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Items: 1 to 50 of 153

1.

IL-10 Signaling Remodels Adipose Chromatin Architecture to Limit Thermogenesis and Energy Expenditure.

Rajbhandari P, Thomas BJ, Feng AC, Hong C, Wang J, Vergnes L, Sallam T, Wang B, Sandhu J, Seldin MM, Lusis AJ, Fong LG, Katz M, Lee R, Young SG, Reue K, Smale ST, Tontonoz P.

Cell. 2018 Jan 11;172(1-2):218-233.e17. doi: 10.1016/j.cell.2017.11.019. Epub 2017 Dec 14.

PMID:
29249357
2.

Defined Sensing Mechanisms and Signaling Pathways Contribute to the Global Inflammatory Gene Expression Output Elicited by Ionizing Radiation.

Purbey PK, Scumpia PO, Kim PJ, Tong AJ, Iwamoto KS, McBride WH, Smale ST.

Immunity. 2017 Sep 19;47(3):421-434.e3. doi: 10.1016/j.immuni.2017.08.017.

3.

A Macrophage Response to Mycobacterium leprae Phenolic Glycolipid Initiates Nerve Damage in Leprosy.

Madigan CA, Cambier CJ, Kelly-Scumpia KM, Scumpia PO, Cheng TY, Zailaa J, Bloom BR, Moody DB, Smale ST, Sagasti A, Modlin RL, Ramakrishnan L.

Cell. 2017 Aug 24;170(5):973-985.e10. doi: 10.1016/j.cell.2017.07.030.

4.

Opposing roles of Toll-like receptor and cytosolic DNA-STING signaling pathways for Staphylococcus aureus cutaneous host defense.

Scumpia PO, Botten GA, Norman JS, Kelly-Scumpia KM, Spreafico R, Ruccia AR, Purbey PK, Thomas BJ, Modlin RL, Smale ST.

PLoS Pathog. 2017 Jul 13;13(7):e1006496. doi: 10.1371/journal.ppat.1006496. eCollection 2017 Jul.

5.

Genetic analysis of Ikaros target genes and tumor suppressor function in BCR-ABL1+ pre-B ALL.

Schjerven H, Ayongaba EF, Aghajanirefah A, McLaughlin J, Cheng D, Geng H, Boyd JR, Eggesbø LM, Lindeman I, Heath JL, Park E, Witte ON, Smale ST, Frietze S, Müschen M.

J Exp Med. 2017 Mar 6;214(3):793-814. doi: 10.1084/jem.20160049. Epub 2017 Feb 11.

6.

The Ly6C(lo)-Down: Targeting Developmental Enhancers for Cell Subset Depletion.

Thomas BJ, Smale ST.

Immunity. 2016 Nov 15;45(5):949-951. doi: 10.1016/j.immuni.2016.10.034.

7.

A Stringent Systems Approach Uncovers Gene-Specific Mechanisms Regulating Inflammation.

Tong AJ, Liu X, Thomas BJ, Lissner MM, Baker MR, Senagolage MD, Allred AL, Barish GD, Smale ST.

Cell. 2016 Mar 24;165(1):165-179. doi: 10.1016/j.cell.2016.01.020. Epub 2016 Feb 25.

8.

Type I and Type II Interferon Coordinately Regulate Suppressive Dendritic Cell Fate and Function during Viral Persistence.

Cunningham CR, Champhekar A, Tullius MV, Dillon BJ, Zhen A, de la Fuente JR, Herskovitz J, Elsaesser H, Snell LM, Wilson EB, de la Torre JC, Kitchen SG, Horwitz MA, Bensinger SJ, Smale ST, Brooks DG.

PLoS Pathog. 2016 Jan 25;12(1):e1005356. doi: 10.1371/journal.ppat.1005356. eCollection 2016 Jan.

9.

Class-specific regulation of pro-inflammatory genes by MyD88 pathways and IκBζ.

Kayama H, Ramirez-Carrozzi VR, Yamamoto M, Mizutani T, Kuwata H, Iba H, Matsumoto M, Honda K, Smale ST, Takeda K.

J Biol Chem. 2015 Sep 11;290(37):22446. doi: 10.1074/jbc.A115.709965. No abstract available.

10.

Regulation of gene expression dynamics during developmental transitions by the Ikaros transcription factor.

Arenzana TL, Schjerven H, Smale ST.

