Department of Cell Biology


Zhou H, Stein CB, Shafiq TA, Shipkovenska G, Kalocsay M, Paulo JA, Zhang J, Luo Z, Gygi SP, Adelman K, Moazed D (2022). Rixosomal RNA degradation contributes to silencing of Polycomb target genes. Nature 604, 167–174.

Xiaoyi Wang, Joao A. Paulo, Xue Li, Haining Zhou, Juntao Yu, Steven P. Gygi, Danesh Moazed, A composite DNA element that functions as a maintainer required for epigenetic inheritance of heterochromatin, Molecular Cell, 2021, ISSN 1097-2765, [pdf]

Shipkovenska G, Durango A, Kalocsay M, Gygi SP, Moazed D (2020). A conserved RNA degradation complex required for spreading and epigenetic inheritance of heterochromatin. elife 2020; 10.7754/elife.54341. Epub 2020 Jun 03. [pdf]

Iglesias N, Paulo JA, Tatarakis A, Wang X, Edwards AL, Bhanu NV, Garcia BA, Haas W, Gygi SP, Moazed D (2020). Native chromatin proteomics reveals a role for specific nucleoporins in heterochromatin organization and maintenance. Mol Cell. 2020; 77 (1):51-66.e8.10.1016/j.molcel.2019.10.018. Epub 2019 Nov 26. [pdf]

Iglesias N, Currie MA, Jih G, Paulo JA, Siuti N, Kalocsay M, Gygi SP, Moazed D (2018). Automethylation-induced conformational switch in Clr4 (Suv39h) maintains epigenetic stability. Nature 2018; 10.1038/s41586-018-0398-2. Epub 2018 Jul 23. [pdf]

Yu R, Wang X, Moazed D (2018). Epigenetic inheritance mediated by coupling of RNAi and histone H3K9 methylation. Nature 2018; 10.1038/s41586-018-0239-3. Epub 2018 Jun 20. [pdf

Jih G, Iglesias N, Currie MA, Bhanu NV, Paulo JA, Gygi SP, Garcia BA, Moazed D (2017). Unique roles for histone H3K9me states in RNAi and heritable silencing of transcription. Nature 2017; 10.1038/nature23267. Epub 2017 Jun 22. [pdf]

Wang X, Moazed D (2017). DNA sequence-dependent epigenetic inheritance of gene silencing and histone H3K9 methylation. Science 2017; 10.1126/science.aaj2114. Epub 2017 Mar 16. [pdf]

Kusevic D, Kudithipudi S, Iglesias N, Moazed D, Jeltsch A (2017). Clr4 specificity and catalytic activity beyond H3K9 methylation. Biochimie 2017; 10.1016/j.biochi.2017.01.013. Epub 2017 Jan 29. [pdf]

Mathew RS*, Tatarakis A*, Rudenko A, Johnson-Venkatesh E, Yang YJ, Murphy E, Todd TP, Schepers SP, Siuti N, Martorell AJ, Falls WA, Hammack SE, Walsh CA, Tsai L-H, Umemori H, Bouton ME, Moazed D (2016) A microRNA negative feedback loop downregulates vesicle transport and inhibits fear memory. eLife 2016;10.7554/eLife.22467. [pdf]

Behrouzi R, Lu C, Currie MA, Jih G, Iglesias N, Moazed D (2016). Heterochromatin assembly by interrupted Sir3 bridges across neighboring nucleosomes. eLife 2016; 10.7554/eLife.17556.1. [pdf]

Jain R*, Iglesias N*, Moazed D (2016). Distinct functions of Argonaute slicer in siRNA maturation and heterochromatin formation. Mol Cell 63, 191-205.1. [pdf]

Yu R, Moazed D (2016). CSR-1 Slices a Balance. Cell 165, 267-9. doi: 10.1016/j.cell.2016.03.019. [pdf]

Martienssen R, Moazed D (2015). RNAi and heterochromatin assembly. Cold Spring Harb Perspect Biol 7(8):a019323. doi: 10.1101/cshperspect.a019323.

