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The CCAAT box in the proximal SERCA2 gene promoter regulates basal and stress-induced transcription in cardiomyocytes
Jorge Fragoso-Medina et. al.
The cardiac sarco/endoplasmic reticulum Ca2+-ATPase-2a (SERCA2a) is vital for the correct handling of calcium concentration in cardiomyocytes. Recent studies showed that the induction of endoplasmic reticulum (ER) stress (ERS) with the SERCA2 inhibitor Thapsigargin (Tg) increases the mRNA and protein levels of SERCA... |
Coordinated Transcriptional Control of Adipocyte Triglyceride Lipase (Atgl) by transcription factors Sp1 and PPARγ during Adipocyte Differentiation
Debasish Roy, Kenneth T. Farabaugh, Jing Wu, Alyssa Charrier, Cynthia Smas, Maria Hatzoglou*, Kavitha Thirumurugan and David A. Buchner
The breakdown of stored fat deposits into its components is a highly regulated process that maintains plasma levels of free fatty acids to supply energy to cells. Insulin-mediated transcription of Atgl, the enzyme that mediates the rate-limiting step in lipolysis, is a key point of this regulation. In conditions suc... |
Novel Molecular Mechanism of Regulation of CD40 Ligand by the Transcription Factor GLI2
Weiguo Han, David A. Jackson, Stephan J. Matissek, Jason A. Misurelli, Matthew S. Neil, Brandon Sklavanitis, Nansalmaa Amarsaikhan and Sherine F. Elsawa
The interaction between tumor cells and their surrounding microenvironment is essential for the growth and persistence of cancer cells. This interaction is mediated, in part, by cytokines. Although the role of cytokines in normal and malignant cell biology is well established, many of the molecular mechanisms regula... |
Foxa2, a novel protein partner of tumour suppressor menin, is deregulated in mouse and human MEN1 glucagonomas
Rémy Bonnavion, Romain Teinturier, Samuele Gherardi, Emmanuelle Leteurtre, Run Yu, Martine Cordier-Bussat, Rui Du, François Pattou, Marie-Christine Vantyghem, Philippe Bertolino, Jieli Lu, Chang Xian Zhang
Foxa2, known as one of the pioneer factors, plays a crucial role in islet development and endocrine functions. Its expression and biological functions are regulated by various factors, including in particular insulin and glucagon. However, its expression and biological role in the adult pancreatic α-cells rema... |
m6A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition
Boxuan Simen Zhao, Xiao Wang, Alana V. Beadell, Zhike Lu, Hailing Shi, Adam Kuuspalu, Robert K. Ho & Chuan He
The maternal-to-zygotic transition (MZT) is one of the most profound and tightly orchestrated processes during the early life of embryos, yet factors that shape the temporal pattern of vertebrate MZT are largely unknown. Here we show that over one-third of zebrafish maternal messenger RNAs (mRNAs) can be N6-methylad... |
A set of novel automated quantitative microproteomics protocols for small sample amounts and its application to kidney tissue substructures
de Graaf, E. L., Pelligrini, D., & McDonnell, L. A.
Here we assessed the ability of an automated sample preparation device equipped with disposable microcolumns to prepare mass-limited samples for high-sensitivity quantitative proteomics, using both label-free and isobaric labeling approaches. First, we compared peptide label-free quantification reproducibility for 1... |
Analysis of Cohesin Function in Gene Regulation and Chromatin Organization in Interphase
Preksha Gupta , Thais Lavagnolli, Hegias Mira-Bontenbal, Matthias Merkenschlager
Cohesin is essential for the maintenance of chromosomes through the cell cycle. In addition, cohesin contributes to the regulation of gene expression and the organization of chromatin in interphase cells. To study cohesin’s role in gene expression and chromatin organization, it is necessary to avoid secondary ... |
DNA fragmentation and quality control analysis
Wassim Lakhal, Irina Panteleeva, Sharon Squazzo, Rini Saxena, Jerome Kroonen, Steve Siembieda, Markus Tilmes & Jonathan Hagopian
Optimal data generation using NGS platforms relies on a few sample-preparation prerequisites, namely, precise DNA fragmentation, size-range analysis, and smear quantification. The Diagenode One, Bioruptor®, Megaruptor®, and Fragment Analyzer™ by Advanced Analytical ensure that these first cri... |
Genome-wide DNA methylation profiling with MeDIP-seq using archived dried blood spots
Nicklas H. Staunstrup et al.
Background In utero and early-life experienced environmental exposures are suggested to play an important role in many multifactorial diseases potentially mediated through lasting effects on the epigenome. As the epigenome in addition remains modifiable throughout life, identifying specific disease-relevant biomarke... |
UMI-4C for quantitative and targeted chromosomal contact profiling
Omer Schwartzman, Zohar Mukamel, Noa Oded-Elkayam, Pedro Olivares-Chauvet, Yaniv Lubling, Gilad Landan, Shai Izraeli and Amos Tanay
We developed a targeted chromosome conformation capture (4C) approach that uses unique molecular identifiers (umis) to derive high-complexity quantitative chromosome contact profiles with controlled signal-to-noise ratios. UMI-4C detects chromosomal interactions with improved sensitivity and specificity, and it can ... |
Characterization of novel Bovine Leukemia Virus (BLV) antisense transcripts by deep sequencing reveals constitutive expression in tumors and transcriptional interaction with viral microRNAs
Durkin K., Rosewick N., Artesi M., Hahaut V., Griebel P., Arsic N., Burny A., Georges M., Van den Broeke A.
