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Items: 1 to 50 of 82

1.

A mass spectrometry-based assay using metabolic labeling to rapidly monitor chromatin accessibility of modified histone proteins.

Sidoli S, Lopes M, Lund PJ, Goldman N, Fasolino M, Coradin M, Kulej K, Bhanu NV, Vahedi G, Garcia BA.

Sci Rep. 2019 Sep 20;9(1):13613. doi: 10.1038/s41598-019-49894-4.

2.

Quantitation of Single and Combinatorial Histone Modifications by Integrated Chromatography of Bottom-up Peptides and Middle-down Polypeptide Tails.

Janssen KA, Coradin M, Lu C, Sidoli S, Garcia BA.

J Am Soc Mass Spectrom. 2019 Sep 11. doi: 10.1007/s13361-019-02303-6. [Epub ahead of print]

PMID:
31512222
3.

Single Cell Proteomics by Data-Independent Acquisition To Study Embryonic Asymmetry in Xenopus laevis.

Saha-Shah A, Esmaeili M, Sidoli S, Hwang H, Yang J, Klein PS, Garcia BA.

Anal Chem. 2019 Jul 16;91(14):8891-8899. doi: 10.1021/acs.analchem.9b00327. Epub 2019 Jun 27.

4.

One minute analysis of 200 histone posttranslational modifications by direct injection mass spectrometry.

Sidoli S, Kori Y, Lopes M, Yuan ZF, Kim HJ, Kulej K, Janssen KA, Agosto LM, Cunha JPCD, Andrews AJ, Garcia BA.

Genome Res. 2019 Jun;29(6):978-987. doi: 10.1101/gr.247353.118. Epub 2019 May 23.

PMID:
31123082
5.

Isotopic Labeling and Quantitative Proteomics of Acetylation on Histones and Beyond.

Lund PJ, Kori Y, Zhao X, Sidoli S, Yuan ZF, Garcia BA.

Methods Mol Biol. 2019;1977:43-70. doi: 10.1007/978-1-4939-9232-4_5.

6.

Interrogating Histone Acetylation and BRD4 as Mitotic Bookmarks of Transcription.

Behera V, Stonestrom AJ, Hamagami N, Hsiung CC, Keller CA, Giardine B, Sidoli S, Yuan ZF, Bhanu NV, Werner MT, Wang H, Garcia BA, Hardison RC, Blobel GA.

Cell Rep. 2019 Apr 9;27(2):400-415.e5. doi: 10.1016/j.celrep.2019.03.057.

7.

Epigenomic Reordering Induced by Polycomb Loss Drives Oncogenesis but Leads to Therapeutic Vulnerabilities in Malignant Peripheral Nerve Sheath Tumors.

Wojcik JB, Marchione DM, Sidoli S, Djedid A, Lisby A, Majewski J, Garcia BA.

Cancer Res. 2019 Jul 1;79(13):3205-3219. doi: 10.1158/0008-5472.CAN-18-3704. Epub 2019 Mar 21.

PMID:
30898839
8.

Regulation of proline-directed kinases and the trans-histone code H3K9me3/H4K20me3 during human myogenesis.

Bhanu NV, Sidoli S, Yuan ZF, Molden RC, Garcia BA.

J Biol Chem. 2019 May 17;294(20):8296-8308. doi: 10.1074/jbc.RA118.004977. Epub 2019 Mar 14.

PMID:
30872405
9.

Histone Acetyltransferase p300 Induces De Novo Super-Enhancers to Drive Cellular Senescence.

Sen P, Lan Y, Li CY, Sidoli S, Donahue G, Dou Z, Frederick B, Chen Q, Luense LJ, Garcia BA, Dang W, Johnson FB, Adams PD, Schultz DC, Berger SL.

Mol Cell. 2019 Feb 21;73(4):684-698.e8. doi: 10.1016/j.molcel.2019.01.021. Epub 2019 Feb 14.

PMID:
30773298
10.

Coordination between TGF-β cellular signaling and epigenetic regulation during epithelial to mesenchymal transition.

