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Changes in chromatin structure regulate gene expression and genome maintenance. Molecules that bind to the nucleosome, the complex of DNA and histone proteins, are key modulators of chromatin structure. Previous work indicated that cholesterol, a ubiquitous cellular lipid, may bind to chromatin in vivo, suggesting a potential function for lipids in modulating chromatin architecture. However, the molecular mechanisms of cholesterol's action on chromatin structure have remained unclear. Here, we explored the biophysical impact of cholesterol on nucleosome and chromatin fibers reconstituted in vitro and characterized in silico the cholesterol binding to the nucleosome. Our findings support that cholesterol assists 10 and 30 nm chromatin formation and induces folding of long chromatin fibers as a result of direct interaction of the cholesterol to six nucleosomal binding sites.

Constant changes in the structure of chromatin regulate gene expression. Molecules that bind to the nucleosome, the complex of DNA and histone proteins, are key modulators of chromatin structure. Conceptually, the nucleosome was first identified as a therapeutic target 14 years ago, when small molecules started to be elegantly designed for nucleosomal DNA binding. Concomitantly, emergent drugs that target enzymes that affect chromatin structure have been developed to a treat myriad of diseases, such as cancer. Here, we discuss the development of more complex molecules, such as peptides and peptidomimetics, to directly target the nucleosome surface to modulate chromatin structure. This new strategy presents great challenges that need to be overcome to develop the exogenous nucleosome-binding molecules (eNBMs) as therapeutic agents.

Our lives changed tracks the day our daughter was born. My wife and I felt settled in the United Kingdom—we'd even bought a house 6 months earlier—but the arrival of our daughter forced a moment of reflection. We wondered whether we should move back to our native Brazil. I remember looking down at our newborn baby and thinking about how different her life would be there. In our native country, we'd be closer to our family and culture. But in the United Kingdom, I had the funding and lab resources I needed for my costly and highly specialized research program. Would such a move sink my career? > “I had been away from my extended family and my culture for too long.” We had left Brazil 10 years earlier so that I could spend the last year of my Ph.D. program in France. Meanwhile, my wife started a Ph.D. in the United Kingdom. We maintained a long-distance relationship for the first few years. But by the time our daughter was born, we'd settled down in the same location; I had a research assistant position and my wife had a postdoc. I was in an amazing scientific environment, working next to Nobel laureates. But I had been away from my extended family and my culture for too long. I missed acai, acaraje, pao de queijo, samba, bossa nova, capoeira, Brazilian jujitsu, and sunny skies. I worried that I might never return to Brazil. My wife missed our homeland as well. As a mathematician, it was also easier for her to imagine doing her work in Brazil; unlike me, she didn't need fancy lab equipment and expensive reagents. So with a newborn baby at home, we started to ask ourselves whether a move was in order. Several events over the next few months nudged us further in the same direction. We heard that new professor positions had opened up at a university in our hometown, in departments that matched both of our research programs. Then, a few weeks later, I received a call in the wee hours of the morning from my brother, who told me that our father had passed away. The great happiness I had felt about my daughter's birth suddenly gave way to a deep sadness. I felt that I was losing precious time with my loved ones. After that, we had no doubt it was the right time to return to Brazil. We applied for the professorships and both received offers. It felt like our personal and professional lives were falling into place. It wasn't easy getting started with my research in Brazil, however. I didn't receive any startup funding for my lab, so I couldn't recruit grad students or hire postdocs. I was able to perform a few experiments myself thanks to reagents I had brought with me from my lab in the United Kingdom, as well as equipment I shared with other professors. Eventually, I secured Brazilian funding, which allowed me to form a team of bright undergraduate and graduate students and buy reagents and lab equipment on my own. Nine years later, I still haven't been able to perform the kind of experiments that U.K. funding would have allowed. And the antiscience views of the current Brazilian government have added to my worries about my squeezed budget. But looking back, I'm happy that my wife and I put our personal well-being first and made the decision to move back to our home country. We've been able to have big meals with our extended family on weekends. We had a second child, and our kids are growing up close to their cousins who are around the same age. And I was able to resume Brazilian jujitsu training, which I hadn't been able to do during my years abroad. We are living the lives we wanted to live—working on rewarding research while staying true to what we feel is best for ourselves and for our family. Any scientist from a developing country who is considering a move home has to weigh the pros and cons, and the situation will be different for everyone. But for us, returning home was worth the costs.

Chromatin is the major regulator of gene expression and genome maintenance. Proteins that bind the nucleosome, the repetitive unit of chromatin, and the histone H4 tail are critical to establishing chromatin architecture and phenotypic outcomes. Intriguingly, nucleosome-binding proteins (NBPs) and the H4 tail peptide compete for the same binding site at an acidic region on the nucleosome surface. Although the essential facts about the nucleosome were revealed 17 years ago, new insights into its atomic structure and molecular mechanisms are still emerging. Several complex nucleosome:NBP structures were recently revealed, characterizing the NBP-binding sites on the nucleosome surface. Here we discuss the potential of the nucleosome surface as a therapeutic target and the impact and development of exogenous nucleosome-binding molecules (eNBMs).

