scholarly journals Unexpected mutual regulation underlies paralogue functional diversification and promotes epithelial tissue maturation in Tribolium

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Daniela Gurska ◽  
Iris M. Vargas Jentzsch ◽  
Kristen A. Panfilio
Keyword(s):  
Feedback Loop ◽  
Single Species ◽  
Epithelial Tissue ◽  
Rna Seq ◽  
Developmental Progression ◽  
Late Embryogenesis ◽  
Mutual Regulation ◽  
Transcriptional Landscape

Abstract Insect Hox3/zen genes represent an evolutionary hotspot for changes in function and copy number. Single orthologues are required either for early specification or late morphogenesis of the extraembryonic tissues, which protect the embryo. The tandemly duplicated zen paralogues of the beetle Tribolium castaneum present a unique opportunity to investigate both functions in a single species. We dissect the paralogues’ expression dynamics (transcript and protein) and transcriptional targets (RNA-seq after RNAi) throughout embryogenesis. We identify an unexpected role of Tc-Zen2 in repression of Tc-zen1, generating a negative feedback loop that promotes developmental progression. Tc-Zen2 regulation is dynamic, including within co-expressed multigene loci. We also show that extraembryonic development is the major event within the transcriptional landscape of late embryogenesis and provide a global molecular characterization of the extraembryonic serosal tissue. Altogether, we propose that paralogue mutual regulation arose through multiple instances of zen subfunctionalization, leading to their complementary extant roles.

scholarly journals Unexpected mutual regulation underlies paralogue functional diversification and promotes maturation of a protective epithelial tissue

2018 ◽  
Author(s):  
Daniela Gurska ◽  
Iris M. Vargas Jentzsch ◽  
Kristen A. Panfilio
Keyword(s):  
Feedback Loop ◽  
Single Species ◽  
Epithelial Tissue ◽  
Rna Seq ◽  
Developmental Progression ◽  
Late Embryogenesis ◽  
Mutual Regulation ◽  
Transcriptional Landscape

ABSTRACTInsect Hox3/zen genes represent an evolutionary hotspot for changes in function and copy number. Single orthologues are required either for early specification or late morphogenesis of the extraembryonic tissues, which protect the embryo. The tandemly duplicated zen paralogues of the beetle Tribolium castaneum present a unique opportunity to investigate both functions in a single species. We dissect the paralogues’ expression dynamics (transcript and protein) and transcriptional targets (RNA-seq after RNAi) throughout embryogenesis. We identify an unexpected role of Tc-Zen2 in repression of Tc-zen1, generating a negative feedback loop that promotes developmental progression. Tc-Zen2 regulation is dynamic, including within co-expressed multigene loci. We also show that extraembryonic development is the major event within the transcriptional landscape of late embryogenesis and provide a global molecular characterization of the extraembryonic serosal tissue. Altogether, we propose that paralogue mutual regulation arose progressively and drove multiple instances of zen subfunctionalization, leading to complementary extant roles.

scholarly journals Human testis-expressed (TEX) genes: a review focused on spermatogenesis and male fertility

2021 ◽  
Vol 31 (1) ◽  
Author(s):  
Hela Bellil ◽  
Farah Ghieh ◽  
Emeline Hermel ◽  
Béatrice Mandon-Pepin ◽  
François Vialard
Keyword(s):  
Current Knowledge ◽  
Gene Mutations ◽  
Subtractive Hybridization ◽  
Human Testis ◽  
Rna Seq ◽  
Reproductive Process ◽  
Complex Process ◽  
Expression Atlas

AbstractSpermatogenesis is a complex process regulated by a multitude of genes. The identification and characterization of male-germ-cell-specific genes is crucial to understanding the mechanisms through which the cells develop. The term “TEX gene” was coined by Wang et al. (Nat Genet. 2001; 27: 422–6) after they used cDNA suppression subtractive hybridization (SSH) to identify new transcripts that were present only in purified mouse spermatogonia. TEX (Testis expressed) orthologues have been found in other vertebrates (mammals, birds, and reptiles), invertebrates, and yeasts. To date, 69 TEX genes have been described in different species and different tissues. To evaluate the expression of each TEX/tex gene, we compiled data from 7 different RNA-Seq mRNA databases in humans, and 4 in the mouse according to the expression atlas database.Various studies have highlighted a role for many of these genes in spermatogenesis. Here, we review current knowledge on the TEX genes and their roles in spermatogenesis and fertilization in humans and, comparatively, in other species (notably the mouse). As expected, TEX genes appear to have a major role in reproduction in general and in spermatogenesis in humans but also in all mammals such as the mouse. Most of them are expressed specifically or predominantly in the testis. As most of the TEX genes are highly conserved in mammals, defects in the male (gene mutations in humans and gene-null mice) lead to infertility. In the future, cumulative data on the human TEX genes’ physiological functions and pathophysiological dysfunctions should become available and is likely to confirm the essential role of this family in the reproductive process. Thirteen TEX genes are now referenced in the OMIM database, and 3 have been linked to a specific phenotype. TEX11 (on Xq13.1) is currently the gene most frequently reported as being associated with azoospermia.

