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Laura F Landweber - One of the best experts on this subject based on the ideXlab platform.
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capture of complete ciliate chromosomes in single sequencing reads reveals widespread chromosome isoforms
BMC Genomics, 2019Co-Authors: John R Bracht, Kelsi A. Lindblad, Robert Sebra, Jananan S Pathmanathan, Sandrine Moreira, Elizabeth Hutton, Laura F LandweberAbstract:Whole-genome shotgun sequencing, which stitches together millions of short sequencing reads into a single genome, ushered in the era of modern genomics and led to a rapid expansion of the number of genome sequences available. Nevertheless, assembly of short reads remains difficult, resulting in fragmented genome sequences. Ultimately, only a sequencing technology capable of capturing complete chromosomes in a single run could resolve all ambiguities. Even “third generation” sequencing technologies produce reads far shorter than most eukaryotic chromosomes. However, the ciliate Oxytricha trifallax has a somatic genome with thousands of chromosomes averaging only 3.2 kbp, making it an ideal candidate for exploring the benefits of sequencing whole chromosomes without assembly. We used single-molecule real-time sequencing to capture thousands of complete chromosomes in single reads and to update the published Oxytricha trifallax JRB310 genome assembly. In this version, over 50% of the completed chromosomes with two telomeres derive from single reads. The improved assembly includes over 12,000 new chromosome isoforms, and demonstrates that somatic chromosomes derive from variable rearrangements between somatic segments encoded up to 191,000 base pairs away. However, while long reads reduce the need for assembly, a hybrid approach that supplements long-read sequencing with short reads for error correction produced the most complete and accurate assembly, overall. This assembly provides the first example of complete eukaryotic chromosomes captured by single sequencing reads and demonstrates that traditional approaches to genome assembly can mask considerable structural variation.
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programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular dna
Nucleic Acids Research, 2019Co-Authors: John R Bracht, Talya V Yerlici, Carla R Hoge, Richard Miller, Rafik Neme, Jaspreet S Khurana, Laura F LandweberAbstract:Extrachromosomal circular DNA (eccDNA) is both a driver of eukaryotic genome instability and a product of programmed genome rearrangements, but its extent had not been surveyed in Oxytricha, a ciliate with elaborate DNA elimination and translocation during development. Here, we captured rearrangement-specific circular DNA molecules across the genome to gain insight into its processes of programmed genome rearrangement. We recovered thousands of circularly excised Tc1/mariner-type transposable elements and high confidence non-repetitive germline-limited loci. We verified their bona fide circular topology using circular DNA deep-sequencing, 2D gel electrophoresis and inverse polymerase chain reaction. In contrast to the precise circular excision of transposable elements, we report widespread heterogeneity in the circular excision of non-repetitive germline-limited loci. We also demonstrate that circular DNAs are transcribed in Oxytricha, producing rearrangement-specific long non-coding RNAs. The programmed formation of thousands of eccDNA molecules makes Oxytricha a model system for studying nucleic acid topology. It also suggests involvement of eccDNA in programmed genome rearrangement.
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Transformation with Artificial Chromosomes in Oxytricha trifallax and Their Applications.
G3: Genes|Genomes|Genetics, 2019Co-Authors: Derek M. Clay, Hoyon Kim, Laura F LandweberAbstract:Oxytricha trifallax, like other ciliates, has separate germline and somatic nuclei. The diploid germline genome in the micronucleus is composed of long conventional chromosomes, the macronucleus, contains a polyploid somatic genome which is naturally fragmented into thousands of kilobase-sized chromosomes. Here, we develop a method to stably incorporate artificial chromosomes into the macronucleus. We report two cases of successful transformation and demonstrate the use of somatic transformation to investigate gene regulation and gene function in Oxytricha. We show that the transformed artificial chromosomes are maintained through multiple asexual divisions. Furthermore, they support the transcriptional regulation of the native chromosome from which they were derived and are translated to produce functional proteins. To test if transformed chromosomes are amenable to practical applications, we generated a tagged version of a representative gene (AL1) and used it to co-precipitate associated proteins. This revealed an association with nucleic acid binding proteins, specifically RNA-binding proteins, and RNA immunoprecipitation of AL1 revealed its association with multiple RNAs. The use of artificial chromosomes in Oxytricha enables an array of genetic and molecular biological assays, as well as new avenues of inquiry into the epigenetic programming of macronuclear development and genome rearrangement.
