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Genomes and Genes | Barbara PanningSummaryAffiliation: University of California Country: USA Publications
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Publications
Xist RNA and the mechanism of X chromosome inactivationKathrin Plath
Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California 94143, USA
Annu Rev Genet 36:233-78. 2002..We are now on the threshold of discovering the factors that regulate and interact with Xist to control X-inactivation, and closer to an understanding of the molecular mechanisms that underlie this complex process...- X chromosomes alternate between two states prior to random X-inactivationSusanna Mlynarczyk-Evans
Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
PLoS Biol 4:e159. 2006.... - Transcriptional regulation: it takes a villageBarbara Panning
Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
Mol Cell 31:622-9. 2008.... - X-chromosome inactivation: the molecular basis of silencingBarbara Panning
Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
J Biol 7:30. 2008..In the first issue of Epigenetics and Chromatin, Nesterova and colleagues investigate the role of the RNA interference pathway enzyme Dicer in DNA methylation of the Xist promoter... - Zinc finger protein Zn72D promotes productive splicing of the maleless transcriptKathleen A Worringer
University of California, San Francisco, Department of Biochemistry and Biophysics, San Francisco, California 94158 2200, USA
Mol Cell Biol 27:8760-9. 2007..Consistent with this, Zn72D colocalizes with elongating RNA polymerase II, implicating it as a more general factor involved in RNA metabolism... - Developmental regulation of Suz 12 localizationCecile C de la Cruz
Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
Chromosoma 114:183-92. 2005..These results suggest that Suz12 may have a function that is not mediated by its association with Eed and Ezh2, and that this additional function is not involved in the regulation of X-inactivation... - The A-repeat links ASF/SF2-dependent Xist RNA processing with random choice during X inactivationMorgan E Royce-Tolland
Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
Nat Struct Mol Biol 17:948-54. 2010..We propose that modulation of Xist RNA processing may be part of the stochastic process that determines which X chromosome will be inactivated... - The polycomb group protein SUZ12 regulates histone H3 lysine 9 methylation and HP1 alpha distributionCecile C de la Cruz
Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
Chromosome Res 15:299-314. 2007..In contrast, EZH2 knockdown caused loss of H3K27me3 but not H3K9me3, indicating that SUZ12 regulates H3-K9 methylation in an EZH2-independent fashion. This work uncovers a role for SUZ12 in H3-K9 methylation... - Condensin complexes regulate mitotic progression and interphase chromatin structure in embryonic stem cellsThomas G Fazzio
Biochemistry and Biophysics Department, University of California, San Francisco, San Francisco, CA 94158, USA
J Cell Biol 188:491-503. 2010..The altered compaction coincided with alterations in the abundance of several epigenetic modifications. These data reveal a unique role for condensin complexes in interphase chromatin compaction in ES cells... - Differences between homologous alleles of olfactory receptor genes require the Polycomb Group protein EedMary Kate Alexander
Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
J Cell Biol 179:269-76. 2007..These results suggest a common mechanism for random monoallelic expression on autosomes and the X chromosome, and implicate Eed in establishing differences between homologous OR loci before and after differentiation... - Chromatin modifications on the inactive X chromosomeHannah R Cohen
Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California 94143, USA
Prog Mol Subcell Biol 38:91-122. 2005.... - The zinc finger protein Zn72D and DEAD box helicase Belle interact and control maleless mRNA and protein levelsKathleen A Worringer
Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
BMC Mol Biol 10:33. 2009..To understand the molecular basis of Zn72D function, we identified proteins that interact with Zn72D... - Role of histone H3 lysine 27 methylation in X inactivationKathrin Plath
Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
