An integrated RNA-Seq and network study reveals a complex regulation process of rice embryo during seed germination

2015 ◽  
Vol 464 (1) ◽  
pp. 176-181 ◽  
Author(s):  
Ting Wei ◽  
Zilong He ◽  
XinYu Tan ◽  
Xue Liu ◽  
Xiao Yuan ◽  
...  
Keyword(s):  
Seed Germination ◽  
Rna Seq ◽  
Regulation Process ◽  
Complex Regulation ◽  
Rice Embryo

scholarly journals AP2M1 Supports TGF-β Signals to Promote Collagen Expression by Inhibiting Caveolin Expression

2021 ◽  
Vol 22 (4) ◽  
pp. 1639
Author(s):  
Saerom Lee ◽  
Ga-Eun Lim ◽  
Yong-Nyun Kim ◽  
Hyeon-Sook Koo ◽  
Jaegal Shim
Keyword(s):  
Rna Seq ◽  
Gene Encoding ◽  
Caveolin 1 ◽  
Collagen Expression ◽  
Disease States ◽  
Tumor Growth Factor ◽  
Complex Process ◽  
Collagen Protein ◽  
Complex Regulation ◽  
Collagen Genes

The extracellular matrix (ECM) is important for normal development and disease states, including inflammation and fibrosis. To understand the complex regulation of ECM, we performed a suppressor screening using Caenorhabditis elegans expressing the mutant ROL-6 collagen protein. One cuticle mutant has a mutation in dpy-23 that encodes the μ2 adaptin (AP2M1) of clathrin-associated protein complex II (AP-2). The subsequent suppressor screening for dpy-23 revealed the lon-2 mutation. LON-2 functions to regulate body size through negative regulation of the tumor growth factor-beta (TGF-β) signaling pathway responsible for ECM production. RNA-seq analysis showed a dominant change in the expression of collagen genes and cuticle components. We noted an increase in the cav-1 gene encoding caveolin-1, which functions in clathrin-independent endocytosis. By knockdown of cav-1, the reduced TGF-β signal was significantly restored in the dpy-23 mutant. In conclusion, the dpy-23 mutation upregulated cav-1 expression in the hypodermis, and increased CAV-1 resulted in a decrease of TβRI. Finally, the reduction of collagen expression including rol-6 by the reduced TGF-β signal influenced the cuticle formation of the dpy-23 mutant. These findings could help us to understand the complex process of ECM regulation in organism development and disease conditions.

scholarly journals Complex Regulation of Chenopodium album Seed Germination

2013 ◽  
Vol 1 (6) ◽  
pp. 133-142 ◽  
Author(s):  
Lindsey M. Altenhofen ◽  
Jack Dekker
Keyword(s):  
Seed Germination ◽  
Chenopodium Album ◽  
Complex Regulation

scholarly journals RNA-seq assembly and analysis of Garcinia mangostana transcriptome during seed germination

Data in Brief ◽  
2017 ◽  
Vol 14 ◽  
pp. 548-550 ◽  
Author(s):  
Nur Diyana Kamal Azlan ◽  
Mohd Noor Mat Isa ◽  
Zamri Zainal
Keyword(s):  
Seed Germination ◽  
Rna Seq ◽  
Garcinia Mangostana

An integrated RNA-Seq and physiological study reveals gene responses involving in the initial imbibition of seed germination in rice

2019 ◽  
Vol 90 (2) ◽  
pp. 249-263 ◽  
Author(s):  
Jia Zhao ◽  
Yongqi He ◽  
Xueying Li ◽  
Xianna Weng ◽  
Defeng Feng ◽  
...  
Keyword(s):  
Seed Germination ◽  
Physiological Study ◽  
Rna Seq

scholarly journals RNA-Seq Study Reveals AP2-Domain-Containing Signalling Regulators Involved in Initial Imbibition of Seed Germination in Rice

Rice Science ◽  
2020 ◽  
Vol 27 (4) ◽  
pp. 302-314
Author(s):  
He Yongqi ◽  
Zhao Jia ◽  
Feng Defeng ◽  
Huang Zhibo ◽  
Liang Jiaming ◽  
...  
Keyword(s):  
Seed Germination ◽  
Rna Seq ◽  
Ap2 Domain

scholarly journals De Novo Assembly and Characterization of the Seed Germination Transcriptomes of Sicyos angulatus

2021 ◽  
Vol 26 (01) ◽  
pp. 31-38
Author(s):  
Helong Si
Keyword(s):  
Signal Transduction ◽  
Seed Germination ◽  
Invasive Plant ◽  
De Novo ◽  
Expression Profiles ◽  
Signal Transduction Pathway ◽  
Pairwise Comparison ◽  
Rna Seq ◽  
Sequencing Data ◽  
Meristem Development