scholarly journals “Single-nucleus RNA-seq2 reveals a functional crosstalk between liver zonation and ploidy”

2020 ◽  
Author(s):  
M. L. Richter ◽  
I.K. Deligiannis ◽  
A. Danese ◽  
E. Lleshi ◽  
P. Coupland ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Dosage ◽  
Cellular Heterogeneity ◽  
Cell Populations ◽  
Rna Seq ◽  
Liver Zonation ◽  
Single Nucleus ◽  
Different Levels

AbstractSingle-cell RNA-seq reveals the role of pathogenic cell populations in development and progression of chronic diseases. In order to expand our knowledge on cellular heterogeneity we have developed a single-nucleus RNA-seq2 method that allows deep characterization of nuclei isolated from frozen archived tissues. We have used this approach to characterize the transcriptional profile of individual hepatocytes with different levels of ploidy, and have discovered that gene expression in tetraploid mononucleated hepatocytes is conditioned by their position within the hepatic lobe. Our work has revealed a remarkable crosstalk between gene dosage and spatial distribution of hepatocytes.

scholarly journals Characterization of epigenetic and transcriptional landscape in infantile hemangiomas with ATAC-seq and RNA-seq

Epigenomics ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 893-905 ◽  
Author(s):  
Xueqing Li ◽  
Yuanzheng Chen ◽  
Cong Fu ◽  
Hongwen Li ◽  
Kun Yang ◽  
...  
Keyword(s):  
Opposite Effect ◽  
Umbilical Vein ◽  
Tube Formation ◽  
Rna Seq ◽  
Epigenetic Landscape ◽  
Normal Tissues ◽  
Umbilical Vein Endothelial Cells ◽  
Accessible Chromatin ◽  
Transcriptional Landscape

Aim: This study was conducted to reveal epigenetic landscape in infantile hemangiomas (IHs) and identify transcription factors (TFs) and their downstream genes active in IHs. Materials & methods: We performed Assay for Transposase Accessible Chromatin (ATAC-seq) with RNA-seq in three pairs of IHs and their adjacent normal tissues. Functions of candidate TFs were investigated in human umbilical vein endothelial cells (HUVECs). Results: Chromatin of IH tissues is less compact. Some candidate genes and TFs were identified. In HUVECs, SPDEF inhibited cell viability and tube formation, and promoted apoptosis; SOX4 exerted the opposite effect. SPDEF may act through EPHA5, ZBTB46 and SASH1; SOX4 may act through MMP12 and HIVEP3. Conclusion: Epigenetics plays a role in IHs. SPDEF and SOX4 may act in IHs.

scholarly journals Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

2011 ◽  
Vol 21 (7) ◽  
pp. 1160-1167 ◽  
Author(s):  
S. Islam ◽  
U. Kjallquist ◽  
A. Moliner ◽  
P. Zajac ◽  
J.-B. Fan ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Seq ◽  
Transcriptional Landscape

scholarly journals Dissecting the Effect of a 3D Microscaffold on the Transcriptome of Neural Stem Cells with Computational Approaches: A Focus on Mechanotransduction

2020 ◽  
Vol 21 (18) ◽  
pp. 6775 ◽  
Author(s):  
Federica Rey ◽  
Cecilia Pandini ◽  
Bianca Barzaghini ◽  
Letizia Messa ◽  
Toniella Giallongo ◽  
...  
Keyword(s):  
Stem Cells ◽  
Regenerative Medicine ◽  
Mechanical Stimuli ◽  
Rna Seq ◽  
3D Cell Cultures ◽  
Different Types ◽  
Strongly Connected ◽  
Molecular Bases

