A full-length transcriptome and gene expression analysis reveal genes and molecular elements expressed during seed development in Gnetum luofuense

Abstract Background Gnetum is an economically important tropical and subtropical gymnosperm genus with various dietary, industrial and medicinal uses. Many carbohydrates, proteins and fibers accumulate during the ripening of Gnetum seeds. However, the molecular mechanisms related to this process remain unknown. Results We therefore assembled a full-length transcriptome from immature and mature G. luofuense seeds using PacBio sequencing reads. We identified a total of 5726 novel genes, 9061 alternative splicing events, 3551 lncRNAs, 2160 transcription factors, and we found that 8512 genes possessed at least one poly(A) site. In addition, gene expression comparisons of six transcriptomes generated by Illumina sequencing showed that 14,323 genes were differentially expressed from an immature stage to a mature stage with 7891 genes upregulated and 6432 genes downregulated. The expression of 14 differentially expressed transcription factors from the MADS-box, Aux/IAA and bHLH families was validated by qRT-PCR, suggesting that they may have important roles in seed ripening of G. luofuense. Conclusions These findings provide a valuable molecular resource for understanding seed development of gymnosperms.

Download Full-text

A full-length transcriptome and gene expression analysis reveal genes and molecular elements expressed during seed development in Gnetum luofuense

10.21203/rs.3.rs-36058/v3 ◽

2020 ◽

Author(s):

Nan deng ◽

Chen Hou ◽

Boxiang He ◽

Fengfeng Ma ◽

Qingan Song ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Seed Development ◽

Molecular Mechanisms ◽

Immature Stage ◽

Full Length ◽

Differentially Expressed ◽

Mature Stage ◽

Medicinal Uses ◽

A Site

Abstract Background: Gnetum is an economically important tropical and subtropical gymnosperm genus with various dietary, industrial and medicinal uses. Many carbohydrates, proteins and fibers accumulate during the ripening of Gnetum seeds. However, the molecular mechanisms related to this process remain unknown.Results: We therefore assembled a full-length transcriptome from immature and mature G. luofuense seeds using PacBio sequencing reads. We identified a total of 5,726 novel genes, 9,061 alternative splicing events, 3,551 lncRNAs, 2,160 transcription factors, and we found that 8,512 genes possessed at least one poly(A) site. In addition, gene expression comparisons of six transcriptomes generated by Illumina sequencing showed that 14,323 genes were differentially expressed from an immature stage to a mature stage with 7,891 genes upregulated and 6,432 genes downregulated. The expression of 14 differentially expressed transcription factors from the MADS-box, Aux/IAA and bHLH families was validated by qRT-PCR, suggesting that they may have important roles in seed ripening of G. luofuense.Conclusions: These findings provide a valuable molecular resource for understanding seed development of gymnosperms.

Download Full-text

A full-length transcriptome and gene expression analysis reveal genes and molecular elements expressed during seed development in Gnetum luofuense

10.21203/rs.3.rs-36058/v2 ◽

2020 ◽

Author(s):

Nan deng ◽

Chen Hou ◽

Boxiang He ◽

Fengfeng Ma ◽

Qingan Song ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Seed Development ◽

Molecular Mechanisms ◽

Immature Stage ◽

Full Length ◽

Differentially Expressed ◽

Mature Stage ◽

Medicinal Uses ◽

A Site

Download Full-text

A Full-length Transcriptome and Gene Expression Analysis Reveal Genes and Molecular Elements Expressed During Seed Development in Gnetum Luofuense

10.21203/rs.3.rs-36058/v1 ◽

2020 ◽

Author(s):

Nan deng ◽

Chen Hou ◽

Boxiang He ◽

Fengfeng Ma ◽

Qingan Song ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Gene Expression Analysis ◽

Molecular Mechanisms ◽

Immature Stage ◽

Full Length ◽

Differentially Expressed ◽

Mature Stage ◽

Medicinal Uses ◽

A Site

Abstract Background: Gnetum is an economically important tropical and subtropical gymnosperm genus with various dietary, industrial and medicinal uses. Many carbohydrates, proteins and secondary metabolic compounds accumulate during the ripening of Gnetum seeds.However, the molecular mechanisms related to this process remain unknown. Results: We therefore assembled a full-length transcriptome from immature and mature G. luofuenseseeds using PacBio sequencingreads. We identified a total of 5,726 novel genes, 9,061 alternative splicing events, 3,551 lncRNAs, 2,160 transcription factors, and 359 fusion genes, and we found that 8,512 genes possessed at least one poly(A) site. In addition, gene expression comparisons of six transcriptomes generated by Illumina sequencing showed that14,323 genes were differentially expressed from an immature stage to a mature stage with 7,891 genes upregulated and 6,432 genes downregulated. The expression of 14 differentially expressed transcription factors from the MADS-box, Aux/IAA and bHLH families was validated by qRT-PCR, suggesting that they may have important roles in seed ripening of G. luofuense. Conclusions:These findings provide a valuable molecular resource for domestication and cultivation of Gnetum species.

