1
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Brovkina MV, Chapman MA, Holding ML, Clowney EJ. Emergence and influence of sequence bias in evolutionarily malleable, mammalian tandem arrays. BMC Biol 2023; 21:179. [PMID: 37612705 PMCID: PMC10463633 DOI: 10.1186/s12915-023-01673-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/01/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND The radiation of mammals at the extinction of the dinosaurs produced a plethora of new forms-as diverse as bats, dolphins, and elephants-in only 10-20 million years. Behind the scenes, adaptation to new niches is accompanied by extensive innovation in large families of genes that allow animals to contact the environment, including chemosensors, xenobiotic enzymes, and immune and barrier proteins. Genes in these "outward-looking" families are allelically diverse among humans and exhibit tissue-specific and sometimes stochastic expression. RESULTS Here, we show that these tandem arrays of outward-looking genes occupy AT-biased isochores and comprise the "tissue-specific" gene class that lack CpG islands in their promoters. Models of mammalian genome evolution have not incorporated the sharply different functions and transcriptional patterns of genes in AT- versus GC-biased regions. To examine the relationship between gene family expansion, sequence content, and allelic diversity, we use population genetic data and comparative analysis. First, we find that AT bias can emerge during evolutionary expansion of gene families in cis. Second, human genes in AT-biased isochores or with GC-poor promoters experience relatively low rates of de novo point mutation today but are enriched for non-synonymous variants. Finally, we find that isochores containing gene clusters exhibit low rates of recombination. CONCLUSIONS Our analyses suggest that tolerance of non-synonymous variation and low recombination are two forces that have produced the depletion of GC bases in outward-facing gene arrays. In turn, high AT content exerts a profound effect on their chromatin organization and transcriptional regulation.
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Affiliation(s)
- Margarita V Brovkina
- Graduate Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Margaret A Chapman
- Neurosciences Graduate Program, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - E Josephine Clowney
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA.
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2
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Bernaola-Galván P, Carpena P, Gómez-Martín C, Oliver JL. Compositional Structure of the Genome: A Review. BIOLOGY 2023; 12:849. [PMID: 37372134 DOI: 10.3390/biology12060849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023]
Abstract
As the genome carries the historical information of a species' biotic and environmental interactions, analyzing changes in genome structure over time by using powerful statistical physics methods (such as entropic segmentation algorithms, fluctuation analysis in DNA walks, or measures of compositional complexity) provides valuable insights into genome evolution. Nucleotide frequencies tend to vary along the DNA chain, resulting in a hierarchically patchy chromosome structure with heterogeneities at different length scales that range from a few nucleotides to tens of millions of them. Fluctuation analysis reveals that these compositional structures can be classified into three main categories: (1) short-range heterogeneities (below a few kilobase pairs (Kbp)) primarily attributed to the alternation of coding and noncoding regions, interspersed or tandem repeats densities, etc.; (2) isochores, spanning tens to hundreds of tens of Kbp; and (3) superstructures, reaching sizes of tens of megabase pairs (Mbp) or even larger. The obtained isochore and superstructure coordinates in the first complete T2T human sequence are now shared in a public database. In this way, interested researchers can use T2T isochore data, as well as the annotations for different genome elements, to check a specific hypothesis about genome structure. Similarly to other levels of biological organization, a hierarchical compositional structure is prevalent in the genome. Once the compositional structure of a genome is identified, various measures can be derived to quantify the heterogeneity of such structure. The distribution of segment G+C content has recently been proposed as a new genome signature that proves to be useful for comparing complete genomes. Another meaningful measure is the sequence compositional complexity (SCC), which has been used for genome structure comparisons. Lastly, we review the recent genome comparisons in species of the ancient phylum Cyanobacteria, conducted by phylogenetic regression of SCC against time, which have revealed positive trends towards higher genome complexity. These findings provide the first evidence for a driven progressive evolution of genome compositional structure.
