Publications
3’UTRs and miRNAs
VHL-Regulated MiR-204 Suppresses Tumor Growth through Inhibition of LC3B-Mediated Autophagy in Renal Clear Cell Carcinoma Olga Mikhaylova, Yiwen Stratton, Daniel Hall, Emily Kellner, Birgit Ehmer, Angela F. Drew, Catherine A. Gallo, David R. Plas, Jacek Biesiada, Jarek Meller, Maria F. Czyzyk-Krzesk. Cancer Cell, April 2012
MicroRNAs Regulate p21Waf1/cip1 Protein Expression and the DNA Damage Response in Human Embryonic Stem Cells Dasa Dolezalova, Marek Mraz, Tomas Barta, Karla Plevova, Vladimir Vinarsky, Zuzana Holubcova, Josef Jaros, Petr Dvorak, Sarka Pospisilova, Ales Hampl. Stem Cells, April 2012
Role of miR-148a in Hepatitis B Associated Hepatocellular Carcinoma Ke Yuan,K., Lian,J., Sun, B., Clayton, M., Ng, I., Feitelson, M. PLoS One, April 2012
Common micro RNAs (miRNAs) target complement factor H (CFH) regulation in Alzheimer’s disease (AD) and in age-related macular degeneration (AMD) Walter J. Lukiw1, Bhattacharjee Surjyadipta1, Prerna Dua2, Peter N. Alexandrov. Int J Biochem, March 2012
miR-125 potentiates early neural specification of human embryonic stem cells Claire Boissart, Xavier Nissan, Karine Giraud-Triboult, Marc Peschanski and Alexandra Benchoua. Development, February 2012
MicroRNA-200b Regulates Cell Proliferation, Invasion, and Migration by Directly Targeting ZEB2 in Gastric Carcinoma H Baba et al. Annals of Surgical Oncology, February 2012
MicroRNA-199a* regulates the expression of cyclooxygenase-2 in human chondrocytes Nahid Akhtar, Tariq M Haqqi. Annals of the Rheumatic Diseases, January 2012
MicroRNA-29b is involved in the Src-ID1 signaling pathway and is dysregulated in human lung adenocarcinoma S I Rothschild, M P Tschan, E A Federzoni, R Jaggi, M F Fey, M Gugger and O Gautschi. Oncogene, January 2012
The miR-183-96-182 cluster is overexpressed in prostate tissue and regulates zinc homeostasis in prostate cells Nonn et. al. Journal of Biological Chemistry. November 2011
MicroRNA-132 targets HB-EGF upon IgE-mediated activation in murine and human mast cells Viktor Molnár, Barbara Érsek, Zoltán Wiener, Zsófia Tömböl, Péter M. Szabó, Péter Igaz, András Falus. Cellular and Molecular Life Sciences, August 2011
Neurotensin Signaling Activates MicroRNAs-21 and-155 and Akt, Promotes Tumor Growth in Mice, and is Increased in Human Colon Tumors Kyriaki Bakirtzi, Maria Hatziapostolou, Iordanes Karagiannides, Christos Polytarchou, Savina Jaeger, Dimitrios Iliopoulos , Charalabos Pothoulakis. Gastroenterology, August 2011
Dickkopf-3 is regulated by the MYCN-induced miR-17-92 cluster in neuroblastoma Sara De Brouwer, Pieter Mestdagh, Irina Lambertz, Filip Pattyn, Anne De Paepe, Frank Westermann, Christina Schroeder, Johannes H. Schulte, Alexander Schramm, Katleen De Preter, Jo Vandesompele, Frank Speleman. International Journal of Cancer, July 2011
Inhibition of miR-193a expression by Max and RXRα activates K-Ras and PLAU to mediate distinct aspects of cellular transformation Iliopoulos, D., Rotem, A., Struhl, K. Cancer Research. 2011 June.
Genome‐wide microRNA downregulation as a negative feedback mechanism in the early phases of liver regeneration Shu, J., Kren, B., Xia, Z, et al. Hepatology. 2011 June.
Porphyromonas gingivalis induction of microRNA-203 expression controls suppressor of cytokine signaling 3 in gingival epithelial cells Moffat, C., Lamont, R. Infection and Immunity. 2011 May.