Structural changes in chromatin regulate gene expression and define phenotypic outcomes. Molecules that bind to the nucleosome, the complex of DNA and histone proteins, are key modulators of chromatin structure. Most recently, the formation of condensed chromatin regions based on phase-separation in the cell, a basic physical mechanism, was proposed. Increased understanding of the mechanisms of interaction between chromatin and lipids suggest that small lipid molecules, such as cholesterol and short-chain fatty acids, can regulate important nuclear functions. New biophysical data has suggested that cholesterol interacts with nucleosome through multiple binding sites and affects chromatin structure in vitro. Regardless of the mechanism of how lipids bind to chromatin, there is currently little awareness that lipids may be stored in chromatin and influence its state. Focusing on lipids that bind to nuclear receptors, clinically relevant transcription factors, we discuss the potential interactions of the nucleosome with steroid hormones, bile acids and fatty acids, which suggest that other lipid chemotypes may also impact chromatin structure through binding to common sites on the nucleosome. Herein, we review the main impacts of lipids on the nuclear environment, emphasizing its role on chromatin architecture. We postulate that lipids that bind to nucleosomes and affect chromatin states are likely to be worth investigating as tools to modify disease phenotypes at a molecular level.

Nuclear receptors are arguably the best understood transcriptional regulators. We know a great deal about the mechanisms through which they activate transcription in response to ligand binding and about the mechanisms through which they repress transcription in the absence of ligand. However, endocrine regulation often requires that ligand-bound receptors repress transcription of a subset of genes. An understanding of the mechanism for ligand-induced repression and how this differs from activation has proven elusive. A number of recent studies have directly or indirectly addressed this problem. Yet it seems the more evidence that accumulates, the more complex the mystery becomes.

Chronic kidney disease is characterized by multiple abnormalities in the thyroid hormone physiology. In the present review, we will briefly discuss the effects of uremia on thyroid hormone synthesis, metabolism, transport, and action.Uremic toxins have been shown to interfere at various levels of the thyroid hormone action, including thyroid hormone transport across plasma membrane and thyroid hormone receptor activity. These abnormalities could explain the resistance to thyroid hormone action in uremia, at least in some tissues.The pathogenesis of thyroid axis abnormalities in uremia is incompletely understood, and its clinical significance remains unclear. The increasing prevalence of chronic kidney disease underscores the need for further efforts to understand the metabolic consequences of uremia and address questions such as the impact of thyroid hormone therapy.

Endoplasmic reticulum (ER) stress triggers the integrated ER‐stress response (IERSR) that ensures cellular survival of ER stress and represents a primordial form of innate immunity. We investigated the role of IERSR during Leishmania amazonensis infection. Treatment of RAW 264.7 infected macrophages with the ER stress‐inducing agent thapsigargin (TG; 1 μM) increased L. amazonensis infectivity in an IFN1‐α receptor (IFNAR)‐dependent manner. In Western blot assays, we showed that L. amazonensis activates the inositol‐requiring enzyme (IRE1)/ X‐box binding protein (XBP)‐1‐splicing arms of the IERSR in host cells. In chromatin immunoprecipitation (ChIP) assays, we showed an increased occupancy of enhancer and promoter sequences for the Ifnb gene by XBP1 in infected RAW 264.7 cells. Knocking down XBP1 expression by transducing RAW 264.7 cells with the short hairpin XBP1 lentiviral vector significantly reduced the parasite proliferation associated with impaired translocation of phosphorylated IFN regulatory transcription factor (IRF)‐3 to the nucleus and a decrease in IFN1‐β expression. Knocking down XBP1 expression also increased NO concentration, as determined by Griess reaction and reduced the expression of antioxidant genes, such as heme oxygenase (HO)‐1, that protect parasites from oxidative stress. We conclude that L. amazonensis activation of XBP1 plays a critical role in infection by protecting the parasites from oxidative stress and increasing IFN1‐β expression.—Dias‐Teixeira, K. L., Calegari‐Silva, T. C., Dos Santos, G. R. R. M., Vitorino dos Santos, J., Lima, C., Medina, J. M., Aktas, B. H., Lopes, U. G. The integrated endoplasmic reticulum stress response in Leishmania amazonensis macrophage infection: the role of X‐box binding protein 1 transcription factor. FASEB J. 30, 1557–1565 (2016). http://www.fasebj.org