Download Full-text

Competition between binding sites determines gene expression at low transcription factor concentrations

10.1101/033753 ◽

2015 ◽

Cited By ~ 1

Author(s):

David van Dijk ◽

Eilon Sharon ◽

Maya Lotan-Pompan ◽

Adina Weinberger ◽

Eran Segal ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Binding Sites ◽

Molecular Mechanisms ◽

Response Curves ◽

Regulate Gene Expression ◽

Extracellular Signals ◽

Absolute Expression ◽

A Site ◽

Target Promoter

AbstractThe response of gene expression to intra-and extra-cellular cues is largely mediated through changes in the activity of transcription factors (TFs), whose sequence specificities are largely known. However, the rules by which promoters decode the amount of active TF into gene expression are not well understood. Here, we measure the activity of 6500 designed promoters at six different levels of TF activity in budding yeast. We observe that maximum promoter activity is determined by TF activity and not by the number of sites. Surprisingly, the addition of an activator-binding site often reduces expression. A thermodynamic model that incorporates competition between neighboring binding sites for a local pool of TF molecules explains this behavior and accurately predicts both absolute expression and the amount by which addition of a site increases or reduces expression. Taken together, our findings support a model in which neighboring binding sites interact competitively when TF is limiting but otherwise act additivelySignificance StatementIn response to intracellular and extracellular signals organisms alter the concentration and activity of transcription factors (TFs), proteins that regulate gene expression. However, the molecular mechanisms that determine the response of a target promoter to changes in the number of active TF molecules are not well understood. By combining mathematical modeling with measurements of TF dose-response curves for thousands of designed promoters, we show that competition for active TF molecules is a major factor in determining gene expression. At low TF concentrations additional activator-binding sites within a promoter can actually reduce expression. Thermodynamic modeling suggests that steric hindrance between neighboring binding sites cannot explain this behavior, but that competition for limiting TF molecules can.

Download Full-text

Transcriptome analyses and virus induced gene silencing identify genes in the Rpp4-mediated Asian soybean rust resistance pathway

Functional Plant Biology ◽

10.1071/fp12296 ◽

2013 ◽

Vol 40 (10) ◽

pp. 1029 ◽

Cited By ~ 30

Author(s):

Aguida M. A. P. Morales ◽

Jamie A. O'Rourke ◽

Martijn van de Mortel ◽

Katherine T. Scheider ◽

Timothy J. Bancroft ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Gene Silencing ◽

Differentially Expressed ◽

Soybean Rust ◽

Phakopsora Pachyrhizi ◽

R Gene ◽

Virus Induced Gene Silencing ◽

Asian Soybean Rust ◽

Defence Responses

Rpp4 (Resistance to Phakopsora pachyrhizi 4) confers resistance to Phakopsora pachyrhizi Sydow, the causal agent of Asian soybean rust (ASR). By combining expression profiling and virus induced gene silencing (VIGS), we are developing a genetic framework for Rpp4-mediated resistance. We measured gene expression in mock-inoculated and P. pachyrhizi-infected leaves of resistant soybean accession PI459025B (Rpp4) and the susceptible cultivar (Williams 82) across a 12-day time course. Unexpectedly, two biphasic responses were identified. In the incompatible reaction, genes induced at 12 h after infection (hai) were not differentially expressed at 24 hai, but were induced at 72 hai. In contrast, genes repressed at 12 hai were not differentially expressed from 24 to 144 hai, but were repressed 216 hai and later. To differentiate between basal and resistance-gene (R-gene) mediated defence responses, we compared gene expression in Rpp4-silenced and empty vector-treated PI459025B plants 14 days after infection (dai) with P. pachyrhizi. This identified genes, including transcription factors, whose differential expression is dependent upon Rpp4. To identify differentially expressed genes conserved across multiple P. pachyrhizi resistance pathways, Rpp4 expression datasets were compared with microarray data previously generated for Rpp2 and Rpp3-mediated defence responses. Fourteen transcription factors common to all resistant and susceptible responses were identified, as well as fourteen transcription factors unique to R-gene-mediated resistance responses. These genes are targets for future P. pachyrhizi resistance research.

Download Full-text

Insights into the seasonal adaptive mechanisms of Chinese alligators (Alligator sinensis) from transcriptomic analyses

Australian Journal of Zoology ◽

10.1071/zo18005 ◽

2018 ◽

Vol 66 (2) ◽

pp. 93 ◽

Cited By ~ 4

Author(s):

Hongji Sun ◽

Xianbo Zuo ◽

Long Sun ◽

Peng Yan ◽

Fang Zhang ◽

...

