The Architecture of a Scrambled Genome Reveals Massive Levels of Genomic Rearrangement during Development

[1]  M. Yao,et al.  The controlling sequence for site-specific chromosome breakage in tetrahymena , 1990, Cell.

[2]  D. Prescott,et al.  Organization of gene and non-gene sequences in micronuclear DNA of Oxytricha nova. , 1983, Nucleic acids research.

[3]  Deqing Hu,et al.  A role for H3K4 monomethylation in gene repression and partitioning of chromatin readers. , 2014, Molecular cell.

[4]  International Human Genome Sequencing Consortium.  Initial sequencing and analysis of the human genome , 2001, Nature.

[5]  David L. Steffen,et al.  The genome of the social amoeba Dictyostelium discoideum , 2005, Nature.

[6]  T. Doak.  A proposed superfamily of transposase-related genes: new members in transposon-like elements of ciliated protozoa and a common "D35E" motif , 1994 .

[7]  W. Ludwig,et al.  SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB , 2007, Nucleic acids research.

[8]  O. Elemento,et al.  Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons , 2012, Cell.

[9]  S. Cartinhour,et al.  Elimination of germ-line tandemly repeated sequences from the somatic genome of the ciliate Oxytricha fallax , 2004, Chromosoma.

[10]  N. Friedman,et al.  Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.

[11]  William Stafford Noble,et al.  Semi-supervised learning for peptide identification from shotgun proteomics datasets , 2007, Nature Methods.

[12]  Laura F. Landweber,et al.  RNA-mediated epigenetic programming of a genome-rearrangement pathway , 2008, Nature.

[13]  L. Katz,et al.  Smith ScholarWorks Smith ScholarWorks Alternative Processing of Scrambled Genes Generates Protein Alternative Processing of Scrambled Genes Generates Protein Diversity in the Ciliate Diversity in the Ciliate Chilodonella uncinata Chilodonella uncinata , 2022 .

[14]  L. Klobutcher,et al.  Consensus inverted terminal repeat sequence of Paramecium IESs: resemblance to termini of Tc1-related and Euplotes Tec transposons. , 1995, Nucleic acids research.

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

[16]  F. Jönsson,et al.  Both subtelomeric regions are required and sufficient for specific DNA fragmentation during macronuclear development in Stylonychia lemnae , 2001, Genome Biology.

[17]  M. Mann,et al.  Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. , 2003, Analytical chemistry.

[18]  J. Vermeesch,et al.  Conserved DNA sequences adjacent to chromosome fragmentation and telomere addition sites in Euplotes crassus. , 1998, Nucleic acids research.

[19]  Sean R. Eddy,et al.  Rfam 11.0: 10 years of RNA families , 2012, Nucleic Acids Res..

[20]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[21]  Sean R. Eddy,et al.  Infernal 1.0: inference of RNA alignments , 2009, Bioinform..

[22]  Zhengwei Zhu,et al.  CD-HIT: accelerated for clustering the next-generation sequencing data , 2012, Bioinform..

[23]  S. Eddy,et al.  Automated de novo identification of repeat sequence families in sequenced genomes. , 2002, Genome research.

[24]  Sara L. Zimmer,et al.  The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions , 2007, Science.

[25]  Michael Roberts,et al.  The MaSuRCA genome assembler , 2013, Bioinform..

[26]  C. Baker,et al.  Genetic Consequences of Programmed Genome Rearrangement , 2012, Current Biology.

[27]  D M Prescott,et al.  The evolutionary scrambling and developmental unscrambling of germline genes in hypotrichous ciliates. , 1999, Nucleic acids research.

[28]  D. Prescott,et al.  DNA of ciliated protozoa , 1971, Chromosoma.

[29]  L. Landweber,et al.  Complex germline architecture: two genes intertwined on two loci. , 2006, Molecular biology and evolution.

[30]  E. Lander,et al.  Genomic mapping by fingerprinting random clones: a mathematical analysis. , 1988, Genomics.

[31]  Bronwen L. Aken,et al.  GENCODE: The reference human genome annotation for The ENCODE Project , 2012, Genome research.

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

[33]  AC Tose.  Cell , 1993, Cell.

[34]  Patricia Siguier,et al.  ISfinder: the reference centre for bacterial insertion sequences , 2005, Nucleic Acids Res..

[35]  G. Crooks,et al.  WebLogo: a sequence logo generator. , 2004, Genome research.

[36]  R. Guigó,et al.  Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia , 2006, Nature.

[37]  M. Mann,et al.  In-gel digestion for mass spectrometric characterization of proteins and proteomes , 2006, Nature Protocols.

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

[39]  J. Matese,et al.  The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes , 2013, PLoS biology.

[40]  William H. Majoros,et al.  Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote , 2006, PLoS biology.

[41]  Benjamin E. Lauderdale,et al.  The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences , 2012, PLoS genetics.

[42]  A. Zahler,et al.  Telomere terminal transferase activity in the hypotrichous ciliate Oxytricha nova and a model for replication of the ends of linear DNA molecules. , 1988, Nucleic acids research.

[43]  L. Landweber,et al.  A Functional Role for Transposases in a Large Eukaryotic Genome , 2009, Science.

[44]  L. Landweber,et al.  Piwi-Interacting RNAs Protect DNA against Loss during Oxytricha Genome Rearrangement , 2012, Cell.

[45]  Thomas G Doak,et al.  Telomere formation on macronuclear chromosomes of Oxytricha trifallax and O. fallax: alternatively processed regions have multiple telomere addition sites , 2002, BMC Genetics.

[46]  L. Klobutcher,et al.  A development‐specific histone H3 localizes to the developing macronucleus of Euplotes , 2000, Genesis.

