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Qian Huang, Xin-Wen Zhang, Yu-Shui Ma, Gai-Xia Lu, Ru-Ting Xie, Hui-Qiong Yang, Zhong-Wei Lv, Xiao-Ming Zhong, Tao Liu, Shi-Xiong Huang, Da Fu, Chun Xie
Background: An increasing understanding of the genes and molecular pathways of glioblastoma multiforme (GBM) can provide us a useful insight for the development of more effective targeted therapeutic. Methods: To investigate the expression and clinical significance of miR-299 and its target genes in GBM, the expression levels of miR-299 and its target gene in human normal brain tissues and GBM were analyzed in silico using genes microarray and hierarchical clustering analysis followed by validation with quantitative RT-PCR...
May 20, 2017: Japanese Journal of Clinical Oncology
Alboukadel Kassambara, Michel Jourdan, Angélique Bruyer, Nicolas Robert, Véronique Pantesco, Olivier Elemento, Bernard Klein, Jérôme Moreaux
MicroRNAs (miRNAs) are small noncoding RNAs that attenuate expression of their mRNA targets. Here, we developed a new method and an R package, to easily infer candidate miRNA-mRNA target interactions that could be functional during a given biological process. Using this method, we described, for the first time, a comprehensive integrated analysis of miRNAs and mRNAs during human normal plasma cell differentiation (PCD). Our results reveal 63 miRNAs with significant temporal changes in their expression during normal PCD...
June 2, 2017: Nucleic Acids Research
A M Olivares, A S Jelcick, J Reinecke, B Leehy, A Haider, M A Morrison, L Cheng, D F Chen, M M DeAngelis, N B Haider
Regulation of biological processes occurs through complex, synergistic mechanisms. In this study, we discovered the synergistic orchestration of multiple mechanisms regulating the normal and diseased state (age related macular degeneration, AMD) in the retina. We uncovered gene networks with overlapping feedback loops that are modulated by nuclear hormone receptors (NHR), miRNAs, and epigenetic factors. We utilized a comprehensive filtering and pathway analysis strategy comparing miRNA and microarray data between three mouse models and human donor eyes (normal and AMD)...
April 6, 2017: Scientific Reports
Xiaonan Qiu, Laura E Pascal, Qiong Song, Yachen Zang, Junkui Ai, Katherine J O'Malley, Joel B Nelson, Zhou Wang
Elongation factor, RNA polymerase II, 2 (ELL2) is expressed and regulated by androgens in the prostate. ELL2 and ELL-associated factor 2 (EAF2) form a stable complex, and their orthologs in Caenorhabditis elegans appear to be functionally similar. In C. elegans, the EAF2 ortholog eaf-1 was reported to interact with the retinoblastoma (RB) pathway to control development and fertility in worms. Because RB loss is frequent in prostate cancer, ELL2 interaction with RB might be important for prostate homeostasis...
March 2017: Neoplasia: An International Journal for Oncology Research
Shiqian Qi, Zichong Li, Ursula Schulze-Gahmen, Goran Stjepanovic, Qiang Zhou, James H Hurley
The intrinsically disordered scaffold proteins AFF1/4 and the transcription elongation factors ELL1/2 are core components of the super elongation complex required for HIV-1 proviral transcription. Here we report the 2.0-Å resolution crystal structure of the human ELL2 C-terminal domain bound to its 50-residue binding site on AFF4, the ELLBow. The ELL2 domain has the same arch-shaped fold as the tight junction protein occludin. The ELLBow consists of an N-terminal helix followed by an extended hairpin that we refer to as the elbow joint, and occupies most of the concave surface of ELL2...
January 30, 2017: Nature Communications
Daniel J Hodson, Arthur L Shaffer, Wenming Xiao, George W Wright, Roland Schmitz, James D Phelan, Yandan Yang, Daniel E Webster, Lixin Rui, Holger Kohlhammer, Masao Nakagawa, Thomas A Waldmann, Louis M Staudt
The requirement for the B-cell transcription factor OCT2 (octamer-binding protein 2, encoded by Pou2f2) in germinal center B cells has proved controversial. Here, we report that germinal center B cells are formed normally after depletion of OCT2 in a conditional knockout mouse, but their proliferation is reduced and in vivo differentiation to antibody-secreting plasma cells is blocked. This finding led us to examine the role of OCT2 in germinal center-derived lymphomas. shRNA knockdown showed that almost all diffuse large B-cell lymphoma (DLBCL) cell lines are addicted to the expression of OCT2 and its coactivator OCA-B...
