Transcription Factors In Human Cells Research Articles

Large-scale mapping and mutagenesis of human transcriptional effector domains.

Human gene expression is regulated by more than 2,000 transcription factors and chromatin regulators1,2. Effector domains within these proteins can activate or repress transcription. However, for many of these regulators we do not know what type of effector domains they contain, their location in the protein, their activation and repression strengths, and the sequences that are necessary for their functions. Here, we systematically measure the effector activity of more than 100,000 protein fragments tiling across most chromatin regulators and transcription factors in human cells (2,047 proteins). By testing the effect they have when recruited at reporter genes, we annotate 374 activation domains and 715 repression domains, roughly 80% of which are new and have not been previously annotated3-5. Rational mutagenesis and deletion scans across all the effector domains reveal aromatic and/or leucine residues interspersed with acidic, proline, serine and/or glutamine residues are necessary for activation domain activity. Furthermore, most repression domain sequences contain sites for small ubiquitin-like modifier (SUMO)ylation, short interaction motifs for recruiting corepressors or are structured binding domains for recruiting other repressive proteins. We discover bifunctional domains that can both activate and repress, some of which dynamically split a cell population into high- and low-expression subpopulations. Our systematic annotation and characterization of effector domains provide a rich resource for understanding the function of human transcription factors and chromatin regulators, engineering compact tools for controlling gene expression and refining predictive models of effector domain function.

Targeted Covalent Inhibition of Small CTD Phosphatase‐1 to Promote the Degradation of REST Transcription Factor in Human Cells

The repressor element‐1 silencing transcription factor (REST) represses neuronal gene expression, whose dysregulation is implicated in brain tumors and neurological diseases. High level of REST protein drives the tumor growth in some glioblastoma cells. While transcription factors like REST are challenging targets for small molecule inhibitors, the inhibition of a regulatory protein, Small CTD Phosphatase 1 (SCP1), promotes REST degradation and reduces transcriptional activity. This study rationally designed a series of α,β‐unsaturated sulfones to serve as potent and selective covalent inhibitors against SCP1. The compounds inactivate SCP1 via covalent modification of Cys181 located at the active site entrance. Cellular studies showed that the inhibitors inactivate SCP1 in a time‐ and dose‐dependent manner with an EC50 ~1.5 µM, reducing REST protein levels and activating specific REST‐suppressed genes. These compounds represent a promising line of small molecule inhibitors as a novel lead for glioblastoma whose growth is driven by REST transcription activity.

Targeted Covalent Inhibition of Small CTD Phosphatase 1 to Promote the Degradation of the REST Transcription Factor in Human Cells.

The repressor element-1 silencing transcription factor (REST) represses neuronal gene expression, whose dysregulation is implicated in brain tumors and neurological diseases. A high level of REST protein drives the tumor growth in some glioblastoma cells. While transcription factors like REST are challenging targets for small-molecule inhibitors, the inactivation of a regulatory protein, small CTD phosphatase 1 (SCP1), promotes REST degradation and reduces transcriptional activity. This study rationally designed a series of α,β-unsaturated sulfones to serve as potent and selective covalent inhibitors against SCP1. The compounds inactivate SCP1 via covalent modification of Cys181 located at the active site entrance. Cellular studies showed that the inhibitors inactivate SCP1 in a time- and dose-dependent manner with an EC50 ∼1.5 μM, reducing REST protein levels and activating specific REST-suppressed genes. These compounds represent a promising line of small-molecule inhibitors as a novel lead for glioblastoma whose growth is driven by REST transcription activity.

The MYST family histone acetyltransferase complex regulates stress resistance and longevity through transcriptional control of DAF-16/FOXO transcription factors.

The well-known link between longevity and the Sir2 histone deacetylase family suggests that histone deacetylation, a modification associated with repressed chromatin, is beneficial to longevity. However, the molecular links between histone acetylation and longevity remain unclear. Here, we report an unexpected finding that the MYST family histone acetyltransferase complex (MYS-1/TRR-1 complex) promotes rather than inhibits stress resistance and longevity in Caenorhabditis elegans. Our results show that these beneficial effects are largely mediated through transcriptional up-regulation of the FOXO transcription factor DAF-16. MYS-1 and TRR-1 are recruited to the promoter regions of the daf-16 gene, where they play a role in histone acetylation, including H4K16 acetylation. Remarkably, we also find that the human MYST family Tip60/TRRAP complex promotes oxidative stress resistance by up-regulating the expression of FOXO transcription factors in human cells. Tip60 is recruited to the promoter regions of the foxo1 gene, where it increases H4K16 acetylation levels. Our results thus identify the evolutionarily conserved role of the MYST family acetyltransferase as a key epigenetic regulator of DAF-16/FOXO transcription factors.