Holoch D, Moazed D (2015). Small-RNA loading licenses Argonaute for assembly into a transcriptional silencing complex. Nat Struct Mol Biol 22, 328-35.1. [pdf]

Ragunathan K, Jih G, Moazed D (2015). Epigenetic inheritance uncoupled from sequence-specific recruitment. Science 348 (6230):1258699. doi: 10.1126/science.1258699. Epub 2014 Nov 20. [pdf]

Egan ED, Braun CR, Gygi SP, Moazed D (2014). Post-transcriptional regulation of meiotic genes by a nuclear RNA silencing complex. RNA 20, 867-81. [pdf]

Yu R, Jih G, Iglesias N, Moazed D (2014). Determinants of Heterochromatic siRNA Biogenesis and Function. Mol Cell 53, 262-76. [pdf]

Johnson A, Wu R, Peetz M, Gygi SP, Moazed D (2014). Heterochromatic gene silencing by activator interference and a transcription elongation barrier. J Biol Chem 288, 28771-82. [pdf]

Heard E, Moazed D (2013). Cell nucleus. Curr Opin Cell Biol 25, 279-80. [pdf]

Moazed D (2013). Chromatin: a tail of repression. Curr Biol 23, R456-9. [pdf]

Wang F, Li G, Altaf M, Lu C, Currie MA, Johnson A, Moazed D (2013). Heterochromatin protein Sir3 induces contacts between the amino terminus of histone H4 and nucleosomal DNA. Proc Natl Acad Sci USA 110, 8495-500. [pdf]

Moazed D (2012). A piRNA to remember. Cell 149, 512-4. [pdf]

Holoch D, Moazed D (2012). RNAi in fission yeast finds new targets and new ways of targeting at the nuclear periphery. Genes Dev 26, 741-5. [pdf]

Moazed D (2011). Mechanisms for the inheritance of chromatin states. Cell 146, 510-8. [pdf]

Gullerova M, Moazed D, Proudfoot NJ (2011). Autoregulation of convergent RNAi genes in fission yeast. Genes Dev 15, 556-568. [pdf]

Gerace EL, Moazed D (2010). Histone demethylation and timely DNA replication. Mol Cell 39, 360-72. [pdf]

Gerae EL, Halic M, Moazed D (2010). The methyltransferase activity of Clr4Suv39h triggers RNAi independently of histone H3K9 methylation. Mol Cell 39, 360-72. [pdf]

Mekhail K, Moazed D (2010). The nuclear envelope in genome organization, expression and stability. Nat Rev Mol Cell Biol 11, 317-28.

Halic M, Moazed D (2010). Dicer-Independent Primal RNAs Trigger RNAi and Heterochromatin Formation. Cell 140, 504-516. [pdf]

Moazed D (2009). Rejoice--RNAi for yeast. Science 326, 533-4. [pdf]

Halic M, Moazed D (2009). 22G-RNAs in transposon silencing and centromere function. Mol Cell 36, 170-1. [pdf]

Johnson A, Li G, Sikorski TW, Buratowski S, Woodcock CL, Moazed D (2009). Reconstitution of heterochromatin-dependent transcriptional gene silencing. Mol Cell 35, 769-81. [pdf]

Sinha M, Watanabe S, Johnson A, Moazed D, Peterson CL (2009). Recombinational repair within heterochromatin requires ATP-dependent chromatin remodeling. Cell 138, 1109-21. [pdf]

Halic M, Moazed D (2009). Transposon silencing by piRNAs. Cell 138, 1058-60. [pdf]

Li H*, Motamedi MR*, Yip CK, Wang Z, Walz T, Patel DJ, Moazed D (2009). An alpha motif at Tas3 C terminus mediates RITS cis spreading and promotes heterochromatic gene silencing. Mol Cell 24, 155-67. [pdf]

