Novel players in X inactivation: insights into Xist-mediated gene silencing and chromosome conformation

The nuclear long noncoding RNA (lncRNA) Xist ensures X-chromosome inactivation (XCI) in female placental mammals. Although Xist is one of the most intensively studied lncRNAs, the mechanisms associated with its capacity to trigger chromosome-wide gene silencing, the formation of facultative heterochromatin and an unusual 3D conformation of the inactive X chromosome (Xi) have remained elusive. Now researchers have identified novel functional partners of Xist in a series of breakthrough studies, using unbiased techniques to isolate Xist-bound proteins, as well as forward genetic screens. In addition, important insights into the 3D organization of Xi and its relation to gene expression have been obtained. In this Review, we discuss how this new information is providing a recipe for deciphering XCI mechanisms by which a multitasking RNA can structurally and functionally transform an active chromosome into uniquely organized facultative heterochromatin.

[1]  Kaoru Inoue,et al.  SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells , 2016, Proceedings of the National Academy of Sciences.

[2]  N. Brockdorff Noncoding RNA and Polycomb recruitment. , 2013, RNA.

[3]  R. Grosschedl,et al.  Satb1 and Satb2 are dispensable for X chromosome inactivation in mice. , 2012, Developmental cell.

[4]  William Stafford Noble,et al.  The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation , 2015, Genome Biology.

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

[6]  J. Sedat,et al.  Spatial partitioning of the regulatory landscape of the X-inactivation centre , 2012, Nature.

[7]  T. Magnuson,et al.  The mouse DXZ4 homolog retains Ctcf binding and proximity to Pls3 despite substantial organizational differences compared to the primate macrosatellite , 2012, Genome Biology.

[8]  Michael J. Sweredoski,et al.  The Xist lncRNA directly interacts with SHARP to silence transcription through HDAC3 , 2015, Nature.

[9]  Samie R. Jaffrey,et al.  m6A RNA methylation promotes XIST-mediated transcriptional repression , 2016, Nature.

[10]  Y. Jan,et al.  Mutations that affect the length, fasciculation, or ventral orientation of specific sensory axons in the Drosophila embryo , 1995, Neuron.

[11]  Carolyn J. Brown,et al.  A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome , 1991, Nature.

[12]  Jeong-Heon Lee,et al.  Rbm15-Mkl1 Interacts with the Setd1b Histone H3-Lys4 Methyltransferase via a SPOC Domain That Is Required for Cytokine-Independent Proliferation , 2012, PloS one.

[13]  L. Kenner,et al.  SATB1 defines the developmental context for gene silencing by Xist in lymphoma and embryonic cells. , 2009, Developmental cell.

[14]  Brian J. Beliveau,et al.  Spatial organization of chromatin domains and compartments in single chromosomes , 2016, Science.

[15]  Howard Y. Chang,et al.  Structural organization of the inactive X chromosome in the mouse , 2016, Nature.

[16]  J. Mcneil,et al.  The X chromosome is organized into a gene-rich outer rim and an internal core containing silenced nongenic sequences , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[17]  William Stafford Noble,et al.  Bipartite structure of the inactive mouse X chromosome , 2015, Genome Biology.

[18]  T B Nesterova,et al.  Characterization of the genomic Xist locus in rodents reveals conservation of overall gene structure and tandem repeats but rapid evolution of unique sequence. , 2001, Genome research.

[19]  Thomas Cremer,et al.  Three-dimensional super-resolution microscopy of the inactive X chromosome territory reveals a collapse of its active nuclear compartment harboring distinct Xist RNA foci , 2014, Epigenetics & Chromatin.

[20]  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.

[21]  Andrew R. Bassett,et al.  Jarid2 binds mono-ubiquitylated H2A lysine 119 to mediate crosstalk between Polycomb complexes PRC1 and PRC2 , 2016, Nature Communications.

[22]  N. Brockdorff,et al.  A Pooled shRNA Screen Identifies Rbm15, Spen, and Wtap as Factors Required for Xist RNA-Mediated Silencing , 2015, Cell reports.

