Cell cloning-based transcriptome analysis in Rett patients: relevance to the pathogenesis of Rett syndrome of new human MeCP2 target genes

AbstractMECP2 and its product, Methyl-CpG binding protein 2 (MeCP2), are mostly known for their association to Rett Syndrome (RTT), a rare neurodevelopmental disorder. Additional evidence suggests that MECP2 may underlie other neuropsychiatric and neurological conditions, and perhaps modulate common presentations and pathophysiology across disorders. To clarify the mechanisms of these interactions, we develop a method that uses the binding properties of MeCP2 to identify its targets, and in particular, the genes recognized by MeCP2 and associated to several neurological and neuropsychiatric disorders. Analysing mechanisms and pathways modulated by these genes, we find that they are involved in three main processes: neuronal transmission, immuno-reactivity, and development. Also, while the nervous system is the most relevant in the pathophysiology of the disorders, additional systems may contribute to MeCP2 action through its target genes. We tested our results with transcriptome analysis on Mecp2-null models and cells derived from a patient with RTT, confirming that the genes identified by our procedure are directly modulated by MeCP2. Thus, MeCP2 may modulate similar mechanisms in different pathologies, suggesting that treatments for one condition may be effective for related disorders.

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Transcriptome Analysis Reveals a Promotion of Carotenoid Production by Copper Ions in Recombinant Saccharomyces cerevisiae

Microorganisms ◽

10.3390/microorganisms9020233 ◽

2021 ◽

Vol 9 (2) ◽

pp. 233

Author(s):

Buli Su ◽

Anzhang Li ◽

Ming-Rong Deng ◽

Honghui Zhu

Keyword(s):

Saccharomyces Cerevisiae ◽

Transcriptome Analysis ◽

Gene Expression Analysis ◽

Target Genes ◽

Copper Ions ◽

Carotenoid Production ◽

Carotenoid Accumulation ◽

Nutritional Components ◽

Differential Gene ◽

First Time

We previously constructed a Saccharomyces cerevisiae carotenoid producer BL03-D-4 which produced much more carotenoid in YPM (modified YPD) media than YPD media. In this study, the impacts of nutritional components on carotenoid accumulation of BL03-D-4 were investigated. When using YPM media, the carotenoid yield was increased 10-fold compared to using the YPD media. To elucidate the hidden mechanism, a transcriptome analysis was performed and showed that 464 genes changed significantly in YPM media. Furthermore, inspired by the differential gene expression analysis which indicated that ADY2, HES1, and CUP1 showed the most remarkable changes, we found that the improvement of carotenoid accumulation in YPM media was mainly due to the copper ions, since supplementation of 0.08 mM CuSO4 in YPD media could increase carotenoid yield 9.2-fold. Reverse engineering of target genes was performed and carotenoid yield could be increased 6.4-fold in YPD media through overexpression of ACE1. The present study revealed for the first time the prominent promotion of carotenoid yield by copper ions in engineered S. cerevisiae and provided a new target ACE1 for genetic engineering of S. cerevisiae for the bioproduction of carotenoids.

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Transcriptome Analysis for Notch3 Target Genes Identifies Grip2 as a Novel Regulator of Myogenic Response in the Cerebrovasculature

Arteriosclerosis Thrombosis and Vascular Biology ◽

10.1161/atvbaha.112.251736 ◽

2013 ◽

Vol 33 (1) ◽

pp. 76-86 ◽

Cited By ~ 15

Author(s):

Charles Fouillade ◽

Céline Baron-Menguy ◽

Valérie Domenga-Denier ◽

Christelle Thibault ◽

Kogo Takamiya ◽

...

Keyword(s):

Transcriptome Analysis ◽

Target Genes ◽

Myogenic Response

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Response of Staphylococcus aureus to Salicylate Challenge

Journal of Bacteriology ◽

10.1128/jb.01149-06 ◽

2006 ◽

Vol 189 (1) ◽

pp. 220-227 ◽

Cited By ~ 30

Author(s):

James T. Riordan ◽

Arunachalam Muthaiyan ◽

Wayne Van Voorhies ◽

Christopher T. Price ◽

James E. Graham ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Antimicrobial Resistance ◽

Transcriptome Analysis ◽

Target Genes ◽

Efflux Pump ◽

Multidrug Efflux ◽

Multidrug Efflux Pump ◽

Antibiotic Target ◽

Unique Mechanism ◽

Formate Metabolism

ABSTRACT Growth of Staphylococcus aureus with the nonsteroidal anti-inflammatory salicylate reduces susceptibility of the organism to multiple antimicrobials. Transcriptome analysis revealed that growth of S. aureus with salicylate leads to the induction of genes involved with gluconate and formate metabolism and represses genes required for gluconeogenesis and glycolysis. In addition, salicylate induction upregulates two antibiotic target genes and downregulates a multidrug efflux pump gene repressor (mgrA) and sarR, which represses a gene (sarA) important for intrinsic antimicrobial resistance. We hypothesize that these salicylate-induced alterations jointly represent a unique mechanism that allows S. aureus to resist antimicrobial stress and toxicity.

