Universal and differential transcriptional regulatory pathways involved in the preparation of summer and winter diapauses in Pieris melete

2021 ◽  
pp. 1-8
Author(s):  
Ting Jiang ◽  
Yulin Zhu ◽  
Yingchuan Peng ◽  
Wanna Zhang ◽  
Haijun Xiao
Keyword(s):  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Orthologous Group ◽  
Seasonal Adaptation ◽  
Environmental Signals ◽  
Regulatory Pathways ◽  
Kegg Pathways ◽  
Summer Diapause ◽  
Transcriptional Regulatory

Abstract Much progress has been made in understanding the environmental and hormonal systems regulating winter diapause. However, transcriptional regulation of summer diapause is still largely unknown, making it difficult to understand an all-around regulation profile of seasonal adaptation. To bridge this gap, comparison RNA-seq to profile the transcriptome and to examine differential gene expression profiles between non-diapause, summer diapause, and winter diapause groups were performed. A total number of 113 million reads were generated and assembled into 79,117 unigenes, with 37,492 unigenes categorized into 58 functional gene ontology groups, 25 clusters of orthologous group categories, and 256 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. KEGG analysis mapped 2108 differentially expressed genes to 48 and 67 pathways for summer and winter diapauses, respectively. Enrichment statistics showed that 11 identical pathways similarly overlapped in the top 20 enriched functional groups both related to summer and winter diapauses. We also identified 35 key candidate genes for universal and differential functions related to summer and winter diapause preparation. Furthermore, we identified some genes involved in the signaling and metabolic pathways that may be the key drivers to integrate environmental signals into the summer and winter diapause preparation. The current study provided valuable insights into global molecular mechanisms underpinning diapause preparation.

scholarly journals Genetic and pharmacological inactivation of adenosine A2A receptor reveals an Egr-2-mediated transcriptional regulatory network in the mouse striatum

2005 ◽  
Vol 23 (1) ◽  
pp. 89-102 ◽  
Author(s):  
Liqun Yu ◽  
Peter M. Haverty ◽  
Juliana Mariani ◽  
Yumei Wang ◽  
Hai-Ying Shen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Regulatory Network ◽  
Molecular Mechanisms ◽  
Transcriptional Regulatory Network ◽  
Expression Profiles ◽  
Mrna Level ◽  
Gene Expression Profiles ◽  
Bioinformatics Analyses ◽  
Mouse Striatum ◽  
Transcriptional Regulatory

The adenosine A2A receptor (A2AR) is highly expressed in the striatum, where it modulates motor and emotional behaviors. We used both microarray and bioinformatics analyses to compare gene expression profiles by genetic and pharmacological inactivation of A2AR and inferred an A2AR-controlled transcription network in the mouse striatum. A comparison between vehicle (VEH)-treated A2AR knockout (KO) mice (A2AR KO-VEH) and wild-type (WT) mice (WT-VEH) revealed 36 upregulated genes that were partially mimicked by treatment with SCH-58261 (SCH; an A2AR antagonist) and 54 downregulated genes that were not mimicked by SCH treatment. We validated the A2AR as a specific drug target for SCH by comparing A2AR KO-SCH and A2AR KO-VEH groups. The unique downregulation effect of A2AR KO was confirmed by comparing A2AR KO-SCH with WT-SCH gene groups. The distinct striatal gene expression profiles induced by A2AR KO and SCH should provide clues to the molecular mechanisms underlying the different phenotypes observed after genetic and pharmacological inactivation of A2AR. Furthermore, bioinformatics analysis discovered that Egr-2 binding sites were statistically overrepresented in the proximal promoters of A2AR KO-affected genes relative to the unaffected genes. This finding was further substantiated by the demonstration that the Egr-2 mRNA level increased in the striatum of both A2AR KO and SCH-treated mice and that striatal Egr-2 binding activity in the promoters of two A2AR KO-affected genes was enhanced in A2AR KO mice as assayed by chromatin immunoprecipitation. Taken together, these results strongly support the existence of an Egr-2-directed transcriptional regulatory network controlled by striatal A2ARs.

scholarly journals De Novo Transcriptome Assembly of Isatis indigotica at Reproductive Stages and Identification of Candidate Genes Associated with Flowering Pathways

2018 ◽  
Vol 143 (1) ◽  
pp. 56-66
Author(s):  
Yu Bai ◽  
Ying Zhou ◽  
Xiaoqing Tang ◽  
Yu Wang ◽  
Fangquan Wang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Orthologous Group ◽  
Rna Seq ◽  
Isatis Indigotica ◽  
Regulatory Pathways ◽  
Kegg Pathways ◽  
Bolting And Flowering

