ShortTalk
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Alterations in methionine metabolism affect histone methylation in a dynamic and reversible manner. Methionine depletion decreases histone H3 lysine 4 trimethylation (H3K4me3) globally and around the transcription start sites of specific genes, including colon cancer genes, decreasing their expression. This suggests a physiological feedback mechanism. Experiments in mice found alterations in methionine metabolism and histone methylation in the liver during methionine restriction, indicating this is a relevant in vivo mechanism for sensing and responding to one-carbon metabolism.
Human
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iet
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on-diet
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ietx
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on-diet
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nexplained
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Results:
High
varia.on
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explained
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by
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altered
H3K4me3
methyla.on](https://image.slidesharecdn.com/700d0bad-e2e9-4be9-a9a5-8a441165ecf6-150928235905-lva1-app6891/85/ShortTalk-18-320.jpg)
ShortTalk
- 1. Histone Methyla.on Dynamics and Gene Regula.on Occur Through the Sensing of One-‐Carbon Metabolism Samantha J. Mentch Locasale Lab Pharmacology & Cancer Biology Departmental Retreat September 18, 2015
- 2. The Methionine Cycle and Methyla.on SAM: S-‐adenosylmethionine SAH: S-‐adenosylhomocysteine HMT: Histone methyltransferase Transsulfura.on pathway me Folate Metabolism or Betaine Cell Membrane HMT
- 3. Histone methylaIon and gene expression me3 me3 me3 me3 me3 me3 me3 me3 me3 me3 me3 me3 H3K4me3 AcIve promoters Open chromaIn H3K27me3 H3K9me3 Closed chromaIn HeterochromaIn HP1 Pol II Vermeulen, et al. (2007) Cell. Nichibushi and Nakayama (2014) Lee and Mahadevan. (2009) J. Cell. Biochem. Barth, T. K., and Imhof, A. (2010) Trends Biochem. Sci
- 4. Ques.ons • Do alteraIons in methionine metabolism affect histone methylaIon? • How are specific genes affected by alteraIons in methionine metabolism? • Is this a physiological mechanism? 1. 2. 3.
- 5. Ques.ons • Do alteraIons in methionine metabolism affect histone methylaIon? • Are specific genes affected by alteraIons in methionine metabolism? • Is this a physiological mechanism? 1. 2. 3.
- 6. Do altera.ons in methionine metabolism affect histone methyla.on? 1. Methods: Liquid Chromatography coupled to Mass Spectrometry (LC-‐MS) Liu, et al (2014) Analy6cal Chem
- 7. Do altera.ons in methionine metabolism affect histone methyla.on? 1. Ques.on: Can methionine restric.on affect methionine metabolism and histone methyla.on? Results: Methionine restric.on alters methionine cycle flux and decreases H3K4me3 M ET SA M SA H hC ystB etaine D M G G LY SER -8 -6 -4 -2 0 2 4 Log2(-MET/+MET)
- 8. Do altera.ons in methionine metabolism affect histone methyla.on? 1. 0 1 2 3 4 5 6 7 8 0.0 0.5 1.0 1.5 Time (Hours) RelativeAbundance SAH MET SAM Ques.on: How dynamic are the changes in methionine metabolism and histone methyla.on during methionine restric.on? Results: Changes in methionine cycle metabolism occur in minutes followed by changes in histone methyla.on
- 9. Do altera.ons in methionine metabolism affect histone methyla.on? 1. Ques.on: Are altera.ons in methionine metabolism and histone methyla.on reversible aWer methionine deple.on? Results: Decreases in methionine cycle flux and histone methyla.on are reversible
- 10. Ques.ons • Do alteraIons in methionine metabolism affect histone methylaIon? • Are specific genes affected by alteraIons in methionine metabolism? • Is this a physiological mechanism? 1. 2. 3.
- 11. Ques.ons • Do alteraIons in methionine metabolism affect histone methylaIon? • Are specific genes affected by alteraIons in methionine metabolism? • Is this a physiological mechanism? 1. 2. 3.