The role of thyroid hormone [L-3,5,3'-triiodothyronine (T3)] and the thyroid hormone receptor (TR) in regulating growth, development, and metabolic homeostasis is well established. It is also emerging that T3 is associated with oxidative stress through the regulation of the activity of superoxide dismutase-1 (SOD-1), a key enzyme in the metabolism of oxygen free radicals. We found that T3 reverses the activation of the SOD-1 promoter caused by the free radical generators paraquat and phorbol 12-myristate 13-acetate through the direct repression of the SOD-1 promoter by liganded TR. Conversely, the SOD-1 promoter is significantly stimulated by unliganded TRs. This regulation requires the DNA-binding domain of the TR, which is recruited to an inhibitory element between -157 and +17 of the SOD-1 promoter. TR mutations, which abolish recruitment of coactivator proteins, block repression of the SOD-1 promoter. Conversely, a mutation that inhibits corepressor binding to the TR prevents activation. Together, our findings suggest a mechanism of negative regulation in which TR binds to the SOD-1 promoter but coactivator and corepressor binding surfaces have an inverted function. This effect may be important in T3 induction of oxidative stress in thyroid hormone excess.

Background Recruiting thermogenic adipocytes in white adipose tissue represents a potential therapeutic strategy for obesity. Interestingly, PPARγ, a major regulator of lipogenesis, is also a key factor in inducing thermogenic genes in adipose tissue. Scope of the review We summarize some of the recent findings regarding the biology of beige adipocytes and their potential significance for metabolic health. We also discuss the role of PPARγ in development of beige adipocyte phenotype and in inducing two apparently divergent processes, namely, lipogenesis and thermogenesis. Major conclusions PPARγ post-translation modifications and differential coregulator recruitment may be key factors in defining adipocyte commitment with lipogenesis or thermogenesis. General significance Dissecting the mechanisms underlying its thermogenic effects may prompt the development of a new generation of PPARγ-based therapies.

Histone deacetylase enzymes (HDACs) are emerging cancer drug targets. They regulate gene expression by removing acetyl groups from lysine residues in histone tails, resulting in chromatin condensation. The enzymatic activity of most class I HDACs requires recruitment into multi-subunit co-repressor complexes, which are in turn recruited to chromatin by repressive transcription factors. Here we report the structure of a complex between an HDAC and a co-repressor, namely, human HDAC3 with the deacetylase activation domain (DAD) from the human SMRT co-repressor (also known as NCOR2). The structure reveals two remarkable features. First, the SMRT-DAD undergoes a large structural rearrangement on forming the complex. Second, there is an essential inositol tetraphosphate molecule--D-myo-inositol-(1,4,5,6)-tetrakisphosphate (Ins(1,4,5,6)P(4))--acting as an 'intermolecular glue' between the two proteins. Assembly of the complex is clearly dependent on the Ins(1,4,5,6)P(4), which may act as a regulator--potentially explaining why inositol phosphates and their kinases have been found to act as transcriptional regulators. This mechanism for the activation of HDAC3 appears to be conserved in class I HDACs from yeast to humans, and opens the way to novel therapeutic opportunities.

SummaryATRX is an X-linked gene of the SWI/SNF family, mutations in which cause syndromal mental retardation and downregulation of α-globin expression. Here we show that ATRX binds to tandem repeat (TR) sequences in both telomeres and euchromatin. Genes associated with these TRs can be dysregulated when ATRX is mutated, and the change in expression is determined by the size of the TR, producing skewed allelic expression. This reveals the characteristics of the affected genes, explains the variable phenotypes seen with identical ATRX mutations, and illustrates a new mechanism underlying variable penetrance. Many of the TRs are G rich and predicted to form non-B DNA structures (including G-quadruplex) in vivo. We show that ATRX binds G-quadruplex structures in vitro, suggesting a mechanism by which ATRX may play a role in various nuclear processes and how this is perturbed when ATRX is mutated.PaperClip

Overexpression of Cu/Zn superoxide dismutase 1 (SOD1) in monocytes blocks reactive oxygen species-induced inhibition of cell growth and apoptosis and renders cells resistant to the toxic effect of tumor necrosis factor (TNF)-alpha, suggesting that TNF-alpha represses the SOD1 gene in these cells. We herein show that TNF-alpha decreases SOD1 mRNA, protein, and promoter activity in U937 cells. Electrophoretic mobility-shift assays (EMSA) show that TNF-alpha decreased binding of three different complexes. Ectopic Sp1 overexpression markedly increased SOD1-basal promoter activity and partially antagonized the TNF-alpha inhibitory effect. In contrast, ectopic c-Jun overexpression mimics TNF-alpha inhibitory effects and antagonizes Sp1 stimulatory effects. In agreement with these findings, EMSA shows a TNF-alpha-induced increase in AP-1 and a decrease in Sp1 DNA binding. Disruption of the C/EBP site decreases, whereas mutation in the Sp1/Egr-1 site completely abolishes DNA-binding and promoter activity. A JNK inhibitor antagonized the negative effects of TNF-alpha on SOD1 promoter activity, suggesting that JNK signaling through c-Jun protein activation is critical for the TNF-alpha-dependent SOD1 repression. A greater understanding of the mechanisms of TNF-alpha-induced SOD1 repression could facilitate the design and development of novel therapeutic drugs for inflammatory conditions.