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identification of a dna n6 adenine methyltransferase complex and its impact on chromatin organization
Cell, 2019Co-Authors: Galia T Debelouchina, John R Bracht, Kelsi A. Lindblad, Derek M. Clay, Robert E Thompson, Elizabeth R Hutton, Robert Sebra, Tom W Muir, Laura F LandweberAbstract:Summary DNA N6-adenine methylation (6mA) has recently been described in diverse eukaryotes, spanning unicellular organisms to metazoa. Here, we report a DNA 6mA methyltransferase complex in ciliates, termed MTA1c. It consists of two MT-A70 proteins and two homeobox-like DNA-binding proteins and specifically methylates dsDNA. Disruption of the catalytic subunit, MTA1, in the ciliate Oxytricha leads to genome-wide loss of 6mA and abolishment of the consensus ApT dimethylated motif. Mutants fail to complete the sexual cycle, which normally coincides with peak MTA1 expression. We investigate the impact of 6mA on nucleosome occupancy in vitro by reconstructing complete, full-length Oxytricha chromosomes harboring 6mA in native or ectopic positions. We show that 6mA directly disfavors nucleosomes in vitro in a local, quantitative manner, independent of DNA sequence. Furthermore, the chromatin remodeler ACF can overcome this effect. Our study identifies a diverged DNA N6-adenine methyltransferase and defines the role of 6mA in chromatin organization.
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Programmed Chromosome Deletion in the Ciliate Oxytricha trifallax
'Genetics Society of America', 2019Co-Authors: Derek M. Clay, Talya V Yerlici, Danylo J. Villano, Laura F LandweberAbstract:The ciliate Oxytricha trifallax contains two nuclei: a germline micronucleus and a somatic macronucleus. These two nuclei diverge significantly in genomic structure. The micronucleus contains approximately 100 chromosomes of megabase scale, while the macronucleus contains 16,000 gene-sized, high ploidy “nanochromosomes.” During its sexual cycle, a copy of the zygotic germline micronucleus develops into a somatic macronucleus via DNA excision and rearrangement. The rearrangement process is guided by multiple RNA-based pathways that program the epigenetic inheritance of sequences in the parental macronucleus of the subsequent generation. Here, we show that the introduction of synthetic DNA molecules homologous to a complete native nanochromosome during the rearrangement process results in either loss or heavy copy number reduction of the targeted nanochromosome in the macronucleus of the subsequent generation. This phenomenon was tested on a variety of nanochromosomes with different micronuclear structures, with deletions resulting in all cases. Deletion of the targeted nanochromosome results in the loss of expression of the targeted genes, including gene knockout phenotypes that were phenocopied using alternative knockdown approaches. Further investigation of the chromosome deletion showed that, although the full length nanochromosome was lost, remnants of the targeted chromosome remain. We were also able to detect the presence of telomeres on these remnants. The chromosome deletions and remnants are epigenetically inherited when backcrossed to wild type strains, suggesting that an undiscovered mechanism programs DNA elimination and cytoplasmically transfers to both daughter cells during conjugation. Programmed deletion of targeted chromosomes provides a novel approach to investigate genome rearrangement and expands the available strategies for gene knockout in Oxytricha trifallax
John R Bracht - One of the best experts on this subject based on the ideXlab platform.