Lu C, Sidoli S, Kulej K, Ross K, Wu CH, Garcia BA.

Epigenetics Chromatin. 2019 Feb 8;12(1):11. doi: 10.1186/s13072-019-0256-y.

11.

Integrated Analysis of Acetyl-CoA and Histone Modification via Mass Spectrometry to Investigate Metabolically Driven Acetylation.

Sidoli S, Trefely S, Garcia BA, Carrer A.

Methods Mol Biol. 2019;1928:125-147. doi: 10.1007/978-1-4939-9027-6_9.

12.

Acetyl-CoA Metabolism Supports Multistep Pancreatic Tumorigenesis.

Carrer A, Trefely S, Zhao S, Campbell SL, Norgard RJ, Schultz KC, Sidoli S, Parris JLD, Affronti HC, Sivanand S, Egolf S, Sela Y, Trizzino M, Gardini A, Garcia BA, Snyder NW, Stanger BZ, Wellen KE.

Cancer Discov. 2019 Mar;9(3):416-435. doi: 10.1158/2159-8290.CD-18-0567. Epub 2019 Jan 9.

PMID:
30626590
13.

H3K9me3-heterochromatin loss at protein-coding genes enables developmental lineage specification.

Nicetto D, Donahue G, Jain T, Peng T, Sidoli S, Sheng L, Montavon T, Becker JS, Grindheim JM, Blahnik K, Garcia BA, Tan K, Bonasio R, Jenuwein T, Zaret KS.

Science. 2019 Jan 18;363(6424):294-297. doi: 10.1126/science.aau0583. Epub 2019 Jan 3.

14.

Impaired cocaine-induced behavioral plasticity in the male offspring of cocaine-experienced sires.

Wimmer ME, Vassoler FM, White SL, Schmidt HD, Sidoli S, Han Y, Garcia BA, Pierce RC.

Eur J Neurosci. 2019 May;49(9):1115-1126. doi: 10.1111/ejn.14310. Epub 2019 Jan 6.

PMID:
30565761
15.

Analysis of the Effect of Intestinal Ischemia and Reperfusion on the Rat Neutrophils Proteome.

Tahir M, Arshid S, Fontes B, Castro MS, Luz IS, Botelho KLR, Sidoli S, Schwämmle V, Roepstorff P, Fontes W.

Front Mol Biosci. 2018 Nov 29;5:89. doi: 10.3389/fmolb.2018.00089. eCollection 2018.

16.

Distinct Roles of Two Histone Methyltransferases in Transmitting H3K36me3-Based Epigenetic Memory Across Generations in Caenorhabditis elegans.

Kreher J, Takasaki T, Cockrum C, Sidoli S, Garcia BA, Jensen ON, Strome S.

Genetics. 2018 Nov;210(3):969-982. doi: 10.1534/genetics.118.301353. Epub 2018 Sep 14.

17.

Extensive Characterization of Heavily Modified Histone Tails by 193 nm Ultraviolet Photodissociation Mass Spectrometry via a Middle-Down Strategy.

Greer SM, Sidoli S, Coradin M, Schack Jespersen M, Schwämmle V, Jensen ON, Garcia BA, Brodbelt JS.

Anal Chem. 2018 Sep 4;90(17):10425-10433. doi: 10.1021/acs.analchem.8b02320. Epub 2018 Aug 16.

18.

Domain-focused CRISPR screen identifies HRI as a fetal hemoglobin regulator in human erythroid cells.

Grevet JD, Lan X, Hamagami N, Edwards CR, Sankaranarayanan L, Ji X, Bhardwaj SK, Face CJ, Posocco DF, Abdulmalik O, Keller CA, Giardine B, Sidoli S, Garcia BA, Chou ST, Liebhaber SA, Hardison RC, Shi J, Blobel GA.

Science. 2018 Jul 20;361(6399):285-290. doi: 10.1126/science.aao0932.

19.

The Tumor Suppressor CIC Directly Regulates MAPK Pathway Genes via Histone Deacetylation.

