elucidate the origin of neoculin at the molecular level.

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