Gene Regulatory Mechanisms

The chromatin remodeling protein BRM regulates the transcription of tight junction proteins: Implication in breast cancer metastasis Publication date: May 2019 Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1862, Issue 5 Author(s): Yuyu Yang, Li Liu, Mingming Fang, Hui Bai, Yong Xu Abstract Claudins are a group of cell tight junction proteins that play versatile roles in cancer biology. Recent studies have correlated down-regulation of Claudins with augmented breast cancer malignancy and poor prognosis. The mechanism underlying repression of Claudin transcription in breast cancer cells is not well understood. Here we report that expression levels of Brahma (BRM) were down-regulated in triple negative breast cancer cells (MDA-231) compared to the less malignant MCF-7 cells and in high-grade human breast cancer specimens compared to low-grade ones. TGF-β treatment in MCF-7 cells repressed BRM transcription likely through targeting C/EBPβ. BRM over-expression suppressed whereas BRM knockdown promoted TGF-β induced migration and invasion of MCF-7 cells. BRM down-regulation was accompanied by the loss of a panel of Claudins in breast cancer cells. BRM directly bound to the promoter region of Claudin genes via interacting with Sp1 and activated transcription by modulating histone modifications. Together, our data have identified a novel epigenetic pathway that links Claudin transcription to breast cancer metastasis.

Inhibition of lysine-specific demethylase LSD1 induces senescence in Glioblastoma cells through a HIF-1α-dependent pathway Publication date: May 2019 Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1862, Issue 5 Author(s): Carmen D. Saccà, Francesca Gorini, Susanna Ambrosio, Stefano Amente, Deriggio Faicchia, Giuseppe Matarese, Luigi Lania, Barbara Majello Abstract Senescence is a stress-responsive cellular program that leads to cell cycle arrest. In cancer cells, senescence has profound implications for tumor aggressiveness and clinical outcome, but the molecular events that provoke cancer cells to undergo senescence remain unclear. Herein, we provide evidence that the histone demethylase LSD1/KDM1A supports the growth of Glioblastoma tumor cells and its inhibition triggers senescence response. LSD1 is a histone modifier that participates in key aspects of gene transcription as well as in the regulation of methylation dynamics of non-histone proteins. We found that down-regulation of LSD1 inhibits Glioblastoma cell growth, impairs mTOR pathway and cell migration and induces senescence. At mechanistic level, we found that LSD1 regulates HIF-1α protein stability. Pharmacological inhibition or siRNA-mediated silencing of LSD1 expression effectively reduces HIF-1α protein levels, which suffices for the induction of senescence. Our findings elucidate a mechanism whereby LSD1 controls senescence in Glioblastoma tumor cells through the regulation of HIF-1α, and we propose the novel defined LSD1/HIF-1α axis as a new target for the therapy of Glioblastoma tumors.

Zbtb7c is a critical gluconeogenic transcription factor that induces glucose-6-phosphatase and phosphoenylpyruvate carboxykinase 1 genes expression during mice fasting Publication date: Available online 5 April 2019 Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms Author(s): Won-Il Choi, Jae-Hyeon Yoon, Ji-Yang Song, Bu-Nam Jeon, Joo-Man Park, Dong-In Koh, Yong-ho Ahn, Kyung-Sup Kim, In-Kyu Lee, Man-Wook Hur Abstract Gluconeogenesis is essential for blood glucose homeostasis during fasting and is regulated by various enzymes, which are encoded by gluconeogenic genes. Those genes are controlled by various transcription factors. Zinc finger and BTB domain–containing 7c (Zbtb7c, also called Kr-pok) is a BTB-POZ family transcription factor with proto-oncogenic activity. Previous findings have indicated that Zbtb7c is involved in the regulation of fatty acid biosynthesis, suggesting an involvement also in primary metabolism. We found here that fasting induced Zbtb7c expression in the mouse liver and in primary liver hepatocytes. We also observed that Zbtb7c-knockout mice have decreased blood glucose levels, so we investigated whether Zbtb7c plays a role in gluconeogenesis. Indeed, differential gene expression analysis of Zbtb7c-knockout versus wild type mouse livers showed downregulated transcription of gluconeogenic genes encoding the glucose 6-phosphatase catalytic subunit (G6pc) and phosphoenolpyruvate carboxykinase 1 (Pck1), while Zbtb7c expression upregulated these two genes, under fasting conditions. Mechanistically, we found that when complexed with histone deacetylase 3 (Hdac3), Zbtb7c binds insulin response elements (IREs) within the G6pc and Pck1 promoters. Moreover, complexed Zbtb7c deacetylated forkhead box O1 (Foxo1), thereby increasing Foxo1 binding to the G6pc and Pck1 IREs, resulting in their transcriptional activation. These results demonstrate Zbtb7c to be a crucial metabolic regulator of blood glucose homeostasis, during mammalian fasting.