A Two-Tiered Approach Identifies a Network of Cancer and Liver Diseases Related Genes Regulated by miR-122.
Boutz,D., Collins, P., Suresh U., Lu M., Ramírez C., Fernández-Hernando C.,Huang, Y., Raquel de Sousa Abreu, Le S.,Shapiro, B., Liu, A., Luk, J., Aldred, S.F., Trinklein, N., Marcotte, E., and Penalva, L. JBC. 2011 Mar.
Deregulation of microRNA-503 Contributes to Diabetes Mellitus–Induced Impairment of Endothelial Function and Reparative Angiogenesis After Limb Ischemia
Andrea Caporali et. al., Molecular Cardiology. 2011 Jan.
Prediction of Associations between microRNAs and Gene Expression in Glioma Biology
Wuchty et. al. PLoS One. 2011 Jan.
A Comprehensive Analysis of MicroRNA ExpressionDuring Human Keratinocyte Differentiation In Vitro and In Vivo.
Hildebrand, J., Rutze1, M., Walz, N., Gallinat,S., Wenck, H., Deppert, W., Grundhoff, A. and Knott, A. Journal of Investigative Dermatology. 2011 Jan.
The miR-17-92 MicroRNA Cluster Regulates Multiple Components of the TGF-β Pathway in Neuroblastoma.
Mestdagh et. Al. Molecular Cell. 2010 Dec
Regulation of Heme Oxygenase-1 Protein Expression by miR-377 in Combination with miR-217.
Beckman, J., Chen, C., Nguyen, J., Thayanithy, V., Subramanian, S., Steer, C.
Journal of Biological Chemistry 2010 Nov.
microRNAs regulate human embryonic stem cell division
Qi et al. Cell Cycle. 2010 Aug.
MicroRNA-205–directed transcriptional activation of tumor suppressor genes in prostate cancer.
Majid, S., Dar, A., Saini, S.,Yamamura, S., Hirata, H., Tanaka, Y., Deng, G., Dahiya, R. Cancer. Aug 2010.
Transcriptome and targetome analysis in MIR155 expressing cells using RNA-Seq.
Xu, G., Fewell, C., Christopher Taylor, C. RNA. 2010 Jun.
hsa-miR-191 Is a Candidate Oncogene Target for Hepatocellular Carcinoma Therapy
Eran Elyakimet. al., Cancer Research. 2010 Apr.
MicroRNAs Distinguish Translational from Transcriptional Silencing during Endotoxin Tolerance.
El Gazzar, M., McCall, C., Journal of Biological Chemistry. 2010 Apr.
MicroRNA-210 Regulates Mitochondrial Free Radical Response to Hypoxia and Krebs Cycle in Cancer Cells by Targeting Iron Sulfur Cluster Protein ISCU.
Favaro et. al., PLoS One. 2010 Mar.
Distinct MicroRNA Alterations Characterize High- and Low-Grade Bladder Cancer.
James Catto, W.F., S., Owen, H. Cancer Research. 2009 Oct.
Functional profiling reveals critical role for miRNA in Differentiation of Human Mesenchymal Stem Cells.
Schoolmeesters A, Eklund T, Leake D, Vermeulen A, Smith Q, Aldred Force S, Fedorov, Y. PLoS ONE. 2009 May;4(5):e5605.
MicroRNAs in the miR-106b Family Regulate p21/CDKN1A and Promote Cell Cycle Progression.
Ivanovska I, Ball AS, Diaz RL, Magnus JF, Kibukawa M, Schelter JM, Kobayashi SV, Lim L, Burchard J, Jackson AL, Linsley PS, Cleary MA. Mol Cell Biol. 2008 Apr;28(7):2167-74.
Coordinated regulation of cell cycle transcripts by p53-Inducible microRNAs, miR-192 and miR-215.
Georges SA, Biery MC, Kim SY, Schelter JM, Guo J, Chang AN, Jackson AL, Carleton MO, Linsley PS, Cleary MA, Chau BN.
Cancer Res. 2008 Dec 15;68(24):10105-12.
Over-represented sequences located on 3’ UTRs are potentially involved in regulatory functions.
Yoon K, Ko D, Doderer M, Livi CB, Penalva LO..
RNA Biol. 2008 Oct-Dec;5(4):255-62.