- 12. Are specific genes affected by altera.ons in methionine metabolism? 2. Ques.on: How does H3K4me3 distribu.on change genome-‐wide? Results: Methionine deple.on alters H3K4me3 peak shape
- 13. Are specific genes affected by altera.ons in methionine metabolism? 2. Ques.on: Does methionine deple.on affect colon cancer genes? Results: Methionine deple.on decreases H3K4me3 around TSS of colon cancer genes and decreases expression D AKT1 MYC TGFR1 MAPK1 RAC3 BIRC5 +M -M +M -M +M -M +M -M +M -M TGFR1 MAPK1 RAC3 BIRC5 RHOA AXIN2 -M +M -M +M -M +M -M +M -M +M -M +M -M +M -M +Met H3K4me3 -Met H3K4me3 RNA-seq
- 14. Are specific genes affected by altera.ons in methionine metabolism? 2. Ques.on: Does methionine deple.on demonstrate regulatory proper.es? Results: Methionine deple.on results in decreased H3K4me3 and gene expression sugges.ng a feedback mechanism
- 15. Ques.ons • Do alteraIons in methionine metabolism affect histone methylaIon? • Are specific genes affected by alteraIons in methionine metabolism? • Is this relevant in vivo? 1. 2. 3.
- 16. Ques.ons • Do alteraIons in methionine metabolism affect histone methylaIon? • Are specific genes affected by alteraIons in methionine metabolism? • Is this a physiological mechanism? 1. 2. 3.
- 17. Is this a physiological mechanism? 3. Liver Control MET Restricted 0 1×107 2×107 3×107 4×107 MSIntensity MET p = N.S. Control MET Restricted 0 2×105 4×105 6×105 8×105 MSIntensity SAM p = 0.0007 Control MET Restricted 0 2×105 4×105 6×105 MSIntensity SAH p = 0.015 SAM/SAH Control MET Restricted 0.0 5.0×107 1.0×108 1.5×108 2.0×108 2.5×108 MSIntensity Betaine p = 0.003 Control MET Restricted 0 2×106 4×106 6×106 8×106 MSIntensity DMG p = 6.2 x 10-6 Control MET Restricted 0.0 5.0×105 1.0×106 1.5×106 MSIntensity Cystathionine p = 0.005 MTA Control MET Restricted 0.0 5.0×106 1.0×107 1.5×107 2.0×107 MSIntensity MET p = 0.001 Control MET Restricted 0 1×104 2×104 3×104 4×104 5×104 MSIntensity SAM p = N.S. Control MET Restricted 0.0 5.0×103 1.0×104 1.5×104 2.0×104 MSIntensity SAH p = N.S. p = N.S. SAM/SAH Control MET Restricted 3×107 4×107 5×107 6×107 7×107 MSIntensity Betaine p = 0.007 Control MET Restricted 0.0 5.0×105 1.0×106 1.5×106 MSIntensity DMG p = 0.0002 Control MET Restricted 0.0 5.0×104 1.0×105 1.5×105 MSIntensity Cystathionine p = 0.006 KMTB Plasma H3K4me3/H3 H3K4me3 Total H3 Control MET Restricted Results: Methionine deple.on can be sustained in vivo and alter histone methyla.on in the liver
- 18. Is this a physiological mechanism? 3. 0 10 20 30 40 [Methionine](µM) Human Serum Samples D iet N on-diet D ietx N on-diet U nexplained 0.0 0.1 0.2 0.3 0.4 0.5 Varianceexplained Results: High varia.on in methionine explained in part by diet and commensurate with levels necessary for altered H3K4me3 methyla.on
- 19. Summary • Decreasing methionine availability decreases methionine cycle flux and H3K4me3 • Decreased H3K4me3 and gene expression of colon cancer genes • Feedback mechanism regulaIng methionine metabolic genes • AlteraIons in methionine metabolism can be sustained by diet in vivo Mentch, et al. (2015) Cell Metabolism
- 20. Acknowledgements CommiZee Members Jason Locasale Sylvia Lee Chris Fromme Locasale Lab Xiaojing Liu Ahmad Cluntun Mahya Mehrmohamadi Lei Huang Marc Warmoes Maria LiberI Elena Turner Louis Vergara Collaborators Saliendra Nichenametla Dwight Maeocks Gene Ables Thalacker-‐Mercer Lab (Anna, Diwakar, Heather) Lee Lab (Erin, MinIe) Cores Cornell InsItute for Biotechnology – Genomics Core Weill Cornell Epigenomics Core Funding Duke University School of Medicine NIH
- 21. Ques.ons?