The appropriate timing of bolting and flowering is one of the keys to the reproductive success of Isatis indigotica. Several flowering regulatory pathways have been reported in plant species, but we know little about flowering regulatory in I. indigotica. In the present study, we performed RNA-seq and annotated I. indigotica transcriptome using RNA from five tissues (leaves, roots, flowers, fruit, and stems). Illumina sequencing generated 149,907,857 high-quality clean reads and 124,508 unigenes were assembled from the sequenced reads. Of these unigenes, 88,064 were functionally annotated by BLAST searches against the public protein databases. Functional classification and annotation assigned 55,991 and 23,072 unigenes to 52 gene ontology (GO) terms and 25 clusters of orthologous group (COG) categories, respectively. A total of 19,927 unigenes were assigned to 124 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and 80 candidate genes related to plant circadian rhythm were identified. We also identified a number of differentially expressed genes (DEG) and 91 potential bolting and flowering-related genes from the RNA-seq data. This study is the first to identify bolting and flowering-related genes based on transcriptome sequencing and assembly in I. indigotica. The results provide foundations for the exploration of flowering pathways in I. indigotica and investigations of the molecular mechanisms of bolting and flowering in Brassicaceae plants.

scholarly journals Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages

2012 ◽  
Vol 13 (11) ◽  
pp. 1118-1128 ◽  
Author(s):  
Emmanuel L Gautier ◽  
◽  
Tal Shay ◽  
Jennifer Miller ◽  
Melanie Greter ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Mouse Tissue ◽  
Regulatory Pathways ◽  
Transcriptional Regulatory

scholarly journals Cyclophilins and Their Functions in Abiotic Stress and Plant–Microbe Interactions

Biomolecules ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1390
Author(s):  
Przemysław Olejnik ◽  
Cezary J. Mądrzak ◽  
Katarzyna Nuc
Keyword(s):  
Abiotic Stress ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Stress Conditions ◽  
Regulatory Pathways ◽  
Isomerase Activity ◽  
Plant Microbe Interaction ◽  
Microbe Interactions ◽  
Fk506 Binding Proteins

Plants have developed a variety of mechanisms and regulatory pathways to change their gene expression profiles in response to abiotic stress conditions and plant–microbe interactions. The plant–microbe interaction can be pathogenic or beneficial. Stress conditions, both abiotic and pathogenic, negatively affect the growth, development, yield and quality of plants, which is very important for crops. In contrast, the plant–microbe interaction could be growth-promoting. One of the proteins involved in plant response to stress conditions and plant–microbe interactions is cyclophilin. Cyclophilins (CyPs), together with FK506-binding proteins (FKBPs) and parvulins, belong to a big family of proteins with peptidyl-prolyl cis-trans isomerase activity (Enzyme Commission (EC) number 5.2.1.8). Genes coding for proteins with the CyP domain are widely expressed in all organisms examined, including bacteria, fungi, animals, and plants. Their different forms can be found in the cytoplasm, endoplasmic reticulum, nucleus, chloroplast, mitochondrion and in the phloem space. They are involved in numerous processes, such as protein folding, cellular signaling, mRNA processing, protein degradation and apoptosis. In the past few years, many new functions, and molecular mechanisms for cyclophilins have been discovered. In this review, we aim to summarize recent advances in cyclophilin research to improve our understanding of their biological functions in plant defense and symbiotic plant–microbe interactions.

scholarly journals Modulation of the Immune Response by Deferasirox in Myelodysplastic Syndrome Patients

2021 ◽  
Vol 14 (1) ◽  
pp. 41
Author(s):  
Hana Votavova ◽  
Zuzana Urbanova ◽  
David Kundrat ◽  
Michaela Dostalova Merkerova ◽  
Martin Vostry ◽  
...  
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Blood Cell ◽  
Myelodysplastic Syndrome ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Adaptive Immune Response ◽  
Gene Expression Profiles ◽  
Iron Chelator ◽  
Multiple Cancer

Deferasirox (DFX) is an oral iron chelator used to reduce iron overload (IO) caused by frequent blood cell transfusions in anemic myelodysplastic syndrome (MDS) patients. To study the molecular mechanisms by which DFX improves outcome in MDS, we analyzed the global gene expression in untreated MDS patients and those who were given DFX treatment. The gene expression profiles of bone marrow CD34+ cells were assessed by whole-genome microarrays. Initially, differentially expressed genes (DEGs) were determined between patients with normal ferritin levels and those with IO to address the effect of excessive iron on cellular pathways. These DEGs were annotated to Gene Ontology terms associated with cell cycle, apoptosis, adaptive immune response and protein folding and were enriched in cancer-related pathways. The deregulation of multiple cancer pathways in iron-overloaded patients suggests that IO is a cofactor favoring the progression of MDS. The DEGs between patients with IO and those treated with DFX were involved predominantly in biological processes related to the immune response and inflammation. These data indicate DFX modulates the immune response mainly via neutrophil-related genes. Suppression of negative regulators of blood cell differentiation essential for cell maturation and upregulation of heme metabolism observed in DFX-treated patients may contribute to the hematopoietic improvement.

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