Gene expression is primarily regulated by cis-regulatory DNA elements and trans-interacting proteins. Transcription factors bind in a DNA sequence-specific manner and recruit activities that modulate the association and activity of transcription complexes at specific genes. Often, transcription factors belong to families of related proteins that interact with similar DNA sequences. Furthermore, genes are regulated by multiple, sometimes redundant, cis-regulatory elements. Thus, the analysis of the role of a specific DNA regulatory sequence and the interacting proteins in the context of intact cells is challenging. In this study, we designed and functionally characterized an artificial DNA-binding domain that neutralizes the function of a cis-regulatory DNA element associated with adult β-globin gene expression. The zinc finger DNA-binding domain (ZF-DBD), comprising six ZFs, interacted specifically with a CACCC site located 90 bp upstream of the transcription start site (-90 β-ZF-DBD), which is normally occupied by KLF1, a major regulator of adult β-globin gene expression. Stable expression of the -90 β-ZF-DBD in mouse erythroleukemia cells reduced the binding of KLF1 with the β-globin gene, but not with locus control region element HS2, and led to reduced transcription. Transient transgenic embryos expressing the -90 β-ZF-DBD developed normally but revealed reduced expression of the adult β-globin gene. These results demonstrate that artificial DNA-binding proteins lacking effector domains are useful tools for studying and modulating the function of cis-regulatory DNA elements.artificial transcription factor | red cell | gene regulation

Summary Mitochondrial diseases comprise a heterogeneous group of genetically inherited disorders that cause failures in energetic and metabolic function. Boosting residual oxidative phosphorylation (OXPHOS) activity can partially correct these failures. Herein, using a high-throughput chemical screen, we identified a bromodomain inhibitor I-BET 525762A as one of the top hits that augments COX5a protein levels in complex I (CI)-mutant cybrid cells. In parallel, Bromodomain-containing protein 4 (Brd4), a target of I-BET 525762A, was identified using a genome-wide CRISPR screen to search for genes whose loss-of-function rescue death of CI-impaired cybrids grown under conditions requiring OXPHOS activity for survival. We show that I-BET525762A or loss-of-Brd4 remodeled the mitochondrial proteome to increase the levels and activity of OXPHOS protein complexes leading to rescue of the bioenergetic defects and cell death caused by mutations or chemical inhibition of CI. These studies show that Brd4 inhibition may have therapeutic implications for the treatment of mitochondrial diseases.

2Helix-loop-helix (HLH) proteins play a profound role in the process of development and cellular differentiation. Among the HLH proteins expressed in differentiating erythroid cells are the ubiquitous proteins Myc, USF1, USF2, and TFII-I, as well as the hematopoiesis-specific transcription factor Tal1/SCL. All of these HLH proteins exhibit distinct functions during the differentiation of erythroid cells. For example, Myc stimulates the proliferation of erythroid progenitor cells, while the USF proteins and Tal1 regulate genes that specify the differentiated phenotype. This minireview summarizes the known activities of Myc, USF, TFII-I, and Tal11/ SCL and discusses how they may function sequentially, cooperatively, or antagonistically in regulating expression programs during the differentiation of erythroid cells.Adult erythroid cells differentiate from hematopoietic stem cells (HSCs) through a cascade of steps (18,132). The most primitive HSC is called a long-term HSC (LT-HSC) for its ability to reconstitute HSCs in the bone marrow of irradiated mice over a long period of time. These slowly dividing cells are attached to a niche in the bone marrow and give rise to shortterm HSCs, which then differentiate into common lymphoid progenitors (CLPs) or common myeloid progenitors (CMPs). The CMPs go on to differentiate into granulocyte/monocyte precursors (GMPs) or into megakaryocyte/erythroid cell precursors (MEPs). MEPs further differentiate into erythropoietin-responsive BFU-E (blast-forming unit-erythroid) and then CFU-E (CFU-erythroid). The CFU-E cells differentiate to form orthochromatic normoblasts, then reticulocytes, and finally enucleated mature erythrocytes (125). The process of erythropoiesis has been extensively studied in vitro and in vivo and led to the identification of key erythroid cell transcription factors that regulate gene expression programs at the various steps of differentiation. The availability of erythroid cells representing different stages of maturation has rendered this system ideal for studying gene regulatory mechanisms.Transcription factors are classified based on the presence of specific protein-protein and protein-DNA interaction motifs which allow them to regulate gene expression by binding to DNA in a sequence-specific manner and to recruit coregulator complexes (98). The class of helix-loop-helix (HLH) transcription factors encompasses many proteins that play important roles during development and differentiation (89). The HLH motif is a characteristic dimerization domain which is accompanied by a basic (b) DNA-binding domain. Some HLH proteins contain an additional leucine zipper (ZIP) protein interaction module; these proteins are referred to as bHLHZIP proteins (89). Erythroid cells express many different HLH proteins. Here, we will review the well-characterized proteins USF1, USF2, Myc, TFII-I, and Tal1/SCL but will also discuss how inhibitor of DNA binding (ID) proteins, which only contain the HLH domain, may interfere with the function of HLH transcription factors in erythro...

