scholarly journals An improved de novo assembling and polishing of Solea senegalensis transcriptome shed light on retinoic acid signalling in larvae

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
José Córdoba-Caballero ◽  
Pedro Seoane ◽  
Fernando M. Jabato ◽  
James R. Perkins ◽  
Manuel Manchado ◽  
...  
Keyword(s):  
Retinoic Acid ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Fine Tuning ◽  
Solea Senegalensis ◽  
Functional Interpretation ◽  
Retinoic Acid Signalling ◽  
Expression Of Genes ◽  
Genome Draft ◽  
De Novo Assembling

AbstractSenegalese sole is an economically important flatfish species in aquaculture and an attractive model to decipher the molecular mechanisms governing the severe transformations occurring during metamorphosis, where retinoic acid seems to play a key role in tissue remodeling. In this study, a robust sole transcriptome was envisaged by reducing the number of assembled libraries (27 out of 111 available), fine-tuning a new automated and reproducible set of workflows for de novo assembling based on several assemblers, and removing low confidence transcripts after mapping onto a sole female genome draft. From a total of 96 resulting assemblies, two “raw” transcriptomes, one containing only Illumina reads and another with Illumina and GS-FLX reads, were selected to provide SOLSEv5.0, the most informative transcriptome with low redundancy and devoid of most single-exon transcripts. It included both Illumina and GS-FLX reads and consisted of 51,348 transcripts of which 22,684 code for 17,429 different proteins described in databases, where 9527 were predicted as complete proteins. SOLSEv5.0 was used as reference for the study of retinoic acid (RA) signalling in sole larvae using drug treatments (DEAB, a RA synthesis blocker, and TTNPB, a RA-receptor agonist) for 24 and 48 h. Differential expression and functional interpretation were facilitated by an updated version of DEGenes Hunter. Acute exposure of both drugs triggered an intense, specific and transient response at 24 h but with hardly observable differences after 48 h at least in the DEAB treatments. Activation of RA signalling by TTNPB specifically increased the expression of genes in pathways related to RA degradation, retinol storage, carotenoid metabolism, homeostatic response and visual cycle, and also modified the expression of transcripts related to morphogenesis and collagen fibril organisation. In contrast, DEAB mainly decreased genes related to retinal production, impairing phototransduction signalling in the retina. A total of 755 transcripts mainly related to lipid metabolism, lipid transport and lipid homeostasis were altered in response to both treatments, indicating non-specific drug responses associated with intestinal absorption. These results indicate that a new assembling and transcript sieving were both necessary to provide a reliable transcriptome to identify the many aspects of RA action during sole development that are of relevance for sole aquaculture.

scholarly journals The Endophytic Fungus Chaetomium cupreum Regulates Expression of Genes Involved in the Tolerance to Metals and Plant Growth Promotion in Eucalyptus globulus Roots

2019 ◽  
Vol 7 (11) ◽  
pp. 490 ◽  
Author(s):  
Javier Ortiz ◽  
Javiera Soto ◽  
Alejandra Fuentes ◽  
Héctor Herrera ◽  
Claudio Meneses ◽  
...  
Keyword(s):  
Plant Growth ◽  
Plant Growth Promotion ◽  
Eucalyptus Globulus ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Growth Promotion ◽  
Metal Stress ◽  
Metal Transporters ◽  
Expression Of Genes ◽  
New Information

The endophytic strain Chaetomium cupreum isolated from metal-contaminated soil was inoculated in Eucalyptus globulus roots to identify genes involved in metal stress response and plant growth promotion. We analyzed the transcriptome of E. globulus roots inoculated with C. cupreum. De novo sequencing, assembly, and analysis were performed to identify molecular mechanisms involved in metal stress tolerance and plant growth promotion. A total of 393,371,743 paired-end reads were assembled into 135,155 putative transcripts. It was found that 663 genes significantly changed their expression in the presence of treatment, of which 369 were up-regulated and 294 were down-regulated. We found differentially expressed genes (DEGs) encoding metal transporters, transcription factors, stress and defense response proteins, as well as DEGs involved in auxin biosynthesis and metabolism. Our results showed that the inoculation of C. cupreum enhanced tolerance to metals and growth promotion on E. globulus. This study provides new information to understand molecular mechanisms involved in plant–microbe interactions under metals stress.

scholarly journals The first formed tooth serves as a signalling centre to induce the formation of the dental row in zebrafish

2019 ◽  
Vol 286 (1904) ◽  
pp. 20190401 ◽  
Author(s):  
Yann Gibert ◽  
Eric Samarut ◽  
Megan K. Ellis ◽  
William R. Jackman ◽  
Vincent Laudet
Keyword(s):  
Retinoic Acid ◽  
Growth Factor ◽  
Fibroblast Growth Factor ◽  
De Novo ◽  
Fine Tuning ◽  
Fibroblast Growth ◽  
Tooth Formation ◽  
Necessary And Sufficient

