This SuperSeries is composed of the SubSeries listed below.
mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues.
Sex, Age, Specimen part, Cell line, Treatment, Time
View SamplesThis SuperSeries is composed of the SubSeries listed below.
HSF1 drives a transcriptional program distinct from heat shock to support highly malignant human cancers.
Specimen part, Cell line, Treatment
View SamplesThis SuperSeries is composed of the SubSeries listed below.
Core transcriptional regulatory circuit controlled by the TAL1 complex in human T cell acute lymphoblastic leukemia.
Disease, Cell line
View SamplesThis SuperSeries is composed of the SubSeries listed below.
Tight coordination of protein translation and HSF1 activation supports the anabolic malignant state.
Specimen part, Cell line, Treatment
View SamplesThe oncogenic transcription factor TAL1/SCL is aberrantly overexpressed in over 40% of cases of T-cell acute lymphoblastic leukemia (T-ALL), emphasizing the importance of the TAL1-regulated transcriptional program in the molecular pathogenesis of T-ALL. Here we identify the core transcriptional regulatory circuit controlled by TAL1 and its regulatory partners HEB, E2A, GATA3, ETS1 and RUNX1 in T-ALL cells. We find that TAL1 forms an interconnected auto-regulatory loop with its partners, which contributes to the sustained upregulation of its direct target genes. Importantly, we also find the MYB oncogenic transcription factor is directly activated by the TAL1 complex and positively regulates many of the same target genes, thus forming a feed-forward positive regulatory loop that further promotes the TAL1-regulated oncogenic program.
Core transcriptional regulatory circuit controlled by the TAL1 complex in human T cell acute lymphoblastic leukemia.
Cell line
View SamplesHeat-Shock Factor 1 (HSF1), master regulator of the heat-shock response, facilitates malignant transformation, cancer cell survival and proliferation in model systems. The common assumption is that these effects are mediated through regulation of heat-shock protein (HSP) expression. However, the transcriptional network that HSF1 coordinates directly in malignancy and its relationship to the heat-shock response have never been defined. By comparing cells with high and low malignant potential alongside their non-transformed counterparts, we identify an HSF1-regulated transcriptional program specific to highly malignant cells and distinct from heat shock. Cancer-specific genes in this program support oncogenic processes: cell-cycle regulation, signaling, metabolism, adhesion and translation. HSP genes are integral to this program, however, even these genes are uniquely regulated in malignancy. This HSF1 cancer program is active in breast, colon and lung tumors isolated directly from human patients and is strongly associated with metastasis and death. Thus, HSF1 rewires the transcriptome in tumorigenesis, with prognostic and therapeutic implications.
HSF1 drives a transcriptional program distinct from heat shock to support highly malignant human cancers.
Cell line, Treatment
View SamplesThe retinal pigment epithelium (RPE) provides vital support to photoreceptor cells and its dysfunction is associated with the onset and progression of age-related macular degeneration (AMD). Surgical provision of RPE cells may ameliorate AMD and thus it would be valuable to develop sources of patient-matched RPE cells for this application of regenerative medicine. We describe here the generation of functional RPE-like cells from fibroblasts that represent an important step toward that goal. We identified candidate master transcriptional regulators of RPEs using a novel computational method and then used these regulators to guide exploration of the transcriptional regulatory circuitry of RPE cells and to reprogram human fibroblasts into RPE-like cells. The RPE-like cells share key features with RPEs derived from healthy individuals, including morphology, gene expression and function, and thus represent a step toward the goal of generating patient-matched RPE cells for treatment of macular degeneration.
A Systematic Approach to Identify Candidate Transcription Factors that Control Cell Identity.
Specimen part
View SamplesThis SuperSeries is composed of the SubSeries listed below.
The Msx1 Homeoprotein Recruits Polycomb to the Nuclear Periphery during Development.
Specimen part, Cell line
View SamplesThe spatial and temporal control of gene expression during development requires the concerted actions of sequence-specific transcriptional regulators and epigenetic chromatin modifiers, which are thought to function within precise nuclear compartments. However, how these activities are coordinated within the dynamic context of the nuclear environment is still largely unresolved. Here we show that transcriptional repression by the Msx1 homeoprotein coordinates recruitment of Polycomb to genomic targets with localization to the nuclear periphery. Using genome-wide ChIP-Seq analyses to identify genomic binding sites for Msx1, we find that repressed target genes are enriched at the nuclear periphery in myoblast cells. We further show that the interaction of Msx1 with the Polycomb repressive complex PRC2 is required for transcriptional repression and regulation of myoblast differentiation, and promotes increased tri-methylation of lysine 27 on histone H3 (H3K27me3) at Msx1 target genes. Furthermore, Msx1 genomic binding promotes the dynamic spatial redistribution of the H3K27me3 repressive mark to the nuclear periphery in developing embryos in vivo. Thus, our findings suggest a hitherto unappreciated spatial coordination of transcription factor binding, Polycomb recruitment, and subnuclear localization in regulation of developmentgene expression programs.
No associated publication
No sample metadata fields
View SamplesA unifying characteristic of aggressive cancers is a profound anabolic shift in metabolism to enable sustained proliferation and biomass expansion. The ribosome is centrally situated to sense metabolic states but whether it impacts systems that promote cellular survival is unknown. Here, through integrated chemical-genetic analyses, we find that a dominant transcriptional effect of blocking protein translation in cancer cells is complete inactivation of heat shock factor 1 (HSF1), a multifaceted transcriptional regulator of the heat-shock response and many other cellular processes essential for tumorigenesis. Translational flux through the ribosome reshapes the transcriptional landscape and links the fundamental anabolic processes of protein production and energy metabolism with HSF1 activity. Targeting this link deprives cancer cells of their energy and chaperone armamentarium thereby rendering the malignant phenotype unsustainable.
Tight coordination of protein translation and HSF1 activation supports the anabolic malignant state.
Specimen part
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