Broadly Applicable Methodology for the Rapid and Dosable Small Molecule-Mediated Regulation of Transcription Factors in Human Cells

Direct and selective small molecule control of transcription factor activity is an appealing avenue for elucidating the cell biology mediated by transcriptional programs. However, pharmacologic tools to modulate transcription factor activity are scarce because transcription factors are not readily amenable to small molecule-mediated regulation. Moreover, existing genetic approaches to regulate transcription factors often lead to high nonphysiologic levels of transcriptional activation that significantly impair our ability to understand the functional implications of transcription factor activity. Herein, we demonstrate that small molecule-mediated conformational control of protein degradation is a generally applicable, chemical biological methodology to obtain small molecule-regulated transcription factors that modulate transcriptional responses at physiologic levels in human cells. Our establishment of this approach allows for the rapid development of genetically encoded, small molecule-regulated transcription factors to explore the biologic and therapeutic impact of physiologic levels of transcription factor activity in cells.

Species-Specific Strategies Underlying Conserved Functions of Metabolic Transcription Factors

The winged helix protein FOXA2 and the nuclear receptor peroxisome proliferator-activated receptor-γ (PPARγ) are highly conserved, regionally expressed transcription factors (TFs) that regulate networks of genes controlling complex metabolic functions. Cistrome analysis for Foxa2 in mouse liver and PPARγ in mouse adipocytes has previously produced consensus-binding sites that are nearly identical to those used by the corresponding TFs in human cells. We report here that, despite the conservation of the canonical binding motif, the great majority of binding regions for FOXA2 in human liver and for PPARγ in human adipocytes are not in the orthologous locations corresponding to the mouse genome, and vice versa. Of note, TF binding can be absent in one species despite sequence conservation, including motifs that do support binding in the other species, demonstrating a major limitation of in silico binding site prediction. Whereas only approximately 10% of binding sites are conserved, gene-centric analysis reveals that about 50% of genes with nearby TF occupancy are shared across species for both hepatic FOXA2 and adipocyte PPARγ. Remarkably, for both TFs, many of the shared genes function in tissue-specific metabolic pathways, whereas species-unique genes fail to show enrichment for these pathways. Nonetheless, the species-unique genes, like the shared genes, showed the expected transcriptional regulation by the TFs in loss-of-function experiments. Thus, species-specific strategies underlie the biological functions of metabolic TFs that are highly conserved across mammalian species. Analysis of factor binding in multiple species may be necessary to distinguish apparent species-unique noise and reveal functionally relevant information.

Probing Target Search Mechanisms of Transcription Factors in Human Cells

Cells control their functions via the expression of specific genes. Over the ∼23 thousands genes present in a human cell only a few thousands are expressed at a given time in order to specify a particular function. Gene expression is regulated through complex protein networks and/or feedback mechanisms that occur at the molecular level. Specific DNA-binding proteins, termed as transcription factors (TFs), play a key role by transiently associating to target sequences on the genome and controlling the genes that are induced or repressed. Therefore, understanding gene expression regulation requires elucidating TFs target search mechanisms and DNA-binding and release kinetics at the target locus. To directly study the target search process, we have decided to insert a binding locus (target) into the genome of a human cell line and to track the dynamics of specific DNA-binding proteins (searchers). To this end, we employ a model system: the SJ-U2OS human cell line, which has a genomic insertion of exogenous binding sites cassettes for two DNA-binding proteins (TetR and LacI). Subsequently, individual - fluorescently labeled - Tet repressors are micro-injected directly inside the cell nucleus and their trajectories are recorded in real-time during the target search by time-lapse single-particle-tracking laser microscopy. In addition, LacI binding sites are used to visualize the position of the binding locus via the expression of NLS-LacI-CFP, while co-injection and imaging of high molecular weight Fluorescein-Dextrans ensures sub-nuclear compartmentalization visualization. The combination of the wealth of information proceeding from individual trajectories, target localization, and nuclear compartmentalization visualization allow us to directly address a variety of important and largely unexplored questions, first of all: how TFs do find their target and what parameters (molecular crowding, nuclear structure, non-specific interaction with DNA, association rate...) primarily determine the search kinetics.