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

[24]  B. Panning,et al.  The Polycomb group protein Eed protects the inactive X-chromosome from differentiation-induced reactivation , 2006, Nature Cell Biology.

[25]  E. Nora,et al.  CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation. , 2016, Annual review of genomics and human genetics.

[26]  J. Gribnau,et al.  Cis- and trans-regulation in X inactivation , 2015, Chromosoma.

[27]  Jeannie T. Lee,et al.  Chromosomes. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation. , 2015, Science.

[28]  N. Little,et al.  Identification of WTAP, a novel Wilms' tumour 1-associating protein. , 2000, Human molecular genetics.

[29]  M. Leeb,et al.  The Trithorax group protein Ash2l and Saf-A are recruited to the inactive X chromosome at the onset of stable X inactivation , 2010, Development.

[30]  T. Cech,et al.  Toward a consensus on the binding specificity and promiscuity of PRC2 for RNA. , 2015, Molecular cell.

[31]  Kyoung-Jae Won,et al.  Nuclear Receptor Corepressors are Required for the Histone Deacetylase Activity of HDAC3 In Vivo , 2012, Nature Structural &Molecular Biology.

[32]  Irmtraud M. Meyer,et al.  A cross-species comparison of X-chromosome inactivation in Eutheria. , 2007, Genomics.

[33]  G. Montana,et al.  Smchd1-Dependent and -Independent Pathways Determine Developmental Dynamics of CpG Island Methylation on the Inactive X Chromosome , 2012, Developmental cell.

[34]  Shinichi Nakagawa,et al.  Xist Exon 7 Contributes to the Stable Localization of Xist RNA on the Inactive X-Chromosome , 2015, PLoS genetics.

[35]  Anton Wutz,et al.  A Chromosomal Memory Triggered by Xist Regulates Histone Methylation in X Inactivation , 2004, PLoS biology.

[36]  G. Dreyfuss,et al.  The pre-mRNA binding K protein contains a novel evolutionarily conserved motif. , 1993, Nucleic acids research.

[37]  Ruslan Sadreyev,et al.  ATRX Directs Binding of PRC2 to Xist RNA and Polycomb Targets , 2014, Cell.

[38]  Noah Ollikainen,et al.  Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing , 2016, Science.

[39]  S. Rastan,et al.  Requirement for Xist in X chromosome inactivation , 1996, Nature.

[40]  M. McArthur,et al.  hnRNP K Is a Haploinsufficient Tumor Suppressor that Regulates Proliferation and Differentiation Programs in Hematologic Malignancies. , 2015, Cancer cell.

[41]  B. Chadwick,et al.  DXZ4 chromatin adopts an opposing conformation to that of the surrounding chromosome and acquires a novel inactive X-specific role involving CTCF and antisense transcripts. , 2008, Genome research.

[42]  Ruslan Sadreyev,et al.  ATRX Directs Binding of PRC2 to Xist RNA and Polycomb Targets , 2014, Cell.

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

[44]  Monika Zwerger,et al.  Lamin B receptor , 2010, Nucleus.

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

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

[47]  H. Aburatani,et al.  Wilms' tumor 1-associating protein regulates G2/M transition through stabilization of cyclin A2 mRNA , 2006, Proceedings of the National Academy of Sciences.

[48]  S. D. Brown XIST and the mapping of the X chromosome inactivation centre. , 1991, BioEssays : news and reviews in molecular, cellular and developmental biology.

[49]  T. Cremer,et al.  A top-down analysis of Xa- and Xi-territories reveals differences of higher order structure at ≥ 20 Mb genomic length scales , 2011, Nucleus.

[50]  T. Honjo,et al.  Regulation of marginal zone B cell development by MINT, a suppressor of Notch/RBP-J signaling pathway. , 2003, Immunity.

[51]  Jesse R. Dixon,et al.  Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions , 2012, Nature.

[52]  Jill P. Mesirov,et al.  RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure , 2016, Cell.

[53]  I. Amit,et al.  Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .

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

[55]  G. Pavlakis,et al.  Nuclear export factor RBM15 facilitates the access of DBP5 to mRNA , 2009, Nucleic acids research.

