Gene expression analysis is a widely used and powerful method for investigating the transcriptional behavior of biological systems, for classifying cell states in disease, and for many other ...purposes. Recent studies indicate that common assumptions currently embedded in experimental and analytical practices can lead to misinterpretation of global gene expression data. We discuss these assumptions and describe solutions that should minimize erroneous interpretation of gene expression data from multiple analysis platforms.
Highlights • Myc is a general regulator that binds to established euchromatin in the cell. • Myc acts as a nonlinear amplifier of transcription. • Miz1 and other regulators shape Myc transcriptional ...amplification.
The multiple myeloma SET domain (MMSET) protein is overexpressed in multiple myeloma (MM) patients with the translocation t(4;14). Although studies have shown the involvement of MMSET/Wolf-Hirschhorn ...syndrome candidate 1 in development, its mode of action in the pathogenesis of MM is largely unknown. We found that MMSET is a major regulator of chromatin structure and transcription in t(4;14) MM cells. High levels of MMSET correlate with an increase in lysine 36 methylation of histone H3 and a decrease in lysine 27 methylation across the genome, leading to a more open structural state of the chromatin. Loss of MMSET expression alters adhesion properties, suppresses growth, and induces apoptosis in MM cells. Consequently, genes affected by high levels of MMSET are implicated in the p53 pathway, cell cycle regulation, and integrin signaling. Regulation of many of these genes required functional histone methyl-transferase activity of MMSET. These results implicate MMSET as a major epigenetic regulator in t(4;14)+ MM.
Reconstructing MYC Levens, David L
Genes & development,
2003-May-01, 20030501, Letnik:
17, Številka:
9
Journal Article
Recenzirano
Odprti dostop
The c-myc protooncogene is a senior administrator of the cell helping to allocate resources and direct proliferation, growth, differentiation, and apoptosis. As an oncogene, MYC is a high-ranking ...member of the gang of molecular thugs that hijacks cells and perpetrates cellular terror. Belying the terrifying organismal consequences of MYC misregulation, its influence on the expression of most target genes is only modest; MYC seldom exerts a dominating influence on natural or artificial targets. Besides acting at the level of chromatin, MYC may also operate at later stages of the transcription cycle, after pre-initiation complex formation. In addition to using generic chromatin complexes to up- or down-regulate transcription, the MYC network also conscripts individual factors to modify expression locally on an ad hoc basis. For example, YY1, AP2, MIZ1, SP1, BRCA1, and other proteins interact directly with MYC, and so may directly modify the output of the MYC network.
While DNA inside the cells is predominantly canonical right-handed double helix, guanine-rich DNAs have potential to fold into four-stranded structures that contain stacks of G-quartets (G4 DNA ...quadruplex). Genome sequencing has revealed G4 sequences tend to localize at the gene control regions, especially in the promoters of oncogenes. A growing body of evidence indicates that G4 DNA quadruplexes might have important regulatory roles in genome function, highlighting the need for techniques to detect genome-wide folding of DNA into this structure. Potassium permanganate in vivo treatment of cells results in oxidizing of nucleotides in single-stranded DNA regions that accompany G4 DNA quadruplexes formation, providing an excellent probe for the conformational state of DNA inside the living cells. Here, we describe a permanganate-based methodology to detect G4 DNA quadruplex, genome-wide. This methodology combined with high-throughput sequencing provides a snapshot of the DNA conformation over the whole genome in vivo.
The first characterised FUSE Binding Protein family member, FUBP1, binds single-stranded DNA to activate MYC transcription. Psi, the sole FUBP protein in Drosophila, binds RNA to regulate P-element ...and mRNA splicing. Our previous work revealed pro-growth functions for Psi, which depend, in part, on transcriptional activation of Myc. Genome-wide functions for FUBP family proteins in transcriptional control remain obscure. Here, through the first genome-wide binding and expression profiles obtained for a FUBP family protein, we demonstrate that, in addition to being required to activate Myc to promote cell growth, Psi also directly binds and activates stg to couple growth and cell division. Thus, Psi knockdown results in reduced cell division in the wing imaginal disc. In addition to activating these pro-proliferative targets, Psi directly represses transcription of the growth inhibitor tolkin (tok, a metallopeptidase implicated in TGFβ signalling). We further demonstrate tok overexpression inhibits proliferation, while tok loss of function increases mitosis alone and suppresses impaired cell division caused by Psi knockdown. Thus, Psi orchestrates growth through concurrent transcriptional activation of the pro-proliferative genes Myc and stg, in combination with repression of the growth inhibitor tok.
