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Genomics Center Publications in Last 5 Years (2014-2018).

  1. Wei R, Dhawan P, Baiocchi RA, Kim K-Y and Christakos S. PU.1 and Epigenetic Signals Modulate Cathelicidin Transcription Induced by C/EBPα and 1,25-Dihydroxyvitamin D3 in Lung Epithelial Cells. J Cell Physiol. Nov 1. doi: 10.1002/jcp.27702. [Epub ahead of print] 2018.
  2. Kurosaki T, Hoque M, Maquat LE. Identifying Cellular Nonsense-Mediated mRNA Decay (NMD) Targets: Immunoprecipitation of Phosphorylated UPF1 Followed by RNA Sequencing (p-UPF1 RIP-Seq). Methods Mol Biol; 1720:175-186. doi: 10.1007/978-1-4939-7540-2_13. PubMed PMID: 29236259. 2018
  3. Roginski RS, Lau CW, Santoiemma PP, Weaver SJ, Du P, Soteropoulos P, Yang J. The human GCOM1 complex gene interacts with the NMDA receptor and internexin-alpha. Gene. Mar 30;648:42-53. doi: 10.1016/j.gene.2018.01.029. Epub Jan 12. PubMed PMID: 29339073. 2018
  4. Korczeniewska OA, Husain S, Khan J, Eliav E, Soteropoulos P, Benoliel R. Differential gene expression in trigeminal ganglia of male and female rats following chronic constriction of the infraorbital nerve. Eur J Pain. May;22(5):875-888. doi: 10.1002/ejp.1174. Epub 2018 Jan 19. PubMed PMID: 29350446. 2018
  5. Yurko N, Liu X, Yamazaki T, Hoque M, Tian B, Manley JL. MPK1/SLT2 Links Multiple Stress Responses with Gene Expression in Budding Yeast by Phosphorylating Tyr1 of the RNAP II CTD. Mol Cell. Dec 7;68(5):913-925.e3. doi: 10.1016/j.molcel.2017.11.020. PubMed PMID: 29220656; PubMed Central PMCID: PMC5736309. 2017
  6. Dhawan P, Veldurthy V, Yehia G, Hsaio C, Porta A, Kim KI, Patel N, Lieben L, Verlinden L, Carmeliet G, Christakos S. Transgenic Expression of the Vitamin D Receptor Restricted to the Ileum, Cecum, and Colon of Vitamin D Receptor Knockout Mice Rescues Vitamin D Receptor-Dependent Rickets. Endocrinology. Nov 1;158(11):3792-3804. doi: 10.1210/en.2017-00258. PubMed PMID: 28938396; PubMed Central PMCID: PMC5695835. 2017
  7. Ngô HM, Zhou Y, Lorenzi H, Wang K, Kim TK, Zhou Y, El Bissati K, Mui E, Fraczek L, Rajagopala SV, Roberts CW, Henriquez FL, Montpetit A, Blackwell JM, Jamieson SE, Wheeler K, Begeman IJ, Naranjo-Galvis C, Alliey-Rodriguez N, Davis RG, Soroceanu L, Cobbs C, Steindler DA, Boyer K, Noble AG, Swisher CN, Heydemann PT, Rabiah P, Withers S, Soteropoulos P, Hood L, McLeod R. Toxoplasma Modulates Signature Pathways of Human Epilepsy, Neurodegeneration & Cancer. Sci Rep. Sep 13;7(1):11496. doi: 10.1038/s41598-017-10675-6. PubMed PMID: 28904337; PubMed Central PMCID: PMC5597608. 2017
  8. Kurthkoti K, Amin H, Marakalala MJ, Ghanny S, Subbian S, Sakatos A, Livny J, Fortune SM, Berney M, Rodriguez GM. The Capacity of Mycobacterium tuberculosis To Survive Iron Starvation Might Enable It To Persist in Iron-Deprived Microenvironments of Human Granulomas. mBio. 8(4). 2017
  9. Veldurthy V, Dhawan P, Patel N, Porta A, Stefa A, et al. Gene expression profiles of selective transcriptome responses in the intestine reveal novel 1,25(OH)2D3 targets and suggest an essential role for the vitamin D receptor in distal as well as proximal intestinal segments. Journal of bone and mineral research: the official journal of the American Society for Bone and Mineral Research; 32(Suppl. 1) S325. 2017