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

Regulation of gene transcription in diverse cell types is determined largely by varied sets of cis-elements where transcription factors bind. Here we demonstrate that data from a single high-throughput DNase I hypersensitivity assay can delineate hundreds of thousands of base-pair resolution in vivo footprints in human cells that precisely mark individual transcription factor-DNA interactions. These annotations provide a unique resource for the investigation of cis-regulatory elements. We find that footprints for specific transcription factors correlate with ChIP-seq enrichment and can accurately identify functional versus nonfunctional transcription factor motifs. We also find that footprints reveal a unique evolutionary conservation pattern that differentiates functional footprinted bases from surrounding DNA. Finally, detailed analysis of CTCF footprints suggests multiple modes of binding and a novel DNA binding motif upstream of the primary binding site.

Osmotic stress response is altered in leiomyoma cells

OBJECTIVE: Clinical treatment of leiomyomas with GnRH analogue produces a rapid reduction in leiomyoma volume. Rapid leiomyoma regrowth when GnRH treatment is withdrawn suggests the reduction in volume is due to transport of water, yet little is known about the response of leiomyoma cells to osmotic stress. Nuclear factor of activated T cells 5 (NFAT5) is the key osmo-sensing transcription factor in human cells. Our goal was to characterize osmosensing via NFAT5 in leiomyoma cells. DESIGN: Prospective, human model experiments MATERIALS AND METHODS: Osmotic stress was induced by culturing immortalized human leiomyoma and myometrial cells in DMEM-10% FBS with additional osmolytes of NaCl at 25, 50 or 100 mM for 8 hours. Proliferation assays were performed by the sulforhodamine B method. Apoptosis was assessed by caspase 3/7 activity assay. Expression of NFAT5 in tissue and cells was determined with qRT-PCR and western blot analysis. RESULTS: Leiomyoma cell growth was inhibited 18% at 50 mM NaCl compared to 48% in myometrial cells (p<0.05), consistent with altered osmosensing in leiomyoma cells. This finding was not due to apoptosis, as evidenced by no change in caspase activity. NFAT5 transcripts were increased in leiomyoma 1.5 fold ± 0.19 compared to myometrium in 4 of 7 patient samples (p<0.05). Concentration dependent upregulation of NFAT5 mRNA was observed in osmotically stressed leiomyoma cells. At 50mM NaCl, NFAT5 transcripts were increased 2.5-fold compared to control. CONCLUSIONS: Leiomyoma cells were more resistant to changes in osmotic stress than myometrial cells, suggesting dysregulation in osmotic signaling in leiomyomas. This change was accompanied by differential expression of NFAT5 in leiomyoma tissue. Altered osmotic signaling in leiomyoma cells suggests a central role for water regulation in the rapid change of leiomyoma volume with GnRH analogue treatment.

Distribution of NF-kappaB-binding sites across human chromosome 22.

We have mapped the chromosomal binding site distribution of a transcription factor in human cells. The NF-kappaB family of transcription factors plays an essential role in regulating the induction of genes involved in several physiological processes, including apoptosis, immunity, and inflammation. The binding sites of the NF-kappaB family member p65 were determined by using chromatin immunoprecipitation and a genomic microarray of human chromosome 22 DNA. Sites of binding were observed along the entire chromosome in both coding and noncoding regions, with an enrichment at the 5' end of genes. Strikingly, a significant proportion of binding was seen in intronic regions, demonstrating that transcription factor binding is not restricted to promoter regions. NF-kappaB binding was also found at genes whose expression was regulated by tumor necrosis factor alpha, a known inducer of NF-kappaB-dependent gene expression, as well as adjacent to genes whose expression is not affected by tumor necrosis factor alpha. Many of these latter genes are either known to be activated by NF-kappaB under other conditions or are consistent with NF-kappaB's role in the immune and apoptotic responses. Our results suggest that binding is not restricted to promoter regions and that NF-kappaB binding occurs at a significant number of genes whose expression is not altered, thereby suggesting that binding alone is not sufficient for gene activation.

Mammalian transcription factors in yeast: strangers in a familiar land.

Many transcription factors in human cells have functional orthologues in yeast, and a common experimental theme has been to define the function of the yeast protein and then test whether the mammalian version behaves similarly. Although, at first glance, this approach does not seem feasible for factors that do not have yeast counterparts, mammalian transcriptional activators or repressors can be expressed directly in yeast. Often, the mammalian factor retains function in yeast, and this allows investigators to exploit the experimental tractability of yeast to ask a diverse set of questions.