scholarly journals Profiling of H3K4me3 and H3K27me3 and Their Roles in Gene Subfunctionalization in Allotetraploid Cotton

2021 ◽  
Vol 12 ◽  
Author(s):  
Aicen Zhang ◽  
Yangyang Wei ◽  
Yining Shi ◽  
Xiaojuan Deng ◽  
Jingjing Gao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Regulatory Networks ◽  
Functional Characterization ◽  
Expression Levels ◽  
Homeologous Genes ◽  
Expression Of Genes ◽  
Differential Gene ◽  
Chromatin Profiling ◽  
Allotetraploid Cotton

Cotton is an excellent model for studying crop polyploidization and domestication. Chromatin profiling helps to reveal how histone modifications are involved in controlling differential gene expression between A and D subgenomes in allotetraploid cotton. However, the detailed profiling and functional characterization of broad H3K4me3 and H3K27me3 are still understudied in cotton. In this study, we conducted H3K4me3- and H3K27me3-related ChIP-seq followed by comprehensively characterizing their roles in regulating gene transcription in cotton. We found that H3K4me3 and H3K27me3 exhibited active and repressive roles in regulating the expression of genes between A and D subgenomes, respectively. More importantly, H3K4me3 exhibited enrichment level-, position-, and distance-related impacts on expression levels of related genes. Distinct GO term enrichment occurred between A/D-specific and homeologous genes with broad H3K4me3 enrichment in promoters and gene bodies, suggesting that broad H3K4me3-marked genes might have some unique biological functions between A and D subgenome. An anticorrelation between H3K27me3 enrichment and expression levels of homeologous genes was more pronounced in the A subgenome relative to the D subgenome, reflecting distinct enrichment of H3K27me3 in homeologous genes between A and D subgenome. In addition, H3K4me3 and H3K27me3 marks can indirectly influence gene expression through regulatory networks with TF mediation. Thus, our study provides detailed insights into functions of H3K4me3 and H3K27me3 in regulating differential gene expression and subfunctionalization of homeologous genes, therefore serving as a driving force for polyploidization and domestication in cotton.

scholarly journals Discovering therapeutic activities from venoms using differential gene expression

2019 ◽  
Author(s):  
Joseph D. Romano ◽  
Hai Li ◽  
Ronald Realubit ◽  
Charles Karan ◽  
Nicholas P. Tatonetti
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Regulatory Networks ◽  
Preliminary Evidence ◽  
Natural Toxins ◽  
Differential Gene ◽  
Public Repositories ◽  
Therapeutic Activities ◽  
Validation Experiments

AbstractVenoms are a diverse and complex group of natural toxins that have been adapted to treat many types of human disease, but rigorous informatics approaches for discovering new therapeutic activities are scarce. We have designed and validated a new platform—named VenomSeq—to systematically generate putative associations between venoms and drugs/diseases via high-throughput transcriptomics and perturbational differential gene expression analysis. In this study, we describe the architecture of VenomSeq, and its evaluation using the crude venoms from 25 diverse animal species. By integrating comparisons to public repositories of differential expression, associations between regulatory networks and disease, and existing knowledge of venom activity, we provide a number of new therapeutic hypotheses linking venoms to human diseases supported by multiple layers of preliminary evidence. We are currently performing validation experiments in vitro to corroborate these findings.

Differential gene expression levels might explain association of LAIR2 polymorphisms with pemphigus

2015 ◽  
Vol 135 (2) ◽  
pp. 233-244 ◽  
Author(s):  
Carolina Maciel Camargo ◽  
Danillo G. Augusto ◽  
Maria Luiza Petzl-Erler
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Expression Levels ◽  
Differential Gene ◽  
Gene Expression Levels

scholarly journals Identification of Differential Gene Expression in Bacteria Associated with Coral Black Band Disease by Using RNA-Arbitrarily Primed PCR

2004 ◽  
Vol 70 (6) ◽  
pp. 3687-3694 ◽  
Author(s):  
Jorge Frias-Lopez ◽  
George T. Bonheyo ◽  
Bruce W. Fouke
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Black Band Disease ◽  
Expression Of Genes ◽  
Black Band ◽  
Differential Gene ◽  
Apoprotein A1 ◽  
Arbitrarily Primed Pcr ◽  
Transporter Systems ◽  
First Time

ABSTRACT RNA-arbitrarily primed PCR techniques have been applied for the first time to identify differential gene expression in black band disease (BBD), a virulent coral infection that affects reef ecosystems worldwide. The gene activity for the BBD mat on infected surfaces of the brain coral Diploria strigosa was compared with that for portions of the BBD mat that were removed from the coral and suspended nearby in the seawater column. The results obtained indicate that three genes (DD 95-2, DD 95-4, and DD 99-9) were up-regulated in the BBD bacterial mat on the coral surface compared to the transcript base levels observed in the BBD mat suspended in seawater. Clone DD 95-4 has homology with known amino acid ABC transporter systems in bacteria, while clone DD 99-9 exhibits homology with chlorophyll A apoprotein A1 in cyanobacteria. This protein is essential in the final conformation of photosystem I P700. DD 95-2, the only gene that was fully repressed in the BBD mat samples suspended in seawater, exhibited homology with the AraC-type DNA binding domain-containing proteins. These transcriptional activators coordinate the expression of genes essential for virulence in many species of gram-negative bacteria.