April 5, 2016: Proceedings of the National Academy of Sciences of the United States of America
Zichong Li, Huasong Lu, Qiang Zhou
Promoter-proximal pausing by RNA polymerase II (Pol II) is a key rate-limiting step in HIV-1 transcription and latency reversal. The viral Tat protein recruits human super elongation complexes (SECs) to paused Pol II to overcome this restriction. Despite the recent progress in understanding the functions of different subsets of SECs in controlling cellular and Tat-activated HIV transcription, little is known about the SEC subtypes that help reverse viral latency in CD4(+) T cells. Here, we used the CRISPR-Cas9 genome-editing tool to knock out the gene encoding the SEC subunit ELL2, AFF1, or AFF4 in Jurkat/2D10 cells, a well-characterized HIV-1 latency model...
April 2016: Molecular and Cellular Biology
Martina Minnich, Hiromi Tagoh, Peter Bönelt, Elin Axelsson, Maria Fischer, Beatriz Cebolla, Alexander Tarakhovsky, Stephen L Nutt, Markus Jaritz, Meinrad Busslinger
The transcription factor Blimp-1 is necessary for the generation of plasma cells. Here we studied its functions in plasmablast differentiation by identifying regulated Blimp-1 target genes. Blimp-1 promoted the migration and adhesion of plasmablasts. It directly repressed genes encoding several transcription factors and Aicda (which encodes the cytidine deaminase AID) and thus silenced B cell-specific gene expression, antigen presentation and class-switch recombination in plasmablasts. It directly activated genes, which led to increased expression of the plasma cell regulator IRF4 and proteins involved in immunoglobulin secretion...
March 2016: Nature Immunology
Bhairavi Swaminathan, Guðmar Thorleifsson, Magnus Jöud, Mina Ali, Ellinor Johnsson, Ram Ajore, Patrick Sulem, Britt-Marie Halvarsson, Guðmundur Eyjolfsson, Vilhelmina Haraldsdottir, Christina Hultman, Erik Ingelsson, Sigurður Y Kristinsson, Anna K Kähler, Stig Lenhoff, Gisli Masson, Ulf-Henrik Mellqvist, Robert Månsson, Sven Nelander, Isleifur Olafsson, Olof Sigurðardottir, Hlif Steingrimsdóttir, Annette Vangsted, Ulla Vogel, Anders Waage, Hareth Nahi, Daniel F Gudbjartsson, Thorunn Rafnar, Ingemar Turesson, Urban Gullberg, Kári Stefánsson, Markus Hansson, Unnur Thorsteinsdóttir, Björn Nilsson
Multiple myeloma (MM) is characterized by an uninhibited, clonal growth of plasma cells. While first-degree relatives of patients with MM show an increased risk of MM, the genetic basis of inherited MM susceptibility is incompletely understood. Here we report a genome-wide association study in the Nordic region identifying a novel MM risk locus at ELL2 (rs56219066T; odds ratio (OR)=1.25; P=9.6 × 10(-10)). This gene encodes a stoichiometrically limiting component of the super-elongation complex that drives secretory-specific immunoglobulin mRNA production and transcriptional regulation in plasma cells...
2015: Nature Communications
Li Xu, Hongwei Tang, Diane W Chen, Adel K El-Naggar, Peng Wei, Erich M Sturgis
BACKGROUND: Salivary gland carcinomas (SGCs) are a rare malignancy with unknown etiology. The objective of the current study was to identify genetic variants modifying the risk of SGC and its major subtypes: adenoid cystic carcinoma and mucoepidermoid carcinoma. METHODS: The authors conducted a genome-wide association study in 309 well-defined SGC cases and 535 cancer-free controls. A single-nucleotide polymorphism (SNP)-level discovery study was performed in non-Hispanic white individuals followed by a replication study in Hispanic individuals...
July 15, 2015: Cancer
Ian Bayles, Christine Milcarek
B cells can be activated by cognate antigen, anti-B-cell receptor antibody, complement receptors, or polyclonal stimulators like lipopolysaccharide; the overall result is a large shift in RNA processing to the secretory-specific form of immunoglobulin (Ig) heavy chain mRNA and an upregulation of Igh mRNA amounts. Associated with this shift is the large-scale induction of Ig protein synthesis and the unfolded protein response to accommodate the massive quantity of secretory Ig that results. Stimulation to secretion also produces major structural accommodations and stress, with extensive generation of endoplasmic reticulum and Golgi as part of the cellular architecture...
2014: Critical Reviews in Immunology
Yasuhito Funahashi, Zhou Wang, Katherine J O'Malley, Pradeep Tyagi, Donald B DeFranco, Jeffrey R Gingrich, Ryosuke Takahashi, Tsuyoshi Majima, Momokazu Gotoh, Naoki Yoshimura
BACKGROUND: Prostatic inflammation is reportedly associated with the development of prostatic hyperplasia. We investigated the effects of prostatic inflammation on expression levels of androgen-responsive genes and growth factors in the rat prostate. METHODS: Prostatic inflammation was induced by Escherichia coli (strain 1677) injection (0.2 ml of 1 × 10(8) CFU/ml) into the prostatic urethra of male Sprague-Dawley rats, and ventral lobes of the prostate were harvested on day 84...
