scholarly journals Control of her1 expression during zebrafish somitogenesis by a Delta-dependent oscillator and an independent wave-front activity

2000 ◽  
Vol 14 (13) ◽  
pp. 1678-1690 ◽  
Author(s):  
Scott A. Holley ◽  
Robert Geisler ◽  
Christiane Nüsslein-Volhard
Keyword(s):  
Gene Expression ◽  
Wave Front ◽  
Expression Pattern ◽  
Molecular Clock ◽  
De Novo ◽  
Presomitic Mesoderm ◽  
Notch Ligand ◽  
Rule Analysis ◽  
Front Model ◽  
Pair Rule

Somitogenesis has been linked both to a molecular clock that controls the oscillation of gene expression in the presomitic mesoderm (PSM) and to Notch pathway signaling. The oscillator, or clock, is thought to create a prepattern of stripes of gene expression that regulates the activity of the Notch pathway that subsequently directs somite border formation. Here, we report that the zebrafish gene after eight (aei) that is required for both somitogenesis and neurogenesis encodes the Notch ligand DeltaD. Additional analysis revealed that stripes of her1 expression oscillate within the PSM and that aei/DeltaDsignaling is required for this oscillation.aei/DeltaD expression does not oscillate, indicating that the activity of the Notch pathway upstream ofher1 may function within the oscillator itself. Moreover, we found that her1 stripes are expressed in the anlage of consecutive somites, indicating that its expression pattern is not pair-rule. Analysis of her1 expression inaei/DeltaD, fused somites (fss), and aei;fss embryos uncovered a wave-front activity that is capable of continually inducing her1 expression de novo in the anterior PSM in the absence of the oscillation of her1. The wave-front activity, in reference to the clock and wave-front model, is defined as such because it interacts with the oscillator-derived pattern in the anterior PSM and is required for somite morphogenesis. This wave-front activity is blocked in embryos mutant for fssbut not aei/DeltaD. Thus, our analysis indicates that the smooth sequence of formation, refinement, and fading ofher1 stripes in the PSM is governed by two separate activities.

Evidence for medial/lateral specification and positional information within the presomitic mesoderm

Development ◽  
2001 ◽  
Vol 128 (24) ◽  
pp. 5139-5147
Author(s):  
Catarina Freitas ◽  
Sofia Rodrigues ◽  
Jean-Baptiste Charrier ◽  
Marie-Aimée Teillet ◽  
Isabel Palmeirim
Keyword(s):  
Expression Pattern ◽  
Molecular Clock ◽  
Positional Information ◽  
Avian Embryo ◽  
Presomitic Mesoderm ◽  
Fate Map ◽  
Expression Of Genes ◽  
Dynamic Expression ◽  
Somite Formation

In the vertebrate embryo, segmentation is built on repetitive structures, named somites, which are formed progressively from the most rostral part of presomitic mesoderm, every 90 minutes in the avian embryo. The discovery of the cyclic expression of several genes, occurring every 90 minutes in each presomitic cell, has shown that there is a molecular clock linked to somitogenesis. We demonstrate that a dynamic expression pattern of the cycling genes is already evident at the level of the prospective presomitic territory. The analysis of this expression pattern, correlated with a quail/chick fate-map, identifies a ‘wave’ of expression travelling along the future medial/lateral presomitic axis. Further analysis also reveals the existence of a medial/lateral asynchrony of expression at the level of presomitic mesoderm. This work suggests that the molecular clock is providing cellular positional information not only along the anterior/posterior but also along the medial/lateral presomitic axis. Finally, by using an in vitro culture system, we show that the information for morphological somite formation and molecular segmentation is segregated within the medial/lateral presomitic axis. Medial presomitic cells are able to form somites and express segmentation markers in the absence of lateral presomitic cells. By contrast, and surprisingly, lateral presomitic cells that are deprived of their medial counterparts are not able to organise themselves into somites and lose the expression of genes known to be important for vertebrate segmentation, such as Delta-1, Notch-1, paraxis, hairy1, hairy2 and lunatic fringe.

