Recipes for Regulation of the Genome: Charge, Grease and Intrinsic Disorder

We are interested in understanding how post-translational modifications and protein intrinsic disorder regulate genome usage, transcriptome regulation, and RNA processing. This has been broadly referred to as epigenetics.

Epigenetics is a phenomenon important for an overall increase in the complexity of the genome without changes in gene sequence. Post-translational modifications of histones, and deposition of histone variants, establish a “histone code” of activation or repression of transcription and other chromatin-mediated transactions, and constitute a major part of the epigenome. Epigenetic information is information content "on top of" the DNA-encoded genetic material. Epigenetic information is the landscape on which the dynamic usage of genetic information is encoded.

We utilize a wide range of techniques to address these questions, including: protein biochemistry and enzymology, structural biology, mass spectrometry, cell culture, and embryos of the frog Xenopus laevis. These tools allow us to probe evolutionarily conserved mechanisms specifying critical events in chromatin biology and epigenetics. Our combined use of rigorous in vitro studies along with in vivo studies provides an uncompromised approach to fully understanding epigenetic phenomena and how to apply this knowledge towards improving human health. We are currently pursuing a number of specific research avenues, including:

• determination of the biochemical mechanisms of arginine methyltransferases (PRMT1-9) using enzymology and structural biology
• analyzing how PRMTs regulate transcription and RNA splicing - we use genomics, sequencing, bioinformatics, and other quantitative approaches
• Determining how TTLL4-mediated post-translational glutamylation of histone chaperones (including Npm1, Npm2, and Nap1) occur, how glutamylation regulate histone chaperones - in normal conditions and in cancers like AML
• Using quantitative techniques (NMR, crystallography, binding studies) to understand histone chaperone intrinsically disordered domains in the binding and release of histones

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You can obtain the TM0936 SAH Deaminase plasmid clone for our EZ-MTase asay (Burgos et al 2017) from DNASU: http://dnasu.org/DNASU/GetCloneDetail.do?cloneid=84735

Lab Chat with Dr. Shechter: http://magazine.einstein.yu.edu/winterspring-2017/lab-chat-5/ and Journal of Molecular Biology biography. 