March 1, 2015: Prostate
Kyung Soo Park, Ian Bayles, Alec Szlachta-McGinn, Joshua Paul, Julie Boiko, Patricia Santos, June Liu, Zhou Wang, Lisa Borghesi, Christine Milcarek
Differentiation of B cells into Ab-secreting cells induces changes in gene transcription, IgH RNA processing, the unfolded protein response (UPR), and cell architecture. The transcription elongation factor eleven nineteen lysine-rich leukemia gene (ELL2) stimulates the processing of the secreted form of the IgH mRNA from the H chain gene. Mice (mus musculus) with the ELL2 gene floxed in either exon 1 or exon 3 were constructed and crossed to CD19-driven cre/CD19(+). The B cell-specific ELL2 conditional knockouts (cKOs; ell2(loxp/loxp) CD19(cre/+)) exhibit curtailed humoral responses both in 4-hydroxy-3-nitrophenyl acetyl-Ficoll and in 4-hydroxy-3-nitrophenyl acetyl-keyhole limpet hemocyanin immunized animals; recall responses were also diminished...
November 1, 2014: Journal of Immunology: Official Journal of the American Association of Immunologists
Melanie C Mann, Sarah Strobel, Bernhard Fleckenstein, Andrea K Kress
The oncoprotein Tax of human T-cell leukemia virus type 1 (HTLV-1) is a potent transactivator of viral and cellular transcription. Here, we identified ELL2 as the sole transcription elongation factor to be specifically upregulated in HTLV-1-/Tax-transformed T-cells. Tax contributes to regulation of ELL2, since transient transfection of Tax increases ELL2 mRNA, Tax transactivates the ELL2 promoter, and repression of Tax results in decrease of ELL2 in transformed T-lymphocytes. However, we also measured upregulation of ELL2 in HTLV-1-transformed cells exhibiting undetectable amounts of Tax, suggesting that ELL2 can still be maintained independent of continuous Tax expression...
September 2014: Virology
Pingyang Liu, Yanhui Xiang, Koh Fujinaga, Koen Bartholomeeusen, Kyle A Nilson, David H Price, B Matija Peterlin
By phosphorylating negative elongation factors and the C-terminal domain of RNA polymerase II (RNAPII), positive transcription elongation factor b (P-TEFb), which is composed of CycT1 or CycT2 and CDK9, activates eukaryotic transcription elongation. In growing cells, it is found in active and inactive forms. In the former, free P-TEFb is a potent transcriptional coactivator. In the latter, it is inhibited by HEXIM1 or HEXIM2 in the 7SK small nuclear ribonucleoprotein (snRNP), which contains, additionally, 7SK snRNA, methyl phosphate-capping enzyme (MePCE), and La-related protein 7 (LARP7)...
April 4, 2014: Journal of Biological Chemistry
Seemay Chou, Heather Upton, Katherine Bao, Ursula Schulze-Gahmen, Avi J Samelson, Nanhai He, Anna Nowak, Huasong Lu, Nevan J Krogan, Qiang Zhou, Tom Alber
The HIV-1 Tat protein stimulates viral gene expression by recruiting human transcription elongation complexes containing P-TEFb, AFF4, ELL2, and ENL or AF9 to the viral promoter, but the molecular organization of these complexes remains unknown. To establish the overall architecture of the HIV-1 Tat elongation complex, we mapped the binding sites that mediate complex assembly in vitro and in vivo. The AFF4 protein emerges as the central scaffold that recruits other factors through direct interactions with short hydrophobic regions along its structurally disordered axis...