  10. Dhawan P, Wei R, Veldurthy V, Christakos S. New Developments in Our Understanding of the Regulation of Calcium Homeostasis by Vitamin D. Molecular, Genetic, and Nutritional Aspects of Major and Trace Minerals; :27-34. 2017
  11. Liu X, Freitas J, Zheng D, Oliveira MS, Hoque M, Martins T, Henriques T, Tian B, Moreira A. Transcription elongation rate has a tissue-specific impact on alternative cleavage and polyadenylation in Drosophila melanogaster. RNA. Dec;23(12):1807-1816. doi: 10.1261/rna.062661.117. Epub 2017 Aug 29. PubMed PMID: 28851752; PubMed Central PMCID: PMC5689002. 2017
  12. Liu X, Hoque M, Larochelle M, Lemay JF, Yurko N, Manley JL, Bachand F, Tian B. Comparative analysis of alternative polyadenylation in S. cerevisiae and S. pombe. Genome Res. Oct;27(10):1685-1695. doi: 10.1101/gr.222331.117. Epub 2017 Sep 15. PubMed PMID: 28916539; PubMed Central PMCID: PMC5630032. 2017
  13. Li W, Li W, Laishram RS, Hoque M, Ji Z, Tian B, Anderson RA. Distinct regulation of alternative polyadenylation and gene expression by nuclear poly(A) polymerases. Nucleic Acids Res. Sep 6;45(15):8930-8942. doi: 10.1093/nar/gkx560. PubMed PMID: 28911096; PubMed Central PMCID: PMC5587728. 2017
  14. Hoque M, Park JY, Chang YJ, Luchessi AD, Cambiaghi TD, Shamanna R, Hanauske-Abel HM, Holland B, Pe'ery T, Tian B, Mathews MB. Regulation of gene expression by translation factor eIF5A: Hypusine-modified eIF5A enhances nonsense-mediated mRNA decay in human cells. Translation (Austin). Aug 14;5(2):e1366294. doi: 10.1080/21690731.2017.1366294. eCollection 2017. PubMed PMID: 29034140; PubMed Central PMCID: PMC5630042. 2017
  15. Ogami K, Richard P, Chen Y, Hoque M, Li W, Moresco JJ, Yates JR 3rd, Tian B, Manley JL. An Mtr4/ZFC3H1 complex facilitates turnover of unstable nuclear RNAs to prevent their cytoplasmic transport and global translational repression. Genes Dev. Jun 15;31(12):1257-1271. doi: 10.1101/gad.302604.117. Epub 2017 Jul 21. PubMed PMID: 28733371; PubMed Central PMCID: PMC5558927. 2017
  16. Sukheja P, Kumar P, Mittal N, Li SG, Singleton E, Russo R, Perryman AL, Shrestha R, Awasthi D, Husain S, Soteropoulos P, Brukh R, Connell N, Freundlich JS, Alland D. A novel small molecule inhibitor of the Mycobacterium tuberculosis demethylmenaquinone methyltransferase MenG is bactericidal to both growing and nutritionally-deprived persister cells. MBio. Feb 14;8(1). pii: e02022-16. doi: 10.1128/mBio.02022-16. 2017
  17. Veldurthy V, Wei R, Oz L, Dhawan P, Jeon YH, Christakos S. Vitamin D, calcium homeostasis and aging. Bone Res. 2016 Oct 18;4:16041. eCollection. PubMed PMID: 27790378; PubMed Central PMCID: PMC5068478. 2016
  18. Veldurthy V, Wei R, Campbell M, Lupicki K, Dhawan P, Christakos S. 25-Hydroxyvitamin D₃ 24-Hydroxylase: A Key Regulator of 1,25(OH)₂D₃ Catabolism and Calcium Homeostasis. Vitam Horm. 2016;100:137-50. doi: 10.1016/bs.vh.2015.10.005. Epub 2016 Jan 2. PubMed PMID: 26827951. 2016