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Transcriptome analysis of a barley breeding program examines gene expression diversity and reveals target genes for malting quality improvement

BMC Genomics ◽

10.1186/1471-2164-11-653 ◽

2010 ◽

Vol 11 (1) ◽

Cited By ~ 20

Author(s):

María Muñoz-Amatriaín ◽

Yanwen Xiong ◽

Mark R Schmitt ◽

Hatice Bilgic ◽

Allen D Budde ◽

...

Keyword(s):

Gene Expression ◽

Quality Improvement ◽

Transcriptome Analysis ◽

Target Genes ◽

Breeding Program ◽

Malting Quality ◽

Barley Breeding

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Transcriptome analysis of microglia in a mouse model of Rett syndrome: differential expression of genes associated with microglia/macrophage activation and cellular stress

Molecular Autism ◽

10.1186/s13229-017-0134-z ◽

2017 ◽

Vol 8 (1) ◽

Cited By ~ 21

Author(s):

Dejian Zhao ◽

Ryan Mokhtari ◽

Erika Pedrosa ◽

Rayna Birnbaum ◽

Deyou Zheng ◽

...

Keyword(s):

Mouse Model ◽

Differential Expression ◽

Rett Syndrome ◽

Transcriptome Analysis ◽

Macrophage Activation ◽

Cellular Stress ◽

Expression Of Genes ◽

Differential Expression Of Genes

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Transcriptome analysis of tetraploid cells identifies cyclin D2 as a facilitator of adaptation to genome doubling in the presence of p53

Molecular Biology of the Cell ◽

10.1091/mbc.e16-05-0268 ◽

2016 ◽

Vol 27 (20) ◽

pp. 3065-3084 ◽

Cited By ~ 25

Author(s):

Tamara A. Potapova ◽

Christopher W. Seidel ◽

Andrew C. Box ◽

Giulia Rancati ◽

Rong Li

Keyword(s):

Gene Expression ◽

Transcriptome Analysis ◽

Cell Cycle Progression ◽

Target Genes ◽

Single Cells ◽

Cyclin D2 ◽

Genome Doubling ◽

Polyploid Cells ◽

Diploid Cells ◽

P53 Target Genes

Tetraploidization, or genome doubling, is a prominent event in tumorigenesis, primarily because cell division in polyploid cells is error-prone and produces aneuploid cells. This study investigates changes in gene expression evoked in acute and adapted tetraploid cells and their effect on cell-cycle progression. Acute polyploidy was generated by knockdown of the essential regulator of cytokinesis anillin, which resulted in cytokinesis failure and formation of binucleate cells, or by chemical inhibition of Aurora kinases, causing abnormal mitotic exit with formation of single cells with aberrant nuclear morphology. Transcriptome analysis of these acute tetraploid cells revealed common signatures of activation of the tumor-suppressor protein p53. Suppression of proliferation in these cells was dependent on p53 and its transcriptional target, CDK inhibitor p21. Rare proliferating tetraploid cells can emerge from acute polyploid populations. Gene expression analysis of single cell–derived, adapted tetraploid clones showed up-regulation of several p53 target genes and cyclin D2, the activator of CDK4/6/2. Overexpression of cyclin D2 in diploid cells strongly potentiated the ability to proliferate with increased DNA content despite the presence of functional p53. These results indicate that p53-mediated suppression of proliferation of polyploid cells can be averted by increased levels of oncogenes such as cyclin D2, elucidating a possible route for tetraploidy-mediated genomic instability in carcinogenesis.

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Construction and analysis of a library of miRNA in gold-coloured mutant leaves of Ginkgo biloba L.

Folia Horticulturae ◽

10.2478/fhort-2019-0005 ◽

2019 ◽

Vol 31 (1) ◽

pp. 81-92 ◽

Cited By ~ 3

Author(s):

Weixing Li ◽

Zhichong He ◽

Shunbo Yang ◽

Yunling Ye ◽

Huiru Jiang ◽

...