Weissmann S, Cloos PA, Sidoli S, Jensen ON, Pollard S, Helin K.

Cancer Res. 2018 Aug 1;78(15):4114-4125. doi: 10.1158/0008-5472.CAN-18-0342. Epub 2018 May 29.

20.

EpiProfile 2.0: A Computational Platform for Processing Epi-Proteomics Mass Spectrometry Data.

Yuan ZF, Sidoli S, Marchione DM, Simithy J, Janssen KA, Szurgot MR, Garcia BA.

J Proteome Res. 2018 Jul 6;17(7):2533-2541. doi: 10.1021/acs.jproteome.8b00133. Epub 2018 May 30.

21.

Middle-Down MS is Ready to Answer Complex Questions in Chromatin Biology.

Sidoli S.

Proteomics. 2018 Jul;18(13):e1800131. doi: 10.1002/pmic.201800131. Epub 2018 Jun 7.

PMID:
29745061
22.

Integrating Proteomics and Targeted Metabolomics to Understand Global Changes in Histone Modifications.

Simithy J, Sidoli S, Garcia BA.

Proteomics. 2018 Sep;18(18):e1700309. doi: 10.1002/pmic.201700309. Epub 2018 Apr 20. Review.

23.

Genomic and Proteomic Resolution of Heterochromatin and Its Restriction of Alternate Fate Genes.

Becker JS, McCarthy RL, Sidoli S, Donahue G, Kaeding KE, He Z, Lin S, Garcia BA, Zaret KS.

Mol Cell. 2017 Dec 21;68(6):1023-1037.e15. doi: 10.1016/j.molcel.2017.11.030.

24.

Protein Kinase C Epsilon Is a Key Regulator of Mitochondrial Redox Homeostasis in Acute Myeloid Leukemia.

Di Marcantonio D, Martinez E, Sidoli S, Vadaketh J, Nieborowska-Skorska M, Gupta A, Meadows JM, Ferraro F, Masselli E, Challen GA, Milsom MD, Scholl C, Fröhling S, Balachandran S, Skorski T, Garcia BA, Mirandola P, Gobbi G, Garzon R, Vitale M, Sykes SM.

Clin Cancer Res. 2018 Feb 1;24(3):608-618. doi: 10.1158/1078-0432.CCR-17-2684. Epub 2017 Nov 10.

25.

Assessment of Quantification Precision of Histone Post-Translational Modifications by Using an Ion Trap and down To 50 000 Cells as Starting Material.

Guo Q, Sidoli S, Garcia BA, Zhao X.

J Proteome Res. 2018 Jan 5;17(1):234-242. doi: 10.1021/acs.jproteome.7b00544. Epub 2017 Nov 21.

26.

Graphical Interpretation and Analysis of Proteins and their Ontologies (GiaPronto): A One-Click Graph Visualization Software for Proteomics Data Sets.

Weiner AK, Sidoli S, Diskin SJ, Garcia BA.

Mol Cell Proteomics. 2018 Jul;17(7):1426-1431. doi: 10.1074/mcp.TIR117.000438. Epub 2017 Nov 8.

27.

Characterization of histone acylations links chromatin modifications with metabolism.

Simithy J, Sidoli S, Yuan ZF, Coradin M, Bhanu NV, Marchione DM, Klein BJ, Bazilevsky GA, McCullough CE, Magin RS, Kutateladze TG, Snyder NW, Marmorstein R, Garcia BA.

Nat Commun. 2017 Oct 26;8(1):1141. doi: 10.1038/s41467-017-01384-9.

28.

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions.

Warneford-Thomson R, He C, Sidoli S, Garcia BA, Bonasio R.

J Vis Exp. 2017 Sep 28;(127). doi: 10.3791/56004.

29.

An HDAC3-PROX1 corepressor module acts on HNF4α to control hepatic triglycerides.

Armour SM, Remsberg JR, Damle M, Sidoli S, Ho WY, Li Z, Garcia BA, Lazar MA.