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Affiliation(s)
- Pedro Bernaola-Galván
- Department of Applied Physics II and Institute Carlos I for Theoretical and Computational Physics, University of Málaga, 29071 Málaga, Spain
| | - Pedro Carpena
- Department of Applied Physics II and Institute Carlos I for Theoretical and Computational Physics, University of Málaga, 29071 Málaga, Spain
| | - Cristina Gómez-Martín
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- Department of Genetics, Faculty of Sciences, 18071 and Laboratory of Bioinformatics, Institute of Biotechnology, Center of Biomedical Research, University of Granada, 18100 Granada, Spain
| | - Jose L Oliver
- Department of Genetics, Faculty of Sciences, 18071 and Laboratory of Bioinformatics, Institute of Biotechnology, Center of Biomedical Research, University of Granada, 18100 Granada, Spain
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3
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Lamolle G, Simón D, Iriarte A, Musto H. Main Factors Shaping Amino Acid Usage Across Evolution. J Mol Evol 2023:10.1007/s00239-023-10120-5. [PMID: 37264211 DOI: 10.1007/s00239-023-10120-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/17/2023] [Indexed: 06/03/2023]
Abstract
The standard genetic code determines that in most species, including viruses, there are 20 amino acids that are coded by 61 codons, while the other three codons are stop triplets. Considering the whole proteome each species features its own amino acid frequencies, given the slow rate of change, closely related species display similar GC content and amino acids usage. In contrast, distantly related species display different amino acid frequencies. Furthermore, within certain multicellular species, as mammals, intragenomic differences in the usage of amino acids are evident. In this communication, we shall summarize some of the most prominent and well-established factors that determine the differences found in the amino acid usage, both across evolution and intragenomically.
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Affiliation(s)
- Guillermo Lamolle
- Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de La República, Montevideo, Uruguay
| | - Diego Simón
- Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de La República, Montevideo, Uruguay
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de La República, Montevideo, Uruguay
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Andrés Iriarte
- Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de La República, Montevideo, Uruguay
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de La República, Montevideo, Uruguay
| | - Héctor Musto
- Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de La República, Montevideo, Uruguay.
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4
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Zeng Y, Fair BJ, Zeng H, Krishnamohan A, Hou Y, Hall JM, Ruthenburg AJ, Li YI, Staley JP. Profiling lariat intermediates reveals genetic determinants of early and late co-transcriptional splicing. Mol Cell 2022; 82:4681-4699.e8. [PMID: 36435176 PMCID: PMC10448999 DOI: 10.1016/j.molcel.2022.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 09/10/2022] [Accepted: 11/02/2022] [Indexed: 11/27/2022]
Abstract
Long introns with short exons in vertebrate genes are thought to require spliceosome assembly across exons (exon definition), rather than introns, thereby requiring transcription of an exon to splice an upstream intron. Here, we developed CoLa-seq (co-transcriptional lariat sequencing) to investigate the timing and determinants of co-transcriptional splicing genome wide. Unexpectedly, 90% of all introns, including long introns, can splice before transcription of a downstream exon, indicating that exon definition is not obligatory for most human introns. Still, splicing timing varies dramatically across introns, and various genetic elements determine this variation. Strong U2AF2 binding to the polypyrimidine tract predicts early splicing, explaining exon definition-independent splicing. Together, our findings question the essentiality of exon definition and reveal features beyond intron and exon length that are determinative for splicing timing.
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Affiliation(s)
- Yi Zeng
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Benjamin J Fair
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Huilin Zeng
- 855 Jefferson Ave. Redwood City, CA 94063, USA
| | - Aiswarya Krishnamohan
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Yichen Hou
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Johnathon M Hall
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Alexander J Ruthenburg
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA; Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Yang I Li
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
| | - Jonathan P Staley
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA.
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5
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Wilcox JJS, Arca-Ruibal B, Samour J, Mateuta V, Idaghdour Y, Boissinot S. Linked-Read Sequencing of Eight Falcons Reveals a Unique Genomic Architecture in Flux. Genome Biol Evol 2022; 14:evac090. [PMID: 35700227 PMCID: PMC9214253 DOI: 10.1093/gbe/evac090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 05/27/2022] [Accepted: 06/06/2022] [Indexed: 11/12/2022] