PRD class homeobox genes in bovine early embryos: function, evolution and overlapping roles
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PROVIDER: PRJNA791233 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:ETCHbox genes are mammalian-specific PRD class homeobox genes with conserved expression in the preimplantation embryo but fast-evolving and highly divergent sequences. We ectopically expressed bovine ARGFX and LEUTX ETCHbox genes, both tagged with 3xFLAG tags, in bovine foetal fibroblasts and completed transcriptome seqencing. We compared the transcriptome of cells with ARGFX or LEUTX ectopic expression with control transfected cells. For ARGFX, we expressed the WT version of the gene and a mutant allele containing a 13bp frameshift deletion.
2022-05-24 | GSE192356 | GEO
Project description:We have ectopically expressed two V5-tagged homeobox genes and a control plasmid in mouse embryonic fibroblasts. Following ectopic expression and chemical selection we used whole transcriptome sequencing to reveal any effect of forced missed expression on the MEF transcriptome.
2020-04-13 | GSE129456 | GEO
Project description:Of eyes and embryos; subfunctionalization of the CRX homeobox gene in mammalian evolution
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Project description:ETCHbox genes are fast-evolving homeobox genes present only in eutherian (placental) mammals which originated by duplication and divergence from a conserved homeobox gene, Cone-rod homeobox (CRX). While expression and function of CRX are restricted to the retina in eutherian mammals, ETCHbox gene expression is specific to preimplantation embryos. This dramatic difference could reflect the acquisition of new functions by duplicated genes or subfunctionalization of pleiotropic roles between CRX and ETCHbox genes. To resolve between these hypotheses, we compared expression, sequence and inferred function between CRX of metatherian (marsupial) mammals and ETCHbox genes of eutherians. We find the metatherian CRX homeobox gene is expressed in early embryos and in eyes, unlike eutherian CRX, and distinct amino acid substitutions were fixed in the metatherian and eutherian evolutionary lineages consistent with altered transcription factor specificity. We find that metatherian CRX is capable of regulating embryonically expressed genes in cultured cells in a comparable way to eutherian ETCHbox. The data are consistent with CRX having a dual role in eyes and embryos of metatherians, providing an early embryonic function comparable to that of eutherian ETCHbox genes; we propose that subfunctionalization of pleiotropic functions occurred after gene duplication along the placental lineage, followed by functional elaboration.
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Project description:Regulons and protein–protein interactions of PRD-containing Bacillus anthracis virulence regulators reveal overlapping but distinct functions
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Project description:LEUTX is a homeodomain transcription factor expressed in the very early embryo with a function around embryonic genome activation. The LEUTX gene is found only in eutherian mammals, including humans, but unlike the majority of homeobox genes, the encoded amino acid sequence is very different between divergent mammalian species. However, whether dynamic evolution has also occurred between closely related mammalian species remains unclear. In this work, we perform a comparative genomics study of LEUTX within the primates, revealing dramatic evolutionary sequence change between closely related species. Positive selection has acted on sites in the LEUTX protein, including six sites within the homeodomain; this suggests that selection may have driven changes in the set of downstream targets. Transfection into cell culture followed by transcriptomic analysis reveals small functional differences between human and marmoset LEUTX, suggesting rapid sequence evolution has fine-tuned the role of this homeodomain protein within the primates.
2023-02-06 | GSE224384 | GEO
Project description:Recently, it has been demonstrated that transcriptionally active leukemia-associated fusion oncogenes alter self-renewal in and generate acute myeloid leukemia (AML) from committed progenitors, linking transformation and self-renewal pathways. AML is a heterogeneous disease, both genetically and biologically, and it is not known whether transformation is mediated by common or overlapping genetic programs downstream of multiple mutations or through the engagement of unique programs downstream of individual mutations. This distinction is important, as the demonstration of common pathways may identify common molecular targets for the treatment of AML. Here we demonstrate that the ability to alter self-renewal in vitro and in vivo is a more generalized property of leukemia-associated oncogenes. We further demonstrate that disparate leukemia-associated oncogenes initiate early common and overlapping transformation and self-renewal gene expression programs to mediate these effects. Furthermore, elements of these programs can be detected in established leukemia stem cells from an animal model and across a large cohort of patients with differing acute myeloid leukemia (AML) subtypes, where they strongly predict for disease biology. Finally, individual genes from the programs are demonstrated to partially phenocopy the leukemia-associated oncogenes and themselves alter self-renewal in committed murine progenitors and generate AML when expressed in murine bone marrow. The dataset comprises granulocyte monocyte precursors (GMP) transduced with either GFP alone or the fusion oncogenes MOZ-TIF2 or NUP98-HOXA9 or AML1-ETO, as labelled. Early gene expression changes (36 hours after transduction) were analysed between these replicate samples in two separate ways; either in a single two-class comparison of all oncogene transduced GMP with empty-vector transduced GMP or in three separate two-class comparisons comparing each oncogene individually with empty-vector transduced GMP. In the first analysis we identified 1082 