January 8, 2013: Proceedings of the National Academy of Sciences of the United States of America
Nora Franceschini, Frank J A van Rooij, Bram P Prins, Mary F Feitosa, Mahir Karakas, John H Eckfeldt, Aaron R Folsom, Jeffrey Kopp, Ahmad Vaez, Jeanette S Andrews, Jens Baumert, Vesna Boraska, Linda Broer, Caroline Hayward, Julius S Ngwa, Yukinori Okada, Ozren Polasek, Harm-Jan Westra, Ying A Wang, Fabiola Del Greco M, Nicole L Glazer, Karen Kapur, Ido P Kema, Lorna M Lopez, Arne Schillert, Albert V Smith, Cheryl A Winkler, Lina Zgaga, Stefania Bandinelli, Sven Bergmann, Mladen Boban, Murielle Bochud, Y D Chen, Gail Davies, Abbas Dehghan, Jingzhong Ding, Angela Doering, J Peter Durda, Luigi Ferrucci, Oscar H Franco, Lude Franke, Grog Gunjaca, Albert Hofman, Fang-Chi Hsu, Ivana Kolcic, Aldi Kraja, Michiaki Kubo, Karl J Lackner, Lenore Launer, Laura R Loehr, Guo Li, Christa Meisinger, Yusuke Nakamura, Christine Schwienbacher, John M Starr, Atsushi Takahashi, Vesela Torlak, André G Uitterlinden, Veronique Vitart, Melanie Waldenberger, Philipp S Wild, Mirna Kirin, Tanja Zeller, Tatijana Zemunik, Qunyuan Zhang, Andreas Ziegler, Stefan Blankenberg, Eric Boerwinkle, Ingrid B Borecki, Harry Campbell, Ian J Deary, Timothy M Frayling, Christian Gieger, Tamara B Harris, Andrew A Hicks, Wolfgang Koenig, Christopher J O' Donnell, Caroline S Fox, Peter P Pramstaller, Bruce M Psaty, Alex P Reiner, Jerome I Rotter, Igor Rudan, Harold Snieder, Toshihiro Tanaka, Cornelia M van Duijn, Peter Vollenweider, Gerard Waeber, James F Wilson, Jacqueline C M Witteman, Bruce H R Wolffenbuttel, Alan F Wright, Qingyu Wu, Yongmei Liu, Nancy S Jenny, Kari E North, Janine F Felix, Behrooz Z Alizadeh, L Adrienne Cupples, John R B Perry, Andrew P Morris
Many disorders are associated with altered serum protein concentrations, including malnutrition, cancer, and cardiovascular, kidney, and inflammatory diseases. Although these protein concentrations are highly heritable, relatively little is known about their underlying genetic determinants. Through transethnic meta-analysis of European-ancestry and Japanese genome-wide association studies, we identified six loci at genome-wide significance (p < 5 × 10(-8)) for serum albumin (HPN-SCN1B, GCKR-FNDC4, SERPINF2-WDR81, TNFRSF11A-ZCCHC2, FRMD5-WDR76, and RPS11-FCGRT, in up to 53,190 European-ancestry and 9,380 Japanese individuals) and three loci for total protein (TNFRS13B, 6q21...
October 5, 2012: American Journal of Human Genetics
Micah J Benson, Tarmo Aijö, Xing Chang, John Gagnon, Utz J Pape, Vivek Anantharaman, L Aravind, Juha-Pekka Pursiheimo, Shalini Oberdoerffer, X Shirley Liu, Riitta Lahesmaa, Harri Lähdesmäki, Anjana Rao
B cells and plasma cells possess distinct RNA processing environments that respectively promote the expression of membrane-associated Ig by B cells versus the secretion of Ig by plasma cells. Through a combination of transcriptional profiling and screening using a lentiviral short-hairpin RNA interference library, we show that both the splicing factor hnRNPLL and the transcription elongation factor ELL2 modulate the ratio of secreted versus membrane-encoding Ighg2b transcripts in MPC11 plasmacytoma cell lines...
October 2, 2012: Proceedings of the National Academy of Sciences of the United States of America
Koen Bartholomeeusen, Yanhui Xiang, Koh Fujinaga, B Matija Peterlin
By phosphorylating elongation factors and the C-terminal domain of RNA polymerase II, the positive transcription elongation factor b (P-TEFb) is the critical kinase for transcription elongation and co-transcriptional processing of eukaryotic genes. It exists in inactive small nuclear ribonucleoprotein (7SK snRNP) and active (free P-TEFb) complexes in cells. The P-TEFb equilibrium determines the state of cellular activation, proliferation, and differentiation. Free P-TEFb, which is required for growth, can be recruited to RNA polymerase II via transcription factors, BRD4, or the super elongation complex (SEC)...
October 19, 2012: Journal of Biological Chemistry
Hui Zhang, Xiaoxiang Hu, Zhipeng Wang, Yuandan Zhang, Shouzhi Wang, Ning Wang, Li Ma, Li Leng, Shengwen Wang, Qigui Wang, Yuxiang Wang, Zhiquan Tang, Ning Li, Yang Da, Hui Li
We conducted a selection signature analysis using the chicken 60k SNP chip in two chicken lines that had been divergently selected for abdominal fat content (AFC) for 11 generations. The selection signature analysis used multiple signals of selection, including long-range allele frequency differences between the lean and fat lines, long-range heterozygosity changes, linkage disequilibrium, haplotype frequencies, and extended haplotype homozygosity. Multiple signals of selection identified ten signatures on chromosomes 1, 2, 4, 5, 11, 15, 20, 26 and Z...
2012: PloS One
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