Promoters
Krüppel-like Factor 7 engineered for transcriptional activation promotes axon regeneration in the adult corticospinal tract Murray G. Blackmore, Zimei Wang, Jessica K. Lerch, Dario Motti, Yi Ping Zhang, Christopher B. Shields, Jae K. Lee, Jeffrey L. Goldberg, Vance P. Lemmon, John L. Bixby. PNAS. April 2012
Antiproliferative Factor Regulates Connective Tissue Growth Factor (CTGF/CCN2) Expression in T24 Bladder Carcinoma Cells Christina A. Matika, Melissa Wasilewski, John A. Arnott, Sonia Lobo Planey,1. Molecular Biology of the Cell, March 2012
Transcriptional provirus silencing as a crosstalk of de novo DNA methylation and epigenomic features at the integration site Filip Šenigl, Miroslav Auxt Jiří Hejnar. Nucleic Acids Research, March 2012
The Mitochondrial ATPase Inhibitory Factor 1 Triggers a ROS-Mediated Retrograde Prosurvival and Proliferative Response Laura Formentini1, María Sánchez-Aragó1, Laura Sánchez-Cenizo1, José M. Cuezva. Molecular Cell, March 2012
The novel function of HINFP as a co-activator in sterol-regulated transcription of PCSK9 in HepG2 cells Hai Li and Jingwen Liu. Biochemical Journal, January 2012
Identification of a pH‐responsive DNA region upstream of the transcription start site of human NBCe1‐B Christian M. Snead, Susan M. Smith, Negar Sadeghein, Rodrigo S. Lacruz, Ping Hu, Ira Kurtz, Michael L. Paine. European Journal of Oral Sciences Janaury 2012
The neuroimmune guidance cue netrin-1 promotes atherosclerosis by inhibiting the emigration of macrophages from plaques Nature Immunology, January 2012
The nuclear receptor TR3 regulates mTORC1 signaling in lung cancer cells expressing wild-type p53 S-O Lee1, T Andey2, U-H Jin1, K Kim1, M Sachdeva2 and S Safe1, Oncogene, November 2011
Acquired STAT4 Deficiency as a Consequence of Cancer Chemotherapy H. Chang et. al. Blood, October 2011
A novel epidermal growth factor receptor variant lacking multiple domains directly activates transcription and is overexpressed in tumors Wong et. Al. Oncogene, October 2011
Endoplasmic reticulum stress-induced CHOP activation mediates the down-regulation of leptin in human neuroblastoma SH-SY5Y cells treated with the oxysterol 27-hydroxycholesterol G Marwarha, B Dasari, O Ghribi. Cellular Signalling, October 2011
The oxysterol 27-hydroxycholesterol regulates α-synuclein and tyrosine hydroxylase expression levels in human neuroblastoma cells through modulation of liver X receptors and estrogen receptors–relevance to Parkinson’s disease Gurdeep Marwarha, Turk Rhen, Trevor Schommer, Othman Ghribi. Journal of Neurochemistry, October 2011
Effect of Brain- and Tumor-Derived Connective Tissue Growth Factor on Glioma Invasion Lincoln A. Edwards, Kevin Woolard, Myung Jin Son, Aiguo Li, Jeongwu Lee, Chibawanye Ene, Samuel A. Mantey, Dragan Maric, Hua Song, Galina Belova, Robert T. Jensen, Wei Zhang and Howard A. Fine. JNCI, July 2011.
A User’s Guide to the Encyclopedia of DNA Elements (ENCODE) B Wold, A Mortazavi, B Williams, G Marinov. PLoS Biology, June 2011
IL-8 signaling plays a critical role in the epithelial-mesenchymal transition of human carcinoma cells Fernando, R., Castillo, M., Litzinger, M., Hamilton, D. Cancer Research. 2011 June.
A User’s Guide to the Encyclopedia of DNA Elements (ENCODE) Gidding, M., et al. ScholarWorks. 2011 June.
p53 Directly Represses Id2 to Inhibit the Proliferation of Neural Progenitor Cells Paolella, B., Havrda, M., Mantani, A., Wray, C., Zhang, Z., Israel, M. Stem Cells. 2011 June.
Identification, Replication, and Functional Fine-Mapping of Expression Quantitative Trait Loci in Primary Human Liver Tissue Innocenti, F., et al. PLoS Genetics. 2011 May.
