scholarly journals Genome-wide phenotypic RNAi screen in the Drosophila wing: Phenotypic description of functional classes

2021 ◽  
Author(s):  
Ana López-Varea ◽  
Patricia Vega-Cuesta ◽  
Ana Ruiz-Gómez ◽  
Cristina M Ostalé ◽  
Cristina Molnar ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Molecular Classification ◽  
Drosophila Genome ◽  
Protein Coding ◽  
Gene Group ◽  
Tissue Organization ◽  
Genome Wide ◽  
Genes Encoding ◽  
Functional Classes ◽  
And Behavior

Abstract The Drosophila genome contains approximately 14.000 protein coding genes encoding all the necessary information to sustain cellular physiology, tissue organization, organism development and behavior. In this manuscript we describe in some detail the phenotypes in the adult fly wing generated after knockdown of approximately 80% of Drosophila genes. We combined this phenotypic description with a comprehensive molecular classification of the Drosophila proteins into classes that summarize the main expected or known biochemical/functional aspect of each protein. This information, combined with mRNA expression levels and in situ expression patterns, provides a simplified atlas of the Drosophila genome, from housekeeping proteins to the components of the signaling pathways directing wing development, that might help to further understand the contribution of each gene group to wing formation.

scholarly journals Emerging Roles of Estrogen-Regulated Enhancer and Long Non-Coding RNAs

2020 ◽  
Vol 21 (10) ◽  
pp. 3711
Author(s):  
Melina J. Sedano ◽  
Alana L. Harrison ◽  
Mina Zilaie ◽  
Chandrima Das ◽  
Ramesh Choudhari ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Expression Patterns ◽  
Biological Significance ◽  
Rna Seq ◽  
Biological Functions ◽  
Protein Coding ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Non Coding Rnas

Genome-wide RNA sequencing has shown that only a small fraction of the human genome is transcribed into protein-coding mRNAs. While once thought to be “junk” DNA, recent findings indicate that the rest of the genome encodes many types of non-coding RNA molecules with a myriad of functions still being determined. Among the non-coding RNAs, long non-coding RNAs (lncRNA) and enhancer RNAs (eRNA) are found to be most copious. While their exact biological functions and mechanisms of action are currently unknown, technologies such as next-generation RNA sequencing (RNA-seq) and global nuclear run-on sequencing (GRO-seq) have begun deciphering their expression patterns and biological significance. In addition to their identification, it has been shown that the expression of long non-coding RNAs and enhancer RNAs can vary due to spatial, temporal, developmental, or hormonal variations. In this review, we explore newly reported information on estrogen-regulated eRNAs and lncRNAs and their associated biological functions to help outline their markedly prominent roles in estrogen-dependent signaling.

scholarly journals Correlation between Bacillus subtilis scoC Phenotype and Gene Expression Determined Using Microarrays for Transcriptome Analysis

2001 ◽  
Vol 183 (24) ◽  
pp. 7329-7340 ◽  
Author(s):  
Robert Caldwell ◽  
Ron Sapolsky ◽  
Walter Weyler ◽  
Randal R. Maile ◽  
Stuart C. Causey ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bacillus Subtilis ◽  
Expression Patterns ◽  
Global Scale ◽  
Complete Sequence ◽  
Dna Arrays ◽  
Genome Wide ◽  
Genes Encoding ◽  
Nucleoside Metabolism

ABSTRACT The availability of the complete sequence of the Bacillus subtilis chromosome (F. Kunst et al., Nature 390:249–256, 1997) makes possible the construction of genome-wide DNA arrays and the study of this organism on a global scale. Because we have a long-standing interest in the effects of scoC on late-stage developmental phenomena as they relate toaprE expression, we studied the genome-wide effects of ascoC null mutant with the goal of furthering the understanding of the role of scoC in growth and developmental processes. In the present work we compared the expression patterns of isogenic B. subtilis strains, one of which carries a null mutation in the scoC locus (scoC4). The results obtained indicate thatscoC regulates, either directly or indirectly, the expression of at least 560 genes in the B. subtilisgenome. ScoC appeared to repress as well as activate gene expression. Changes in expression were observed in genes encoding transport and binding proteins, those involved in amino acid, carbohydrate, and nucleotide and/or nucleoside metabolism, and those associated with motility, sporulation, and adaptation to atypical conditions. Changes in gene expression were also observed for transcriptional regulators, along with sigma factors, regulatory phosphatases and kinases, and members of sensor regulator systems. In this report, we discuss some of the phenotypes associated with the scoCmutant in light of the transcriptome changes observed.

scholarly journals Genome-wide transcriptomic analysis of n-caproic acid production in Ruminococcaceae bacterium CPB6 with lactate supplementation