scholarly journals Transcriptome Sequencing of Trichoderma Koningiopsis Strain Tk1 to Identify and Analyze Differential Gene Expression Patterns

2020 ◽  
Author(s):  
Mei Luo ◽  
Zhangyong Dong ◽  
Yongxin Shu ◽  
Mobing Chen
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Differential Gene Expression ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Antimicrobial Effect ◽  
Carbohydrate Active Enzymes ◽  
Differential Gene

Abstract Background: Trichoderma koningiopsis strain Tk1 shows good biocontrol potential. However, its biocontrol function may differ under different conditions. The objective of this study is to elucidate the biological and transcriptome differences of T. koningiopsis Tk1 under different media. Results: In this study, the mycelium weight and sporulation of T. koningiopsis Tk1 was found to differ in various media. Further, the Tk1 strain inhibited the growth of the pathogen Fusarium oxysporum in the three media tested. Fries3, PD, and PS were collected for RNA sequencing of Tk1 mycelia to identify the genes that are differentially expressed genes (DEGs) between Tk1 grown on different media. De novo transcriptome assembly resulted in identification of 14,208 unigenes. The differential gene expression pattern was more similar between the Fries3 and PS samples, whereas PD samples showed a different expression pattern. The DEGs were enriched in some metabolic and biosynthetic pathways. Additional analysis of the DEGs identified a set of carbohydrate-active enzymes that are upregulated or downregulated under different conditions.Conclusions: These results indicate that the Tk1 strain cultured in Fires3 and PS mediums can produce specific metabolic and carbohydrate-active enzymes to enhance their antimicrobial effect, providing a foundation for the subsequent mining of specific genes.

Leukemic Pattern Of HOX Gene Expression Is Driven By Genetic Aberrations Through Epigenetic Modifiers

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 2504-2504
Author(s):  
Julia Starkova ◽  
Karolina Kramarzova ◽  
Karel Fiser ◽  
Ester Mejstrikova ◽  
Katerina Rejlova ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Hox Genes ◽  
De Novo ◽  
In Vitro Experiments ◽  
Genetic Aberrations ◽  
Hox Gene ◽  
Epigenetic Modifiers ◽  
Fab Classification

