ATRX Directs Binding of PRC2 to Xist RNA and Polycomb Targets

(Cell 159, 869–883; November 6, 2014) During the final revision process, we inadvertently removed a key reference to prior work linking ATRX to macroH2A. On page 871, the sentence ‘‘ATRX caught our attention, as it was shown to be enriched on the Xi by immunofluorescence (Baumann and De La Fuente, 2009) and has an ATPase and helicase domain (Clynes et al., 2013; Ratnakumar and Bernstein, 2013)’’ should have cited the paper by Ratnakumar et al. (2012). The text and reference list have been corrected online.

[1]  T. Cech,et al.  Promiscuous RNA binding by Polycomb Repressive Complex 2 , 2013, Nature Structural &Molecular Biology.

[2]  Jürg Müller,et al.  Biochemical mechanisms of gene regulation by polycomb group protein complexes. , 2009, Current opinion in genetics & development.

[3]  Carolyn J. Brown,et al.  The human XIST gene: Analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus , 1992, Cell.

[4]  J. Gribnau,et al.  Different flavors of X-chromosome inactivation in mammals. , 2013, Current opinion in cell biology.

[5]  Jeannie T. Lee,et al.  Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome , 2008, Science.

[6]  Jeannie T. Lee,et al.  Jpx RNA Activates Xist by Evicting CTCF , 2013, Cell.

[7]  Robert E. Kingston,et al.  Occupying chromatin: Polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put. , 2013, Molecular cell.

[8]  Huntington F Willard,et al.  Multiple spatially distinct types of facultative heterochromatin on the human inactive X chromosome. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Forest M White,et al.  Molecular Characterization of EGFR and EGFRvIII Signaling Networks in Human Glioblastoma Tumor Xenografts* , 2012, Molecular & Cellular Proteomics.

[10]  Jeannie T. Lee.  Epigenetic Regulation by Long Noncoding RNAs , 2012, Science.

[11]  Jeannie T. Lee,et al.  A transient heterochromatic state in Xist preempts X inactivation choice without RNA stabilization. , 2006, Molecular cell.

[12]  Jeannie T. Lee,et al.  X-Inactivation, Imprinting, and Long Noncoding RNAs in Health and Disease , 2013, Cell.

[13]  S. Rafii,et al.  Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions , 2010, Cell.

[14]  Jeannie T. Lee,et al.  Tsix, a gene antisense to Xist at the X-inactivation centre , 1999, Nature Genetics.

[15]  J. Qin,et al.  The ATRX syndrome protein forms a chromatin-remodeling complex with Daxx and localizes in promyelocytic leukemia nuclear bodies , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[16]  Rudolf Jaenisch,et al.  Chromosomal silencing and localization are mediated by different domains of Xist RNA , 2002, Nature Genetics.

[17]  P. Park,et al.  Design and analysis of ChIP-seq experiments for DNA-binding proteins , 2008, Nature Biotechnology.

[18]  Sarah K. Bowman,et al.  High-resolution Xist binding maps reveal 2-step spreading during X-inactivation , 2013, Nature.

[19]  P. Sharp,et al.  14-3-3sigma controls mitotic translation to facilitate cytokinesis. , 2007, Nature.

[20]  Rolf Backofen,et al.  Tandem stem-loops in roX RNAs act together to mediate X chromosome dosage compensation in Drosophila. , 2013, Molecular cell.

[21]  Jeannie T. Lee,et al.  Perinucleolar Targeting of the Inactive X during S Phase: Evidence for a Role in the Maintenance of Silencing , 2007, Cell.

[22]  D. Higgs,et al.  Loss of Atrx Affects Trophoblast Development and the Pattern of X-Inactivation in Extraembryonic Tissues , 2006, PLoS genetics.

[23]  Jeannie T. Lee,et al.  The Long Noncoding RNA, Jpx, Is a Molecular Switch for X Chromosome Inactivation , 2010, Cell.

[24]  K. Stuart,et al.  Determinants for association and guide RNA-directed endonuclease cleavage by purified RNA editing complexes from Trypanosoma brucei. , 2008, Journal of molecular biology.

[25]  Richard A Young,et al.  Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2. , 2010, Molecular cell.

[26]  Kristian Helin,et al.  Chromatin proteins and modifications as drug targets , 2013, Nature.

[27]  A. Wutz.  Gene silencing in X-chromosome inactivation: advances in understanding facultative heterochromatin formation , 2011, Nature Reviews Genetics.

[28]  J. Mcneil,et al.  XIST RNA paints the inactive X chromosome at interphase: evidence for a novel RNA involved in nuclear/chromosome structure , 1996, The Journal of cell biology.

[29]  Forest M White,et al.  Computer aided manual validation of mass spectrometry-based proteomic data. , 2013, Methods.