Tomson BN, Rahal R, Reiser V, Monje-Casas F, Mekhail K, Moazed D, Amon A (2009) .Regulation of Spo12 phosphorylation and its essential role in the FEAR network. Curr Biol 19, 449-60. Epub 2009 Mar 5. [pdf]

Moazed D (2009). Small RNAs in transcriptional gene silencing and genome defense. Nature 457, 413-420. [pdf]

Motamedi M, Hong EE, Li X, Gerber S, Denison C, Gygi SP, Moazed D (2008). HP1 Proteins Form Distinct Complexes and Mediate Heterochromatic Gene Silencing by Non-Overlapping Mechanisms. Mol. Cell 32, 778-790. [pdf]

Buchberger J, Onishi M, Li G, Seebacher J, Rudner AD, Gygi SP, Moazed D (2008). Sir3-Nucleosome Interactions in Spreading of Silent Chromatin in Saccharomyces cerevisiae. Mol. Cell Biol. 28, 6903-6918. [pdf]

Mekhail K, Seebacher J, Gygi SP, Moazed D (2008). Role for perinuclear chromosome tethering in maintenance of genome stability. Nature 456, 667-670. [pdf]

Kanfi Y, Shalman R, Peshti V, Pilosof SN, Gozlan YM, Pearson KJ, Lerrer B, Moazed D, Marine JC, de Cabo R, Cohen HY (2008). Regulation of SIRT6 protein levels by nutrient availability. FEBS Lett. 582, 543-8. [pdf]

Bühler M, Spies N, Bartel D, Moazed D (2008). TRAMP-mediated RNA surveillance prevents spurious entry of RNAs into the S. pombe siRNA pathway. Nature Structural Molecular Biology 15, 1025-1023. [pdf]

Iida T, Nakayama J, Moazed D (2008). siRNA-mediated heterochromatin establishment requires HP1 and is associated with antisense transcription. Mol. Cell 31, 178-189. [pdf]

Onishi M, Liou G, Buchberger J, Walz T, Moazed D (2007). Role of the conserved Sir3-BAH domain in nucleosome binding and silent chromatin assembly. Mol. Cell 28, 1015-28. [pdf]

Bühler M, Moazed D (2007). RNAi and Transcription in Heterochromatic Gene Silencing. Nature Structural Molecular Biology 4, 1041-1048. [pdf]

Colmenares SU, Buker S, Bühler, M, Dlakic M, Moazed D (2007). Coupling of double-stranded RNA synthesis and siRNA generation in fission yeast RNAi. Mol. Cell, 449-461. [pdf]

Bühler M, Haas W, Gygi SP, and Moazed D (2007). RNAi-dependent and independent RNA turnover mechanisms contribute to heterochromatic gene silencing in fission yeast. Cell 129, 707-721. [pdf]

Buker SM, Iida T, Bühler M, Villén J, Gygi SP, Nakayama J, Moazed D (2007). Two different Argonaute complexes are required for siRNA generation and heterochromatin assembly. Nature Structural Molecular Biology 14, 200-207. [pdf]

Morris CA, Moazed D (2007). Centromere Assembly and Propagation. Cell 128, 647-50. [pdf]

Skiniotis G, Moazed D, Walz T (2007). Acetylated histone-tail peptides induce structural rearrangements in the RSC chromatin remodeling complex. J Biol Chem. 282, 20804-20808. [pdf] [supplement]

Niu H, Li X, Job E, Park C, Moazed D, Gygi SP, Hollingsworth NM (2007). Mek1 kinase is regulated to suppress double-strand break repair between sister chromatids during budding yeast meiosis. Mol Cell Biol. 7, 5456-5467. [pdf]

Moazed D, Bühler M, Buker SM, Colmenares SU, Gerace EL, Gerber SA, Hong EJ, Motamedi MR, Verdel A, Villen J, Gygi SP (2007). Studies on the mechanism of RNAi-dependent heterochromatin assembly. Cold Spring Harb Symp Quant Biol. 71, 461-71.