Science 300:131-5. 2003..Together, our results suggest a role for Eed-Ezh2-mediated H3-K27 methylation during initiation of both imprinted and random X inactivation and demonstrate that H3-K27 methylation is not sufficient for silencing of the Xi... - The histone domain of macroH2A1 contains several dispersed elements that are each sufficient to direct enrichment on the inactive X chromosomeDmitri A Nusinow
Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
J Mol Biol 371:11-8. 2007..These sequences map to the surface of the macroH2A1/H2B dimer, but are buried in the crystal structure of the macroH2A1 containing nucleosome, suggesting that they may contribute to recognition by macroH2A1/H2B deposition factors... - X inactivation in mouse ES cells: histone modifications and FISHBarbara Panning
Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448, USA
Methods Enzymol 376:419-28. 2004 - Chromatin regulation Tip(60)s the balance in embryonic stem cell self-renewalThomas G Fazzio
The G W Hooper Research Foundation, University of California San Francisco, San Francisco, California 94143 0552, USA
Cell Cycle 7:3302-6. 2008..Rather, we propose that the impact of specific modifications at each promoter is determined by the chromatin context in which they are found... - The site-specific installation of methyl-lysine analogs into recombinant histonesMatthew D Simon
Department of Chemistry, University of California, Berkeley, CA 94720, USA
Cell 128:1003-12. 2007.... - Counting chromosomes: not as easy as 1, 2, 3Mary Kate Alexander
University of California, San Francisco, Department of Biochemistry and Biophysics, 600 16th Street, Box 2200, San Francisco, California 94158, USA
Curr Biol 15:R834-6. 2005..Mammalian cells must count their X chromosomes to determine whether to initiate X chromosome inactivation. A region that may be important for X chromosome counting has been identified, but the puzzle pieces still do not quite fit... - Polycomb repressive complex 2 is necessary for the normal site-specific O-GlcNAc distribution in mouse embryonic stem cellsSamuel A Myers
Department of Pharmaceutical Chemistry and Biochemistry, University of California, San Francisco, CA 94158, USA
Proc Natl Acad Sci U S A 108:9490-5. 2011..Together, these results provide insight into how OGT may regulate transcription in early development, possibly by modifying proteins important to maintain the ESC transcriptional repertoire... - Poly(ADP-ribose) polymerase 1 is inhibited by a histone H2A variant, MacroH2A, and contributes to silencing of the inactive X chromosomeDmitri A Nusinow
Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, USA
J Biol Chem 282:12851-9. 2007..These results suggest that one function of macroH2A in gene silencing is to inhibit PARP-1 enzymatic activity, and this may affect PARP-1 association with chromatin... - Mapping post-translational modifications of the histone variant MacroH2A1 using tandem mass spectrometryFeixia Chu
Mass Spectrometry Facility and Department of Pharmaceutical Chemistry, University of California, San Francisco, 94143, USA
Mol Cell Proteomics 5:194-203. 2006..2, suggesting that, like canonical H2A, this variant H2A is subject to regulation by combinatorial use of covalent modifications... - Epigenetic gene regulation by noncoding RNAsAngela A Andersen
Department of Biochemistry and Biophysics, University of California San Francisco, Genentech Hall, Room S374, 600 16th Street, San Francisco, CA 94143 2200, USA
Curr Opin Cell Biol 15:281-9. 2003..However, given that RNA has been shown to be at the catalytic core of other ribonucleoprotein complexes, it is also possible that RNA also plays a role in modulating changes in chromatin structure... - Recognition and modification of seX chromosomesDmitri A Nusinow
Department of Biochemistry and Biophysics, Genentech Hall, S374, University of California-San Francisco, 600 16th Street, San Francisco, CA 94143-2200, USA
Curr Opin Genet Dev 15:206-13. 2005..Finally, evidence from mammals suggests that the chromatin modifications that mediate dosage compensation are very dynamic, because they are established, reversed and re-established early in development... - IRE1 signaling affects cell fate during the unfolded protein responseJonathan H Lin
Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA 94158, USA