scholarly journals Differential gene expression is associated with degeneration of mating-type chromosomes in the absence of sexual antagonism

2019 ◽  
Author(s):  
Wen-Juan Ma ◽  
Fantin Carpentier ◽  
Tatiana Giraud ◽  
Michael Hood
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Differential Gene Expression ◽  
Mating Type ◽  
Mating Types ◽  
Antagonistic Selection ◽  
Expression Of Genes ◽  
Sexually Antagonistic Selection ◽  
Differential Gene ◽  
Anther Smut

AbstractIn animals and plants, differential expression of genes on sex chromosomes is widespread and it is usually considered to result from sexually antagonistic selection; however differential expression can also be caused by asymmetrical sequence degeneration in non-recombining sex chromosomes, which has been very little studied. The anther-smut fungus Microbotryum lychnidis-dioicae is ideal to investigate the extent to which differential gene expression is associated with sequence degeneration because: 1) separate haploid cultures of opposite mating types help identify differential expression, 2) its mating-type chromosomes display multiple evolutionary strata reflecting successive events of gene linkage to the mating-type loci, and 3) antagonistic selection is unlikely between isogamous haploid mating types. We therefore tested the hypothesis that differential gene expression between mating types resulted from sequence degeneration. We found that genes showing differential expression between haploid mating types were enriched only on the oldest evolutionary strata of the mating-type chromosomes and were associated with multiple signatures of sequence degeneration. We found that differential expression between mating types was associated with elevated differences between alleles in non-synonymous substitution rates, indels and premature stop codons, transposable element insertions, and altered intron and GC content. Our findings strongly suggest that degenerative mutations are important in the evolution of differential expression in non-recombining regions. Our results are relevant for a broad range of taxa where mating compatibility or sex is determined by genes located in large regions of recombination suppression, showing that differential expression should not be taken as necessarily arising from antagonistic selection.Author SummaryDifferences between males and females, from morphology to behavior and physiology, are considered to largely reflect differential expression of genes that maximize fitness benefits relative to costs that are specific to one sex. However, there is an unexplored alternative to such ‘sexually antagonistic selection’ to explain differential expression. Reproductive compatibility is often determined by genes located in large non-recombining chromosomal regions, where degenerative mutations are expected to accumulate and may separately affect the expression of alternate alleles of genes. We tested the role of genetic degeneration in determining differential expression between the isogamous haploid mating types of the anther-smut fungus, Microbotryum lychnidis-dioicae, where sexually antagonistic selection is not a confounding factor. We show that differentially expressed genes are highly enriched in the non-recombining mating-type chromosomes, and that they are associated with various forms of degenerative mutations, some of which indicate that the less expressed allele suffers greater mutational effects. Our finding of the role for degenerative mutations in the evolution of differential expression is relevant for a broad range of organisms where reproductive compatibility or sex is determined by genes in regions of suppressed recombination, and shows that differential expression should not be taken as necessarily arising from antagonistic selection.

scholarly journals Assessment of the differential gene expression in anthracnose treated seedlings of yellow lupin

2021 ◽  
Vol 65 (3) ◽  
pp. 330-336
Author(s):  
E. N. Sysoliatin ◽  
V. S. Anokhina ◽  
N. V. Anisimova ◽  
O. G. Babak ◽  
A. V. Kilchevsky
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Differential Gene Expression ◽  
Genetic Determinants ◽  
Yellow Lupin ◽  
Expression Of Genes ◽  
Differential Gene ◽  
Colletotrichum Lupini ◽  
Yellow Lupine ◽  
Differential Expression Of Genes

Seedlings of yellow lupine treated with Colletotrichum lupini isolate were studied by the method of SRAP-analysis with the purpose to assess the differential expression of genes. As a result, the PCR fragment corresponding to tolerant seedlings was found. The genetic determinants found are likely involved in the control of the resistance (tolerance) of lupine plants to anthracnose.