  19. Wei R, Dhawan P, Salgame P, Bhatt K, Christakos S. Epigenetic Signals and Mycobacterium tuberculosis Infection Modulate 1,25(OH)2D3 Regulation of Innate Immune Responses in Lung Epithelial Cells. Journal of bone and mineral research: the official journal of the American Society for Bone and Mineral Research; 31(Suppl. 1). 2016
  20. Goswami S, S Y, J F, Dhawan P, Christakos S, et al. 1,25-Dihydroxyvitamin D3 or high dietary vitamin D Alleviates Inflammatory Bowel Phenotypes in a Genetic Mouse Model with a High Disease Susceptibility. Journal of bone and mineral research: the official journal of the American Society for Bone and Mineral Research. 31(Suppl. 1). 2016
  21. Veldurthy V, Kim K, Dhawan P, Oz L, Mady L, et al. Evidence for a Key Role of Histone Methylation in the Control of the Biological Function of Vitamin D: Aberrant Regulation with Aging. Journal of bone and mineral research: the official journal of the American Society for Bone and Mineral Research; 31(Suppl. 1). 2016
  22. Christakos S, Dhawan P, Verstuyf A, Verlinden L, Carmeliet G. Vitamin D: Metabolism, Molecular Mechanism of Action, and Pleiotropic Effects. Physiol Rev. Jan;96(1):365-408. doi: 10.1152/physrev.00014.2015. PubMed PMID: 26681795; PubMed Central PMCID: PMC4839493. 2016
  23. Kimani SG, Kumar S, Davra V, Chang YJ, Kasikara C, Geng K, Tsou WI, Wang S, Hoque M, Boháč A, Lewis-Antes A, De Lorenzo MS, Kotenko SV, Birge RB. Normalization of TAM post-receptor signaling reveals a cell invasive signature for Axl tyrosine kinase.Cell Commun Signal. Sep 6;14(1):19. doi: 10.1186/s12964-016-0142-1. PubMed PMID: 27595981; PubMed Central PMCID: PMC5011882. 2016
  24. Lemay JF, Marguerat S, Larochelle M, Liu X, van Nues R, Hunyadkürti J, Hoque M, Tian B, Granneman S, Bähler J, Bachand F. The Nrd1-like protein Seb1 coordinates cotranscriptional 3' end processing and polyadenylation site selection. Genes Dev. Jul 1;30(13):1558-72. doi: 10.1101/gad.280222.116. PubMed PMID: 27401558; PubMed Central PMCID: PMC4949328. 2016
  25. Devany E, Park JY, Murphy MR, Zakusilo G, Baquero J, Zhang X, Hoque M, Tian B, Kleiman FE. Intronic cleavage and polyadenylation regulates gene expression during DNA damage response through U1 snRNA. Cell Discov. Jun 14;2:16013. doi: 10.1038/celldisc.2016.13. eCollection 2016. PubMed PMID: 27462460; PubMed Central PMCID: PMC4906801. 2016
  26. Yang Y, Li W, Hoque M, Hou L, Shen S, Tian B, Dynlacht BD. Correction: PAF Complex Plays Novel Subunit-Specific Roles in Alternative Cleavage and Polyadenylation. PLoS Genet. Feb 18;12(2):e1005883. doi: 10.1371/journal.pgen.1005883. eCollection Feb. PubMed PMID: 26890028; PubMed Central PMCID: PMC4758808. 2016
  27. Li W, Park JY, Zheng D, Hoque M, Yehia G, Tian B. Alternative cleavage and polyadenylation in spermatogenesis connects chromatin regulation with post-transcriptional control. BMC Biol. Jan 22;14:6. doi: 10.1186/s12915-016-0229-6. PubMed PMID: 26801249; PubMed Central PMCID: PMC4724118. 2016