Keyword(s):

Gene Expression ◽

Skeletal Muscle ◽

Molecular Mechanisms ◽

Differentially Expressed ◽

Model Organisms ◽

Seasonal Adaptation ◽

Cold Temperatures ◽

Chinese Alligator ◽

Adaptive Mechanisms ◽

Alligator Sinensis

The Chinese alligator (Alligator sinensis) is an endemic and rare species in China, and is considered to be one of the most endangered vertebrates in the world. It is known to hibernate, an energy-saving strategy against cold temperatures and food deprivation. Changes in gene expression during hibernation remain largely unknown. To understand these complex seasonal adaptive mechanisms, we performed a comprehensive survey of differential gene expression in heart, skeletal muscle, and kidney of hibernating and active Chinese alligators using RNA-Sequencing. In total, we identified 4780 genes differentially expressed between the active and hibernating periods. GO and KEGG pathway analysis indicated the likely role of these differentially expressed genes (DEGs). The upregulated DEGs in the active Chinese alligator, CSRP3, MYG and PCKGC, may maintain heart and skeletal muscle contraction, transport and storage of oxygen, and enhance the body’s metabolism, respectively. The upregulated DEGs in the dormant Chinese alligator, ADIPO, CIRBP and TMM27, may improve insulin sensitivity and glucose/lipid metabolism, protect cells against harmful effects of cold temperature and hypoxia, regulate amino acid transport and uptake, and stimulate the proliferation of islet cells and the secretion of insulin. These results provide a foundation for understanding the molecular mechanisms of the seasonal adaptation required for hibernation in Chinese alligators, as well as effective information for other non-model organisms research.

Download Full-text

Shank3 Modulates Sleep and Expression of Circadian Transcription Factors

10.1101/465799 ◽

2018 ◽

Author(s):

Ashley M. Ingiosi ◽

Taylor Wintler ◽

Hannah Schoch ◽

Kristan G. Singletary ◽

Dario Righelli ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Molecular Mechanisms ◽

Sleep Problems ◽

Wheel Running ◽

The United States ◽

Autism Spectrum ◽

Wheel Running Activity ◽

Falling Asleep ◽

Circadian Transcription

AbstractAutism Spectrum Disorder (ASD) is the most prevalent neurodevelopmental disorder in the United States and often co-presents with sleep problems. Sleep problems in ASD predict the severity of ASD core diagnostic symptoms and have a considerable impact on the quality of life of caregivers. Little is known, however, about the underlying molecular mechanisms. We investigated the role of Shank3, a high confidence ASD gene candidate, in sleep architecture and regulation. We show that mice lacking exon 21 of Shank3 have problems falling asleep even when sleepy. Using RNA-seq we show that sleep deprivation increases the differences in gene expression between mutants and wild types, downregulating circadian transcription factors Per3, Dec2, Hlf, Tef, and Reverbα. Shank3 mutants also have trouble regulating wheel-running activity in constant darkness. Overall our study shows that Shank3 is an important modulator of sleep and clock gene expression.

Download Full-text

Insight into Molecular Profile Changes after Skeletal Muscle Contusion Using Microarray and Bioinformatics Analyses

10.21203/rs.3.rs-85830/v1 ◽

2020 ◽

Author(s):

Na Li ◽

Ru-feng Bai ◽

Chun Li ◽

Li-hong Dang ◽

Qiu-xiang Du ◽

...

Keyword(s):

Gene Expression ◽

Network Analysis ◽

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Expression Profiles ◽

Healing Process ◽

Differentially Expressed ◽

Molecular Profile ◽

Wound Age ◽

Functional Modules

Abstract Background: Muscle trauma frequently occurs in daily life. However, the molecular mechanisms of muscle healing, which partly depend on the extent of the damage, are not well understood. This study aimed to investigate gene expression profiles following mild and severe muscle contusion, and to provide more information about the molecular mechanisms underlying the repair process.Methods: A total of 33 rats were divided randomly into control (n = 3), mild contusion (n = 15), and severe contusion (n = 15) groups; the contusion groups were further divided into five subgroups (1, 3, 24, 48, and 168 h post-injury; n = 3 per subgroup). Then full genome microarray of RNA isolated from muscle tissue was performed to access the gene expression changes during healing process.Results: A total of 2,844 and 2,298 differentially expressed genes were identified in the mild and severe contusion groups, respectively. The analysis of the overlapping differentially expressed genes showed that there are common mechanisms of transcriptomic repair of mild and severe contusion within 48 h post-contusion. This was supported by the results of principal component analysis, hierarchical clustering, and weighted gene co‐expression network analysis of the 1,620 coexpressed genes in mildly and severely contused muscle. From these analyses, we discovered that the gene profiles in functional modules and temporal clusters were similar between the mild and severe contusion groups; moreover, the genes showed time-dependent patterns of expression, which allowed us to identify useful markers of wound age. We then performed an analysis of the functions of genes (including Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway annotation, and protein–protein interaction network analysis) in the functional modules and temporal clusters, and the hub genes in each module–cluster pair were identified. Interestingly, we found that genes downregulated within 24−48 h of the healing process were largely associated with metabolic processes, especially oxidative phosphorylation of reduced nicotinamide adenine dinucleotide phosphate, which has been rarely reported. Conclusions: These results improve our understanding of the molecular mechanisms underlying muscle repair, and provide a basis for further studies of wound age estimation.