Mitochondrial oxidative and thermogenic functions in brown and beige adipose tissues modulate rates of energy expenditure. It is unclear, however, how beige or white adipose tissue contributes to brown fat thermogenic function or compensates for partial deficiencies in this tissue and protects against obesity. Here, we show that the transcription factor Yin Yang 1 (YY1) in brown adipose tissue activates the canonical thermogenic and uncoupling gene expression program. In contrast, YY1 represses a series of secreted proteins, including fibroblast growth factor 21 (FGF21), bone morphogenetic protein 8b (BMP8b), growth differentiation factor 15 (GDF15), angiopoietin-like 6 (Angptl6), neuromedin B, and nesfatin, linked to energy expenditure. Despite substantial decreases in mitochondrial thermogenic proteins in brown fat, mice lacking YY1 in this tissue are strongly protected against diet-induced obesity and exhibit increased energy expenditure and oxygen consumption in beige and white fat depots. The increased expression of secreted proteins correlates with elevation of energy expenditure and promotion of beige and white fat activation. These results indicate that YY1 in brown adipose tissue controls antagonistic gene expression programs associated with energy balance and maintenance of body weight.T he incidence of obesity has become a global epidemic, leading to an increase in associated pathologies such as cardiovascular disease, type 2 diabetes, and cancer (1). Obesity is the result of a net imbalance between the energy intake and the energy expenditure (2). An important component of energy expenditure is adaptive thermogenesis caused by the heat dissipated in response to lower temperatures or diet and produced in the mitochondria of brown adipose tissue (BAT) and skeletal muscle. In BAT, this thermogenic process is largely dependent on inducible mitochondrial uncoupling respiration mediated by uncoupling protein 1 (UCP1) (3, 4). In addition to brown adipocytes, the presence of clusters of inducible thermogenic adipocytes within subcutaneous white fat depots, referred to as browning, has been proposed as an additional or compensatory site of energy dissipation and body weight control (5-7). Although these adipocytes, named "beige" (or "brite"), are derived from a different developmental lineage than BAT, they express UCP1 and similar thermogenic components (5, 8, 9). Moreover, under some conditions, white adipocytes activate thermogenic processes that contribute to energy expenditure (6, 10). In humans, the presence of these inducible thermogenic adipocytes opens the possibility to identify targets to therapeutically treat obesity. Toward this goal, it is necessary to identify the molecular and cellular mechanisms governing beige or white adipocyte thermogenesis that, despite recent advances (11-15), are currently not completely understood.At the transcriptional level, activation of the canonical thermogenic program in BAT (often in response to adrenergic agonism) (16), involves inducible coactivation of peroxi...