  28. Yang Y, Li W, Hoque M, Hou L, Shen S, Tian B, Dynlacht BD. PAF Complex Plays Novel Subunit-Specific Roles in Alternative Cleavage and Polyadenylation. PLoS Genet. Jan 14;12(1):e1005794. doi: 10.1371/journal.pgen.1005794. eCollection 2016 Jan. Erratum in: PLoS Genet. Feb;12(2):e1005883. PubMed PMID: 26765774; PubMed Central PMCID: PMC4713055. 2016
  29. Neve J, Burger K, Li W, Hoque M, Patel R, Tian B, Gullerova M, Furger A. Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation. Genome Res. Jan;26(1):24-35. doi: 10.1101/gr.193995.115. Epub 2015 Nov 6. PubMed PMID: 26546131; PubMed Central PMCID: PMC4691748. 2016
  30. Tasker C, Subbian S, Gao P, Couret J, Levine C, Ghanny S, Soteropoulos P, Zhao X, Landau N, Lu W, Chang TL. IFN- protects primary macrophages against HIV infection. JCI Insight. Dec 8;1(20):e88255. PubMed PMID: 27942584; PubMed Central PMCID: PMC5135270. 2016
  31. Henry EK, Sy CB, Inclan-Rico JM, Espinosa V, Ghanny S, Dwyer DF, Soteropoulos P, Rivera A, Siracusa MC. Carbonic anhydrase enzymes regulate mast cell-mediated inflammation. J Exp Med. Aug 22;213(9):1663-73. doi: 10.1084/jem.20151739. Epub 2016 Aug 15. PubMed PMID: 27526715; PubMed Central PMCID: PMC4995079 2016
  32. Irene C, Theis JF, Gresham D, Soteropoulos P and Newlon CS. Hst3p, a histone deacetylase, promotes maintenance of Saccharomyces cerevisiae chromosome III lacking efficient replication origins. Mol Genet Genomics. Feb;291(1):271-83. doi: 10.1007/s00438-015-1105-8. Epub 2015 Aug 29. PubMed PMID: 26319649; PubMed Central PMCID: PMC4729790. 2016
  33. Wu S, Marie Lutz B, Miao X, Liang L, Mo K, Chang YJ, Du P, Soteropoulos P, Tian B, Kaufman AG, Bekker A, Hu Y, Tao YX. Dorsal root ganglion transcriptome analysis following peripheral nerve injury in mice. Mol Pain. Mar 11;12. pii: 1744806916629048. doi: 10.1177/1744806916629048. Print 2016. PubMed PMID: 27030721. 2016
  34. Dhawan P, Wei R, Sun C, Gombart AF, Koeffler HP, Diamond G, Christakos S. C/EBPα and the Vitamin D Receptor Cooperate in the Regulation of Cathelicidin in Lung Epithelial Cells. J Cell Physiol. Feb;230(2):464-72. doi: 10.1002/jcp.24729. PubMed PMID: 25078430. 2015
  35. Veldurthy V, Dhawan P, Kim K, Frenken F, Mady L, et al. Altered Calcium Homeostasis in the Klotho Mutant Mouse Does Not Reflect Changes in Calcium Homeostasis that Occur with Aging. Journal of bone and mineral research: the official journal of the American Society for Bone and Mineral Research. 30(Suppl. 1). 2015
  36. Pandey R, Russo R, Ghanny S, Huang X, Helmann J, Rodriguez GM. MntR (Rv2788): a transcriptional regulator that controls manganese homeostasis in Mycobacterium tuberculosis. Molecular microbiology. 98(6):1168-83. NIHMSID: NIHMS791305. 2015
  37. Soroceanu L, Matlaf L, Khan S, Akhavan A, Singer E, Bezrookove V, Decker S, Ghanny S, Hadaczek P, Bengtsson H, Ohlfest J, Luciani-Torres MG, Harkins L, Perry A, Guo H, Soteropoulos P, Cobbs CS. Cytomegalovirus Immediate-Early Proteins Promote Stemness Properties in Glioblastoma. Cancer research. 75(15):3065-76. NIHMSID: NIHMS697797 PubMed [journal] PMID: 26239477 PMCID: PMC4526117. 2015
