The shared genomic architecture of human nucleolar organizer regions

The short arms of the five acrocentric human chromosomes harbor sequences that direct the assembly and function of the nucleolus, one of the key functional domains of the nucleus, yet they are absent from the current human genome assembly. Here we describe the genomic architecture of these human nucleolar organizers. Sequences distal and proximal to ribosomal gene arrays are conserved among the acrocentric chromosomes, suggesting they are sites of frequent recombination. Although previously believed to be heterochromatic, characterization of these two flanking regions reveals that they share a complex genomic architecture similar to other euchromatic regions of the genome, but they have distinct genomic characteristics. Proximal sequences are almost entirely segmentally duplicated, similar to the regions bordering centromeres. In contrast, the distal sequence is predominantly unique to the acrocentric short arms and is dominated by a very large inverted repeat. We show that the distal element is localized to the periphery of the nucleolus, where it appears to anchor the ribosomal gene repeats. This, combined with its complex chromatin structure and transcriptional activity, suggests that this region is involved in nucleolar organization. Our results provide a platform for investigating the role of NORs in nucleolar formation and function, and open the door for determining the role of these regions in the well-known empirical association of nucleoli with pathology.

[1]  Data production leads,et al.  An integrated encyclopedia of DNA elements in the human genome , 2012 .

[2]  Carleen Cullinane,et al.  Inhibition of RNA polymerase I as a therapeutic strategy to promote cancer-specific activation of p53. , 2012, Cancer cell.

[3]  ENCODEConsortium,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[4]  Manolis Kellis,et al.  ChromHMM: automating chromatin-state discovery and characterization , 2012, Nature Methods.

[5]  F. Recillas-Targa,et al.  Changes of the Nucleolus Architecture in Absence of the Nuclear Factor CTCF , 2012, Cytogenetic and Genome Research.

[6]  Nathan C. Sheffield,et al.  Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. , 2011, Genome research.

[7]  G. Längst,et al.  Genome organization in and around the nucleolus. , 2011, Trends in genetics : TIG.

[8]  Timothy J. Durham,et al.  "Systematic" , 1966, Comput. J..

[9]  Timothy J. Durham,et al.  Systematic analysis of chromatin state dynamics in nine human cell types , 2011, Nature.

[10]  N. Galjart,et al.  CTCF regulates the local epigenetic state of ribosomal DNA repeats , 2010, Epigenetics & Chromatin.

[11]  A. Lamond,et al.  High-Resolution Whole-Genome Sequencing Reveals That Specific Chromatin Domains from Most Human Chromosomes Associate with Nucleoli , 2010, Molecular biology of the cell.

[12]  Mary Goldman,et al.  The UCSC Genome Browser database: update 2011 , 2010, Nucleic Acids Res..

[13]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[14]  A. Conesa,et al.  Initial Genomics of the Human Nucleolus , 2010, PLoS genetics.

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

[16]  Takehiko Kobayashi,et al.  The effect of replication initiation on gene amplification in the rDNA and its relationship to aging. , 2009, Molecular cell.

[17]  V. Corces,et al.  CTCF: Master Weaver of the Genome , 2009, Cell.

[18]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[19]  Steven J. M. Jones,et al.  Abyss: a Parallel Assembler for Short Read Sequence Data Material Supplemental Open Access , 2022 .

[20]  L. Montanaro,et al.  What the nucleolus says to a tumour pathologist , 2009, Histopathology.

[21]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[22]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[23]  I. Grummt,et al.  The epigenetics of rRNA genes: from molecular to chromosome biology. , 2008, Annual review of cell and developmental biology.

[24]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[25]  Terrence S. Furey,et al.  F-Seq: a feature density estimator for high-throughput sequence tags , 2008, Bioinform..

[26]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[27]  Jonathan E. Allen,et al.  Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments , 2007, Genome Biology.

[28]  A. Pierce,et al.  Genomic architecture and inheritance of human ribosomal RNA gene clusters. , 2007, Genome research.

[29]  D. Hernandez-Verdun,et al.  Nucleolus: the fascinating nuclear body , 2007, Histochemistry and Cell Biology.

[30]  Antony V. Cox,et al.  Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21. , 2007, Genome research.

[31]  B. McStay,et al.  Recruitment of factors linking transcription and processing of pre-rRNA to NOR chromatin is UBF-dependent and occurs independent of transcription in human cells. , 2007, Genes & development.

[32]  F. Boisvert,et al.  The multifunctional nucleolus , 2007, Nature Reviews Molecular Cell Biology.

[33]  V. Iyer,et al.  FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. , 2007, Genome research.

[34]  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.

[35]  E. Eichler,et al.  Primate segmental duplications: crucibles of evolution, diversity and disease , 2006, Nature Reviews Genetics.

[36]  Terrence S. Furey,et al.  The UCSC Genome Browser Database: update 2006 , 2005, Nucleic Acids Res..

[37]  S. Edelstein,et al.  Human ribosomal RNA gene arrays display a broad range of palindromic structures. , 2005, Genome research.

[38]  J. Jurka,et al.  Repbase Update, a database of eukaryotic repetitive elements , 2005, Cytogenetic and Genome Research.