Genes Dev. 2015 Sep 1;29(17):1801-16. doi: 10.1101/gad.266999.115. Epub 2015 Aug 27.

11.

Age-Related Gene Expression Differences in Monocytes from Human Neonates, Young Adults, and Older Adults.

Lissner MM, Thomas BJ, Wee K, Tong AJ, Kollmann TR, Smale ST.

PLoS One. 2015 Jul 6;10(7):e0132061. doi: 10.1371/journal.pone.0132061. eCollection 2015.

12.

Divergence of transcriptional landscape occurs early in B cell activation.

Fowler T, Garruss AS, Ghosh A, De S, Becker KG, Wood WH, Weirauch MT, Smale ST, Aronow B, Sen R, Roy AL.

Epigenetics Chromatin. 2015 May 14;8:20. doi: 10.1186/s13072-015-0012-x. eCollection 2015.

13.

Class-specific regulation of pro-inflammatory genes by MyD88 pathways and IκBζ.

Kayama H, Ramirez-Carrozzi VR, Yamamoto M, Mizutani T, Kuwata H, Iba H, Matsumoto M, Honda K, Smale ST, Takeda K.

J Biol Chem. 2015 Feb 20;290(8):4815. doi: 10.1074/jbc.A114.709965. No abstract available.

14.

Transcriptional control of inflammatory responses.

Smale ST, Natoli G.

Cold Spring Harb Perspect Biol. 2014 Sep 11;6(11):a016261. doi: 10.1101/cshperspect.a016261. Review.

15.

Restriction of IL-22-producing T cell responses and differential regulation of regulatory T cell compartments by zinc finger transcription factor Ikaros.

Heller JJ, Schjerven H, Li S, Lee A, Qiu J, Chen ZM, Smale ST, Zhou L.

J Immunol. 2014 Oct 15;193(8):3934-46. doi: 10.4049/jimmunol.1401234. Epub 2014 Sep 5.

16.

Toward an understanding of the gene-specific and global logic of inducible gene transcription.

Smale ST, Plevy SE, Weinmann AS, Zhou L, Ramirez-Carrozzi VR, Pope SD, Bhatt DM, Tong AJ.

Cold Spring Harb Symp Quant Biol. 2013;78:61-8. doi: 10.1101/sqb.2013.78.020313. Epub 2014 Apr 19.

PMID:
24747344
17.

Transcriptional regulation in the immune system: a status report.

Smale ST.

Trends Immunol. 2014 May;35(5):190-4. doi: 10.1016/j.it.2014.03.003. Epub 2014 Apr 2.

18.

Pten null prostate epithelium promotes localized myeloid-derived suppressor cell expansion and immune suppression during tumor initiation and progression.

Garcia AJ, Ruscetti M, Arenzana TL, Tran LM, Bianci-Frias D, Sybert E, Priceman SJ, Wu L, Nelson PS, Smale ST, Wu H.

Mol Cell Biol. 2014 Jun;34(11):2017-28. doi: 10.1128/MCB.00090-14. Epub 2014 Mar 24. Erratum in: Mol Cell Biol. 2014 Sep;34(17):3354.

19.

Chromatin contributions to the regulation of innate immunity.

Smale ST, Tarakhovsky A, Natoli G.

Annu Rev Immunol. 2014;32:489-511. doi: 10.1146/annurev-immunol-031210-101303. Epub 2014 Feb 6. Review.

PMID:
24555473
20.

Selective regulation of lymphopoiesis and leukemogenesis by individual zinc fingers of Ikaros.

Schjerven H, McLaughlin J, Arenzana TL, Frietze S, Cheng D, Wadsworth SE, Lawson GW, Bensinger SJ, Farnham PJ, Witte ON, Smale ST.

Nat Immunol. 2013 Oct;14(10):1073-83. doi: 10.1038/ni.2707. Epub 2013 Sep 8.

21.

PCR-mediated site-directed mutagenesis.

Carey MF, Peterson CL, Smale ST.

Cold Spring Harb Protoc. 2013 Aug 1;2013(8):738-42. doi: 10.1101/pdb.prot076505.

PMID:
23906918
22.

Electrophoretic mobility-shift assays.

Carey MF, Peterson CL, Smale ST.

Cold Spring Harb Protoc. 2013 Jul 1;2013(7):636-9. doi: 10.1101/pdb.prot075861.

PMID:
23818676
23.