  38. Dai W, Li W, Hoque M, Li Z, Tian B, Makeyev EV. A post-transcriptional mechanism pacing expression of neural genes with precursor cell differentiation status. Nat Commun. Jul 6; 6:7576. doi: 10.1038/ncomms8576. PubMed PMID: 26144867; PubMed Central PMCID: PMC4506538. 2015
  39. Pfister NT, Fomin V, Regunath K, Zhou JY, Zhou W, Silwal-Pandit L, Freed-Pastor WA, Laptenko O, Neo SP, Bargonetti J, Hoque M, Tian B, Gunaratne J, Engebraaten O, Manley JL, Børresen-Dale AL, Neilsen PM, Prives C. Mutant p53 cooperates with the SWI/SNF chromatin remodeling complex to regulate VEGFR2 in breast cancer cells. Genes Dev. Jun 15;29(12):1298-315. doi: 10.1101/gad.263202.115. Epub 2015 Jun 16. PubMed PMID: 26080815; PubMed Central PMCID: PMC4495400. 2015
  40. Li W, You B, Hoque M, Zheng D, Luo W, Ji Z, Park JY, Gunderson SI, Kalsotra A, Manley JL, Tian B. Systematic profiling of poly(A)+ transcripts modulated by core 3' end processing and splicing factors reveals regulatory rules of alternative cleavage and polyadenylation. PLoS Genet. Apr 23;11(4):e1005166. doi: 10.1371/journal.pgen.1005166. eCollection 2015 Apr. PubMed PMID: 25906188; PubMed Central PMCID: PMC4407891. 2015
  41. Jin Y, Geisberg JV, Moqtaderi Z, Ji Z, Hoque M, Tian B, Struhl K. Mapping 3' mRNA isoforms on a genomic scale. Curr Protoc Mol Biol. Apr 1;110:4.23.1-17. doi: 10.1002/0471142727.mb0423s110. PubMed PMID: 25827089; PubMed Central PMCID: PMC4397975. 2015
  42. Soroceanu L, Matlaf L, Khan S, Akhavan A, Singer E, Bezrookove V, Decker S, Ghanny S, Hadaczek P, Bengtsson H, Ohlfest J, Luciani-Torres MG, Harkins L, Perry A, Guo H, Soteropoulos P, and Cobbs CS. Cytomegalovirus Immediate-Early Proteins Promote Stemness Properties in Glioblastoma. Cancer Res. Aug 1;75(15):3065-76. doi: 10.1158/0008-5472.CAN-14-3307. PubMed PMID: 26239477; PubMed Central PMCID: PMC4526117. 2015
  43. Singer E, Judkins J, Salomonis N, Matlaf L, Soteropoulos P, McAllister S, Soroceanu L. Reactive oxygen species-mediated therapeutic response and resistance in glioblastoma. Cell Death Dis. Jan 15;6:e1601. doi: 10.1038/cddis.2014.566. PubMed PMID: 25590811; PubMed Central PMCID: PMC4669764. 2015
  44. Subbian S, Pandey R, Soteropoulos P, Rodriguez GM. Vaccination with an attenuated ferritin mutant protects mice against virulent Mycobacterium tuberculosis. J Immunol Res. 2015:385402. doi: 10.1155/2015/385402. Epub 2015 Aug 3. PubMed PMID: 26339659; PubMed Central PMCID: PMC4539171. 2015
  45. Seth-Vollenweider T, Joshi S, Dhawan P, Sif S, Christakos S. Novel mechanism of negative regulation of 1,25-dihydroxyvitamin D3-induced 25-hydroxyvitamin D3 24-hydroxylase (Cyp24a1) Transcription: epigenetic modification involving cross-talk between protein-arginine methyltransferase 5 and the SWI/SNF complex. J Biol Chem. Dec 5;289(49):33958-70. doi: 10.1074/jbc.M114.583302. Epub 2014 Oct 16. PubMed PMID: 25324546; PubMed Central PMCID: PMC4256333. 2014
  46. Christakos S, Seth T, Wei R, Veldurthy V, Sun C, Kim KI, Kim KY, Tariq U, Dhawan P. Vitamin D and health: beyond bone. MD Advis. 2014 Summer;7(3):28-32. Review. PubMed PMID: 25485749. 2014