Abstract Introduction Homeobox (HOX) genes encode transcription factors crucial in embryogenesis. They are often dysregulated in malignancies including leukemias. The aberrant HOX gene expression and its regulation in leukemic cells is neither completely described nor understood. Aims Our main aim was to determine whether the leukemic HOX gene expression pattern is driven by differentiation stage of hematopoietic cells or determined de novo during the process of malignant transformation. Consequentially, we aimed to study the role epigenetic modifiers in regulation of HOX gene expression in normal and malignant hematopoiesis. Methods The expression pattern of HOX genes (cluster of HOX A and B) and epigenetic modifiers (DNMT1, DNMT3a, DNMT3b, EZH2, BMI-1, MLL, JMJD3, UTX) was assessed by qPCR in 8 FACS-sorted subpopulations of healthy BM representing stages of myeloid differentiation (each sample representing a pool of cells sorted from five individuals). The leukemic expression pattern of these genes was analyzed in diagnostic BM samples of childhood AML patients with typical genotypic and morphological (FAB classification) characteristics (N=46). In vitro experiments were performed using NB4 cell line. Results As expected HOX genes were gradually downregulated during normal differentiation of granulocytic and monocytic lineages (assessed in four consecutive differentiation stages for each lineage). In AML samples, HOX gene expression patterns differed significantly among morphological subtypes. However, HOX gene expression did not correlate among subtypes of AML and their physiologically differentiated counterparts. Interestingly, unsupervised hierarchical clustering (HCA) divided AML patients into four main clusters characterized by the presence of prevalent gene rearrangement (PML-RARa, AML1-ETO, MLL rearrangements and NK-AML). The presence of PML/RARa rearrangement was strongly associated with the lowest expression of both HOXA and HOXB clusters, while the other groups had more variable expression of HOX genes. Moreover, the effect of genetic aberrations on HOX gene expression was clearly apparent within AML M2 and M4 subtypes, where AML1/ETO+ or CBFb/MYH11+ patients had significantly lower expression of HOX genes compared to patients with the same FAB classification but without the rearrangements. The expression pattern of epigenetic modifiers in sorted subpopulations of healthy BM followed their expected role in transcriptional regulation during differentiation. However, there was no relation of this pattern to HOX gene expression. On the contrary, in AML samples, the expression levels of epigenetic modifiers clearly correlated with expression profile of HOX genes. These results were supported by unsupervised HCA based on the expression of epigenetic modifiers that showed upregulation of histon demethylases JMJD3 and UTX together with downregulation of DNMT3b in concordance with high levels of HOX genes. Negative correlation between JMJD3 and DNMT3b expression was observed in all leukemic samples (p=0.03); most apparently in PML/RARa+ patients. Therefore we further studied the impact of genetic aberrations on the epigenetic regulation of HOX gene expression in vitrowith PML-RARa+ cell line. Treatment of NB4 cells with ATRA (8, 24hours, 1uM, 10uM) increased the levels of particular HOX genes (HOXA5, A7, B4, B7; FCA=2.8; 1.7; 4; 4 respectively) as well as JMJD3 (FCA=3) and UTX (FCA=1.6). Concordantly, the expression of DNMT3b (FCA=5) was downregulated. The hypothetical driving effect of PML-RARa on de novo determination of leukemic HOX gene expression is further supported by our Results. PML-RARa+ patients had the lowest HOX gene expression regardless of their FLT3/ITD status – previously shown to upregulate strongly HOX genes expression. Conclusion We conclude that the leukemic expression pattern of HOX genes does not reflect the differentiation stages of malignant cells. Our data also demonstrate different contribution of epigenetic modifiers to the HOX gene expression in healthy and malignant hematopoiesis. Moreover, HCA and expression data together with the results of in vitro experiments suggest that the specific molecular aberrations (as exemplified by PML-RARa) participate in regulation of leukemic HOX gene expression through epigenetic changes. Supported by GACR P304/12/2214, GAUK 568213, 00064203. Disclosures: No relevant conflicts of interest to declare.

scholarly journals 25 MATERNAL-TO-EMBRYONIC TRANSITION FOLLOWING NUCLEAR TRANSFER OR PARTHENOGENETIC ACTIVATION

2006 ◽  
Vol 18 (2) ◽  
pp. 121
Author(s):  
T. Brevini ◽  
S. Antonini ◽  
F. Cillo ◽  
I. Lagutina ◽  
S. Colleoni ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Nuclear Transfer ◽  
De Novo ◽  
Gene Expression Pattern ◽  
Mrna Levels ◽  
Cell Stage ◽  
Specific Expression ◽  
Parthenogenetic Activation