Keyword(s):

Expression Pattern ◽

Transcriptome Analysis ◽

Ginkgo Biloba ◽

Regulatory Networks ◽

Target Genes ◽

Chloroplast Development ◽

Glutathione Metabolism ◽

Hormone Metabolism ◽

Srna Library ◽

Normal Green

AbstractTo gain insights into the regulatory networks of miRNAs related to golden colour formation in Ginkgo biloba leaves, we constructed an sRNA library of golden-green striped mutant leaves. A total of 213 known miRNAs comprising 54 miRNA families were obtained, and 214 novel miRNAs were identified in the mutant leaves. We further constructed a normal green leaf sRNA library as a control and compared the expression of miRNAs between mutant and normal leaves. We found 42 known and 54 novel differential expression candidate miRNAs; 39 were up-regulated and 57 down-regulated in mutants compared to normal leaves. Our transcriptome analysis and annotation of the predicted targets indicated that the potential roles of miRNAs in G. biloba leaves included involvement in the ‘Glutathione metabolism’, ‘Plant circadian rhythm’, and ‘Phenylalanine metabolism’ categories. miRNAs and their targets were further validated by qRT-PCR. The expression of miR159a and miR159c, in particular, was significantly higher in mutant leaves than in normal leaves, while their potential target gene CLT3, which is associated with chloroplast development, displayed the opposite expression pattern. In addition, the expression of miR396g-3p and miR396h was also significantly higher in mutant leaves than in normal leaves, while the target genes ABP1 (auxin-related gene) and PPR32 (chloroplast RNA editing protein), respectively, showed the opposite expression pattern. Combined with the transcriptome analysis, these data suggest that miR159, miR396, and their targets may participate in chloroplast development and hormone metabolism to regulate colour formation in G. biloba leaves.

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Transcriptome Analysis to Identify the Potential Role of Long non-coding RNAs in Enteric Glial Cells under Hyperglycemia

10.21203/rs.3.rs-118235/v1 ◽

2020 ◽

Author(s):

Xuping Zhu ◽

Yanyu Li ◽

Xue Zhu ◽

Yanmin Jiang ◽

Xiaowei Zhu ◽

...

Keyword(s):

Autonomic Neuropathy ◽

Glial Cells ◽

Transcriptome Analysis ◽

Target Genes ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Protein Protein Interaction ◽

Enteric Glial Cells ◽

Non Coding Rnas

Abstract Background Long non-coding RNAs (lncRNAs) are important mediators in the pathogenesis of diabetic gastrointestinal autonomic neuropathy, which has just been reported to have a relation to enteric glial cells (EGCs). However, the role of lncRNAs in the pathogenesis of diabetic gastrointestinal autonomic neuropathy, especially EGCs-related gastrointestinal dysfunction, has never been reported. Methods RNA sequencing technology (RNA-Seq) was used to screen the differential lncRNAs and mRNAs in EGCs under hyperglycemia (300 mmol L− 1 high glucose). Results Totally 4678 differentially expressed lncRNAs (DE lncRNAs) and 6244 differentially expressed mRNAs (DE mRNAs) were obtained. GO enrichment analysis and KEGG pathway analysis showed significant differences. 2910 and 1549 co-expressed mRNAs were respectively expressed in up-regulated and down-regulated DE lncRNA target genes. Several up- or down-regulated lncRNAs were at the key junction points of the regulatory network. Protein-protein interaction networks showed highly connected clusters were TP53, AKT1, Casp9, Casp8, Casp3, TNF, etc, which are known closely related to apoptosis. FLRT3, Fras1, and other related target genes, which revealed the potential function of lncRNAs, may be important targets for differential lncRNAs to regulate the apoptosis of glial cells induced by hyperglycemia. Conclusion In this study, the involvement of lncRNAs in EGCs under hyperglycemia was analyzed using transcriptome analysis.

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Identification of Candidate Carboxylesterases Associated With Odorant Degradation in Holotrichia parallela Antennae Based on Transcriptome Analysis

Frontiers in Physiology ◽

10.3389/fphys.2021.674023 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jiankun Yi ◽

Shang Wang ◽

Zhun Wang ◽

Xiao Wang ◽

Gongfeng Li ◽

...

Keyword(s):

Transcriptome Analysis ◽

Target Genes ◽

Expression Profiles ◽

Sequence Alignments ◽

Olfactory Neurons ◽

Holotrichia Parallela ◽

Qpcr Analysis ◽

Olfactory Systems ◽

Selection Of

Insects rely on their olfactory systems in antennae to recognize sex pheromones and plant volatiles in surrounding environments. Some carboxylesterases (CXEs) are odorant-degrading enzymes (ODEs), degrading odorant signals to protect the olfactory neurons against continuous excitation. However, there is no report about CXEs in Holotrichia parallela, one of the most major agricultural underground pests in China. In the present study, 20 candidate CXEs were identified based on transcriptome analysis of female and male antennae. Sequence alignments and phylogenetic analysis were performed to investigate the characterization of these candidate CXEs. The expression profiles of CXEs were compared by RT-qPCR analysis between olfactory and non-olfactory tissues of both genders. HparCXE4, 11, 16, 17, 18, 19, and 20 were antenna-biased expressed genes, suggesting their possible roles as ODEs. HparCXE6, 10, 11, 13, and 16 showed significantly higher expression profiles in male antennae, whereas HparCXE18 was expressed more in female antennae. This study highlighted candidate CXE genes linked to odorant degradation in antennae, and provided a useful resource for further work on the H. parallela olfactory mechanism and selection of target genes for integrative control of H. parallela.

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