Preparation of (32)P-end-labeled DNA fragments for performing DNA-binding experiments.

Carey MF, Peterson CL, Smale ST.

Cold Spring Harb Protoc. 2013 May 1;2013(5):464-8. doi: 10.1101/pdb.prot074336.

PMID:
23637369
24.

DNase I footprinting.

Carey MF, Peterson CL, Smale ST.

Cold Spring Harb Protoc. 2013 May 1;2013(5):469-78. doi: 10.1101/pdb.prot074328.

PMID:
23637368
25.

Splicing kinetics and transcript release from the chromatin compartment limit the rate of Lipid A-induced gene expression.

Pandya-Jones A, Bhatt DM, Lin CH, Tong AJ, Smale ST, Black DL.

RNA. 2013 Jun;19(6):811-27. doi: 10.1261/rna.039081.113. Epub 2013 Apr 24.

26.

The RNase protection assay.

Carey MF, Peterson CL, Smale ST.

Cold Spring Harb Protoc. 2013 Mar 1;2013(3). pii: pdb.prot071910. doi: 10.1101/pdb.prot071910.

PMID:
23457339
27.

The primer extension assay.

Carey MF, Peterson CL, Smale ST.

Cold Spring Harb Protoc. 2013 Feb 1;2013(2):164-73. doi: 10.1101/pdb.prot071902.

PMID:
23378648
28.

Genome-wide identification of Ikaros targets elucidates its contribution to mouse B-cell lineage specification and pre-B-cell differentiation.

Ferreirós-Vidal I, Carroll T, Taylor B, Terry A, Liang Z, Bruno L, Dharmalingam G, Khadayate S, Cobb BS, Smale ST, Spivakov M, Srivastava P, Petretto E, Fisher AG, Merkenschlager M.

Blood. 2013 Mar 7;121(10):1769-82. doi: 10.1182/blood-2012-08-450114. Epub 2013 Jan 9.

29.

Designing an enhancer landscape.

Xu J, Smale ST.

Cell. 2012 Nov 21;151(5):929-31. doi: 10.1016/j.cell.2012.11.007.

30.

Regulation of cooperative function of the Il12b enhancer and promoter by the interferon regulatory factors 3 and 5.

Koshiba R, Yanai H, Matsuda A, Goto A, Nakajima A, Negishi H, Nishio J, Smale ST, Taniguchi T.

Biochem Biophys Res Commun. 2013 Jan 4;430(1):95-100. doi: 10.1016/j.bbrc.2012.11.006. Epub 2012 Nov 12.

PMID:
23154183
31.

Restraint of inflammatory signaling by interdependent strata of negative regulatory pathways.

Murray PJ, Smale ST.

Nat Immunol. 2012 Oct;13(10):916-24. doi: 10.1038/ni.2391. Epub 2012 Sep 18. Review.

32.

Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions.

Bhatt DM, Pandya-Jones A, Tong AJ, Barozzi I, Lissner MM, Natoli G, Black DL, Smale ST.

Cell. 2012 Jul 20;150(2):279-90. doi: 10.1016/j.cell.2012.05.043.

33.

Confirming the functional importance of a protein-DNA interaction.

Carey MF, Peterson CL, Smale ST.

Cold Spring Harb Protoc. 2012 Jul 1;2012(7):733-57. doi: 10.1101/pdb.top070060.

PMID:
22753608
34.

Cross-interference of RLR and TLR signaling pathways modulates antibacterial T cell responses.

Negishi H, Yanai H, Nakajima A, Koshiba R, Atarashi K, Matsuda A, Matsuki K, Miki S, Doi T, Aderem A, Nishio J, Smale ST, Honda K, Taniguchi T.

Nat Immunol. 2012 May 20;13(7):659-66. doi: 10.1038/ni.2307.

PMID:
22610141
35.

Dimer-specific regulatory mechanisms within the NF-κB family of transcription factors.

Smale ST.

Immunol Rev. 2012 Mar;246(1):193-204. doi: 10.1111/j.1600-065X.2011.01091.x. Review.

PMID:
22435556
36.

Identifying cis-acting DNA elements within a control region.

Carey MF, Peterson CL, Smale ST.

Cold Spring Harb Protoc. 2012 Mar 1;2012(3):279-96. doi: 10.1101/pdb.top068171. Review.

PMID:
22383646
37.

Experimental strategies for cloning or identifying genes encoding DNA-binding proteins.