IsomiRs: Expanding the miRNA repression toolbox beyond the seed Publication date: Available online 4 April 2019 Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms Author(s): Xavier Bofill-De Ros, Acong Yang, Shuo Gu Abstract MicroRNAs (miRNAs) are a class of small non-coding RNAs that play increasingly appreciated roles in gene regulation. In animals, miRNAs silence gene expression by binding to partially complementary sequences within target mRNAs. It is well-established that miRNAs recognize canonical target sites by base-pairing in the 5′region. However, the development of biochemical methods has identified many novel, non-canonical target sites, suggesting additional modes of miRNA-target association. Here, we review the current knowledge of miRNA-target recognition and how new evidence supports or challenges existing models. We also review the process by which microRNA isoforms achieve functional diversification via modulation of target recognition.

Adaptor proteins in long noncoding RNA biology Publication date: Available online 2 April 2019 Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms Author(s): Emily Dangelmaier, Ashish Lal Abstract Long noncoding RNAs (lncRNAs) are a heterogeneous class of noncoding RNAs that have gained increasing attention due to their vital roles in the regulation of diverse cellular processes. Because lncRNAs are generally expressed at low levels, are poorly conserved, and can act via diverse mechanisms, investigating the molecular mechanisms by which lncRNAs act is challenging. Similar to mRNAs, lncRNAs bind to RNA-binding proteins (RBPs) and in some cases, have been shown to regulate the activity of the RBP they bind to. Furthermore, recent studies have shown that some lncRNAs directly bind to a specific RBP that, in turn, forms a complex with other proteins that mediate the effects of the lncRNA. We termed such RBPs as adaptor proteins because they function as adaptors to recruit other proteins that indirectly associate with the lncRNA. Here, we discuss the emerging roles of adaptor proteins in lncRNA function and propose mechanistic scenarios and strategies to identify adaptor proteins that could play vital roles in the biology of a lncRNA. This article is part of a Special Issue entitled: ncRNA in control of gene expression edited by Kotb Abdelmohsen.

A non-autonomous role of MKL1 in the activation of hepatic stellate cells Publication date: Available online 2 April 2019 Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms Author(s): Zilong Li, Ping Li, Yunjie Lu, Dongli Sun, Xiaoying Zhang, Yong Xu Abstract Although hepatic stellate cells (HSC) represent the major source of fibrogenesis in the liver under various pathological conditions, other cell types including hepatic parenchymal cells (hepatocytes) also contribute to HSC activation and hence liver fibrosis. The underlying mechanism, however, is poorly defined. Here we report that hepatocytes exposed to high concentrations of glucose (HG) emit a pro-fibrogenic cue as evidenced by the observation that primary HSCs cultured in conditioned media (CM) collected from hepatocytes exposed to HG up-regulated the production of extracellular matrix (ECM) proteins compared to CM collected from hepatocytes exposed to low glucose. We further identified the pro-fibrogenic cue from hepatocytes to be connective tissue growth factor (CTGF) because either depletion of endogenous CTGF in hepatocytes with siRNA or the addition of a CTGF-specific neutralizing antibody to the CM blunted the pro-fibrogenic effect elicit by HG treatment. Of interest, we discovered that genetic ablation or pharmaceutical inhibition of the transcriptional modulator MKL1 in hepatocytes also abrogated the HG-induced pro-fibrogenic effects. Mechanistically, MKL1 interacted with AP-1 and SMAD3 to trans-activate CTGF in response to HG treatment. In conclusion, our data suggest that MKL1 contribute to HSC activation in a non-autonomous fashion by promoting CTGF transcription in hepatocytes.