3D cell cultures are becoming more and more important in the field of regenerative medicine due to their ability to mimic the cellular physiological microenvironment. Among the different types of 3D scaffolds, we focus on the Nichoid, a miniaturized scaffold with a structure inspired by the natural staminal niche. The Nichoid can activate cellular responses simply by subjecting the cells to mechanical stimuli. This kind of influence results in different cellular morphology and organization, but the molecular bases of these changes remain largely unknown. Through RNA-Seq approach on murine neural precursors stem cells expanded inside the Nichoid, we investigated the deregulated genes and pathways showing that the Nichoid causes alteration in genes strongly connected to mechanobiological functions. Moreover, we fully dissected this mechanism highlighting how the changes start at a membrane level, with subsequent alterations in the cytoskeleton, signaling pathways, and metabolism, all leading to a final alteration in gene expression. The results shown here demonstrate that the Nichoid influences the biological and genetic response of stem cells thorough specific alterations of cellular signaling. The characterization of these pathways elucidates the role of mechanical manipulation on stem cells, with possible implications in regenerative medicine applications.

scholarly journals Identification and Characterization of lncRNA and mRNA in Testes of Landrace and Hezuo Boars

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2263
Author(s):  
Bo Zhang ◽  
Zunqiang Yan ◽  
Pengfei Wang ◽  
Qiaoli Yang ◽  
Xiaoyu Huang ◽  
...  
Keyword(s):  
Precocious Puberty ◽  
Sexual Maturity ◽  
Testicular Development ◽  
Rna Seq ◽  
Kegg Pathways ◽  
Wnt Pathways ◽  
Molecular Regulatory Mechanisms ◽  
Identification And Characterization

Chinese HZ boars are typical plateau miniature boars characterized by precocious puberty, which is closely related to testicular development and spermatogenesis. Accumulating evidence indicates that lncRNA is involved in the testicular development and regulation of spermatogenesis. However, little is known about the lncRNA precocious regulation in testicular development and spermatogenesis on early sexual maturity of HZ boars. Thus, we investigated the expression and characterization of lncRNA and mRNA in 30-day-old and 120-day-old HZ boar testes using transcriptome to explore precocious puberty. Landrace (LC) boar was treated as the control. Histological analyses indicated that HZ boar underwent puberty development at an earlier stage than LC boar and had achieved sexual maturity at 120 days old. RNA-Seq yielded a total of 187 lncRNAs and 984 mRNAs; these molecules were identified as possible candidates for precocious puberty. GO terms and KEGG pathways enrichment analyses revealed that the differentially expressed lncRNA and their targeted genes were involved in metabolic pathways regulating testis development and spermatogenesis, such as the PI3K-Akt, TGF-beta and Wnt pathways. Further screening, some lncRNA (such as LOC102166140, LOC110259451, and MSTRG.15011.2), and mRNA (such as PDCL2, HSD17B4, SHCBP1L, CYP21A2, and SPATA3) were found to be possibly associated with precocious puberty, which would add to our understanding of the molecular regulatory mechanisms of precocious puberty. This study provided valuable information for further study of the role of lncRNA and mRNA in the process of precocious puberty.

scholarly journals An RNA-Seq-Based Framework for Characterizing Canine Prostate Cancer and Prioritizing Clinically Relevant Biomarker Candidate Genes

2021 ◽  
Vol 22 (21) ◽  
pp. 11481
Author(s):  
Heike Thiemeyer ◽  
Leila Taher ◽  
Jan Torben Schille ◽  
Eva-Maria Packeiser ◽  
Lisa K. Harder ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Cell Cycle ◽  
Malignant Disease ◽  
Pi3k Signaling ◽  
Rna Seq ◽  
Promising Candidate ◽  
Fine Needle ◽  
Human Counterpart ◽  
Transcriptional Landscape

Prostate cancer (PCa) in dogs is a highly malignant disease akin to its human counterpart. In contrast to the situation in humans, multi-gene approaches facilitating risk stratification of canine PCa are barely established. The aims of this study were the characterization of the transcriptional landscape of canine PCa and the identification of diagnostic, prognostic and/or therapeutic biomarkers through a multi-step screening approach. RNA-Sequencing of ten malignant tissues and fine-needle aspirations (FNA), and 14 nonmalignant tissues and FNAs was performed to find differentially expressed genes (DEGs) and deregulated pathways. The 4098 observed DEGs were involved in 49 pathways. These 49 pathways could be grouped into five superpathways summarizing the hallmarks of canine PCa: (i) inflammatory response and cytokines; (ii) regulation of the immune system and cell death; (iii) cell surface and PI3K signaling; (iv) cell cycle; and (v) phagosome and autophagy. Among the highly deregulated, moderately to strongly expressed DEGs that were members of one or more superpathways, 169 DEGs were listed in relevant databases and/or the literature and included members of the PCa pathway, oncogenes, prostate-specific genes, and druggable genes. These genes are novel and promising candidate diagnostic, prognostic and/or therapeutic canine PCa biomarkers.

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