[56]  Makoto Naito,et al.  Identification of Wilms' Tumor 1-associating Protein Complex and Its Role in Alternative Splicing and the Cell Cycle* , 2013, The Journal of Biological Chemistry.

[57]  N. Brockdorff,et al.  Control of Chromosomal Localization of Xist by hnRNP U Family Molecules. , 2016, Developmental cell.

[58]  Samie R. Jaffrey,et al.  The dynamic epitranscriptome: N6-methyladenosine and gene expression control , 2014, Nature Reviews Molecular Cell Biology.

[59]  M. Mann,et al.  Stable isotope labeling by amino acids in cell culture for quantitative proteomics. , 2007, Methods in molecular biology.

[60]  T. Magnuson,et al.  Imprinted X inactivation maintained by a mouse Polycomb group gene , 2001, Nature Genetics.

[61]  E. Heard,et al.  Evolutionary diversity and developmental regulation of X-chromosome inactivation , 2011, Human Genetics.

[62]  N. Brockdorff,et al.  The matrix protein hnRNP U is required for chromosomal localization of Xist RNA. , 2010, Developmental cell.

[63]  Mariko Ariyoshi,et al.  A conserved structural motif reveals the essential transcriptional repression function of Spen proteins and their role in developmental signaling. , 2003, Genes & development.

[64]  R. Jaenisch,et al.  Xist-deficient mice are defective in dosage compensation but not spermatogenesis. , 1997, Genes & development.

[65]  W. V. van IJcken,et al.  The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA. , 2011, Genes & development.

[66]  Schraga Schwartz,et al.  Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites. , 2014, Cell reports.

[67]  Samir Adhikari,et al.  Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase , 2014, Cell Research.

[68]  Walter N. Moss,et al.  Probing Xist RNA Structure in Cells Using Targeted Structure-Seq , 2015, PLoS genetics.

[69]  A. Belmont,et al.  The facultative heterochromatin of the inactive X chromosome has a distinctive condensed ultrastructure , 2008, Journal of Cell Science.

[70]  E. Heard,et al.  A novel role for Xist RNA in the formation of a repressive nuclear compartment into which genes are recruited when silenced. , 2006, Genes & development.

[71]  M. Guttman,et al.  Methods for comprehensive experimental identification of RNA-protein interactions , 2014, Genome Biology.

[72]  Neva C. Durand,et al.  Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture , 2016, Proceedings of the National Academy of Sciences.

[73]  Dean Nizetic,et al.  Fusion of two novel genes, RBM15 and MKL1, in the t(1;22)(p13;q13) of acute megakaryoblastic leukemia , 2001, Nature Genetics.

[74]  R. Evans,et al.  Sharp, an inducible cofactor that integrates nuclear receptor repression and activation. , 2001, Genes & development.

[75]  G. Kay,et al.  SmcHD1, containing a structural-maintenance-of-chromosomes hinge domain, has a critical role in X inactivation , 2008, Nature Genetics.

[76]  Dominic P. Norris,et al.  The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus , 1992, Cell.

[77]  Neva C. Durand,et al.  A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.

[78]  S. Thore,et al.  Identification of Spen as a Crucial Factor for Xist Function through Forward Genetic Screening in Haploid Embryonic Stem Cells , 2015, Cell reports.

[79]  Qiangfeng Cliff Zhang,et al.  Systematic Discovery of Xist RNA Binding Proteins , 2015, Cell.

[80]  S. Thore,et al.  The crystal structure of the Split End protein SHARP adds a new layer of complexity to proteins containing RNA recognition motifs , 2014, Nucleic acids research.

[81]  J. Lawrence,et al.  SAF-A Requirement in Anchoring XIST RNA to Chromatin Varies in Transformed and Primary Cells. , 2016, Developmental cell.

[82]  Eric S. Lander,et al.  A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2015, Cell.

[83]  R. Jaenisch,et al.  A shift from reversible to irreversible X inactivation is triggered during ES cell differentiation. , 2000, Molecular cell.

[84]  E. Heard,et al.  X-chromosome inactivation: new insights into cis and trans regulation. , 2015, Current opinion in genetics & development.