Dicer1 is required for pigment cell and craniofacial development in zebrafish Publication date: April 2019 Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1862, Issue 4 Author(s): Andrea M.J. Weiner, Nadia L. Scampoli, Tomás J. Steeman, Christopher M. Dooley, Elisabeth M. Busch-Nentwich, Robert N. Kelsh, Nora B. Calcaterra Abstract The multidomain RNase III endoribonuclease DICER is required for the generation of most functional microRNAs (miRNAs). Loss of Dicer affects developmental processes at different levels. Here, we characterized the zebrafish Dicer1 mutant, dicer1sa9205, which has a single point mutation induced by N-ethyl-N-nitrosourea mutagenesis. Heterozygous dicer1sa9205 developed normally, being phenotypically indistinguishable from wild-type siblings. Homozygous dicer1sa9205 mutants display smaller eyes, abnormal craniofacial development and aberrant pigmentation. Reduced numbers of both iridophores and melanocytes were observed in the head and ventral trunk of dicer1sa9205 homozygotes; the effect on melanocytes was stronger and detectable earlier in development. The expression of microphthalmia-associated transcription factor a (mitfa), the master gene for melanocytes differentiation, was enhanced in dicer1-depleted fish. Similarly, the expression of SRY-box containing gene 10 (sox10), required for mitfa activation, was higher in mutants than in wild types. In silico and in vivoanalyses of either sox10 or mitfa 3'UTRs revealed conserved potential miRNA binding sites likely involved in the post-transcriptional regulation of both genes. Based on these findings, we propose that dicer1 participates in the gene regulatory network governing zebrafish melanocyte differentiation by controlling the expression of mitfa and sox10.

Dose dependent gene expression is dynamically modulated by the history, physiology and age of yeast cells Publication date: April 2019 Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1862, Issue 4 Author(s): Amparo Pascual-Ahuir, Eva González-Cantó, Pauline Juyoux, Julia Pable, Daniel Poveda-Huertes, Sandra Saiz-Balbastre, Sonia Squeo, Alvaro Ureña-Marco, Elena Vanacloig-Pedros, Laura Zaragoza-Infante, Markus Proft Abstract Cells respond to external stimuli with transient gene expression changes in order to adapt to environmental alterations. However, the dose response profile of gene induction upon a given stress depends on many intrinsic and extrinsic factors. Here we show that the accurate quantification of dose dependent gene expression by live cell luciferase reporters reveals fundamental insights into stress signaling. We make the following discoveries applying this non-invasive reporter technology. (1) Signal transduction sensitivities can be compared and we apply this here to salt, oxidative and xenobiotic stress responsive transcription factors. (2) Stress signaling depends on where and how the damage is generated within the cell. Specifically we show that two ROS-generating agents, menadione and hydrogen peroxide, differ in their dependence on mitochondrial respiration. (3) Stress signaling is conditioned by the cells history. We demonstrate here that positive memory or an acquired resistance towards oxidative stress is induced dependent on the nature of the previous stress experience. (4) The metabolic state of the cell impinges on the sensitivity of stress signaling. This is shown here for the shift towards higher stress doses of the response profile for yeast cells moved from complex to synthetic medium. (5) The age of the cell conditions its transcriptional response capacity, which is demonstrated by the changes of the dose response to oxidative stress during both replicative and chronological aging. We conclude that capturing dose dependent gene expression in real time will be of invaluable help to understand stress signaling and its dynamic modulation.

The nuclear receptors PXR and LXR are regulators of the scaffold protein PDZK1 Publication date: April 2019 Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1862, Issue 4 Author(s): Celio Ferreira, Ramona Meyer, Henriette E. Meyer zu Schwabedissen Abstract PDZK1 (NHERF3) interacts with membrane proteins whereby modulating their spatial arrangement, membrane stability, and function. One of the membrane proteins shown to be stabilized by interaction with PDZK1 is the HDL-receptor SR-BI (SCARB1). Testing the influence of TO 901317, a known activator of liver X receptor alpha (LXRα, NR1H3) which is a central regulator of the lipid homeostasis, Grefhorst et al. reported in 2012 that administration of TO 901317 did not affect PDZK1 expression and reduced the amount of SR-BI protein in mouse liver. Considering that TO 901317 also activates the xenosensor pregnane X receptor (PXR, NR1I2), it was aim of this study to further investigate the influence of LXRα and PXR activation on transcription of PDZK1. First, we tested the transactivation of PDZK1 by LXRα or PXR in cell-based reporter gene assays comparing the effect of prototypical ligands to that of TO 901317. Ligand mediated activation of LXRα increased, while that of PXR lowered luciferase activity. Further, we located the most likely binding site for LXRα and PXR on the PDZK1 promoter between −85 bp and −54 bp. The transcriptional regulation by LXRα was further supported showing enhanced mRNA expression of PDZK1 in HepG2 cells treated with the selective LXRα-agonist GW3965, while treatment with TO 901317 reduced the protein amount of PDZK1. Taken together, we provide evidence that both LXRα and PXR are transcriptional regulators of PDZK1 supporting the previous notion that the scaffold protein is part of cholesterol homeostasis and drug metabolism.

Editorial Board Publication date: April 2019 Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1862, Issue 4 Author(s):