SAF-A Regulates Interphase Chromosome Structure through Oligomerization with Chromatin-Associated RNAs

[1]  D. Norman,et al.  Quantitative FLIM-FRET Microscopy to Monitor Nanoscale Chromatin Compaction In Vivo Reveals Structural Roles of Condensin Complexes. , 2017, Cell reports.

[2]  J. Rinn,et al.  "Cat's Cradling" the 3D Genome by the Act of LncRNA Transcription. , 2016, Molecular cell.

[3]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using MODELLER , 2016, Current protocols in bioinformatics.

[4]  Davide Marenduzzo,et al.  Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains , 2016, Nucleic acids research.

[5]  J. Lawrence,et al.  RNA as a fundamental component of interphase chromosomes: could repeats prove key? , 2016, Current opinion in genetics & development.

[6]  Leonid A. Mirny,et al.  Super-resolution imaging reveals distinct chromatin folding for different epigenetic states , 2015, Nature.

[7]  R. Baldock,et al.  eMouseAtlas informatics: embryo atlas and gene expression database , 2015, Mammalian Genome.

[8]  J. Tapia,et al.  hnRNP U protein is required for normal pre-mRNA splicing and postnatal heart development and function , 2015, Proceedings of the National Academy of Sciences.

[9]  S. Lees-Miller,et al.  Phosphorylation of SAF-A/hnRNP-U Serine 59 by Polo-Like Kinase 1 Is Required for Mitosis , 2015, Molecular and Cellular Biology.

[10]  Michael J E Sternberg,et al.  The Phyre2 web portal for protein modeling, prediction and analysis , 2015, Nature Protocols.

[11]  D. Gallie Faculty Opinions recommendation of The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. , 2015 .

[12]  L. Hurst,et al.  Neighboring Genes Show Correlated Evolution in Gene Expression , 2015, Molecular biology and evolution.

[13]  Tomas W. Fitzgerald,et al.  Large-scale discovery of novel genetic causes of developmental disorders , 2014, Nature.

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

[15]  C. Delteil,et al.  DNA damage triggers SAF-A and RNA biogenesis factors exclusion from chromatin coupled to R-loops removal , 2014, Nucleic acids research.

[16]  N. Gilbert,et al.  Interphase Chromatin LINEd with RNA , 2014, Cell.

[17]  J. Lawrence,et al.  Stable C0T-1 Repeat RNA Is Abundant and Is Associated with Euchromatic Interphase Chromosomes , 2014, Cell.

[18]  Andrew S. Belmont,et al.  Large-scale chromatin organization: the good, the surprising, and the still perplexing. , 2014, Current opinion in cell biology.

[19]  S. Richard,et al.  Defining the RGG/RG motif. , 2013, Molecular cell.

[20]  M. Durante,et al.  Clustered DNA damage induces pan-nuclear H2AX phosphorylation mediated by ATM and DNA–PK , 2013, Nucleic acids research.

[21]  S. Cockroft,et al.  Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures , 2013, Nature Structural &Molecular Biology.

[22]  J. Rappsilber,et al.  Mitotic chromosomes are compacted laterally by KIF4 and condensin and axially by topoisomerase IIα , 2012, The Journal of cell biology.

[23]  K. Rippe,et al.  Nuclear architecture by RNA. , 2012, Current opinion in genetics & development.

[24]  C. Shao,et al.  Nuclear matrix factor hnRNP U/SAF-A exerts a global control of alternative splicing by regulating U2 snRNP maturation. , 2012, Molecular cell.

[25]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[26]  David R. Kelley,et al.  Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.

[27]  Peter J. Stuckey,et al.  Automatic generation of protein structure cartoons with Pro-origami , 2011, Bioinform..

[28]  N. Horton Faculty Opinions recommendation of DNA stretching by bacterial initiators promotes replication origin opening. , 2011 .

[29]  N. Gilbert,et al.  Analysis of Active and Inactive X Chromosome Architecture Reveals the Independent Organization of 30 nm and Large-Scale Chromatin Structures , 2010, Molecular cell.

[30]  J. Berger,et al.  Origin Remodeling and Opening in Bacteria Rely on Distinct Assembly States of the DnaA Initiator , 2010, The Journal of Biological Chemistry.

[31]  Miki Ebisuya,et al.  Ripples from neighbouring transcription , 2008, Nature Cell Biology.