Matecic M, Martins-Taylor K, Hickman M, Tanny J, Moazed D, Holmes SG (2006). New alleles of SIR2 define cell-cycle-specific silencing functions. Genetics, 1939-1950. [pdf]

Lan F, Zaratiegui M, Villen J, Vaughn MW, Verdel A, Huarte M, Shi Y, Gygi SP, Moazed D, Martienssen RA, Shi Y (2007). S. pombe LSD1 homologs regulate heterochromatin propagation and euchromatic gene transcription. Mol Cell 26, 89-101. [pdf]

Huang J, Brito I, Villen J, Amon A, and Moazed D (2006). Inhibition of homologous recombination by a cohesin-associated clamp complex recruited to the rDNA recombination enhancer. Genes Dev Dec 15, 2887-2901. [pdf] [supplement]

Bühler M, Verdel A, and Moazed D (2006). Tethering the RITS complex to a nascent transcripts initiates RNAi- and heterochromatin-dependent gene silencing. Cell 125, 873-886. [pdf]

Martienssen R, Moazed D (2006). RNAi and Heterochromatin Assembly. CSHL Epigenetics textbook. Editors: David Allis, Thomas Jenuwein, Danny Reinberg. Cold Spring Harbor Laboratory Press, NY, USA.

Liou GG, Tanny JC, Kruger RG, Walz T, Moazed D (2005). Assembly of the SIR Complex and its Regulation by O-acetyl-ADP-ribose, a Product of NAD-Dependent Histone Deacetylation. Cell 121, 515-527. [pdf]

Rudner AD, Hall BE, Ellenberger T, Moazed D (2005). A non-histone protein-protein interaction required for assembly of the SIR complex and silent chromatin. Mol. Cell Biol. 25, 4514-4528. [pdf]

Denison C, Rudner AD, Gerber SA, Bakalarski CE, Moazed D, Gygi SP (2005). A proteomic strategy for gaining insights into protein sumoylation in yeast. Mol Cell Proteomics 2005; 4:246-54. [pdf] [supplement]

Verdel A, Moazed D (2005). RNAi-directed assembly of heterochromatin in fission yeast. FEBS lett. 579: 5872-5878. [pdf]

Hong EE, Villén J, Gerace EL, Gygi SP, Moazed D (2005). A Cullin E3 ubiquitin ligase complex associates with Rik1 and the Clr4 histone H3-K9 methyltransferase and is required for heterochromatin formation. RNA Biology 2-3: 106-111.

Sugiyama T, Cam H, Verdel A, Moazed D, Grewal SI (2005). RNA-dependent RNA polymerase is an essential component of a self-enforcing loop coupling heterochromatin assembly to siRNA production. Proc Natl Acad Sci U S A 102,152-157. [pdf] [supplement]

Motamedi MR*, Verdel A*, Colmenares SU*, Gerber S, Gygi SP, and Moazed D (2004). Two RNAi Complexes, RITS and RDRC, Physically Interact and Localize to Noncoding Centromeric RNAs. Cell 119, 789-802. [pdf]

Noma K, Sugiyama T, Cam H, Verdel A, Zofall M, Jia S, Moazed D, Grewal SI (2004). RITS acts in cis to promote RNA interference-mediated transcriptional and post-transcriptional silencing. Nat Genet 36, 1174-1180. [pdf]

Tanny JC, Kirkpatrick D, Gygi SP, and Moazed D (2004). Budding yeast silencing complexes and the regulation of Sir2 activity by protein-protein interactions. Mol. Cell Biol. 24, 6931-6946. [pdf]

Verdel A, Moazed D (2004). Association of siRNAs with the RITS complex. Meth. Enzymol. 392, 297-307. [pdf]

Stegmeier F, Huang J, Rahal R, Zmolik J, Moazed D, and Amon A (2004). The replication fork block protein Fob1 functions as a negative regulator of the FEAR network. Curr Biol. 23, 467-80. [pdf]

Moazed D, Rudner AD, Huang J, Hoppe GJ, and Tanny JC (2004). A model for step-wise assembly of heterochromatin in yeast. Novartis Found Symp. 259:48-56; discussion 56-62, 163-9.