2020 ◽  
Author(s):  
Yong Tao ◽  
Shaowen Lu ◽  
Yi Wang ◽  
Cuicui Wei ◽  
Hong Jin ◽  
...  
Keyword(s):  
Stationary Phases ◽  
Expression Patterns ◽  
Caproic Acid ◽  
Transcriptional Analysis ◽  
Chain Elongation ◽  
Transcriptional Level ◽  
Phosphotransferase System ◽  
Oxidation Pathway ◽  
Genome Wide ◽  
Genes Encoding

Abstract Background n-Caproic acid (CA) is gaining increased attention due to its high value as a chemical feedstock. Ruminococcaceae bacterium strain CPB6 is an anaerobic mesophilic bacterium that is highly prolific in its ability to perform chain elongation of lactate to CA. However, little is known about the genome-wide transcriptional analysis of strain CPB6 for CA production triggered by the supplementation of exogenous lactate. Results In this study, 0.5% lactate was supplemented into the fermentation with Ruminococcaceae bacterium CPB6 for CA production. Compared to the control (without lactate supplementation), lactate supplementation led to earlier CA production and higher final CA titer and productivity. Transcriptional analysis was carried out using RNA-Seq for the culture with and without lactate supplementation (two groups) at growth and stationary phases, respectively. It has been indicated that 295 genes whose changes in expression patterns were substrate and/or growth dependent. These genes cover crucial functional categories. Specifically, 5 genes responsible for the reverse β-oxidation pathway, 11 genes encoding ATP-binding cassette (ABC) transporters, 6 genes encoding substrate-binding protein (SBP) and 4 genes encoding phosphotransferase system (PTS) transporters were strikingly upregulated in response to the addition of lactate. These genes would be candidates for future studies aiming at understanding the regulatory mechanism of lactate conversion into CA, as well as for the improvement of CA production in strain CPB6. Conclusions This study suggested that lactate supplementation can promote CA production by altering the expression patterns of genes involved in the essential metabolic pathways, such as central pyruvate metabolism, the reverse β-oxidation pathway, ABC and PTS transports. The findings presented herein reveal unique insights into the biomolecular effects of lactate on CA production at the gene transcriptional level.

scholarly journals Genome-Wide Analysis and Hormone Regulation of Chitin Deacetylases in Silkworm

2019 ◽  
Vol 20 (7) ◽  
pp. 1679 ◽  
Author(s):  
Ziyu Zhang ◽  
Jiamin Yan ◽  
Qing Liu ◽  
Yuhao Zhang ◽  
Jing Gong ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Critical Role ◽  
Embryo Cell ◽  
Hormone Regulation ◽  
Juvenile Hormone Analog ◽  
Genome Wide ◽  
Hormone Analog ◽  
Lepidopteran Insects ◽  
Genes Encoding ◽  
Silkworm Genome

Chitin deacetylases (CDAs) are a group of enzymes involved in chitin metabolism in insects; they play a critical role in molting, pupation, and the modification of chitin. In this study, we identified several CDAs in the silkworm, Bombyx mori (BmCDA), and investigated the effect of various hormones on their expression in B. mori larvae and embryo cell lines (BmE). Eight genes encoding BmCDAs were identified in the silkworm genome. They showed different expression patterns in different tissues, and were classified into three types based on where they were expressed: the exoskeleton, digestive organs, and genital organs. Moreover, we found that some BmCDAs showed upregulated expression during the molting period, especially during the fourth molting period in larvae. We also verified that the expression of BmCDA1–6 was upregulated by treatment with 20-hydroxyecdysone not only in larvae, but also in BmE cells. Interestingly, juvenile hormone analog treatment also upregulated the expression of some BmCDAs. The overexpression of several transcription factors revealed that the POU transcription factor POUM2 may play a major role in the regulation of BmCDA expression. Finally, the silencing of BmCDA1 and BmCDA2 did not lead to abnormal phenotypes or death, but may have led to delays in silkworm pupation. These results provide important information about lepidopteran insects in terms of chitin deacetylases and the regulation of their expression.

scholarly journals Comparative genomics of muskmelon reveals a potential role for retrotransposons in the modification of gene expression

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Ryoichi Yano ◽  
Tohru Ariizumi ◽  
Satoko Nonaka ◽  
Yoichi Kawazu ◽  
Silin Zhong ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fruit Ripening ◽  
Expression Patterns ◽  
Rna Seq ◽  
Protein Coding ◽  
Genome Wide ◽  
Oxford Nanopore ◽  
Melon Genome ◽  
Number Variation ◽  
Genome Assemblies