To now, there are no studies reporting whether thyroid hormones (THs) transport play a role in thyroid hormone dysfunction observed in chronic renal failure (CRF). Therefore, the aim of this study was to investigate the transport of THs in erythrocytes from patients with CRF on hemodialysis (HD).[125I]-L-triiodothyronine ([125I]T3) and [125I]-L-thyroxine ([125I]T4) erythrocytes uptake was measured at 1 min and 5 min. To study L-triiodothyronine (LT3) and L-thyroxine (LT4) efflux from erythrocytes, we preloaded the cells during 180 min with [125I]T3 or [125I]T4 and measured their [125I]T3 or [125I]T4 efflux during 60 min.[125I]T3 uptake in erythrocytes from uremic patients pre-HD was higher than control subjects by 50% at 1 min and by 55% at 5 min. However, [125I]T4 uptake in erythrocytes from uremic patients was significantly lower at 1min (88%) and at 5 min (63%). LT3 efflux rate was lower and LT4 efflux was significantly higher than in control subjects. After 60-min of efflux, LT3 remained in erythrocytes was 80% higher and LT4 was 57% lower than in normal individuals. Neither [125I]T3 and [125I]T4 uptake, nor efflux rates were changed by hemodialysis.Despite the fact that uremic patients on hemodialysis show low serum levels of LT3, changes in LT3 influx and efflux could act as a compensatory mechanism that neutralize thyroid hormone dysfunction in order to maintain the euthyroid state.

Background: Much is known about how genes regulated by nuclear receptors (NRs) are switched on in the presence of a ligand. However, the molecular mechanism for gene down-regulation by liganded NRs remains a conundrum. The interaction between two zinc-finger transcription factors, Nuclear Receptor and GATA, was described almost a decade ago as a strategy adopted by the cell to up- or down-regulate gene expression. More recently, cell-based assays have shown that the Zn-finger region of GATA2 (GATA2-Zf) has an important role in down-regulation of the thyrotropin gene (TSHb )b y liganded thyroid hormone receptor (TR). Methodology/Principal Findings: In an effort to better understand the mechanism that drives TSHb down-regulation by a liganded TR and GATA2, we have carried out equilibrium binding assays using fluorescence anisotropy to study the interaction of recombinant TR and GATA2-Zf with regulatory elements present in the TSHb promoter. Surprisingly, we observed that ligand (T3) weakens TR binding to a negative regulatory element (NRE) present in the TSHb promoter. We also show that TR may interact with GATA2-Zf in the absence of ligand, but T3 is crucial for increasing the affinity of this complex for different GATA response elements (GATA-REs). Importantly, these results indicate that TR complex formation enhances DNA binding of the TR-GATA2 in a ligand-dependent manner. Conclusions: Our findings extend previous results obtained in vivo, further improving our understanding of how liganded nuclear receptors down-regulate gene transcription, with the cooperative binding of transcription factors to DNA forming the core of this process.

There is a substantial clinical overlap between chronic renal failure (CRF) and hypothyroidism, suggesting the presence of hypothyroidism in uremic patients. Although CRF patients have low T3 and T4 levels with normal thyroid-stimulating hormone (TSH), they show a higher prevalence of goiter and evidence for blunted tissue responsiveness to T3 action. However, there are no studies examining whether thyroid hormone receptors (TRs) play a role in thyroid hormone dysfunction in CRF patients. To evaluate the effects of an uremic environment on TR function, we investigated the effect of uremic plasma on TRβ1 binding to DNA as heterodimers with the retinoid X receptor alpha (RXRα) and on T3-dependent transcriptional activity. We demonstrated that uremic plasma collected prior to hemodialysis (Pre-HD) significantly reduced TRβ1-RXRα binding to DNA. Such inhibition was also observed with a vitamin D receptor (VDR) but not with a peroxisome proliferator-activated receptor gamma (PPARγ). A cell-based assay confirmed this effect where uremic pre-HD ultrafiltrate inhibited the transcriptional activation induced by T3 in U937 cells. In both cases, the inhibitory effects were reversed when the uremic plasma and the uremic ultrafiltrate were collected and used after hemodialysis (Post-HD). These results suggest that dialyzable toxins in uremic plasma selectively block the binding of TRβ1-RXRα to DNA and impair T3 transcriptional activity. These findings may explain some features of hypothyroidism and thyroid hormone resistance observed in CRF patients.