Effects of Thai Medicinal Herb Extracts with Anti-Psoriatic Activity on the Expression on NF-κB Signaling Biomarkers in HaCaT Keratinocytes Saelee, C., Thongrakard, V., Tencomnao, T. Molecules. 2011 May.
Suppression of Latent TGF-beta1 Restores Growth Inhibitory TGFBeta Signaling Through microRNAs.
Dogar, A., Towbin, H., Hall, J. JBC. 2011 Mar.
The Endothelial-Dependent Effect of RTEF-1 in Pressure Overload Cardiac Hypertrophy – Role of VEGF-B.
Xu, M., Jin, Y., Song, Q., Wu, J., Philbrick, M., Cully, B., An, X., Gao, F., Li, J. Cardiovascular Research. 2010 Dec.
Phospho-ΔNp63α/Rpn13-dependent regulation of LKB1 degradation modulates autophagy in cancer cells.
Huang, Y. and Ratovitski, E. Aging. 2010 Dec.
Glycogen synthase kinase−3β inhibitors suppress leukemia cell growth
Songab, E., Palladinettibc, P., Klamerbc, G., Koab, K, Lindemanbd, R., O’Brienab, T., Dolnikovab, A. Experimental Hematology. 2010 Oct.
G-protein-coupled receptor for short-chain fatty acids suppresses colon cancer.
Tang, Y., Chen, Y., Jiang, H. Robbins, G., Nie, D. International Journal of Cancer. 2010 Oct.
Characterization of the Contradictory Chromatin Signatures at the 3′ Exons of Zinc Finger Genes.
Blahnik et. al. PLoS One. 2010 Oct.
GIP increases human adipocyte LPL expression through CREB and TORC2-mediated trans-activation of the LPL gene.
Kim, S., Nian, C., McIntosh, C., Journal of Lipid Research. 2010 Aug.
Estradiol Suppresses NF-κB Activation through Coordinated Regulation of let-7a and miR-125b in Primary Human Macrophages.
Murphy, A., Guyre, P., Pioli, P., Journal of Immunology. 2010 Aug.
Glucose-dependent insulinotropic polypeptide (GIP) increases human adipocyte lipoprotein lipase (LPL) expression through cyclic AMP (cAMP) response element binding protein (CREB) and cAMP-responsive CREB coactivator 2 (TORC2) mediated trans-activation of the LPL gene.
Kim, S., Nian, C., McIntosh, H.S. Journal of Lipid Research. 2010 Aug.
14-3-3τ Regulates Beclin 1 and Is Required for Autophagy.
Wang, B., Ling, S., Lin, W. PLoS One. 2010 Apr.
An extended set of PRDM1/BLIMP1 target genes links binding motif type to dynamic repression.
Doody, G., Care, M., Burgoyne, N., Bradford, J., Bota, M., Bonifer, C., Westhead, D., Tooze, R. Nucleic Acids Research. 2010 Mar.
Pathway Reporter Assays Reveal Small Molecule Mechanisms of Action.
King, F., Selinger, D., Mapa, F., Janes, J., Wu, H., Smith, T., Wang, Q., Niyomrattanakitand, P., Sipes, D., Brinker, A., Porter, J., Myer, V. Journal of the Association for Laboratory Automation. 2009 Dec.
Insulin enhances biogenesis of the nuclear SREBP-1c by posttranscriptional downregulation of Insig-2a and its dissociation from SCAP-SREBP-1c complex.
Yellaturu, C., Deng, X., Park, E. Raghow, R. JBC. 2009 Dec.
Caveolin-1 Promotes Autoregulatory, Akt-Mediated Induction of Cancer-Promoting Growth Factors in Prostate Cancer Cells.
Li, L., Ren, C., Yang, G. Golstov, A., Tabata, K., Thompson, T. Molecular Cancer Research. 2009 Nov
Gene Product Modulates TIS11B Expression in Renal Cell Carcinoma:Impact on Vascular Endothelial Growth Factor Expression in Hypoxia.
Sinha, S., Dutta, S., Datta, K., Ghosh, A., Mukhopadhyay, D. JBC 2009 Sep.
KLF4 suppresses HDACi induced caspase activation and the SAPK pathway by targeting p57.