AbstractMelon exhibits substantial natural variation especially in fruit ripening physiology, including both climacteric (ethylene-producing) and non-climacteric types. However, genomic mechanisms underlying such variation are not yet fully understood. Here, we report an Oxford Nanopore-based high-grade genome reference in the semi-climacteric cultivar Harukei-3 (378 Mb + 33,829 protein-coding genes), with an update of tissue-wide RNA-seq atlas in the Melonet-DB database. Comparison between Harukei-3 and DHL92, the first published melon genome, enabled identification of 24,758 one-to-one orthologue gene pairs, whereas others were candidates of copy number variation or presence/absence polymorphisms (PAPs). Further comparison based on 10 melon genome assemblies identified genome-wide PAPs of 415 retrotransposon Gag-like sequences. Of these, 160 showed fruit ripening-inducible expression, with 59.4% of the neighboring genes showing similar expression patterns (r > 0.8). Our results suggest that retrotransposons contributed to the modification of gene expression during diversification of melon genomes, and may affect fruit ripening-inducible gene expression.

scholarly journals Gene Expression Patterns for Proteins With Lectin Domains in Flax Stem Tissues Are Related to Deposition of Distinct Cell Wall Types

2021 ◽  
Vol 12 ◽  
Author(s):  
Natalia Petrova ◽  
Alsu Nazipova ◽  
Oleg Gorshkov ◽  
Natalia Mokshina ◽  
Olga Patova ◽  
...  
Keyword(s):  
Cell Wall ◽  
Higher Plants ◽  
Expression Patterns ◽  
Transcript Level ◽  
Genome Wide ◽  
Distinct Cell ◽  
A Genome ◽  
Genes Encoding ◽  
Genome Wide Search ◽  
Encoding Genes

The genomes of higher plants encode a variety of proteins with lectin domains that are able to specifically recognize certain carbohydrates. Plants are enriched in a variety of potentially complementary glycans, many of which are located in the cell wall. We performed a genome-wide search for flax proteins with lectin domains and compared the expression of the encoding genes in different stem tissues that have distinct cell wall types with different sets of major polysaccharides. Over 400 genes encoding proteins with lectin domains that belong to different families were revealed in the flax genome; three quarters of these genes were expressed in stem tissues. Hierarchical clustering of the data for all expressed lectins grouped the analyzed samples according to their characteristic cell wall type. Most lectins differentially expressed in tissues with primary, secondary, and tertiary cell walls were predicted to localize at the plasma membrane or cell wall. These lectins were from different families and had various architectural types. Three out of four flax genes for proteins with jacalin-like domains were highly upregulated in bast fibers at the stage of tertiary cell wall deposition. The dynamic changes in transcript level of many genes for lectins from various families were detected in stem tissue over the course of gravitropic response induced by plant gravistimulation. The data obtained in this study indicate a large number of lectin-mediated events in plants and provide insight into the proteins that take part in tissue specialization and reaction to abiotic stress.

scholarly journals A genome-wide resource for the analysis of protein localisation in Drosophila

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Mihail Sarov ◽  
Christiane Barz ◽  
Helena Jambor ◽  
Marco Y Hein ◽  
Christopher Schmied ◽  
...  
Keyword(s):  
Protein Expression ◽  
Large Fraction ◽  
Drosophila Genome ◽  
Systematic Analysis ◽  
Protein Coding ◽  
Endogenous Expression ◽  
Genome Wide ◽  
A Genome ◽  
Transgenic Lines ◽  
Interaction Proteomics

The Drosophila genome contains >13000 protein-coding genes, the majority of which remain poorly investigated. Important reasons include the lack of antibodies or reporter constructs to visualise these proteins. Here, we present a genome-wide fosmid library of 10000 GFP-tagged clones, comprising tagged genes and most of their regulatory information. For 880 tagged proteins, we created transgenic lines, and for a total of 207 lines, we assessed protein expression and localisation in ovaries, embryos, pupae or adults by stainings and live imaging approaches. Importantly, we visualised many proteins at endogenous expression levels and found a large fraction of them localising to subcellular compartments. By applying genetic complementation tests, we estimate that about two-thirds of the tagged proteins are functional. Moreover, these tagged proteins enable interaction proteomics from developing pupae and adult flies. Taken together, this resource will boost systematic analysis of protein expression and localisation in various cellular and developmental contexts.

scholarly journals A genome-wide resource for the analysis of protein localisation inDrosophila

2015 ◽  
Author(s):  
Mihail Sarov ◽  
Chritiane Barz ◽  
Helena Jambor ◽  
Marco Y Hein ◽  
Christopher Schmied ◽  
...  
Keyword(s):  
Protein Expression ◽  
Large Fraction ◽  
Drosophila Genome ◽  
Systematic Analysis ◽  
Protein Coding ◽  
Endogenous Expression ◽  
Genome Wide ◽  
A Genome ◽  
Transgenic Lines ◽  
Interaction Proteomics