Nat Commun. 2017 Sep 15;8(1):549. doi: 10.1038/s41467-017-00772-5.

30.

Phosphoproteomics reveals that glycogen synthase kinase-3 phosphorylates multiple splicing factors and is associated with alternative splicing.

Shinde MY, Sidoli S, Kulej K, Mallory MJ, Radens CM, Reicherter AL, Myers RL, Barash Y, Lynch KW, Garcia BA, Klein PS.

J Biol Chem. 2017 Nov 3;292(44):18240-18255. doi: 10.1074/jbc.M117.813527. Epub 2017 Sep 15.

31.

Proteome-wide acetylation dynamics in human cells.

Kori Y, Sidoli S, Yuan ZF, Lund PJ, Zhao X, Garcia BA.

Sci Rep. 2017 Aug 31;7(1):10296. doi: 10.1038/s41598-017-09918-3.

32.

Identification of Nidogen 1 as a lung metastasis protein through secretome analysis.

Alečković M, Wei Y, LeRoy G, Sidoli S, Liu DD, Garcia BA, Kang Y.

Genes Dev. 2017 Jul 15;31(14):1439-1455. doi: 10.1101/gad.301937.117. Epub 2017 Aug 21.

33.

Metabolic labeling in middle-down proteomics allows for investigation of the dynamics of the histone code.

Sidoli S, Lu C, Coradin M, Wang X, Karch KR, Ruminowicz C, Garcia BA.

Epigenetics Chromatin. 2017 Jul 6;10(1):34. doi: 10.1186/s13072-017-0139-z.

34.

Middle-down proteomics: a still unexploited resource for chromatin biology.

Sidoli S, Garcia BA.

Expert Rev Proteomics. 2017 Jul;14(7):617-626. doi: 10.1080/14789450.2017.1345632. Epub 2017 Jun 28. Review.

35.

Quantitative chromatin proteomics reveals a dynamic histone post-translational modification landscape that defines asexual and sexual Plasmodium falciparum parasites.

Coetzee N, Sidoli S, van Biljon R, Painter H, Llinás M, Garcia BA, Birkholtz LM.

Sci Rep. 2017 Apr 4;7(1):607. doi: 10.1038/s41598-017-00687-7.

36.

Abnormal levels of histone methylation in the retinas of diabetic rats are reversed by minocycline treatment.

Wang W, Sidoli S, Zhang W, Wang Q, Wang L, Jensen ON, Guo L, Zhao X, Zheng L.

Sci Rep. 2017 Mar 24;7:45103. doi: 10.1038/srep45103.

37.

Paternal cocaine taking elicits epigenetic remodeling and memory deficits in male progeny.

Wimmer ME, Briand LA, Fant B, Guercio LA, Arreola AC, Schmidt HD, Sidoli S, Han Y, Garcia BA, Pierce RC.

Mol Psychiatry. 2017 Nov;22(11):1653. doi: 10.1038/mp.2017.71. Epub 2017 Mar 21.

PMID:
28322277
38.

Paternal cocaine taking elicits epigenetic remodeling and memory deficits in male progeny.

Wimmer ME, Briand LA, Fant B, Guercio LA, Arreola AC, Schmidt HD, Sidoli S, Han Y, Garcia BA, Pierce RC.

Mol Psychiatry. 2017 Nov;22(11):1641-1650. doi: 10.1038/mp.2017.8. Epub 2017 Feb 21. Erratum in: Mol Psychiatry. 2017 Nov;22(11):1653.

39.

Multicellular Tumor Spheroids Combined with Mass Spectrometric Histone Analysis To Evaluate Epigenetic Drugs.

Feist PE, Sidoli S, Liu X, Schroll MM, Rahmy S, Fujiwara R, Garcia BA, Hummon AB.

Anal Chem. 2017 Mar 7;89(5):2773-2781. doi: 10.1021/acs.analchem.6b03602. Epub 2017 Feb 21.

40.

Time-resolved Global and Chromatin Proteomics during Herpes Simplex Virus Type 1 (HSV-1) Infection.