genes/1119 probesets whose expression levels significantly differed (FDR level 0.05). There is a loss of self-renewal potential in the transition from the LSK to GMP population and to further enrich for potential self-renewal genes we compared the expression of these genes/probes in sorted normal LSK versus GMP populations. Genes which were not significantly (p<0.05) and similarly differentially expressed between LSK and GMP were excluded, allowing us to prioritize an immediate “leukemia initiation” program of 167 genes (182 probesets). Our second analysis demonstrated differential expression of 5750, 1161, and 5109 genes, when MOZ-TIF2, NUP98-HOXA9 and AML1-ETO transduced GMP were respectively compared with empty-vector transduced GMP (p<0.05). When our “leukemia initiation” signature was compared to the single comparisons, 127/167 (76%) genes overlapped. To assess the evolutionary nature of transcriptional programs critical for leukemia induction and maintenance, the gene expression profiles of replicate functionally validated leukemic stem cells from a MOZ-TIF2 model of leukemia (L-GMP) were then compared to their normal phenotypic counterpart (normal GMP). 2715 genes were differentially expressed between normal and leukemic GMP (p<0.05). Similarities were seen between our immediate pre-leukemic signatures and the gene expression profiles in the overt leukemias. The overlap with the leukemia initiation and leukemia self-renewal signatures was highly significant at 59/167 genes (35%) and 29/91 genes (32%), respectively (both p<0.0001). Gene expression levels were measured using Affymetrix (Santa Clara, CA) GeneChip Mouse Genome 430A 2.0 arrays (22,690 probesets) with hybridisation and washes as per the manufacturers specifications. The starting point for all analyses was the ''.CEL'' files from the MAS5 software. Data was analyzed using the R statistical package bioconductor18. Data quality was assessed using functions in the affy and affyPLM packages and outlier arrays were removed from subsequent analysis. The GCRMA algorithm (ver. 2.4.1) was used to obtain normalized expression estimates. Genes were selected for further analysis on the following basis: genes that had probesets for which the expression value was greater than 60 (which in our study constitute the average background reading of all probesets) and that had a present flag call in at least two of three samples. To detect significant changes in the expression levels, two-sample Welch t-tests (parametric; assuming unequal variances; Benjamini and Hochberg step-up multiple testing correction at a False Discovery Rate <0.05) was applied to the resulting genes.
2011-06-27 | E-GEOD-24797 | biostudies-arrayexpress
Project description:The genome of V. volvacea revealed 47 genes encoding homeobox transcription factors. Of them, 8 differentially expressed homeobox transcription factors were obtained by comparing the gene expression during primordia and elongation formation. Furthermore, quantitative real-time PCR was performed on selected genes with different expression levels to demonstrate the utility of digital gene expression for gene expression profiles during fruiting body formation. The results showed that five homeobox transcription factors were up-regulated during primordia formation, and three homeobox transcription factors were down-regulated from the egg stage to elongation stage. Overall, a critical role for homeobox transcription factor was believed to contribute to the fruiting body formation. Using the 3'-tag digital gene expression (DGE), we compared the gene expression profiles in fruiting body development of V. volvacea.
2014-12-19 | E-GEOD-43297 | biostudies-arrayexpress
Project description:Homeobox genes encode transcription factors regulating basic processes in cell differentiation during embryogenesis and in the adult. Recently, we have reported the NKL-code which describes physiological expression patterns of nine NKL homeobox genes in early hematopoiesis and in lymphopoiesis including main stages of T-, B- and NK-cell development. Aberrant activity of NKL homeobox genes is involved in the generation of hematological malignancies including T-cell leukemia. Here, we searched for deregulated NKL homeobox genes in main entities of T-cell lymphomas comprising peripheral T-cell lymphoma (PTCL), angioimmunoblastic T-cell lymphoma (AITL), anaplastic large cell lymphoma (ALCL), adult T-cell leukemia/lymphoma (ATLL), hepatospleenic T-cell lymphoma (HSTL), and NK/T-cell lymphoma (NKTL). Our data revealed in all types altogether 19 aberrantly overexpressed genes, demonstrating that deregulated NKL homeobox genes play a significant role in T-cell lymphomas as well. For detailed analyses we focused on NKL homeobox gene MSX1 which is normally expressed in NK-cells and aberrantly activated in T-cell leukemia. This gene was overexpressed in subsets of HSTL patients and HSTL-derived sister cell lines DERL-2 and DERL-7 which served as models to identify mechanisms of deregulation. We performed genomic and expression profiling and whole genome sequencing and revealed mutated and deregulated gene candidates including the fusion gene CD53-PDGFRB exclusively expressed in DERL-2. Subsequent knockdown experiments allowed the construction of an aberrant network involved in MSX1 deregulation containing chromatin factors AUTS2 and H3B/H3.1, PDGF- and BMP-signalling pathways, and homeobox genes NKX2-2 and PITX1. The gene encoding AUTS2 is located at 7q11 and may represent a basic target of the HSTL hallmark aberration i(7q). Our data indicate both oncogenic and tumor suppressor functions of MSX1 in HSTL, reflecting its activity in early lineage differentiation of T- and NK-cells and the presence of NK-cell like characteristics in malignant HSTL cells. In this context, NKL homeobox gene MSX1 may represent a selective target in HSTL tumor evolution. Together, the data highlight an oncogenic role of deregulated NKL homeobox genes in T-cell lymphoma and identified MSX1 as a novel player in HSTL, involved in aberrant NK- and T-cell differentiation.
2019-11-01 | E-MTAB-7734 | biostudies-arrayexpress