Publications

3’UTRs and miRNAs

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

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.

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.