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capture of complete ciliate chromosomes in single sequencing reads reveals widespread chromosome isoforms
BMC Genomics, 2019Co-Authors: John R Bracht, Kelsi A. Lindblad, Robert Sebra, Jananan S Pathmanathan, Sandrine Moreira, Elizabeth Hutton, Laura F LandweberAbstract:Whole-genome shotgun sequencing, which stitches together millions of short sequencing reads into a single genome, ushered in the era of modern genomics and led to a rapid expansion of the number of genome sequences available. Nevertheless, assembly of short reads remains difficult, resulting in fragmented genome sequences. Ultimately, only a sequencing technology capable of capturing complete chromosomes in a single run could resolve all ambiguities. Even “third generation” sequencing technologies produce reads far shorter than most eukaryotic chromosomes. However, the ciliate Oxytricha trifallax has a somatic genome with thousands of chromosomes averaging only 3.2 kbp, making it an ideal candidate for exploring the benefits of sequencing whole chromosomes without assembly. We used single-molecule real-time sequencing to capture thousands of complete chromosomes in single reads and to update the published Oxytricha trifallax JRB310 genome assembly. In this version, over 50% of the completed chromosomes with two telomeres derive from single reads. The improved assembly includes over 12,000 new chromosome isoforms, and demonstrates that somatic chromosomes derive from variable rearrangements between somatic segments encoded up to 191,000 base pairs away. However, while long reads reduce the need for assembly, a hybrid approach that supplements long-read sequencing with short reads for error correction produced the most complete and accurate assembly, overall. This assembly provides the first example of complete eukaryotic chromosomes captured by single sequencing reads and demonstrates that traditional approaches to genome assembly can mask considerable structural variation.
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programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular dna
Nucleic Acids Research, 2019Co-Authors: John R Bracht, Talya V Yerlici, Carla R Hoge, Richard Miller, Rafik Neme, Jaspreet S Khurana, Laura F LandweberAbstract:Extrachromosomal circular DNA (eccDNA) is both a driver of eukaryotic genome instability and a product of programmed genome rearrangements, but its extent had not been surveyed in Oxytricha, a ciliate with elaborate DNA elimination and translocation during development. Here, we captured rearrangement-specific circular DNA molecules across the genome to gain insight into its processes of programmed genome rearrangement. We recovered thousands of circularly excised Tc1/mariner-type transposable elements and high confidence non-repetitive germline-limited loci. We verified their bona fide circular topology using circular DNA deep-sequencing, 2D gel electrophoresis and inverse polymerase chain reaction. In contrast to the precise circular excision of transposable elements, we report widespread heterogeneity in the circular excision of non-repetitive germline-limited loci. We also demonstrate that circular DNAs are transcribed in Oxytricha, producing rearrangement-specific long non-coding RNAs. The programmed formation of thousands of eccDNA molecules makes Oxytricha a model system for studying nucleic acid topology. It also suggests involvement of eccDNA in programmed genome rearrangement.
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identification of a dna n6 adenine methyltransferase complex and its impact on chromatin organization
Cell, 2019Co-Authors: Galia T Debelouchina, John R Bracht, Kelsi A. Lindblad, Derek M. Clay, Robert E Thompson, Elizabeth R Hutton, Robert Sebra, Tom W Muir, Laura F LandweberAbstract:Summary DNA N6-adenine methylation (6mA) has recently been described in diverse eukaryotes, spanning unicellular organisms to metazoa. Here, we report a DNA 6mA methyltransferase complex in ciliates, termed MTA1c. It consists of two MT-A70 proteins and two homeobox-like DNA-binding proteins and specifically methylates dsDNA. Disruption of the catalytic subunit, MTA1, in the ciliate Oxytricha leads to genome-wide loss of 6mA and abolishment of the consensus ApT dimethylated motif. Mutants fail to complete the sexual cycle, which normally coincides with peak MTA1 expression. We investigate the impact of 6mA on nucleosome occupancy in vitro by reconstructing complete, full-length Oxytricha chromosomes harboring 6mA in native or ectopic positions. We show that 6mA directly disfavors nucleosomes in vitro in a local, quantitative manner, independent of DNA sequence. Furthermore, the chromatin remodeler ACF can overcome this effect. Our study identifies a diverged DNA N6-adenine methyltransferase and defines the role of 6mA in chromatin organization.