Sicyos angulatus has become an important invasive plant exhibiting good ecological adaptability and strong competitive ability. However, studies on this plant at the molecular level are limited by a lack of sequencing data. The present study obtained transcriptome sequences and gene expression profiles using RNA-Seq during S. angulatus seed germination. In total, RNA-Seq generated 491,967,468 reads, which were de novo assembled and 127,874 unigenes with N50 length of 807 bp. About 34.9% of the unigenes (44,660) were annotated against the protein databases, and 35,176 coding sequences were determined. During S. angulatus seed germination, over 127,860 unigenes were expressed and 66,664 unigenes differentially expressed genes (DEGs), among which 8919 DEGs were similar in pairwise comparison. Gene Ontology (GO) analysis of DEGs revealed that genes related to post-embryonic development, meristem development, and photosynthesis were enriched. In addition, the GO term “plant hormone signal transduction pathway” was also enriched in the DEGs. Important changes in genes expression related to auxin and gibberellin signal transduction might possibly be associated with S. angulatus seed germination. The findings of this study provide a foundation for research on S. angulatus that may contribute to prevent further invasion of this plant, consequently protecting the environment. © 2021 Friends Science Publishers

scholarly journals INVESTIGATING DYNAMICS OF AGE-ASSOCIATED TRANSCRIPTIONAL NETWORKS WITH INTERVENTIONS TARGETING AGING

2019 ◽  
Vol 3 (Supplement_1) ◽  
pp. S559-S559
Author(s):  
Ameya S Kulkarni ◽  
Jessica C Mar ◽  
Nir Barzilai
Keyword(s):  
Gene Networks ◽  
Gene Network ◽  
Physiological Function ◽  
Biological Aging ◽  
Transcriptional Networks ◽  
Rna Seq ◽  
Short Term ◽  
Progressive Decline ◽  
Topology Changes ◽  
Complex Regulation

Abstract Biological aging is characterized by a progressive decline in physiological function from molecular to organismal levels, manifesting through adaptive transcriptional networks. We present an overview of the complex regulation of transcriptional networks in species- and tissue-specific aging. We aimed to: 1) capture the age-associated changes in gene-gene connectivity, and 2) evaluate the effect of two interventions targeting biological aging (metformin, acarbose) on the regulation of gene networks. Aim 1) Using RNA-Seq we modeled co-expression networks and identified differentially co-expressed gene-pairs between young, middle-aged and older-aged groups. Aim 2) Using short-term clinical studies in older humans (metformin: MILES-trial; acarbose: SAIL-trial), and complementary mouse studies, we revealed the genes and novel pathways underlying the drugs’ effects on biological aging in muscle and adipose. Importantly, these interventions shifted transcripts to a more youthful expression. Overall, we provide evidence of age-associated gene-network topology changes and identify upstream transcriptional factors affected by age-targeting drugs.

scholarly journals In-Depth Proteomic Analysis of Rice Embryo Reveals its Important Roles in Seed Germination

2014 ◽  
Vol 55 (10) ◽  
pp. 1826-1847 ◽  
Author(s):  
Chao Han ◽  
Dongli He ◽  
Ming Li ◽  
Pingfang Yang
Keyword(s):  
Seed Germination ◽  
Proteomic Analysis ◽  
Rice Embryo

scholarly journals The Rice Small Auxin-Up RNA Gene OsSAUR33 Regulates Seed Vigor via Sugar Pathway during Early Seed Germination

2021 ◽  
Vol 22 (4) ◽  
pp. 1562
Author(s):  
Jia Zhao ◽  
Wenjun Li ◽  
Shan Sun ◽  
Liling Peng ◽  
Zhibo Huang ◽  
...  
Keyword(s):  
Seed Germination ◽  
Sugar Content ◽  
Soluble Sugar ◽  
Seedling Emergence ◽  
Seed Vigor ◽  
Rna Seq ◽  
Sugar Signaling ◽  
Early Germination ◽  
Germinating Seeds ◽  
Insight Into

Seed vigor affects seed germination and seedling emergence, and therefore is an important agronomic trait in rice. Small auxin-up RNAs (SAURs) function in a range of developmental processes, but their role in seed vigor remains unclear. Here, we observed that disruption of OsSAUR33 resulted in reduced germination rates and low seed uniformity in early germination. Expression of OsSAUR33 was higher in mature grains and early germinating seeds. RNA-seq analysis revealed that OsSAUR33 modulated seed vigor by affecting the mobilization of stored reserves during germination. Disruption of OsSAUR33 increased the soluble sugar content in dry mature grains and seeds during early germination. OsSAUR33 interacted with the sucrose non-fermenting-1-related protein kinase OsSnRK1A, a regulator of the sugar signaling pathway, which influences the expression of sugar signaling-related genes during germination. Disruption of OsSAUR33 increased sugar-sensitive phenotypes in early germination, suggesting OsSAUR33 likely affects seed vigor through the sugar pathway. One elite haplotype of OsSAUR33 associated with higher seed vigor was identified mainly in indica accessions. This study provides insight into the effects of OsSAUR33 on seed vigor in rice.

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