Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA98039 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To examine the effects of disrupting the AML1/ETO MYND-SMRT interaction with the W692A substitution on AML1/ETO function, the global gene expression profile of mouse bone marrow LSK cells transduced with GFP was compared to that of cells transduced with either wild-type AML1/ETO or AML1/ETO harboring the W692A substitution in the MYND domain. Three independent biological replicates were assessed for both the control (GFP/MigR1) and AML1/ETO (intact MYND-SMRT interaction) conditions, whereas four independent biological replicates were assessed for the W692A (disrupted MYND-SMRT interaction) condition. The three GFP replicates were used to establish a baseline signal for comparison to both the AML1/ETO and W692A samples. Keywords: genetic modification
2007-03-21 | GSE7324 | GEO
Project description:To examine the effects of disrupting the AML1/ETO MYND-SMRT interaction with the W692A substitution on AML1/ETO function, the global gene expression profile of mouse bone marrow LSK cells transduced with GFP was compared to that of cells transduced with either wild-type AML1/ETO or AML1/ETO harboring the W692A substitution in the MYND domain. Three independent biological replicates were assessed for both the control (GFP/MigR1) and AML1/ETO (intact MYND-SMRT interaction) conditions, whereas four independent biological replicates were assessed for the W692A (disrupted MYND-SMRT interaction) condition. The three GFP replicates were used to establish a baseline signal for comparison to both the AML1/ETO and W692A samples. Experiment Overall Design: Global gene expression profiles of FACS-sorted Lin-Sca1+cKit+ mouse bone marrow cells transduced with empty vector (GFP-MigR1), AML1/ETO, or AML1/ETO with the W692A substitution (W692A).
2008-06-15 | E-GEOD-7324 | biostudies-arrayexpress
Project description:This study characterizes the genome-side occupancy of AML1, AML1-ETO and the cofactors N-CoR and p300 in leukemics cells (Kasumi-1) to discover novel regulatory mechanisms involving genes bound by the t(8:21) fusion protein AML1-ETO. A significant discovery of our study is the co-localization of AML1-ETO with the N-CoR co-repressor on genomic regions that are primarily distal to the transcriptional start sites (TSSs). These regions exhibit over-representation of the PU.1 motif: PU.1 is a key hematopoietic regulator and member of the ETS family of transcription factors. Functionally, genes co-occupied by AML1-ETO and N-CoR (e.g., TYROBP and LAPTM5) are associated with the leukemic phenotype, as determined by analyses of gene ontology and by the observation that these genes are predominantly up-regulated upon AML1-ETO depletion. To further probe the regulatory context of these leukemic cells, genome-wide enrichment of the transcriptional initiation-associated histone modification H3K4me3 was also measured.
2015-05-26 | GSE62847 | GEO
Project description:Piwi-interacting RNAs (piRNAs) guide Piwi Argonautes to suppress transposon activity in animal gonads. Known piRNA populations are extremely complex, with millions of individual sequences present in a single organism. Despite this complexity, specific Piwi proteins incorporate piRNAs with distinct nucleotide- and transposon strand-biases (antisense or sense) of unknown origin. Here we examined the contribution of structural domains in Piwi proteins towards defining these biases. We report the first crystal structure of the MID domain from a Piwi Argonaute and use docking experiments to show its ability to specify recognition of 5M-bM-^@M-2 uridine (1U-bias) of piRNAs. Mutational analyses reveal the importance of 5M-bM-^@M-^Y end-recognition within the MID domain for piRNA biogenesis in vivo. Finally, domain-swapping experiments uncover an unexpected role for the MID-PIWI module of a Piwi protein in dictating the strand-orientation of its bound piRNAs. Our work identifies structural features that allow distinguishing individual Piwi members during piRNA biogenesis Immunoprecipitated small RNA were purified from Bmn4 cells for preparation of high-throughput sequencing libraries.
2014-07-01 | E-GEOD-55451 | biostudies-arrayexpress
Project description:This study characterizes the genome-side occupancy of AML1, AML1-ETO and the cofactors N-CoR and p300 in leukemics cells (Kasumi-1) to discover novel regulatory mechanisms involving genes bound by the t(8:21) fusion protein AML1-ETO. A significant discovery of our study is the co-localization of AML1-ETO with the N-CoR co-repressor on genomic regions that are primarily distal to the transcriptional start sites (TSSs). These regions exhibit over-representation of the PU.1 motif: PU.1 is a key hematopoietic regulator and member of the ETS family of transcription factors. Functionally, genes co-occupied by AML1-ETO and N-CoR (e.g., TYROBP and LAPTM5) are associated with the leukemic phenotype, as determined by analyses of gene ontology and by the observation that these genes are predominantly up-regulated upon AML1-ETO depletion. To further probe the regulatory context of these leukemic cells, genome-wide enrichment of the transcriptional initiation-associated histone modification H3K4me3 was also measured. Genome-wide study of transcription factor-DNA binding for AML1 (RUNX1) and the t(8;21) fusion protien AML1-ETO (RUNX1T1) in the Kasumi-1 leukemia cell line. The genome-wide binding of the disease-related cofactors N-CoR and p300 was assayed, along with enrichments of the H3K4me3 and H3K27me3 histone modifications.
2015-05-26 | E-GEOD-62847 | biostudies-arrayexpress
Project description:Piwi-interacting RNAs (piRNAs) guide Piwi Argonautes to suppress transposon activity in animal gonads. Known piRNA populations are extremely complex, with millions of individual sequences present in a single organism. Despite this complexity, specific Piwi proteins incorporate piRNAs with distinct nucleotide- and transposon strand-biases (antisense or sense) of unknown origin. Here we examined the contribution of structural domains in Piwi proteins towards defining these biases. We report the first crystal structure of the MID domain from a Piwi Argonaute and use docking experiments to show its ability to specify recognition of 5′ uridine (1U-bias) of piRNAs. Mutational analyses reveal the importance of 5’ end-recognition within the MID domain for piRNA biogenesis in vivo. Finally, domain-swapping experiments uncover an unexpected role for the MID-PIWI module of a Piwi protein in dictating the strand-orientation of its bound piRNAs. Our work identifies structural features that allow distinguishing individual Piwi members during piRNA biogenesis
2014-07-01 | GSE55451 | GEO
Project description:Approximately 20% of Acute Myelogenous Leukemia (AML) cases carry the t(8;21) translocation, which involves the AML1 and ETO genes, and express the resulting AML1/ETO fusion protein that functions as a transcriptional repressor by recruiting NCoR/SMRT/HDAC complexes to DNA. We used microarrays to identify human promoters bound by AML1/ETO in U937 cells. Keywords: ChIP-chip
2008-12-22 | GSE10531 | GEO
Project description:The progesterone receptor (PR) is a steroid-responsive nuclear receptor with two isoforms: PR-A and PR-B. Disruption of PR-A:PR-B signaling is associated with breast cancer through interactions with oncogenic co-regulatory proteins (CoRs). However, molecular details of isoform-specific PR-CoR interactions remain poorly understood. Using structural mass spectrometry, we investigate the sequential binding mechanism of purified full-length PR and intact CoRs, steroid receptor coactivator 3 (SRC3) and p300, as complexes on target DNA. Our findings reveal selective CoR NR-box binding by PR and novel interaction surfaces between PR and CoRs during complex assembly, providing a structural basis for CoR sequential binding on PR. Antagonist-bound PR showed persistent CoR interactions, challenging the classical model of nuclear receptor activation and repression. Collectively, we offer a peptide-level perspective on the organization of the PR transcriptional complex and infer the mechanisms behind the interactions of these proteins, both in active and inactive conformations.
2025-04-07 | PXD056360 | Pride