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Oxytricha trifallax macronuclear genome fosmids
2016Co-Authors: Estienne C. Swart, John R Bracht, Xiao Chen, Jaspreet S Khurana, Vincent Magrini, Patrick Minx, Yi Zhou, Aaron D. Goldman, Mariusz Nowacki, Klaas SchotanusAbstract:Oxytricha trifallax macronuclear genome fosmid
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Oxytricha trifallax macronuclear PCAP 2.1.8 assembly
2016Co-Authors: Estienne C. Swart, John R Bracht, Xiao Chen, Jaspreet S Khurana, Vincent Magrini, Patrick Minx, Yi Zhou, Aaron D. Goldman, Mariusz Nowacki, Klaas SchotanusAbstract:Oxytricha trifallax macronuclear PCAP 2.1.8 assembl
Steve C Schultz - One of the best experts on this subject based on the ideXlab platform.
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crystal structure of the n terminal domain of Oxytricha nova telomere end binding protein alpha subunit both uncomplexed and complexed with telomeric ssdna
Journal of Molecular Biology, 2001Co-Authors: Scott Classen, James A Ruggles, Steve C SchultzAbstract:Abstract Oxytricha nova telomere end-binding protein specifically recognizes and caps single strand (T 4 G 4 ) n telomeric DNA at the very 3′-ends of O. nova macronuclear chromosomes. Proteins homologous to the N-terminal domain of On TEBP α subunit have now been identified in Oxytricha trifallax , Stylonychia mytilis , Euplotes crassus , Schizosaccharomyces pombe , and Homo sapiens , suggesting that this protein is widely distributed in eukaryotes. We describe here the crystal structures of the N-terminal single-stranded DNA (ssDNA)-binding domain of O. nova telomere end-binding protein α subunit both uncomplexed and complexed with single strand telomeric DNA. These structures show how the N-terminal domain of α alone, in the absence of the β subunit and without α dimerization, can bind single-stranded telomeric DNA in a sequence-specific and 3′-end-specific manner. Furthermore, comparison of the uncomplexed and complexed forms of this protein shows that the ssDNA-binding site is largely pre-organized in the absence of ssDNA with modest, but interesting, rearrangements of amino acid side-chains that compose the ssDNA-binding site. The structures described here extend our understanding of structures of O. nova telomeric complexes by adding uncomplexed and complexed forms of monomeric α to previously described structures for (α56/ssDNA) 2 dimer and α56/β28/ssDNA ternary complexes. We believe that each of these four structures represent intermediates in an ordered assembly/disassembly pathway for O. nova telomeric complexes.
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crystal structure of the Oxytricha nova telomere end binding protein complexed with single strand dna
Cell, 1998Co-Authors: Martin P Horvath, James A Ruggles, Viloya L Schweiker, Joanne M Bevilacqua, Steve C SchultzAbstract:Telomeres are specialized protein-DNA complexes that compose the ends of eukaryotic chromosomes. Telomeres protect chromosome termini from degradation and recombination and act together with telomerase to ensure complete genome replication. We have determined the crystal structure of the two-subunit Oxytricha nova telomere end binding protein (OnTEBP) complexed with single strand telomeric DNA at 2.8 A resolution. The structure reveals four oligonucleotide/oligosaccharide-binding folds, three of which form a deep cleft that binds the ssDNA, and a fourth that forms an unusual protein-protein interaction between the alpha and beta subunits. This structure provides a molecular description of how the two subunits of OnTEBP recognize and bind ssDNA to form a sequence-specific, telomeric nucleoprotein complex that caps the very 3' ends of chromosomes.