[32]  Kengo Kinoshita,et al.  Prediction of disordered regions in proteins based on the meta approach , 2008, Bioinform..

[33]  Jan Koster,et al.  The Three-Dimensional Structure of Human Interphase Chromosomes Is Related to the Transcriptome Map , 2007, Molecular and Cellular Biology.

[34]  A. Sali,et al.  Statistical potential for assessment and prediction of protein structures , 2006, Protein science : a publication of the Protein Society.

[35]  S. Guil,et al.  hnRNP A1 Relocalization to the Stress Granules Reflects a Role in the Stress Response , 2006, Molecular and Cellular Biology.

[36]  J. Berger,et al.  Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling , 2006, Nature Structural &Molecular Biology.

[37]  J. Berger,et al.  Evolutionary relationships and structural mechanisms of AAA+ proteins. , 2006, Annual review of biophysics and biomolecular structure.

[38]  H. Ruley,et al.  Hypomorphic mutation in hnRNP U results in post-implantation lethality , 2005, Transgenic Research.

[39]  Nick Gilbert,et al.  Chromatin Architecture of the Human Genome Gene-Rich Domains Are Enriched in Open Chromatin Fibers , 2004, Cell.

[40]  Tom Misteli,et al.  Global Nature of Dynamic Protein-Chromatin Interactions In Vivo: Three-Dimensional Genome Scanning and Dynamic Interaction Networks of Chromatin Proteins , 2004, Molecular and Cellular Biology.

[41]  F. O. Fackelmayer,et al.  Scaffold attachment factor A (SAF-A) is concentrated in inactive X chromosome territories through its RGG domain , 2003, Chromosoma.

[42]  Wendy A Bickmore,et al.  Chromatin Motion Is Constrained by Association with Nuclear Compartments in Human Cells , 2002, Current Biology.

[43]  R. Hancock A new look at the nuclear matrix , 2000, Chromosoma.

[44]  E. Koonin,et al.  SAP - a putative DNA-binding motif involved in chromosomal organization. , 2000, Trends in biochemical sciences.

[45]  D. Jackson,et al.  The balance sheet for transcription: an analysis of nuclear RNA metabolism in mammalian cells , 2000, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[46]  Hong Ma,et al.  Association of Chromosome Territories with the Nuclear Matrix , 1999, The Journal of cell biology.

[47]  Peter Teague,et al.  Differences in the Localization and Morphology of Chromosomes in the Human Nucleus , 1999, The Journal of cell biology.

[48]  Patrice Gouet,et al.  ESPript: analysis of multiple sequence alignments in PostScript , 1999, Bioinform..

[49]  J Schultz,et al.  SMART, a simple modular architecture research tool: identification of signaling domains. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[50]  T. Pederson Thinking about a nuclear matrix. , 1998, Journal of molecular biology.

[51]  B. Schwab,et al.  The novel SAR‐binding domain of scaffold attachment factor A (SAF‐A) is a target in apoptotic nuclear breakdown , 1997, The EMBO journal.

[52]  P Bork,et al.  SPRY domains in ryanodine receptors (Ca(2+)-release channels). , 1997, Trends in biochemical sciences.

[53]  S. Bell,et al.  Coordinate Binding of ATP and Origin DNA Regulates the ATPase Activity of the Origin Recognition Complex , 1997, Cell.

[54]  F. O. Fackelmayer,et al.  Characterization of SAF‐A, a novel nuclear DNA binding protein from HeLa cells with high affinity for nuclear matrix/scaffold attachment DNA elements. , 1992, The EMBO journal.

[55]  G. Dreyfuss,et al.  Primary structure and binding activity of the hnRNP U protein: binding RNA through RGG box. , 1992, The EMBO journal.

[56]  David A. Agard,et al.  Large-scale chromatin structural domains within mitotic and interphase chromosomes in vivo and in vitro , 1989, Chromosoma.

[57]  A. Kornberg,et al.  ATP activates dnaA protein in initiating replication of plasmids bearing the origin of the E. coli chromosome , 1987, Cell.

[58]  S. Penman,et al.  Association of RNA with the Cytoskeleton and the Nuclear Matrix , 1986, Journal of Cell Science.

[59]  R Berezney,et al.  Identification of a nuclear protein matrix. , 1974, Biochemical and biophysical research communications.

[60]  D. Holmes,et al.  Chromosomal RNA: Its Properties , 1972, Science.