The successful development of embryos generated by somatic cell nuclear transfer (SCNT) requires the ooplasm to reprogram the nucleus. This establishes the gene expression pattern necessary for full development by mechanisms that are currently being clarified. The ooplasm action on somatic nuclei shows many common aspects to the process that leads to the creation of a functional embryonic genome from the differentiated sperm and egg genomes. In order to investigate this aspect we studied a critical phase of early embryonic development: the maternal to embryonic transition (MET). We compared the pattern and level of gene expression between bovine embryos derived from in vitro fertilization (IVF), from nuclear transfer of adult fibroblasts (NT), or from parthenogenetic activation (PG). The study was performed in cattle because MET, in this species, occurs over four cell cycles, making it easier to detect even small deviations. Oocytes, matured for 22 h and fertilized in vitro or after cumulus removal, were enucleated and fused to fibroblast cells. Nuclear transfer and Met II oocytes were activated at 24-26 h of maturation with ionomycin (5 �M) for 5 min and 6DMAP (2 mM) for 4 h and then cultured in mSOFaa. Embryos were harvested at the required time for analysis at the 2-, 4-, 8-, and 16-cell; morula; and blastocyst stages and stored snap-frozen in a minimal volume of medium in groups of 5-10 embryos. Semiquantitative RT-PCR was used to study the expression of Nanog, Oct-4, Zar-1, and Par-3, because these genes are directly involved in early embryo development and have a specific expression pattern during MET. Data were analyzed with one-way ANOVA followed by Student-Newman-Keuls All Pairwise Multiple Comparison. No difference in pre-implantation development was observed among the three groups. The Nanog expression pattern was unchanged in all three groups, becoming detectable from the 8-16-cell stage onward. Oct-4 mRNA was detected at all stages in every group, but only in NT embryos did a significant increase occur at the 16-cell stage, suggesting the onset of an anticipated embryonic transcription. the Zar-1 expression pattern, with the characteristic de-novo transcription peak at the 4-cell stage, was observed in both IVF and NT embryos but not in PG embryos. In this group, Zar-1 mRNA levels were significantly higher at the 2- and 4-cell stage than in all of the following stages. The Par-3 gene showed the biggest differences among groups: IVF embryos expressed this gene from the 8-cell stage onward, whereas NT embryos showed high levels of Par-3 mRNA already at the 2-cell stage. Surprisingly, PG embryos showed no detectable Par-3 levels at any stages. The results indicate that, although in vitro development was not affected, gene-specific expression differences during MET occurred among groups. Relating the specific functions exerted by each of these genes in early development to the changes observed following the different manipulations provides useful data toward a better understanding of the role of these genes and of the mechanisms of nuclear reprogramming. This work was supported by FIRB RBNE01HPMX, FIRST 2004, and ESF-EuroStells.

Expression domains of a zebrafish homologue of the Drosophila pair-rule gene hairy correspond to primordia of alternating somites

Development ◽  
1996 ◽  
Vol 122 (7) ◽  
pp. 2071-2078 ◽  
Author(s):  
M. Muller ◽  
E. Weizsacker ◽  
J.A. Campos-Ortega
Keyword(s):  
Expression Pattern ◽  
Bhlh Protein ◽  
Presomitic Mesoderm ◽  
Tail Bud ◽  
Expression Domain ◽  
Somite Formation ◽  
Pair Rule Gene ◽  
Pair Rule ◽  
Time Point

her1 is a zebrafish cDNA encoding a bHLH protein with all features characteristic of members of the Drosophila HAIRY-E(SPL) family. During late gastrulation stages, her1 is expressed in the epibolic margin and in two distinct transverse bands of hypoblastic cells behind the epibolic front. After completion of epiboly, this pattern persists essentially unchanged through postgastrulation stages; the marginal domain is incorporated in the tail bud and, depending on the time point, either two or three paired bands of expressing cells are present within the paraxial presomitic mesoderm separated by regions devoid of transcripts. Labelling of cells within the her1 expression domains with fluorescein-dextran shows that the cells in the epibolic margin and the tail bud are not allocated to particular somites. However, allocation of cells to somites occurs between the marginal expression domain and the first expression band, anterior to it. Moreover, the her1 bands, and the intervening non-expressing zones, each represents the primordium of a somite. This expression pattern is highly reminiscent of that of Drosophila pair-rule genes. A possible participation of her1 in functions related to somite formation is discussed.

AML with Translocation T(8;16) Shows Unique Cytomorphological, Cytogenetic, Molecular, and Prognostic Features and Therefore Qualifies as An Own Entity According to WHO Criteria.