Here, we report novel tumour suppressor activity for the
Argonaute family RNA-binding protein AGO1, a component of the miRNA-dependent RNA-induced silencing complex (RISC). The mechanism for growth ...inhibition does not, however, involve canonical roles as part of the RISC; rather, AGO1 controls cell and tissue growth by functioning as a direct transcriptional repressor of the master regulator of growth, Myc. AGO1 depletion in wing imaginal discs drives a significant increase in ribosome biogenesis, nucleolar expansion and cell growth in a manner dependent on Myc abundance. Moreover, increased
promoter activity and elevated
mRNA in AGO1-depleted animals requires RNA polymerase II transcription. Further support for transcriptional AGO1 functions is provided by physical interaction with the RNA polymerase II transcriptional machinery (chromatin remodelling factors and Mediator Complex), punctate nuclear localisation in euchromatic regions and overlap with Polycomb Group transcriptional silencing loci. Moreover, significant AGO1 enrichment is observed on the
promoter and AGO1 interacts with the
transcriptional activator Psi. Together, our data show that
AGO1 functions outside of the RISC to repress
transcription and inhibit developmental cell and tissue growth.This article has an associated 'The people behind the papers' interview.
Despite two decades of research, the major function of FBP-family KH domain proteins during animal development remains controversial. The literature is divided between RNA processing and ...transcriptional functions for these single stranded nucleic acid binding proteins. Using Drosophila, where the three mammalian FBP proteins (FBP1-3) are represented by one ortholog, Psi, we demonstrate the primary developmental role is control of cell and tissue growth. Co-IP-mass spectrometry positioned Psi in an interactome predominantly comprised of RNA Polymerase II (RNA Pol II) transcriptional machinery and we demonstrate Psi is a potent transcriptional activator. The most striking interaction was between Psi and the transcriptional mediator (MED) complex, a known sensor of signaling inputs. Moreover, genetic manipulation of MED activity modified Psi-dependent growth, which suggests Psi interacts with MED to integrate developmental growth signals. Our data suggest the key target of the Psi/MED network in controlling developmentally regulated tissue growth is the transcription factor MYC. As FBP1 has been implicated in controlling expression of the MYC oncogene, we predict interaction between MED and FBP1 might also have implications for cancer initiation and progression.
We identified the far upstream element binding protein 1 (FBP1), an activator of transcription of the proto‐oncogene c‐myc, in a functional yeast survival screen for tumor‐related antiapoptotic ...proteins and demonstrated strong overexpression of FBP1 in human hepatocellular carcinoma (HCC). Knockdown of the protein in HCC cells resulted in increased sensitivity to apoptotic stimuli, reduced cell proliferation, and impaired tumor formation in a mouse xenograft transplantation model. Interestingly, analysis of gene regulation in these cells revealed that c‐myc levels were not influenced by FBP1 in HCC cells. Instead, we identified the cell cycle inhibitor p21 as a direct target gene repressed by FBP1, and in addition, expression levels of the proapoptotic genes tumor necrosis factor α, tumor necrosis factor–related apoptosis‐inducing ligand, Noxa, and Bik were elevated in the absence of FBP1. Conclusion: Our data establish FBP1 as an important oncoprotein overexpressed in HCC that induces tumor propagation through direct or indirect repression of cell cycle inhibitors and proapoptotic target genes. (HEPATOLOGY 2009.)
To investigate the association of DNA nucleotide excision repair (NER) defects with neurological degeneration, cachexia and cancer, we performed autopsies on 4 adult xeroderma pigmentosum (XP) ...patients with different clinical features and defects in NER complementation groups XP-A, XP-C or XP-D.
The XP-A (XP12BE) and XP-D (XP18BE) patients exhibited progressive neurological deterioration with sensorineural hearing loss. The clinical spectrum encompassed severe cachexia in the XP-A (XP12BE) patient, numerous skin cancers in the XP-A and two XP-C (XP24BE and XP1BE) patients and only few skin cancers in the XP-D patient. Two XP-C patients developed internal neoplasms including glioblastoma in XP24BE and uterine adenocarcinoma in XP1BE. At autopsy, the brains of the 44 yr XP-A and the 45 yr XP-D patients were profoundly atrophic and characterized microscopically by diffuse neuronal loss, myelin pallor and gliosis. Unlike the XP-A patient, the XP-D patient had a thickened calvarium, and the brain showed vacuolization of the neuropil in the cerebrum, cerebellum and brainstem, and patchy Purkinje cell loss. Axonal neuropathy and chronic denervation atrophy of the skeletal muscles were observed in the XP-A patient, but not in the XP-D patient.
These clinical manifestations and autopsy findings indicate advanced involvement of the central and peripheral nervous system. Despite similar defects in DNA repair, different clinicopathological phenotypes are seen in the four cases, and therefore distinct patterns of neurodegeneration characterize XP-D, XP-A and XP-C patients.
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