Kulej K, Avgousti DC, Sidoli S, Herrmann C, Della Fera AN, Kim ET, Garcia BA, Weitzman MD.

Mol Cell Proteomics. 2017 Apr;16(4 suppl 1):S92-S107. doi: 10.1074/mcp.M116.065987. Epub 2017 Feb 8.

41.

Recent Achievements in Characterizing the Histone Code and Approaches to Integrating Epigenomics and Systems Biology.

Janssen KA, Sidoli S, Garcia BA.

Methods Enzymol. 2017;586:359-378. doi: 10.1016/bs.mie.2016.10.021. Epub 2017 Jan 6. Review.

42.

Roles of H3K27me2 and H3K27me3 Examined during Fate Specification of Embryonic Stem Cells.

Juan AH, Wang S, Ko KD, Zare H, Tsai PF, Feng X, Vivanco KO, Ascoli AM, Gutierrez-Cruz G, Krebs J, Sidoli S, Knight AL, Pedersen RA, Garcia BA, Casellas R, Zou J, Sartorelli V.

Cell Rep. 2017 Jan 3;18(1):297. doi: 10.1016/j.celrep.2016.12.036. No abstract available.

43.

Why proteomics is not the new genomics and the future of mass spectrometry in cell biology.

Sidoli S, Kulej K, Garcia BA.

J Cell Biol. 2017 Jan 2;216(1):21-24. doi: 10.1083/jcb.201612010. Epub 2016 Dec 12.

45.

Roles of H3K27me2 and H3K27me3 Examined during Fate Specification of Embryonic Stem Cells.

Juan AH, Wang S, Ko KD, Zare H, Tsai PF, Feng X, Vivanco KO, Ascoli AM, Gutierrez-Cruz G, Krebs J, Sidoli S, Knight AL, Pedersen RA, Garcia BA, Casellas R, Zou J, Sartorelli V.

Cell Rep. 2016 Oct 25;17(5):1369-1382. doi: 10.1016/j.celrep.2016.09.087. Erratum in: Cell Rep. 2017 Jan 3;18(1):297.

46.

High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells.

He C, Sidoli S, Warneford-Thomson R, Tatomer DC, Wilusz JE, Garcia BA, Bonasio R.

Mol Cell. 2016 Oct 20;64(2):416-430. doi: 10.1016/j.molcel.2016.09.034.

47.

Nuclear phosphoproteome analysis of 3T3-L1 preadipocyte differentiation reveals system-wide phosphorylation of transcriptional regulators.

Rabiee A, Schwämmle V, Sidoli S, Dai J, Rogowska-Wrzesinska A, Mandrup S, Jensen ON.

Proteomics. 2017 Mar;17(6). doi: 10.1002/pmic.201600248. Epub 2016 Dec 14.

PMID:
27717184
48.

High performance mass spectrometry based proteomics reveals enzyme and signaling pathway regulation in neutrophils during the early stage of surgical trauma.

Arshid S, Tahir M, Fontes B, de Souza Montero EF, Castro MS, Sidoli S, Roepstorff P, Fontes W.

Proteomics Clin Appl. 2017 Jan;11(1-2). doi: 10.1002/prca.201600001. Epub 2016 Nov 9.

PMID:
27672009
49.

Identification and Quantification of Histone PTMs Using High-Resolution Mass Spectrometry.

Karch KR, Sidoli S, Garcia BA.

Methods Enzymol. 2016;574:3-29. doi: 10.1016/bs.mie.2015.12.007. Epub 2016 Feb 1.

50.

Systems Level Analysis of Histone H3 Post-translational Modifications (PTMs) Reveals Features of PTM Crosstalk in Chromatin Regulation.

Schwämmle V, Sidoli S, Ruminowicz C, Wu X, Lee CF, Helin K, Jensen ON.

Mol Cell Proteomics. 2016 Aug;15(8):2715-29. doi: 10.1074/mcp.M115.054460. Epub 2016 Jun 14.

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