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 1197-1197
Author(s):  
Alexander Kohlmann ◽  
Martin Dugas ◽  
Hans-Ulrich Klein ◽  
Christian Ruckert ◽  
Wolfgang Kern ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
De Novo ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Gene Expression Patterns ◽  
Specific Gene ◽  
Differentiation Potential ◽  
Who Criteria ◽  
Prognostic Features

Abstract Balanced chromosomal rearrangements define distinct biological subsets in acute myeloid leukemia (AML). It is recognized that recurrent balanced aberrations, such as t(15;17), t(8;21), inv(16), and 11q23/MLL translocations, show a close correlation to cytomorphology and also harbor specific gene expression signatures. We here present a cohort of 13 AML cases with t(8;16)(p11;p13). This translocation is rare with only 13 cases (6 males, 7 females) diagnosed from our overall cohort of 6124 cases of AML over recent years, and is more frequently found in therapy-related AML than in de novo AML (7/438 t-AML, and 6/5686 de novo, p=0.00001). Prognosis was poor with median overall survival of 4.7 months. Five patients deceased within the first month after diagnosis. AML with t(8;16) is characterized by striking cytomorphologic features: In all 13 cases the positivity for myeloperoxidase (MPO) on bone marrow smears was >30% (median: 85%) and intriguingly, in parallel also >40% (median: 88%) of blast cells stained strongly positive for non-specific esterase (NSE) in the same cell, suggesting that AML with t(8;16) arise from a very early stem cell with both myeloid and monoblastic differentiation potential. Therefore, AML with t(8;16) cases can not be classified according to standard FAB categories. Morphologically we also detected erythrophagocytosis in 7/13 cases, a specific feature in AML with t(8;16) that was previously described. With respect to cytogenetics, 6/13 patients had t(8;16)(p11;p13) as sole abnormality. 7/13 patients demonstrated additional non-recurrent abnormalities, 4 cases with single additional aberrations, and 3 cases with two or more additional aberrations. Molecular analyses detected the MYST3- CREBBP fusion transcript in all cases tested (12/12). We then compared gene expression patterns in 7 cases of AML with t(8;16) to: (i) AML FAB subtypes M1 and M4/5 with strong MPO or NSE with normal karyotype and to (ii) distinct AML subtypes with balanced chromosomal aberrations according to WHO classification. In a first series using Affymetrix HG-U133A+B microarrays 4 cases of AML with t(8;16) were compared to FAB M1 (n=46), M4 (n=41), M5a (n=9), and M5b (n=16). Hierarchical clustering and principal component analyses revealed that AML with t(8;16) were intercalating rather with FAB subtypes M4 and M5b and did not cluster near to FAB M1, although strong positivity for MPO was seen in all t(8;16) cases. Thus, monocytic characteristics influence the gene expression pattern stronger than myeloid features. When further compared to AML WHO subtypes t(15;17) (n=43), t(8;21) (n=43), inv(16) (n=49), and 11q23/MLL (n=50), AML with t(8;16) samples were repeatedly grouped in the vicinity of the 11q23/MLL cases. This can be explained by a similar expression of genes such as EAF2, HOXA9, HOXA10, PRKCD, or HNMT. Yet, in a subsequent pairwise comparison AML with t(8;16) could also be clearly discriminated from 11q23/MLL with differentially expressed genes including CAPRIN1, RAN, SMARCD2, LRRC41, or H2BFS, higher expressed in AML with t(8;16) and SOCS2, PRAME, RUNX3, or TPT1, lower expressed in AML with t(8;16), respectively. Moreover, the respective FAB-type or WHO-type signatures were validated on a separate cohort of patients (n=3 AML with t(8;16); n=107 other AML subtypes as above), all prospectively analyzed with the successor HG-U133 Plus 2.0 microarray. Again, in direct comparison to FAB-type or WHO-type cases, dominant and unique gene expression patterns were seen for AML with t(8;16), confirming the molecular distinctiveness of this rare AML entity. Using a classification algorithm we were able to correctly predict all AML with t(8;16) cases by their gene expression pattern. This accuracy was observed not only for both FAB-type and WHO-type signatures, but also correctly classified the cases across the different patient cohorts and microarray designs. In conclusion, AML with t(8;16) is a specific subtype of AML with very poor prognosis that often presents as treatment-related AML and with particular characteristics not only in morphology and clinical profile, but also on a molecular level. Due to these unique features, it qualifies as a specific recurrent entity according to WHO criteria.

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