253 DIFFERENTIAL GENE EXPRESSION IN IN VIVO-DERIVED v. IN VITRO-PRODUCED EQUINE BLASTOCYSTS AS DETERMINED BY RT-qPCR

2010 ◽  
Vol 22 (1) ◽  
pp. 284
Author(s):  
K. Smits ◽  
K. Goossens ◽  
A. Van Soom ◽  
L. Peelman
Keyword(s):  
Gene Expression ◽  
Real Time ◽  
Differential Gene Expression ◽  
Real Time Pcr ◽  
Calf Serum ◽  
Fatty Acid Binding ◽  
Expression Levels ◽  
Differential Gene

Although in vitro production of equine embryos has greatly evolved in recent years, there are still substantial differences between in vitro-produced and in vivo-derived equine embryos. Fundamental insight into these differences could lead to optimization of equine assisted reproductive techniques. Reverse transcription quantitative real-time PCR (RT-qPCR) is a highly specific and sensitive tool to compare mRNA expression levels of specific genes and was used in this study to determine differences in gene expression between equine in vivo and in vitro embryos. In vivo embryos (n = 8) were derived by uterine flushing of artificially inseminated mares at 7 days after ovulation. For the production of the in vitro embryos (n = 8), oocytes from slaughtered mares were matured in DMEM-F12-based medium (Galli et al. 2007 Anim. Reprod. Sci. 98, 39-55) in 5% CO2 in air (maturation rate: 57%), fertilized by intracytoplasmic sperm injection, and cultured in DMEM-F12 with 10% fetal calf serum in 5% CO2, 5% O2, and 90% N2 for 9.5 days (cleavage rate: 74%; blastocyst rate: 7%). RNA was extracted from single early to expanded blastocysts and amplified and converted into cDNA with the WT-Ovation RNA Amplification System (NuGEN, San Carlos, CA, USA). Based on the presumed gene functions and differential gene expression as determined in a previously performed suppression subtractive hybridization (SSH; Smits et al. 2009 Reprod. Dom. Anim. 44, 75), 5 genes [brain expressed X-linked 2 (BEX2), Mps one binder kinase activator-like 3 (MOBKL3), fatty acid binding protein 3 (FABP3), minichromosome maintenance complex component 7 (MCM7), and ornithine decarboxylase (ODC)] were selected for quantification by RT-qPCR with the KAPA SYBR® FAST qPCR Kit (Kapa Biosystems, Belgium) on the iCycler iQ Real-Time PCR Detection System (Bio-Rad, Nazareth, Belgium). All data were normalized with previously determined stable reference genes (beta actin, ubiquitin C, ribosomal protein L32, and glyceraldehyde-3-phosphate dehydrogenase) and statistically analyzed by means of a Mann-Whitney test. The fact that all genes were expressed at greater levels in the in vivo-derived blastocysts than in the in vitro-produced blastocysts confirmed the results of the SSH. This difference was highly significant for MOBKL3, BEX2, and ODC (P < 0.005), significant for FABP3 (P < 0.05), and not significant for MCM7. These genes have already been shown to be important for embryonic cell survival (ODC), oocyte maturation and pre- implantation development (MOBKL3) in mice, regulation during embryonic development (BEX2) and fetal development (FABP3) in human, and genome replication in eukaryotes (MCM7) (Pendeville et al. 2001 Mol. Cell Biol. 21, 6549-6558; Han et al. 2005 Nucleic Acids Res. 33, 6555-6565). In conclusion, 4 genes (MOBKL3, BEX2, ODC, and FABP3) with greater expression levels in in vivo-derived equine blastocysts have been identified. Whether the up-regulation of these genes is important for normal embryonic differentiation in the horse embryo is currently under investigation.

scholarly journals Differential gene expression in Drosophila melanogaster and D. nigrosparsa infected with the same Wolbachia strain

2020 ◽  
Author(s):  
Matsapume Detcharoen ◽  
Martin P. Schilling ◽  
Wolfgang Arthofer ◽  
Birgit C. Schlick-Steiner ◽  
Florian M. Steiner
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Differential Gene Expression ◽  
Expression Patterns ◽  
Specific Gene ◽  
Positive Effects ◽  
Arthropod Species ◽  
Expression Of Genes ◽  
Novel Host ◽  
Differential Gene

AbstractWolbachia, maternally inherited endosymbionts, infect nearly half of all arthropod species. Wolbachia manipulate their hosts to maximize their transmission, but they can also provide benefits such as nutrients and resistance to viruses for their hosts. The Wolbachia strain wMel was recently found to increase locomotor activities and possibly trigger cytoplasmic incompatibility in the fly Drosophila nigrosparsa. Here, we compared differential gene expression in Drosophila melanogaster (original host) and D. nigrosparsa (novel host), both uninfected and infected with wMel, using RNA sequencing to see if the two Drosophila species respond to the infection in the same or different ways. A total of 2164 orthologous genes were used. We found species-specific gene expression patterns. Significant changes shared by the fly species were confined to the expression of genes involved in heme binding and oxidation-reduction; the two host species differently changed the expression of genes when infected. Some of the genes were down-regulated in the infected D. nigrosparsa, which might indicate small positive effects of Wolbachia. We discuss our findings also in the light of how Wolbachia survive within both the native and the novel host.

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