Verdel A, Jia S, Gerber S, Sugiyama T, Gygi SP, Grewal SI, and Moazed D (2004). RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303, 672-676. [pdf]

Huang J, Moazed D (2003). Association of the RENT complex with non-transcribed and coding regions of rDNA and a regional requirement for the replication fork block protein Fob1 in rDNA silencing. Genes & Dev. 17, 2162-2176. [pdf]

Shankaranarayana G, Motamedi MR, Moazed D, and Grewal SI (2003). Sir2 regulates histone H3 lysine 9 methylation and heterochromatin assembly in fission yeast. Curr Biol 13, 1240-1246. [pdf]

Grewal SI, Moazed D (2003). Heterochromatin and epigenetic regulation of gene expression. Science 301, 798-802. [pdf]

Chang JF, Hall BE, Tanny JC, Moazed D, Filman D, Ellenberger T (2003). Structure of the coiled-coil dimerization motif of Sir4 and its interaction with Sir3. Structure 11, 637-49. [pdf]

Kellogg D, Moazed D (2002). Protein- and immuno-affinity purification of multiprotein complexes. Meth. Enzymol. 351, 172-183. [pdf]

Li J, Moazed D, Gygi SP (2002). Association of the Histone Methyltransferase Set2 with RNA Polymerase II Plays a Role in Transcription Elongation. J. Biol. Chem. 277, 49383-8. [pdf]

Hoppe G. H., Tanny, J. C., Rudner, A. D., Gerber, S. A., Danaie, S., Gygi, S. and Moazed, D. (2002). Steps in assembly of silent chromatin in yeast: Sir3-independent binding of a Sir2/Sir4 complex to silencers and a role for Sir2-dependent deacetylation. Mol. Cell Biol. 22, 4167-4180. [pdf]

Tanny JC, Moazed D (2002). Recognition of acetylated proteins: lessons from an ancient family of enzymes. Structure 10, 1290-1292. [pdf]

Grozinger CM, Chao ED, Blackwell HE, Moazed D, and Schreiber SL (2001). Identification of a class of small molecule inhibitors of the sirtuin family of NAD-dependent deacetylases by phenotypic screening. J Biol Chem. 276, 38837-43. [pdf]

Moazed D (2001). Common themes in mechanisms of gene silencing. Molecular Cell 8, 489-498. [pdf]

Moazed D (2001). Sir2 and its enzymatic activities in chromatin silencing. Current Opinions in Cell Biology 13, 232-238. [pdf]

Tanny JC, Moazed D (2001). Coupling of histone deacetylation to NAD breakdown by the yeast silencing protein Sir2: evidence for acetyl transfer from substrate to an NAD breakdown product. Proc Natl Acad Sci USA 98, 415-420. (published on line December 26, 2000). [pdf]

Tanny JC, Huang J, Dowd G, Hilz H, and Moazed D (1999). An enzymatic activity in the yeast Sir2 protein that is essential for gene silencing. Cell 99, 735-745. [pdf]

Straight AF, Shou W, Dowd GJ, Turck C, Deshaies RJ, Johnson AD, and Moazed D (1999). Net1, a Sir2-associated nucleolar protein required for rDNA silencing and nucleolar integrity. Cell 97, 245-256. [pdf]

Moazed D, Kistler A, Axelrod A, Rine J, and Johnson AD (1997). SIR protein complexes in S. cerevisiae: A SIR2/SIR4 complex and evidence for a regulatory domain in SIR4 that inhibits its interaction with SIR3. Proc Natl Acad Sci USA 94, 2186-2191. [pdf]

Moazed D, Johnson AD (1996). A deubiquitinating enzyme interacts with SIR4 and regulates silencing in S. cerevisiae. Cell 86, 667-677. [pdf]

Moazed D, O'Farrell PH (1992). Maintenance of the engrailed expression pattern by Polycomb group genes in Drosophila. Development 116, 805-810. [pdf]