[30]  B. Garcia,et al.  ATRX-mediated chromatin association of histone variant macroH2A1 regulates α-globin expression. , 2012, Genes & development.

[31]  J. Rinn,et al.  Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression , 2009, Proceedings of the National Academy of Sciences.

[32]  D. Reinberg,et al.  Interactions between JARID2 and noncoding RNAs regulate PRC2 recruitment to chromatin. , 2014, Molecular cell.

[33]  Combinatorial readout of histone H3 modifications specifies localization of ATRX to heterochromatin , 2011 .

[34]  M. Sternberg,et al.  Functional significance of mutations in the Snf2 domain of ATRX. , 2011, Human molecular genetics.

[35]  J. Starmer,et al.  A new model for random X chromosome inactivation , 2009, Development.

[36]  P. Becker,et al.  ATP-dependent roX RNA remodeling by the helicase maleless enables specific association of MSL proteins. , 2013, Molecular cell.

[37]  R. Shiekhattar,et al.  A Novel Transcription Regulatory Complex Containing Death Domain-associated Protein and the ATR-X Syndrome Protein* , 2004, Journal of Biological Chemistry.

[38]  Emilia Dimitrova,et al.  The ATRX-ADD domain binds to H3 tail peptides and reads the combined methylation state of K4 and K9. , 2011, Human molecular genetics.

[39]  Jeannie T. Lee,et al.  YY1 Tethers Xist RNA to the Inactive X Nucleation Center , 2011, Cell.

[40]  Dmitri A. Nusinow,et al.  Poly(ADP-ribose) Polymerase 1 Is Inhibited by a Histone H2A Variant, MacroH2A, and Contributes to Silencing of the Inactive X Chromosome* , 2007, Journal of Biological Chemistry.

[41]  Jeannie T. Lee,et al.  Intersection of the RNA Interference and X-Inactivation Pathways , 2008, Science.

[42]  S. Timsit,et al.  Specific interaction between the XNP/ATR-X gene product and the SET domain of the human EZH2 protein. , 1998, Human molecular genetics.

[43]  E. Bernstein,et al.  ATRX: the case of a peculiar chromatin remodeler. , 2013, Epigenetics.

[44]  Jeannie T. Lee,et al.  Regulatory interactions between RNA and polycomb repressive complex 2. , 2014, Molecular cell.

[45]  Toshiro K. Ohsumi,et al.  Genome-wide identification of polycomb-associated RNAs by RIP-seq. , 2010, Molecular cell.

[46]  C. Allis,et al.  Daxx is an H3.3-specific histone chaperone and cooperates with ATRX in replication-independent chromatin assembly at telomeres , 2010, Proceedings of the National Academy of Sciences.

[47]  D. Reinberg,et al.  Jarid2 Is Implicated in the Initial Xist-Induced Targeting of PRC2 to the Inactive X Chromosome. , 2014, Molecular cell.

[48]  C. Costanzi,et al.  Histone macroH2A1 is concentrated in the inactive X chromosome of female mammals , 1998, Nature.

[49]  T. Ohhata,et al.  A proximal conserved repeat in the Xist gene is essential as a genomic element for X-inactivation in mouse , 2009, Development.

[50]  R. D. L. Fuente,et al.  ATRX marks the inactive X chromosome (Xi) in somatic cells and during imprinted X chromosome inactivation in trophoblast stem cells , 2009, Chromosoma.

[51]  D. Higgs,et al.  The chromatin remodeller ATRX: a repeat offender in human disease. , 2013, Trends in biochemical sciences.

[52]  Toshiro K. Ohsumi,et al.  Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations , 2012, Genome research.

[53]  Steven J. M. Jones,et al.  ATR-X Syndrome Protein Targets Tandem Repeats and Influences Allele-Specific Expression in a Size-Dependent Manner , 2010, Cell.

[54]  V. Rybin,et al.  The Xist RNA A-repeat comprises a novel AUCG tetraloop fold and a platform for multimerization. , 2011, RNA.

[55]  D. Reinberg,et al.  PRC2 binds to active promoters and contacts nascent RNAs in embryonic stem cells , 2013, Nature Structural &Molecular Biology.

[56]  D. Patel,et al.  ATRX ADD domain links an atypical histone methylation recognition mechanism to human mental-retardation syndrome. , 2011, Nature structural & molecular biology.

[57]  I. Krantz,et al.  Mutations in the chromatin‐associated protein ATRX , 2008, Human mutation.

[58]  Jeannie T. Lee,et al.  X-chromosome hyperactivation in mammals via nonlinear relationships between chromatin states and transcription , 2011, Nature Structural &Molecular Biology.

[59]  J. Shendure,et al.  Global survey of escape from X inactivation by RNA-sequencing in mouse. , 2010, Genome research.

[60]  P. Avner,et al.  2-D Structure of the A Region of Xist RNA and Its Implication for PRC2 Association , 2010, PLoS biology.