[47]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[48]  J. Fillingham,et al.  A Non-Long Terminal Repeat Retrotransposon Family Is Restricted to the Germ Line Micronucleus of the Ciliated Protozoan Tetrahymena thermophila , 2004, Eukaryotic Cell.

[49]  T. Doak,et al.  A proposed superfamily of transposase genes: transposon-like elements in ciliated protozoa and a common "D35E" motif. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[50]  N. Lennon,et al.  Characterizing and measuring bias in sequence data , 2013, Genome Biology.

[51]  D. Shippen,et al.  Developmentally Programmed Gene Elimination in Euplotes crassus Facilitates a Switch in the Telomerase Catalytic Subunit , 2003, Cell.

[52]  Makedonka Mitreva,et al.  Silencing of germline-expressed genes by DNA elimination in somatic cells. , 2012, Developmental cell.

[53]  T. Ried,et al.  Faculty Opinions recommendation of Massive genomic rearrangement acquired in a single catastrophic event during cancer development. , 2011 .

[54]  L. Klobutcher,et al.  Developmental genome reorganization in ciliated protozoa: the transposon link. , 1997, Progress in nucleic acid research and molecular biology.

[55]  Robert D. Finn,et al.  HMMER web server: interactive sequence similarity searching , 2011, Nucleic Acids Res..

[56]  L. Landweber,et al.  RNA-mediated epigenetic regulation of DNA copy number , 2010, Proceedings of the National Academy of Sciences.

[57]  J. Seger,et al.  Selection on the protein-coding genes of the TBE1 family of transposable elements in the ciliates Oxytricha fallax and O. trifallax. , 1997, Molecular biology and evolution.

[58]  D M Prescott,et al.  Internal Eliminated Segments (IESs) of Oxytrichidae 1 , 1996, Journal of Eukaryotic Microbiology.

[59]  Sergey Koren,et al.  Aggressive assembly of pyrosequencing reads with mates , 2008, Bioinform..

[60]  Gertraud Burger,et al.  AutoFACT: An Automatic Functional Annotation and Classification Tool , 2005, BMC Bioinformatics.

[61]  L. Klobutcher.  Micronuclear organization of macronuclear genes in the hypotrichous ciliate Oxytricha nova. , 1987, The Journal of protozoology.

[62]  R. Durbin,et al.  Efficient de novo assembly of large genomes using compressed data structures. , 2012, Genome research.

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

[64]  M. Batzer,et al.  Repetitive Elements May Comprise Over Two-Thirds of the Human Genome , 2011, PLoS genetics.

[65]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[66]  Siu-Ming Yiu,et al.  IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth , 2012, Bioinform..

[67]  Laura F. Landweber,et al.  MDS_IES_DB: a database of macronuclear and micronuclear genes in spirotrichous ciliates , 2005, Nucleic Acids Res..

[68]  B. Spear,et al.  Polytene chromosomes of Oxytricha: Biochemical and morphological changes during macronuclear development in a ciliated protozoan , 1976, Chromosoma.

[69]  Huanming Yang,et al.  De novo assembly of human genomes with massively parallel short read sequencing. , 2010, Genome research.

[70]  Olivier Arnaiz,et al.  ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia , 2010, Nucleic Acids Res..

[71]  T. Fennell,et al.  Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries , 2011, Genome Biology.

[72]  Dalong Ma,et al.  Nested genes in the human genome. , 2005, Genomics.

[73]  Nikhil A. Joshi,et al.  Genome-Scale Analysis of Programmed DNA Elimination Sites in Tetrahymena thermophila , 2011, G3: Genes | Genomes | Genetics.

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

[75]  D. Prescott,et al.  DNA of ciliated protozoa: DNA sequence diminution during macronuclear development of oxytricha , 1976, Cell.

[76]  Terrence S. Furey,et al.  The UCSC Table Browser data retrieval tool , 2004, Nucleic Acids Res..

[77]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[78]  L. Holm,et al.  The Pfam protein families database , 2005, Nucleic Acids Res..

[79]  Lawrence A. Klobutcher,et al.  Alternative use of chromosome fragmentation sites in the ciliated protozoan Oxytricha nova , 1988, Nucleic Acids Res..

[80]  Michael P. Snyder,et al.  Extensive genetic variation in somatic human tissues , 2012, Proceedings of the National Academy of Sciences.

[81]  Philippe Dessen,et al.  Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: a somatic view of the germline. , 2008, Genome research.

[82]  Robert C. Edgar,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2001 .

[83]  M. R. Esteban,et al.  Chromosome elimination in sciarid flies , 2001, BioEssays : news and reviews in molecular, cellular and developmental biology.

[84]  Andre R. O. Cavalcanti,et al.  Sequence features of Oxytricha trifallax (class Spirotrichea) macronuclear telomeric and subtelomeric sequences. , 2004, Protist.

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

[86]  D. Ang,et al.  Mobile elements bounded by C4A4 telomeric repeats in oxytricha fallax , 1985, Cell.

[87]  N. Carter,et al.  Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development , 2011, Cell.

[88]  E. Mardis,et al.  The Oxytricha trifallax Mitochondrial Genome , 2011, Genome biology and evolution.

[89]  Glenn Tesler,et al.  Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory , 2012, BMC Bioinformatics.

[90]  Pavel A. Pevzner,et al.  De novo identification of repeat families in large genomes , 2005, ISMB.

[91]  Aaron A. Klammer,et al.  Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data , 2013, Nature Methods.

[92]  Anuj Kumar,et al.  An Overview of Nested Genes in Eukaryotic Genomes , 2009, Eukaryotic Cell.

[93]  Burkhard Morgenstern,et al.  AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints , 2005, Nucleic Acids Res..