Download Full-text

A Comparison of Gene Expression Changes in the Blood of Individuals Consuming Diets Supplemented with Olives, Nuts or Long-Chain Omega-3 Fatty Acids

Nutrients ◽

10.3390/nu12123765 ◽

2020 ◽

Vol 12 (12) ◽

pp. 3765

Author(s):

Virginie Bottero ◽

Judith A. Potashkin

Keyword(s):

Gene Expression ◽

Alzheimer’S Disease ◽

Fatty Acids ◽

Transcription Factors ◽

Mediterranean Diet ◽

Differentially Expressed ◽

Omega 3 Fatty Acids ◽

Omega 3 ◽

The Mediterranean ◽

Long Chain

Background: The Mediterranean diet, which is rich in olive oil, nuts, and fish, is considered healthy and may reduce the risk of chronic diseases. Methods: Here, we compared the transcriptome from the blood of subjects with diets supplemented with olives, nuts, or long-chain omega-3 fatty acids and identified the genes differentially expressed. The dietary genes obtained were subjected to network analysis to determine the main pathways, as well as the transcription factors and microRNA interaction networks to elucidate their regulation. Finally, a gene-associated disease interaction network was performed. Results: We identified several genes whose expression is altered after the intake of components of the Mediterranean diets compared to controls. These genes were associated with infection and inflammation. Transcription factors and miRNAs were identified as potential regulators of the dietary genes. Interestingly, caspase 1 and sialophorin are differentially expressed in the opposite direction after the intake of supplements compared to Alzheimer’s disease patients. In addition, ten transcription factors were identified that regulated gene expression in supplemented diets, mild cognitive impairment, and Alzheimer’s disease. Conclusions: We identified genes whose expression is altered after the intake of the supplements as well as the transcription factors and miRNAs involved in their regulation. These genes are associated with schizophrenia, neoplasms, and rheumatic arthritis, suggesting that the Mediterranean diet may be beneficial in reducing these diseases. In addition, the results suggest that the Mediterranean diet may also be beneficial in reducing the risk of dementia.

Download Full-text

The Western Diet Regulates Hippocampal Microvascular Gene Expression: An Integrated Genomic Analyses in Female Mice

Scientific Reports ◽

10.1038/s41598-019-55533-9 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 4

Author(s):

Saivageethi Nuthikattu ◽

Dragan Milenkovic ◽

John Rutledge ◽

Amparo Villablanca

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Differential Expression ◽

Differential Gene Expression ◽

Gene Networks ◽

Molecular Mechanisms ◽

Western Diet ◽

Protein Coding ◽

Female Mice ◽

Differential Gene

AbstractHyperlipidemia is a risk factor for dementia, and chronic consumption of a Western Diet (WD) is associated with cognitive impairment. However, the molecular mechanisms underlying the development of microvascular disease in the memory centers of the brain are poorly understood. This pilot study investigated the nutrigenomic pathways by which the WD regulates gene expression in hippocampal brain microvessels of female mice. Five-week-old female low-density lipoprotein receptor deficient (LDL-R−/−) and C57BL/6J wild type (WT) mice were fed a chow or WD for 8 weeks. Metabolics for lipids, glucose and insulin were determined. Differential gene expression, gene networks and pathways, transcription factors, and non-protein coding RNAs were evaluated by genome-wide microarray and bioinformatics analysis of laser captured hippocampal microvessels. The WD resulted in differential expression of 2,412 genes. The majority of differential gene expression was attributable to differential regulation of cell signaling proteins and their transcription factors, approximately 7% was attributable to differential expression of miRNAs, and a lesser proportion was due to other non-protein coding RNAs, primarily long non-coding RNAs (lncRNAs) and small nucleolar RNAs (snoRNAs) not previously described to be modified by the WD in females. Our findings revealed that chronic consumption of the WD resulted in integrated multilevel molecular regulation of the hippocampal microvasculature of female mice and may provide one of the mechanisms underlying vascular dementia.

Download Full-text