  47. Veldurthy V, Dhawan P, Seth T, Kim K, Porta A, et al. Gene expression profiles identify selective transcriptome responses of the duodenum and distal intestine to modulation by calcium or vitamin D. Journal of bone and mineral research: the official journal of the American Society for Bone and Mineral Research. 29:MO0145. 2014
  48. Dhawan P, Wei R, Sun C, Gombart AF, Koeffler HP, et al. Evidence that C/EBP alpha, PU.1 and the SWI/SNF complex are key mediators of 1,25-dihydroxyvitamin D3 regulation of innate immune responses in lung epithelial cells. Journal of bone and mineral research: the official journal of the American Society for Bone and Mineral Research. 29(Suppl. 1):MO0144. 2014
  49. Di Giammartino DC, Li W, Ogami K, Yashinskie JJ, Hoque M, Tian B, Manley JL. RBBP6 isoforms regulate the human polyadenylation machinery and modulate expression of mRNAs with AU-rich 3' UTRs. Genes Dev. Oct 15;28(20):2248-60. doi: 10.1101/gad.245787.114. PubMed PMID: 25319826; PubMed Central PMCID: PMC4201286. 2014
  50. Kurosaki T, Li W, Hoque M, Popp MW, Ermolenko DN, Tian B, Maquat LE. A post-translational regulatory switch on UPF1 controls targeted mRNA degradation. Genes Dev. Sep 1;28(17):1900-16. doi: 10.1101/gad.245506.114. PubMed PMID: 25184677; PubMed Central PMCID: PMC4197951. 2014
  51. Rosonina E, Yurko N, Li W, Hoque M, Tian B, Manley JL. Threonine-4 of the budding yeast RNAP II CTD couples transcription with Htz1-mediated chromatin remodeling. Proc Natl Acad Sci U S A. Aug 19;111(33):11924-31. doi: 10.1073/pnas.1412802111. Epub 2014 Jul 28. PubMed PMID: 25071213; PubMed Central PMCID: PMC4143052. 2014
  52. Hsin JP, Li W, Hoque M, Tian B, Manley JL. RNAP II CTD tyrosine 1 performs diverse functions in vertebrate cells. Elife. May 8;3:e02112. doi: 10.7554/eLife.02112. PubMed PMID: 24842995; PubMed Central PMCID: PMC4042873. 2014
  53. Mémin E, Hoque M, Jain MR, Heller DS, Li H, Cracchiolo B, Hanauske-Abel HM, Pe'ery T, Mathews MB. Blocking eIF5A modification in cervical cancer cells alters the expression of cancer-related genes and suppresses cell proliferation. Cancer Res. Jan 15;74(2):552-62. doi: 10.1158/0008-5472.CAN-13-0474. Epub 2013 Nov 12. PubMed PMID: 24220243; PubMed Central PMCID: PMC4745653. 2014
  54. Hoque M, Li W, Tian B. Accurate mapping of cleavage and polyadenylation sites by 3' region extraction and deep sequencing. Methods Mol Biol. 2014;1125:119-29. doi: 10.1007/978-1-62703-971-0_10. PubMed PMID: 24590784. 2014
  55. Saglam O, Dai F, Husain S, Zhan Y, Toruner G, Haines III KG. Matricellular protein CCN1 (CYR61) expression is associated with high-grade ductal carcinoma in situ. Hum Pathol. Jun; 45(6):1269-75. doi: 10.1016/j.humpath. 2014.02.007. Epub 2014 Feb 20. 2014
  56. Tsenova L, O’Brien P, Holloway J, Peixoto B, Soteropoulos P, Fallows D, Kaplan G and Subbian S. Etanercept exacerbates inflammation and pathology in a rabbit model of active pulmonary tuberculosis. J Interferon Cytokine Res. 2014 Sep;34(9):716-26. doi: 10.1089/jir.2013.0123. Epub 2014 May 15. PubMed PMID: 24831609; PubMed Central PMCID: PMC4150396. 2014