Mitochondrial mutations cause bioenergetic defects associated with failures to use the electron transfer chain and oxidize substrates. These defects are exacerbated under energetic stress conditions and ultimately cause cell deterioration and death. However, little is known about cellular strategies that rescue mitochondrial stress failures and maintain cell survival under these conditions. Here, we have designed and performed a high-throughput chemical screen to identify small molecules that rescue human mitochondrial complex I mutations from energetic stress-induced cell death. The top positive hits were a series of sulfonylureas that efficiently maintain prolonged cell survival and growth under energetic stress conditions. The addition of galactose instead of glucose, to experimentally force mitochondrial respiration, triggered an initial ER stress response that was associated with IRE1α-dependent inflammatory signals including JNK and p38 MAP kinases in mutant cells. Sulfonylureas, similar to inhibition of IRE1α and p38 MAP kinase, potently blocked this ER stress inflammatory and cell death pathway and maintained viability and cell growth under severe energetic stress conditions. These studies reveal that sulfonylureas and specific inhibition of the IRE1α inflammatory pathway protect against cell death and can be used to rescue bioenergetic failures in mitochondrial complex I-mutated cells under stress conditions.

Genome editing and alteration of gene expression by synthetic DNA binding activities gained a lot of momentum over the last decade. This is due to the development of new DNA binding molecules with enhanced binding specificity. The most commonly used DNA binding modules are zinc fingers (ZFs), TALE-domains, and the RNA component of the CRISPR/Cas9 system. These binding modules are fused or linked to either nucleases that cut the DNA and induce DNA repair processes, or to protein domains that activate or repress transcription of genes close to the targeted site in the genome. This review focuses on the structure, design, and applications of ZF DNA binding domains (ZFDBDs). ZFDBDs are relatively small and have been shown to penetrate the cell membrane without additional tags suggesting that they could be delivered to cells without a DNA or RNA intermediate. Advanced algorithms that are based on extensive knowledge of the mode of ZF/DNA interactions are used to design the amino acid composition of ZFDBDs so that they bind to unique sites in the genome. Off-target binding has been a concern for all synthetic DNA binding molecules. Thus, increasing the specificity and affinity of ZFDBDs will have a significant impact on their use in analytical or therapeutic settings.

Developmental stage-specific expression of the β-type globin genes is regulated by many cis- and trans-acting components. The adult β-globin gene contains an E-box located 60 bp downstream of the transcription start site that has been shown to bind transcription factor upstream stimulatory factor (USF) and to contribute to efficient in vitro transcription. We expressed an artificial zinc finger DNA-binding domain (ZF-DBD) targeting this site (+60 ZF-DBD) in murine erythroleukemia cells. Expression of the +60 ZF-DBD reduced the recruitment and elongation of RNA polymerase II (Pol II) at the adult β-globin gene and at the same time increased the binding of Pol II at locus control region (LCR) element HS2, suggesting that Pol II is transferred from the LCR to the globin gene promoters. Expression of the +60 ZF-DBD also reduced the frequency of interactions between the LCR and the adult β-globin promoter. ChIP-exonuclease-sequencing revealed that the +60ZF-DBD was targeted to the adult β-globin downstream promoter and that the binding of the ZF-DBD caused alterations in the association of USF2 containing protein complexes. The data demonstrate that targeting a ZF-DBD to the adult β-globin downstream promoter region interferes with the LCR-mediated recruitment and activity of Pol II.

Zinc finger proteins are the most common among families of DNA-binding transcription factors. Designer transcription factors generated by the fusion of engineered zinc finger DNA-binding domains (ZF-DBDs) to effector domains have been valuable tools for the modulation of gene expression and for targeted genome editing. However, ZF-DBDs without effector domains have also been shown to effectively modulate gene expression by competing with sequence-specific DNA-binding transcription factors. Here, we describe the methodology and provide a detailed workflow for the cloning, expression, purification, and direct cell delivery of engineered ZF-DBDs. Using this protocol, ZF-DBDs can be generated with high efficiency in less than 2 weeks. We also describe a nonradioactive method for measuring DNA binding affinity of the purified ZF-DBD proteins as well as a method for direct delivery of the purified ZF-DBDs to mammalian cells.