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crystal structure of the Oxytricha nova telomere end binding protein complexed with single strand dna
Cell, 1998Co-Authors: Martin P Horvath, James A Ruggles, Viloya L Schweiker, Joanne M Bevilacqua, Steve C SchultzAbstract:Abstract Telomeres are specialized protein–DNA complexes that compose the ends of eukaryotic chromosomes. Telomeres protect chromosome termini from degradation and recombination and act together with telomerase to ensure complete genome replication. We have determined the crystal structure of the two-subunit Oxytricha nova telomere end binding protein ( On TEBP) complexed with single strand telomeric DNA at 2.8 A resolution. The structure reveals four oligonucleotide/oligosaccharide–binding folds, three of which form a deep cleft that binds the ssDNA, and a fourth that forms an unusual protein–protein interaction between the α and β subunits. This structure provides a molecular description of how the two subunits of On TEBP recognize and bind ssDNA to form a sequence-specific, telomeric nucleoprotein complex that caps the very 3′ ends of chromosomes.
Mariusz Nowacki - One of the best experts on this subject based on the ideXlab platform.
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Oxytricha trifallax macronuclear genome fosmids
2016Co-Authors: Estienne C. Swart, John R Bracht, Xiao Chen, Jaspreet S Khurana, Vincent Magrini, Patrick Minx, Yi Zhou, Aaron D. Goldman, Mariusz Nowacki, Klaas SchotanusAbstract:Oxytricha trifallax macronuclear genome fosmid
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Oxytricha trifallax macronuclear PCAP 2.1.8 assembly
2016Co-Authors: Estienne C. Swart, John R Bracht, Xiao Chen, Jaspreet S Khurana, Vincent Magrini, Patrick Minx, Yi Zhou, Aaron D. Goldman, Mariusz Nowacki, Klaas SchotanusAbstract:Oxytricha trifallax macronuclear PCAP 2.1.8 assembl
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the Oxytricha trifallax macronuclear genome a complex eukaryotic genome with 16 000 tiny chromosomes
PLOS Biology, 2013Co-Authors: Estienne C. Swart, John R Bracht, Xiao Chen, Jaspreet S Khurana, Vincent Magrini, Patrick Minx, Yi Zhou, Mariusz Nowacki, Aaron David GoldmanAbstract:The macronuclear genome of the ciliate Oxytricha trifallax displays an extreme and unique eukaryotic genome architecture with extensive genomic variation. During sexual genome development, the expressed, somatic macronuclear genome is whittled down to the genic portion of a small fraction (,5%) of its precursor ‘‘silent’’ germline micronuclear genome by a process of ‘‘unscrambling’’ and fragmentation. The tiny macronuclear ‘‘nanochromosomes’’ typically encode single, proteincoding genes (a small portion, 10%, encode 2–8 genes), have minimal noncoding regions, and are differentially amplified to an average of ,2,000 copies. We report the high-quality genome assembly of ,16,000 complete nanochromosomes (,50 Mb haploid genome size) that vary from 469 bp to 66 kb long (mean ,3.2 kb) and encode ,18,500 genes. Alternative DNA fragmentation processes ,10% of the nanochromosomes into multiple isoforms that usually encode complete genes. Nucleotide diversity in the macronucleus is very high (SNP heterozygosity is ,4.0%), suggesting that Oxytricha trifallax may have one of the largest known effective population sizes of eukaryotes. Comparison to other ciliates with nonscrambled genomes and long macronuclear chromosomes (on the order of 100 kb) suggests several candidate proteins that could be involved in genome rearrangement, including domesticated MULE and IS1595-like DDE transposases. The assembly of the highly fragmented Oxytricha macronuclear genome is the first completed genome with such an unusual architecture. This genome sequence provides tantalizing glimpses into novel molecular biology and evolution. For example, Oxytricha maintains tens of millions of telomeres per cell and has also evolved an intriguing expansion of telomere end-binding proteins. In conjunction with the micronuclear genome in progress, the O. trifallax macronuclear genome will provide an invaluable resource for investigating programmed genome rearrangements, complementing studies of rearrangements arising during evolution and disease.
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Comparison of key ciliate macronuclear genomes.