The diversity of teeth patterns in actinopterygians is impressive with tooth rows in many locations in the oral and pharyngeal regions. The first-formed tooth has been hypothesized to serve as an initiator controlling the formation of the subsequent teeth. In zebrafish, the existence of the first tooth (named 4 V 1 ) is puzzling as its replacement is induced before the opening of the mouth. Functionally, it has been shown that 4 V 1 formation requires fibroblast growth factor (FGF) and retinoic acid (RA) signalling. Here, we show that the ablation of 4 V 1 prevents the development of the dental row demonstrating its dependency over it. If endogenous levels of FGF and RA are restored after 4 V 1 ablation, embryonic dentition starts again by de novo formation of a first tooth, followed by the dental row. Similarly, induction of anterior ectopic teeth induces subsequent tooth formation, demonstrating that the initiator tooth is necessary and sufficient for dental row formation, probably via FGF ligands released by 4 V 1 to induce the formation of subsequent teeth. Our results show that by modifying the formation of the initiator tooth it is possible to control the formation of a dental row. This could help to explain the diversity of tooth patterns observed in actinopterygians and more broadly, how diverse traits evolved through molecular fine-tuning.

scholarly journals Comparison of Transcriptomic Profiles of MiaPaCa-2 Pancreatic Cancer Cells Treated with Different Statins

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3528
Author(s):  
Silvie Rimpelová ◽  
Michal Kolář ◽  
Hynek Strnad ◽  
Tomáš Ruml ◽  
Libor Vítek ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Mevalonate Pathway ◽  
Posttranslational Regulation ◽  
Cycle Arrest ◽  
Pancreatic Cancer Cells ◽  
Expression Of Genes ◽  
Beneficial Impact ◽  
Coa Reductase

Statins have been widely used for the treatment of hypercholesterolemia due to their ability to inhibit HMG-CoA reductase, the rate-limiting enzyme of de novo cholesterol synthesis, via the so-called mevalonate pathway. However, their inhibitory action also causes depletion of downstream intermediates of the pathway, resulting in the pleiotropic effects of statins, including the beneficial impact in the treatment of cancer. In our study, we compared the effect of all eight existing statins on the expression of genes, the products of which are implicated in cancer inhibition and suggested the molecular mechanisms of their action in epigenetic and posttranslational regulation, and in cell-cycle arrest, death, migration, or invasion of the cancer cells.

scholarly journals A regulatory cascade involving retinoic acid, Cbfa1, and matrix metalloproteinases is coupled to the development of a process of perichondrial invasion and osteogenic differentiation during bone formation

2001 ◽  
Vol 155 (7) ◽  
pp. 1333-1344 ◽  
Author(s):  
Maria J.G. Jiménez ◽  
Milagros Balbín ◽  
Jesús Alvarez ◽  
Toshihisa Komori ◽  
Paolo Bianco ◽  
...  
Keyword(s):  
Retinoic Acid ◽  
Bone Formation ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
De Novo ◽  
Bone Matrix ◽  
Type Ii Collagen ◽  
Mitogen Activated Protein Kinase ◽  
Regulatory Cascade ◽  
The Matrix

Tissue-remodeling processes are largely mediated by members of the matrix metalloproteinase (MMP) family of endopeptidases whose expression is strictly controlled both spatially and temporally. In this article, we have examined the molecular mechanisms that could contribute to modulate the expression of MMPs like collagenase-3 and MT1-MMP during bone formation. We have found that all-trans retinoic acid (RA), which usually downregulates MMPs, strongly induces collagenase-3 expression in cultures of embryonic metatarsal cartilage rudiments and in chondrocytic cells. This effect is dose and time dependent, requires the de novo synthesis of proteins, and is mediated by RAR-RXR heterodimers. Analysis of the signal transduction mechanisms underlying the upregulating effect of RA on collagenase-3 expression demonstrated that this factor acts through a signaling pathway involving p38 mitogen-activated protein kinase. RA treatment of chondrocytic cells also induces the production of MT1-MMP, a membrane-bound metalloproteinase essential for skeletal formation, which participates in a proteolytic cascade with collagenase-3. The production of these MMPs is concomitant with the development of an RA-induced differentiation program characterized by formation of a mineralized bone matrix, downregulation of chondrocyte markers like type II collagen, and upregulation of osteoblastic markers such as osteocalcin. These effects are attenuated in metatarsal rudiments in which RA induces the invasion of perichondrial osteogenic cells from the perichondrium into the cartilage rudiment. RA treatment also resulted in the upregulation of Cbfa1, a transcription factor responsible for collagenase-3 and osteocalcin induction in osteoblastic cells. The dynamics of Cbfa1, MMPs, and osteocalcin expression is consistent with the fact that these genes could be part of a regulatory cascade initiated by RA and leading to the induction of Cbfa1, which in turn would upregulate the expression of some of their target genes like collagenase-3 and osteocalcin.

scholarly journals Development of whole-genome multiplex assays and construction of an integrated genetic map using SSR markers in Senegalese sole

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Israel Guerrero-Cózar ◽  
Cathaysa Perez-Garcia ◽  
Hicham Benzekri ◽  
J. J. Sánchez ◽  
Pedro Seoane ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Genetic Map ◽  
De Novo ◽  
Pedigree Analysis ◽  
Solea Senegalensis ◽  
Whole Genome ◽  
Senegalese Sole ◽  
A Genome ◽  
Genome Draft ◽  
Integrated Genetic Map

AbstractThe Senegalese sole (Solea senegalensis) is an economically important flatfish species. In this study, a genome draft was analyzed to identify microsatellite (SSR) markers for whole-genome genotyping. A subset of 224 contigs containing SSRs were preselected and validated by using a de novo female hybrid assembly. Overall, the SSR density in the genome was 886.7 markers per megabase of genomic sequences and the dinucleotide motif was the most abundant (52.4%). In silico comparison identified a set of 108 SSRs (with di-, tetra- or pentanucleotide motifs) widely distributed in the genome and suitable for primer design. A total of 106 markers were structured in thirteen multiplex PCR assays (with up to 10-plex) and the amplification conditions were optimized with a high-quality score. Main genetic diversity statistics and genotyping reliability were assessed. A subset of 40 high polymorphic markers were selected to optimize four supermultiplex PCRs (with up to 11-plex) for pedigree analysis. Theoretical exclusion probabilities and real parentage allocation tests using parent–offspring information confirmed their robustness and effectiveness for parental assignment. These new SSR markers were combined with previously published SSRs (in total 229 makers) to construct a new and improved integrated genetic map containing 21 linkage groups that matched with the expected number of chromosomes. Synteny analysis with respect to C. semilaevis provided new clues on chromosome evolution in flatfish and the formation of metacentric and submetacentric chromosomes in Senegalese sole.

scholarly journals HP1 drives de novo 3D genome reorganization in early Drosophila embryos

Nature ◽  
2021 ◽  
Author(s):  
Fides Zenk ◽  
Yinxiu Zhan ◽  
Pavel Kos ◽  
Eva Löser ◽  
Nazerke Atinbayeva ◽  
...  
Keyword(s):  
Genome Organization ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Early Embryo ◽  
Heterochromatin Protein ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Genome Reorganization

AbstractFundamental features of 3D genome organization are established de novo in the early embryo, including clustering of pericentromeric regions, the folding of chromosome arms and the segregation of chromosomes into active (A-) and inactive (B-) compartments. However, the molecular mechanisms that drive de novo organization remain unknown1,2. Here, by combining chromosome conformation capture (Hi-C), chromatin immunoprecipitation with high-throughput sequencing (ChIP–seq), 3D DNA fluorescence in situ hybridization (3D DNA FISH) and polymer simulations, we show that heterochromatin protein 1a (HP1a) is essential for de novo 3D genome organization during Drosophila early development. The binding of HP1a at pericentromeric heterochromatin is required to establish clustering of pericentromeric regions. Moreover, HP1a binding within chromosome arms is responsible for overall chromosome folding and has an important role in the formation of B-compartment regions. However, depletion of HP1a does not affect the A-compartment, which suggests that a different molecular mechanism segregates active chromosome regions. Our work identifies HP1a as an epigenetic regulator that is involved in establishing the global structure of the genome in the early embryo.

scholarly journals Copy number-dependent DNA methylation of the Pyricularia oryzae MAGGY retrotransposon is triggered by DNA damage

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Ba Van Vu ◽  
Quyet Nguyen ◽  
Yuki Kondo-Takeoka ◽  
Toshiki Murata ◽  
Naoki Kadotani ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Copy Number ◽  
Rna Silencing ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Pyricularia Oryzae ◽  
Transcriptional Gene Silencing ◽  
Physical Interaction ◽  
Uncharacterized Protein ◽  
Form Complex

AbstractTransposable elements are common targets for transcriptional and post-transcriptional gene silencing in eukaryotic genomes. However, the molecular mechanisms responsible for sensing such repeated sequences in the genome remain largely unknown. Here, we show that machinery of homologous recombination (HR) and RNA silencing play cooperative roles in copy number-dependent de novo DNA methylation of the retrotransposon MAGGY in the fungusPyricularia oryzae. Genetic and physical interaction studies revealed thatRecAdomain-containing proteins, includingP. oryzaehomologs ofRad51, Rad55, andRad57, together with an uncharacterized protein, Ddnm1, form complex(es) and mediate either the overall level or the copy number-dependence of de novo MAGGY DNA methylation, likely in conjunction with DNA repair. Interestingly,P. oryzaemutants of specific RNA silencing components (MoDCL1andMoAGO2)were impaired in copy number-dependence of MAGGY methylation. Co-immunoprecipitation of MoAGO2 and HR components suggested a physical interaction between the HR and RNA silencing machinery in the process.

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