Background
Bovine Leukemia Virus (BLV) is a deltaretrovirus closely related to the Human T cell leukemia virus-1 (HTLV-1). Cattle are the natural host of BLV where it integrates into B-cells, producing a lifelong infection. Most infected animals remain asymptomatic but following a protracted latency period about 5 ... |
Parental epigenetic asymmetry of PRC2-mediated histone modifications in the Arabidopsis endosperm
Moreno-Romero J et al.
Parental genomes in the endosperm are marked by differential DNA methylation and are therefore epigenetically distinct. This epigenetic asymmetry is established in the gametes and maintained after fertilization by unknown mechanisms. In this manuscript, we have addressed the key question whether parentally inherited... |
Histamine 1 receptor-Gβγ-cAMP/PKA-CFTR pathway mediates the histamine-induced resetting of the suprachiasmatic circadian clock
Yoon Sik Kim, Young-Beom Kim, Woong Bin Kim, Seung Won Lee, Seog Bae Oh, Hee-Chul Han, C. Justin LeeEmail author, Christopher S. Colwell and Yang In Kim
Background
Recent evidence indicates that histamine, acting on histamine 1 receptor (H1R), resets the circadian clock in the mouse suprachiasmatic nucleus (SCN) by increasing intracellular Ca2+ concentration ([Ca2+]i) through the activation of CaV1.3 L-type Ca2+ channels and Ca2+-induced Ca2+ release from ryan... |
Methylated DNA Immunoprecipitation Analysis of Mammalian Endogenous Retroviruses.
Rebollo R, Mager DL
Endogenous retroviruses are repetitive sequences found abundantly in mammalian genomes which are capable of modulating host gene expression. Nevertheless, most endogenous retrovirus copies are under tight epigenetic control via histone-repressive modifications and DNA methylation. Here we describe a common method us... |
TLK1B mediated phosphorylation of Rad9 regulates its nuclear/cytoplasmic localization and cell cycle checkpoint
Sanket Awate and Arrigo De Benedetti
The Tousled like kinase 1B (TLK1B) is critical for DNA repair and survival of cells. Upon DNA damage, Chk1 phosphorylates TLK1B at S457 leading to its transient inhibition. Once TLK1B regains its kinase activity it phosphorylates Rad9 at S328. In this work we investigated the significance of this mechanism by overex... |
The transcription factor SOX6 contributes to the developmental origins of obesity by promoting adipogenesis
Shi Chi Leow, Jeremie Poschmann, Peh Gek Too, Juan Yin, Roy Joseph, Craig McFarlane, Shaillay Dogra, Asim Shabbir, Philip W. Ingham, Shyam Prabhakar, Melvin K. S. Leow, Yung Seng Lee, Kai Lyn Ng, Yap Seng Chong, Peter D. Gluckman, Walter Stünkel
The association between impaired fetal growth and postnatal development of obesity has been demonstrated before. By comparing adipocytes differentiated from Mesenchymal Stem Cells (MSCs) taken from the umbilical cord and derived from normal and growth restricted neonates, we identified the transcription factor SOX6 ... |
Desensitization and incomplete recovery of hepatic target genes after chronic thyroid hormone treatment and withdrawal in male adult mice
Kenji Ohba, Melvin Khee-Shing Leow, Brijesh Kumar Singh, Rohit Anthony Sinha, Ronny Lesmana,Xiao-Hui Liao, Paul Michael Yen
Here, we examined changes in hepatic gene expression and serum TH/thyrotropin (TSH) levels in adult male mice treated either with a single T3 (20 g/100 g body weight) injection (acute T3) or daily injections for 14 days (chronic T3) followed by 10 days withdrawal. Chromatin immunoprecipitation analysis of repre... |
Transducin-like enhancer of split-1 is expressed and functional in human macrophages
Federica De Paoli, Corinne Copin, Jonathan Vanhoutte, Bruno Derudas, Manjula Vinod, Christophe Zawadzki, Sophie Susen, Giulia Chinetti-Gbaguid
Macrophages display heterogeneous phenotypes, including the classical M1 proinflammatory and the alternative M2 anti-inflammatory polarization states. The transducin-like enhancer of split-1 (TLE1) is a transcriptional corepressor whose functions in macrophages have not been studied yet. We report that TLE1 is highl... |
Standardizing chromatin research: a simple and universal method for ChIP-seq
Laura Arrigoni, Andreas S. Richter, Emily Betancourt, Kerstin Bruder, Sarah Diehl, Thomas Manke and Ulrike Bönisch
Here we demonstrate that harmonization of ChIP-seq workflows across cell types and conditions is possible when obtaining chromatin from properly isolated nuclei. We established an ultrasound-based nuclei extraction method (Nuclei Extraction by Sonication) that is highly effective across various organisms, cell ... |
The Deacetylase Sirtuin 1 Regulates Human Papillomavirus Replication by Modulating Histone Acetylation and Recruitment of DNA Damage Factors NBS1 and Rad51 to Viral Genomes