1. Maxim I Maron, Alyssa D Casill, Varun Gupta, Jacob S Roth, Simone Sidoli, Charles C Query, Matthew J Gamble, David Shechter. Type I and II PRMTs inversely regulate post-transcriptional intron detention through Sm and CHTOP methylation. eLife, 2022; 11:e72867 DOI: 10.7554/eLife.72867, PMCID: PMC8765754
2. Maxim I. Maron, Stephanie M. Lehman, Sitaram Gayatri, Joseph D. DeAngelo, Subray Hegde, Benjamin M. Lorton, Yan Sun, Dina L. Bai, Simone Sidoli, Varun Gupta, Matthew R. Marunde, James R. Bone, Zu-Wen Sun, Mark T. Bedford, Jeffrey Shabanowitz, Hongshan Chen, Donald F. Hunt, David Shechter, Independent transcriptomic and proteomic regulation by type I and II protein arginine methyltransferases, iScience, Volume 24, Issue 9, 2021
3. Christopher Warren, Jeffery B. Bonanno, Steven C. Almo, David Shechter. Structure of a Single Chain H2A/H2B Dimer. Acta Cryst. F 2020
4. Benjamin M. Lorton, Rajesh K. Harijan, Emmanuel S. Burgos, Jeffrey B. Bonanno, Steven C. Almo, and David Shechter. “A binary arginine methylation switch on histone H3 Arginine 2 regulates its interaction with WDR5. Biochemistry, Jun 2020.
5. Benjamin Lorton and David Shechter. Cellular consequences of arginine methylation. Cellular and Molecular Life Sciences, Aug 2019.
6. Wei-Lin Wang, Takashi Onikubo, and David Shechter. Chromatin characterization in Xenopus laevis cell-free egg extracts and embryos. Cold Spring Harbor Protocols, Feb 2019.
7. Christopher Warren, Tsutomu Matsui, Jerome Karp, Takashi Onikubo, Sean Cahil, Michael Brenowitz, David Cowburn, Mark Girvin, and David Shechter. Dynamic intramolecular regulation of the histone chaperone nucleoplasmin controls histone binding and release. Nature Communications, 2017
8. Emmanuel S. Burgos,  Ryan O. Walters, Derek M. Huffman and David Shechter. A simplified characterization of S-adenosyl-L-methionine-consuming enzymes with 1-Step EZ-MTase: a universal and straightforward coupled-assay for in vitro and in vivo setting. Chem. Sci., 2017
9. Christopher Warren and David Shechter. Fly Fishing for Histones: Catch and Release by Histone Chaperone Intrinsically Disordered Regions and Acidic Stretches. J Mol Biol. 2017 doi:10.1016/j.jmb.2017.06.005
10. Wei-lin Wang and David Shechter. Chromatin assembly and transcriptional cross-talk in Xenopus laevis oocyte and egg extracts. Int J. Dev. Biol. 2016. doi: 10.1387/ijdb.160161ds
11. Hongshan Chen, Benjamin Lorton, Varun Gupta, and David Shechter. A TGFβ-PRMT5-MEP50 axis regulates cancer cell invasion through histone H3 and H4 arginine methylation coupled transcriptional activation and repression. Oncogene, Jun 2016.
12. Takashi Onikubo, Joshua J. Nicklay, Li Xing, Christopher Warren, Brandon Anson, Wei-Lin Wang, Emmanuel S. Burgos, Sophie E. Ruff, Jeffrey Shabanowitz, R. Holland Cheng, Donald F. Hunt, and David Shechter. Developmentally Regulated Post-Translational Modification of Nucleoplasmin Controls Histone Sequestration and Deposition. Cell Reports, Mar 11 2015; doi:10.1016/j.celrep.2015.02.038
13. Histone H2A and H4 N-Terminal Tails are Positioned by the MEP50 WD-Repeat Protein for Efficient Methylation by the PRMT5 Arginine Methyltransferase. Emmanuel S. Burgos, Carola Wilczek, Takashi Onikubo, Jeffrey B. Bonanno, Janina Jansong, Ulf Reimer and David Shechter. Journal of Biological Chemistry, 2015.
14. The PRMT5 arginine methyltransferase: many roles in development, cancer, and beyond. Nicole Stopa, Jocelyn Krebs, David Shechter. Cellular and Molecular Life Sciences, 2015. 
15. Phosphorylation and arginine methylation mark histone H2A prior to deposition during Xenopus laevis development
    Wei-Lin Wang, Lissa C Anderson, Joshua J Nicklay, Hongshan Chen, Matthew J Gamble, Jeffrey Shabanowitz, Donald F Hunt and David Shechter. Epigenetics & Chromatin, 2014.  7:22
16. Structure of the Arginine Methyltransferase PRMT5-MEP50 Reveals a Mechanism for Substrate Specificity Ho MC, Wilczek C, Bonanno JB, Xing L, Seznec J, Matsui T, Carter LG, Onikubo T, Kumar PR, Chan MK, Brenowitz M, Cheng RH, Reimer U, Almo SC, Shechter D.(2013).PLoS ONE 8(2): e57008. doi:10.1371/journal.pone.0057008.
17. Protein Arginine Methyltransferase Prmt5-Mep50 Methylates Histones H2A and H4 and the Histone Chaperone Nucleoplasmin in Xenopus laevis Eggs. Wilczek C, Chitta R, Woo E, Shabanowitz J, Chait BT, Hunt DF, Shechter D.. J Biol Chem. 2011 Dec 9;286(49):42221-31.  
18. Laura Banszynski, C. David Allis, David Shechter. Analysis of histones and chromatin in Xenopus laevis egg and ooctye extracts. Methods. 2010. Vol 51:1.
19. Extraction, purification and analysis of histones. Shechter D, Dormann HL, Allis CD, Hake SB. Nature Protocols 2007;2(6):1445-57.