[39]  Gregory Kucherov,et al.  YASS: enhancing the sensitivity of DNA similarity search , 2005, Nucleic Acids Res..

[40]  Mark Borodovsky,et al.  GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses , 2005, Nucleic Acids Res..

[41]  Carla Grandori,et al.  c-Myc binds to human ribosomal DNA and stimulates transcription of rRNA genes by RNA polymerase I , 2005, Nature Cell Biology.

[42]  Ewan Birney,et al.  Automated generation of heuristics for biological sequence comparison , 2005, BMC Bioinformatics.

[43]  Anthony K. L. Leung,et al.  Nucleolar proteome dynamics , 2005, Nature.

[44]  Steven Salzberg,et al.  TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders , 2004, Bioinform..

[45]  E. Lander,et al.  Finishing the euchromatic sequence of the human genome , 2004 .

[46]  J. Bonfield,et al.  Finishing the euchromatic sequence of the human genome , 2004, Nature.

[47]  D. Haussler,et al.  The structure and evolution of centromeric transition regions within the human genome , 2004, Nature.

[48]  Lior Pachter,et al.  VISTA: computational tools for comparative genomics , 2004, Nucleic Acids Res..

[49]  Stephen M. Mount,et al.  Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. , 2003, Nucleic acids research.

[50]  I. Grummt.  Life on a planet of its own: regulation of RNA polymerase I transcription in the nucleolus. , 2003, Genes & development.

[51]  E. Birney,et al.  Apollo: a sequence annotation editor , 2002, Genome Biology.

[52]  T. Misteli,et al.  A Kinetic Framework for a Mammalian RNA Polymerase in Vivo , 2002, Science.

[53]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[54]  M. Mann,et al.  Directed Proteomic Analysis of the Human Nucleolus , 2002, Current Biology.

[55]  W. Bickmore,et al.  Human acrocentric chromosomes with transcriptionally silent nucleolar organizer regions associate with nucleoli , 2001, The EMBO journal.

[56]  M. Rocchi,et al.  The structure of duplications on human acrocentric chromosome short arms derived by the analysis of 15p , 2001, Human Genetics.

[57]  J. D. De Mey,et al.  Nucleolar Assembly of the Rrna Processing Machinery in Living Cells , 2001, The Journal of cell biology.

[58]  B. Trask,et al.  Segmental duplications: organization and impact within the current human genome project assembly. , 2001, Genome research.

[59]  S. Smith,et al.  Rb and p130 regulate RNA polymerase I transcription: Rb disrupts the interaction between UBF and SL-1 , 2000, Oncogene.

[60]  I. Longden,et al.  EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.

[61]  V. Solovyev,et al.  Ab initio gene finding in Drosophila genomic DNA. , 2000, Genome research.

[62]  Angelika Amon,et al.  Cfi1 prevents premature exit from mitosis by anchoring Cdc14 phosphatase in the nucleolus , 1999, Nature.

[63]  A. Budde,et al.  p53 represses ribosomal gene transcription , 1999, Oncogene.

[64]  J. Sylvester,et al.  Beyond ribosomal DNA: on towards the telomere , 1997, Chromosoma.

[65]  S. Karlin,et al.  Prediction of complete gene structures in human genomic DNA. , 1997, Journal of molecular biology.

[66]  P. D. de Jong,et al.  Human ribosomal RNA gene cluster: identification of the proximal end containing a novel tandem repeat sequence. , 1995, Genomics.

[67]  A Bensimon,et al.  Alignment and sensitive detection of DNA by a moving interface. , 1994, Science.

[68]  C. Denniston,et al.  The nonrandom participation of human acrocentric chromosomes in Robertsonian translocations , 1989, Annals of human genetics.

[69]  Prof. Dr. Asen A. Hadjiolov.  The Nucleolus and Ribosome Biogenesis , 1985, Cell Biology Monographs.

[70]  A. Henderson,et al.  Location of ribosomal DNA in the human chromosome complement. , 1972, Proceedings of the National Academy of Sciences of the United States of America.

[71]  Kazutaka Katoh,et al.  Multiple alignment of DNA sequences with MAFFT. , 2009, Methods in molecular biology.

[72]  B. McStay,et al.  UBF-binding site arrays form pseudo-NORs and sequester the RNA polymerase I transcription machinery. , 2005, Genes & development.

[73]  B. Mcclintock.  The relation of a particular chromosomal element to the development of the nucleoli in Zea mays , 2004, Zeitschrift für Zellforschung und Mikroskopische Anatomie.

[74]  N. Blin,et al.  A novel centromeric repetitive DNA from human chromosome 22 , 2004, Chromosoma.

[75]  Ravi Kumar,et al.  Structure and Evolution Of , 2004 .

[76]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

[77]  R G Worton,et al.  Human ribosomal RNA genes: orientation of the tandem array and conservation of the 5' end. , 1988, Science.

[78]  R. Schmickel.  Quantitation of Human Ribosomal DNA: Hybridization of Human DNA with Ribosomal RNA for Quantitation and Fractionation , 1973, Pediatric Research.