Carey MF, Peterson CL, Smale ST.

Cold Spring Harb Protoc. 2012 Feb 1;2012(2):183-92. doi: 10.1101/pdb.top067900.

PMID:
22301659
38.

Transcriptional regulation in the innate immune system.

Smale ST.

Curr Opin Immunol. 2012 Feb;24(1):51-7. doi: 10.1016/j.coi.2011.12.008. Epub 2012 Jan 7. Review.

39.

Experimental strategies for the identification of DNA-binding proteins.

Carey MF, Peterson CL, Smale ST.

Cold Spring Harb Protoc. 2012 Jan 1;2012(1):18-33. doi: 10.1101/pdb.top067470. Review.

PMID:
22194258
40.

Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding.

Siggers T, Chang AB, Teixeira A, Wong D, Williams KJ, Ahmed B, Ragoussis J, Udalova IA, Smale ST, Bulyk ML.

Nat Immunol. 2011 Nov 20;13(1):95-102. doi: 10.1038/ni.2151.

41.

Hierarchies of NF-κB target-gene regulation.

Smale ST.

Nat Immunol. 2011 Jul 19;12(8):689-94. doi: 10.1038/ni.2070. Review.

42.

A distal enhancer in Il12b is the target of transcriptional repression by the STAT3 pathway and requires the basic leucine zipper (B-ZIP) protein NFIL3.

Smith AM, Qualls JE, O'Brien K, Balouzian L, Johnson PF, Schultz-Cherry S, Smale ST, Murray PJ.

J Biol Chem. 2011 Jul 1;286(26):23582-90. doi: 10.1074/jbc.M111.249235. Epub 2011 May 12.

43.

NFIL3 is a regulator of IL-12 p40 in macrophages and mucosal immunity.

Kobayashi T, Matsuoka K, Sheikh SZ, Elloumi HZ, Kamada N, Hisamatsu T, Hansen JJ, Doty KR, Pope SD, Smale ST, Hibi T, Rothman PB, Kashiwada M, Plevy SE.

J Immunol. 2011 Apr 15;186(8):4649-55. doi: 10.4049/jimmunol.1003888. Epub 2011 Mar 7.

44.

Magnesium-agarose electrophoretic mobility shift assay (EMSA) of transcription factor IID binding to DNA.

Carey MF, Peterson CL, Smale ST.

Cold Spring Harb Protoc. 2010 Nov 1;2010(11):pdb.prot5514. doi: 10.1101/pdb.prot5514.

PMID:
21041387
45.

Immune inhibitory ligand CD200 induction by TLRs and NLRs limits macrophage activation to protect the host from meningococcal septicemia.

Mukhopadhyay S, Plüddemann A, Hoe JC, Williams KJ, Varin A, Makepeace K, Aknin ML, Bowdish DM, Smale ST, Barclay AN, Gordon S.

Cell Host Microbe. 2010 Sep 16;8(3):236-47. doi: 10.1016/j.chom.2010.08.005.

46.

Potassium permanganate probing of Pol II open complexes.

Carey MF, Peterson CL, Smale ST.

Cold Spring Harb Protoc. 2010 Aug 1;2010(8):pdb.prot5479. doi: 10.1101/pdb.prot5479. No abstract available.

PMID:
20679388
47.

Protein complex binding to promoter DNA: immobilized template assay.

Carey MF, Peterson CL, Smale ST.

Cold Spring Harb Protoc. 2010 Aug 1;2010(8):pdb.prot5465. doi: 10.1101/pdb.prot5465. No abstract available.

PMID:
20679374
48.

Purification of mediator from HeLa cell lines expressing a flag-tagged mediator subunit.

Carey MF, Peterson CL, Smale ST.

Cold Spring Harb Protoc. 2010 Jul 1;2010(7):pdb.prot5451. doi: 10.1101/pdb.prot5451.

PMID:
20647355
49.

Purification of epitope-tagged transcription factor IID.

Carey MF, Peterson CL, Smale ST.

Cold Spring Harb Protoc. 2010 Jul 1;2010(7):pdb.prot5450. doi: 10.1101/pdb.prot5450.

PMID:
20647354
50.

Pioneer factors in embryonic stem cells and differentiation.

Smale ST.

Curr Opin Genet Dev. 2010 Oct;20(5):519-26. doi: 10.1016/j.gde.2010.06.010. Epub 2010 Jul 16. Review.

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