Ky, N., Lim, C., Li, J., Tam, J., Hamza, M., Zhao, Y. Apoptosis. 2009 Jun.
The T-box transcription factor Brachyury promotes epithelial-mesenchymal transition in human tumor cells.
Fernando R, Litzinger M, Trono P, Hamilton D, Schlom J, Palena C. J. Clin Invest. 2010 Jan.
Overlapping promoter targeting by Elk-1 and other divergent ETS-domain transcription factor family members.
Boros J, O’Donnell A, Donaldson I, Kasza A, Zeef L, Sharrocks A. Nucleic Acids Research. 2009 Dec.
A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays.
Hartzell D, Trinklein ND*, Mendez J, Murphy N, Aldred Force S, Wood K, Marjeta U. Biomed Central. 2009 Oct.
Identification of Chemical Compunds that induce HIF-1alpha Activity.
Xia M, Huang R, Sun Y, Semenza G, Aldred Force S, Witt K, Inglese J, Tice R, Austin C. Toxicological Sciences. 2009 Jun.
Comprehensive Analysis of Transcriptional Promoter Structure and Function in 1% of the Human Genome.
Cooper SJ, Trinklein ND*, Anton EA, Nguyen L, Myers RM.
Genome Res. 2005 Dec 12 Epub. (*corresponding author)
Identification and functional analysis of human transcriptional promoters.
Trinklein ND*, Aldred SJ*, Saldanha AJ, Myers RM.
Genome Res. 2003 Feb;13(2):308-12. (*equal contribution)
An abundance of bidirectional promoters in the human genome.
Trinklein ND, Aldred SF, Hartman SJ, Schroeder DI, Otillar RP, Myers RM.
Genome Res. 2004 Jan;14(1):62-6.
Direct isolation and identification of promoters in the human genome.
Kim TH, Barrera LO, Qu C, Van Calcar S, Trinklein ND, Cooper SJ, Luna RM, Glass CK, Rosenfeld MG, Myers RM, Ren B.
Genome Res. 2005 Jun;15(6):830-9.
Polymorphisms within the C-reactive protein (CRP) promoter region are associated with plasma CRP levels.
Carlson CS, Aldred SF, Lee PK, Tracy RP, Schwartz SM, Rieder M, Liu K, Williams OD, Iribarren C, Lewis EC, Fornage M, Boerwinkle E, Gross M, Jaquish C, Nickerson DA, Myers RM, Siscovick DS, Reiner AP.
Am J Hum Genet. 2005 Jul;77(1):64-77.
Functional profiling reveals critical role for miRNA in Differentiation of Human Mesenchymal Stem Cells.
Schoolmeesters A, Eklund T, Leake D, Vermeulen A, Smith Q, Aldred Force S, Fedorov, Y. PLoS ONE. 2009 May;4(5):e5605.
MicroRNAs in the miR-106b Family Regulate p21/CDKN1A and Promote Cell Cycle Progression.
Ivanovska I, Ball AS, Diaz RL, Magnus JF, Kibukawa M, Schelter JM, Kobayashi SV, Lim L, Burchard J, Jackson AL, Linsley PS, Cleary MA. Mol Cell Biol. 2008 Apr;28(7):2167-74.
Coordinated regulation of cell cycle transcripts by p53-Inducible microRNAs, miR-192 and miR-215.
Georges SA, Biery MC, Kim SY, Schelter JM, Guo J, Chang AN, Jackson AL, Carleton MO, Linsley PS, Cleary MA, Chau BN.
Cancer Res. 2008 Dec 15;68(24):10105-12.
The ENCODE (ENCyclopedia Of DNA Elements) Project.
ENCODE Project Consortium.
Science. 2004 Oct 22;306(5696):636-40.
The role of heat shock transcription factor 1 in the genome-wide regulation of the mammalian heat shock response.
Trinklein ND, Murray JI, Hartman SJ, Botstein D, Myers RM.
Mol Biol Cell. 2004 Mar;15(3):1254-61.
Transcriptional regulation and binding of heat shock factor 1 and heat shock factor 2 to 32 human heat shock genes during thermal stress and differentiation.
Trinklein ND, Chen WC, Kingston RE, Myers RM.
Cell Stress Chaperones. 2004 Mar;9(1):21-8.