Erika S. Langsfeld, Jason M. Bodily, Laimonis A. Laimins
Human papillomaviruses (HPV) regulate their differentiation-dependent life cycles by activating a number of cellular pathways, such as the DNA damage response, through control of post-translational protein modification. Sirtuin 1 (SIRT1) is a protein deacetylase that modulates the acetylation of a number of cellular... |
The MEF2-HDAC axis controls proliferation of mammary epithelial cells and acini formation in vitro
Andrea Clocchiatti, Eros Di Giorgio, Giulia Viviani, Charles Streuli, Andrea Sgorbissa, Raffaella Picco, Valentina Cutano, Claudio Brancolini
The MEF2-HDAC axis is a master regulator of different developmental programs and adaptive responses in adults. In this manuscript we have investigated the contribution of the axis to the regulation of epithelial morphogenesis, using 3D organotypic cultures of MCF10A cells as a model. We have demonstrated that MEF2 t... |
LXR-Mediated ABCA1 Expression and Function Are Modulated by High Glucose and PRMT2
Maryem A. Hussein, Elina Shrestha, Mireille Ouimet, Tessa J. Barrett, Sarah Leone, Kathryn J. Moore, Yann Hérault, Edward A. Fisher, Michael J. Garabedian
High cholesterol and diabetes are major risk factors for atherosclerosis. Regression of atherosclerosis is mediated in part by the Liver X Receptor (LXR) through the induction of genes involved in cholesterol transport and efflux. In the context of diabetes, regression of atherosclerosis is impaired. We proposed tha... |
Runx1 Transcription Factor Is Required for Myoblasts Proliferation during Muscle Regeneration
Kfir Baruch Umansky, Yael Gruenbaum-Cohen, Michael Tsoory, Ester Feldmesser, Dalia Goldenberg, Ori Brenner, Yoram Groner
Following myonecrosis, muscle satellite cells proliferate, differentiate and fuse, creating new myofibers. The Runx1 transcription factor is not expressed in naïve developing muscle or in adult muscle tissue. However, it is highly expressed in muscles exposed to myopathic damage yet, the role of Runx1 in muscle... |
Concurrent whole-genome haplotyping and copy-number profiling of single cells.
Zamani Esteki M, Dimitriadou E, Mateiu L, Melotte C, Van der Aa N, Kumar P, Das R, Theunis K, Cheng J, Legius E, Moreau Y, Debrock S, D'Hooghe T, Verdyck P, De Rycke M, Sermon K, Vermeesch JR, Voet T
Methods for haplotyping and DNA copy-number typing of single cells are paramount for studying genomic heterogeneity and enabling genetic diagnosis. Before analyzing the DNA of a single cell by microarray or next-generation sequencing, a whole-genome amplification (WGA) process is required, but it substantially disto... |
High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq.
Vanhille L, Griffon A, Maqbool MA, Zacarias-Cabeza J, Dao LT, Fernandez N, Ballester B, Andrau JC, Spicuglia S
Cell-type specific regulation of gene expression requires the activation of promoters by distal genomic elements defined as enhancers. The identification and the characterization of enhancers are challenging in mammals due to their genome complexity. Here we develop CapStarr-Seq, a novel high-throughput strategy to ... |
Mitogenomic phylogeny of the common long-tailed macaque (Macaca fascicularis fascicularis).
Liedigk R, Kolleck J, Böker KO, Meijaard E, Md-Zain BM, Abdul-Latiff MA, Ampeng A, Lakim M, Abdul-Patah P, Tosi AJ, Brameier M, Zinner D, Roos C
BACKGROUND: Long-tailed macaques (Macaca fascicularis) are an important model species in biomedical research and reliable knowledge about their evolutionary history is essential for biomedical inferences. Ten subspecies have been recognized, of which most are restricted to small islands of Southeast Asia. In contras... |
Phylogenomics of Phrynosomatid Lizards: Conflicting Signals from Sequence Capture versus Restriction Site Associated DNA Sequencing
Leaché AD, Chavez AS, Jones LN, Grummer JA, Gottscho AD, Linkem CW
Sequence capture and restriction site associated DNA sequencing (RADseq) are popular methods for obtaining large numbers of loci for phylogenetic analysis. These methods are typically used to collect data at different evolutionary timescales; sequence capture is primarily used for obtaining conserved loci, whereas R... |
Modulation of p53 and met expression by Krüppel-like factor 8 regulates zebrafish cerebellar development.
Tsai MY, Lu YF, Liu YH, Lien HW, Huang CJ, Wu JL, Hwang SL
Krüppel-like factor 8 (Klf8) is a zinc-finger transcription factor implicated in cell proliferation, and cancer cell survival and invasion; however, little is known about its role in normal embryonic development. Here, we show that Klf8 is required for normal cerebellar development in zebrafish embryos. Morphol... |