The Drosophila genome contains >13,000 protein coding genes, the majority of which remain poorly investigated. Important reasons include the lack of antibodies or reporter constructs to visualise these proteins. Here we present a genome-wide fosmid library of ≈10,000 GFP-tagged clones, comprising tagged genes and most of their regulatory information. For 880 tagged proteins we have created transgenic lines and for a total of 207 lines we have assessed protein expression and localisation in ovaries, embryos, pupae or adults by stainings and live imaging approaches. Importantly, we can visualise many proteins at endogenous expression levels and find a large fraction of them localising to subcellular compartments. Using complementation tests we demonstrate that two-thirds of the tagged proteins are fully functional. Moreover, our clones enable interaction proteomics from developing pupae and adult flies. Taken together, this resource will enable systematic analysis of protein expression and localisation in various cellular and developmental contexts.

scholarly journals Genome-Wide Transcriptomic Analysis of N-Caproic Acid Production in Ruminococcaceae Bacterium CPB6 with Lactate Supplementation

2020 ◽  
Author(s):  
YONG TAO ◽  
Shaowen Lu ◽  
Yi Wang ◽  
Cuicui Wei
Keyword(s):  
Expression Patterns ◽  
Caproic Acid ◽  
Transcriptional Analysis ◽  
Transcriptional Level ◽  
Rna Seq ◽  
Phosphotransferase System ◽  
Oxidation Pathway ◽  
Genome Wide ◽  
Genes Encoding ◽  
Substrate Binding Protein

Abstract Background: n-Caproic acid (CA) is gaining increased attention due to its high value as a chemical feedstock. Our recent studies have demonstrated that lactate can be an attractive energy substrate for the production of CA. However, little is known about the potential molecular mechanism for CA production triggered by the supplementation of exogenous lactate at the gene transcriptional level. Results: 5% lactate was supplemented into the fermentation with Ruminococcaceae bacterium CPB6 for CA production. Results showed that lactate supplementation led to earlier CA production and higher final CA titer and productivity. Transcriptional analysis was carried out using RNA-Seq for the culture with lactate supplementation compared to the control (without lactate supplementation). It has been indicated that there were only 34 differentially expressed genes (DEGs) between the two groups at the exponential phase, of which 15 were upregulated, and 19 were downregulated by more than two-fold. A total of 245 DEGs were identified between the two groups at the stationary phase, of which 123 were upregulated and 122 were downregulated. These DEGs cover crucial functional categories. Specifically, 5 genes responsible for the reverse β-oxidation pathway, 11 genes encoding ATP-binding cassette (ABC) transporters, 6 genes encoding substrate-binding protein (SBP) and 4 genes encoding phosphotransferase system (PTS) transporters were strikingly upregulated in response to the addition of lactate. These genes would be candidates for future studies aiming at understanding the regulatory mechanism of lactate conversion into CA, as well as for the improvement of CA production in strain CPB6. Conclusion: This study suggested that lactate supplementation can promote CA production by altering the expression patterns of genes involved in the essential metabolic pathways, such as central pyruvate metabolism, the reverse β-oxidation pathway, ABC and PTS transports. The findings presented herein reveal unique insights into the biomolecular effects of lactate on CA production at the gene transcriptional level.

scholarly journals Genome-Wide Identification of OSC Gene Family and Potential Function in the Synthesis of Ursane- and Oleanane-Type Triterpene in Momordica charantia

2021 ◽  
Vol 23 (1) ◽  
pp. 196
Author(s):  
Yutong Han ◽  
Ya Yang ◽  
Yan Li ◽  
Xin Yin ◽  
Zhiyu Chen ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Momordica Charantia ◽  
Bitter Gourd ◽  
Active Components ◽  
Oxidosqualene Cyclase ◽  
Genome Wide ◽  
Genes Encoding ◽  
Triterpene Biosynthesis ◽  
Different Tissues

The triterpenes in bitter gourd (Momordica charantia) show a variety of medicinal activities. Oxidosqualene cyclase (OSC) plays an indispensable role in the formation of triterpene skeletons during triterpene biosynthesis. In this study, we identified nine genes encoding OSCs from bitter gourd (McOSC1–9). Analyses of their expression patterns in different tissues suggested that characteristic triterpenoids may be biosynthesized in different tissues and then transported. We constructed a hairy root system in which McOSC7 overexpression led to an increased accumulation of camaldulenic acid, enoxolone, and quinovic acid. Thus, the overexpression of McOSC7 increased the active components content in bitter gourd. Our data provide an important foundation for understanding the roles of McOSCs in triterpenoid synthesis.

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