2013Co-Authors: Estienne C. Swart, John R Bracht, Xiao Chen, Jaspreet S Khurana, Vincent Magrini, Patrick Minx, Yi Zhou, Aaron D. Goldman, Mariusz Nowacki, Klaas SchotanusAbstract:The phylogeny represents the bootstrap consensus of 100 replicates from PhyML (with the HKY85 substitution model) based on a MUSCLE multiple sequence alignment of 18S rRNA genes from seven ciliates (Oxytricha trifallax—FJ545743; Stylonychia lemnae—AJJRB310497; Euplotes crassus—AJJRB310492; Nyctotherus ovalis—AJ222678; Tetrahymena thermophila—M10932; Ichthyophthirius multifiliis—IMU17354; and Paramecium tetraurelia—AB252009) rooted with two other alveolates (Perkinsus marinus—X75762 and Plasmodium falciparum—NC_004325). All bootstrap values are ≥80, except for the node between Nyctotherus and Oxytricha/Stylonychia/Euplotes, which has a boostrap value of 60. Euplotes and Nyctotherus both have nanochromosomes, like Oxytricha. Other than the genome statistics for Oxytricha trifallax, which were determined in this study, table statistics were obtained from the following sources: a - [2], b - [22],[116], c - [117], d - [99], e - [94], f - [56] (the number of chromosomes is an estimate), g -[118], h - [119], i - [120], j- [64] (for a single stage of the Ichthyophthirius life cycle), k - [121], l - [69], m - [122]. Table statistics for Perkinsus marinus are for the current assembly deposited in GenBank (GCA_000006405.1).
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Telomere end-binding protein-α paralogs in ciliates.
2013Co-Authors: Estienne C. Swart, John R Bracht, Xiao Chen, Jaspreet S Khurana, Vincent Magrini, Patrick Minx, Yi Zhou, Aaron D. Goldman, Mariusz Nowacki, Klaas SchotanusAbstract:The phylogeny is an ML tree generated by PhyML [123] with a single substitution rate category and the JTT substitution model, optimized for tree topology and branch length. Bootstrap percentages for 1,000 replicates are indicated at the tree nodes. The multiple sequence alignments underlying the phylogeny were produced with MAFFT (v 6.418b [124]) (default parameters; BLOSUM 62 substitution matrix) and were trimmed with trimal1.2 [125] with the “-automated1” parameter to remove excess gaps and poorly aligned regions. GenBank accessions are provided for the taxa unless otherwise indicated. Euplotes crassus is indicated in blue (Q06184 and Q06183), and an additional match from our preliminary Euplotes genome assembly is EUP_contig393834_f1_1. Perkinsus marinus is purple (EER00428) and Oxytricha nova is light green (P29549). Tetrahymena thermophila (salmon color) accessions are from the Tetrahymena genome database [126]—TTHERM_00378980 and TTHERM_00378990; Paramecium tetraurelia's TeBP-α protein (pink) is from ParameciumDB [127] (GSPATP00001065001). All the nodes beginning with “Contig” are Oxytricha trifallax TeBP-α paralogs (dark green) and Contig22209.0.g66 is TeBP-α1, the original TeBP-α. The tree is rooted at the midpoint of the branch between Arabidopsis thaliana (Pot1a—AAX78213 and Pot1b—AAS99712) and Homo sapiens (Pot1—EAW83616; black) and the rest of the phylogeny. Gene expression levels are normalized RNA-seq counts (see Text S1; Supporting Materials and Methods) before (“fed”) and during conjugation (0–60 h) are shown for the Oxytricha trifallax TeBP-α paralogs; coding sequence lengths are also indicated (in bp) for each of these paralogs.
Xiao Chen - One of the best experts on this subject based on the ideXlab platform.