Science 318:944-9. 2007..Key findings from our studies in cell culture were recapitulated in photoreceptors expressing mutant rhodopsin in animal models of retinitis pigmentosa... - An RNAi screen of chromatin proteins identifies Tip60-p400 as a regulator of embryonic stem cell identityThomas G Fazzio
Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
Cell 134:162-74. 2008..Depletion of Nanog reduces p400 binding to target promoters without affecting H3K4me3 levels. Together, these data indicate that Tip60-p400 integrates signals from Nanog and H3K4me3 to regulate gene expression in ESCs... - Fine-tuning silencingBarbara Panning
Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
Cell Stem Cell 6:3-4. 2010..Two reports in Cell by Peng et al. (2009) and Shen et al. (2009) identify Jarid2/Jumonji, a new component of PRC2, which inhibits PRC2 enzymatic activity to fine-tune silencing... - X-inactivation: it takes two to countMorgan Royce-Tolland
Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, USA
Curr Biol 18:R255-6. 2008..Recent reports suggest homologous X chromosome pairing may be a prerequisite for silencing, providing a basis for counting by ensuring that silencing only occurs in cells with two X chromosomes... - High resolution electron transfer dissociation studies of unfractionated intact histones from murine embryonic stem cells using on-line capillary LC separation: determination of abundant histone isoforms and post-translational modificationsShannon M Eliuk
Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158 2517, USA
Mol Cell Proteomics 9:824-37. 2010..From a single LC-electron transfer dissociation run, this strategy permits the identification of the most abundant intact proteins, determination of the isoforms present, and the localization of post-translational modifications... - XIST RNA exhibits nuclear retention and exhibits reduced association with the export factor TAP/NXF1Hannah R Cohen
Department of Biochemistry and Biophysics, University of California San Francisco, Genentech Hall, Room S372B, 600 16th Street, San Francisco, CA 94143 2200, USA
Chromosoma 116:373-83. 2007..We present evidence that the export factor TAP/NXF1 binds poorly to XIST RNA in comparison to exported mRNAs, suggesting that reduced TAP/NFX1 binding may contribute to nuclear retention of XIST RNA... - The Polycomb group protein Eed protects the inactive X-chromosome from differentiation-induced reactivationSundeep Kalantry
Department of Genetics and the Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC 27599 7264, USA
Nat Cell Biol 8:195-202. 2006..Instead, PcG proteins seem to propagate cellular memory by preventing transcriptional activation of facultative heterochromatin during differentiation... - Developmentally regulated alterations in Polycomb repressive complex 1 proteins on the inactive X chromosomeKathrin Plath
Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
J Cell Biol 167:1025-35. 2004..Our results implicate mPRC1 in X inactivation and suggest that the regulated assembly of PcG protein complexes on the Xi contributes to this multistep process... - Stable X chromosome inactivation involves the PRC1 Polycomb complex and requires histone MACROH2A1 and the CULLIN3/SPOP ubiquitin E3 ligaseInmaculada Hernández-Muñoz
Division of Molecular Genetics, The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
Proc Natl Acad Sci U S A 102:7635-40. 2005..We further demonstrate that MACROH2A1 deposition is regulated by the CULLIN3/SPOP ligase complex and is actively involved in stable X inactivation, likely through the formation of an additional layer of epigenetic silencing... - Epigenomics: a roadmap, but to where?Hiten D Madhani
Science 322:43-4. 2008 - The colocalization transition of homologous chromosomes at meiosisMario Nicodemi
Department of Physics and Complexity Science, University of Warwick, Coventry, United Kingdom
Phys Rev E Stat Nonlin Soft Matter Phys 77:061913. 2008.... - The XIST noncoding RNA functions independently of BRCA1 in X inactivationCuiying Xiao
Genetics of Development and Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, 10 9N105, National Institutes of Health, Bethesda, MD 20892, USA
Cell 128:977-89. 2007..Together, these results do not support a role for BRCA1 in promoting XIST RNA localization to the Xi or regulating XIST-dependent functions in maintaining the stability of facultative heterochromatin...