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a comparative study of genome organization and epigenetic mechanisms in model ciliates with an emphasis on tetrahymena paramecium and Oxytricha
European Journal of Protistology, 2017Co-Authors: Yurui Wang, Xiao Chen, Yuanyuan Wang, Yalan Sheng, Jie Huang, Khaled A S Alrasheid, Shan GaoAbstract:As a group of unicellular eukaryotes, ciliates offer a unique system to explore epigenetic regulation, mostly due to their nuclear dualism. Ciliates launched a successful radiation after their early evolutionary branching, therefore harboring an unexpectedly rich pool of diverse biological functions and mechanisms. In this review, we compare distinct features of different ciliates in mating type determination, genome organization, DNA methylation, and removal of internal eliminated sequences (IES), with emphasis on Tetrahymena, Paramecium and Oxytricha. Firstly, we review studies on mating type determination in Paramecium, one of the foundational phenomena that defined the field of epigenetics, and compare this process with that in Tetrahymena. Secondly, we showcase the high diversity in genome structure of several ciliates, such as genome size, gene copy numbers, genome rearrangement, etc. Thirdly, we present a brief description of features and potential functions of 5-methylcytosine (5mC) and N6-methyladenine (6mA) in ciliates so far studied. Fourthly, we describe both the initial and the continuously optimized scan RNA (scnRNA) model for IES elimination in Tetrahymena and contrast it with that in Paramecium and Oxytricha. Finally, we discuss the importance of integrative approaches to the study of epigenetic diversity in ciliates and provide possible directions for future research.
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Recurring patterns among scrambled genes in the encrypted genome of the ciliate Oxytricha trifallax.
Journal of Theoretical Biology, 2016Co-Authors: Jonathan Burns, Masahico Saito, Denys Kukushkin, Laura F Landweber, Xiao Chen, Nataša JonoskaAbstract:Abstract Some genera of ciliates, such as Oxytricha and Stylonychia, undergo massive genome reorganization during development and provide model organisms to study DNA rearrangement. A common feature of these ciliates is the presence of two types of nuclei: a germline micronucleus and a transcriptionally-active somatic macronucleus containing over 16,000 gene sized “nano-chromosomes”. During conjugation the old parental macronucleus disintegrates and a new macronucleus forms from a copy of the zygotic micronucleus. During this process, macronuclear chromosomes assemble through DNA processing events that delete 90–98% of the DNA content of the micronucleus. This includes the deletion of noncoding DNA segments that interrupt precursor DNA regions in the micronucleus, as well as transposons and other germline-limited DNA. Each macronuclear locus may be present in the micronucleus as several nonconsecutive, permuted, and/or inverted DNA segments. Here we investigate the genome-wide range of scrambled gene architectures that describe all precursor-product relationships in Oxytricha trifallax, the first completely sequenced scrambled genome. We find that five general, recurrent patterns in the sets of scrambled micronuclear precursor pieces can describe over 80% of Oxytricha's scrambled genes. These include instances of translocations and inversions, and other specific patterns characterized by alternating stretches of consecutive odd and even DNA segments. Moreover, we find that iterating patterns of alternating odd–even segments up to four times can describe over 96% of the scrambled precursor loci. Recurrence of these highly structured genetic architectures within scrambled genes presumably reflects recurrent evolutionary events that gave rise to over 3000 of scrambled loci in the germline genome.
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Oxytricha trifallax macronuclear genome fosmids
2016Co-Authors: Estienne C. Swart, John R Bracht, Xiao Chen, Jaspreet S Khurana, Vincent Magrini, Patrick Minx, Yi Zhou, Aaron D. Goldman, Mariusz Nowacki, Klaas SchotanusAbstract:Oxytricha trifallax macronuclear genome fosmid
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Oxytricha trifallax macronuclear PCAP 2.1.8 assembly
2016Co-Authors: Estienne C. Swart, John R Bracht, Xiao Chen, Jaspreet S Khurana, Vincent Magrini, Patrick Minx, Yi Zhou, Aaron D. Goldman, Mariusz Nowacki, Klaas SchotanusAbstract:Oxytricha trifallax macronuclear PCAP 2.1.8 assembl
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Additional file 1: of Phylogenomic analysis reveals genome-wide purifying selection on TBE transposons in the ciliate Oxytricha
2016Co-Authors: Xiao Chen, Laura LandweberAbstract:Annotation of TBE sequences in Oxytricha micronuclear genome in gff format. (GFF 2.38 mb
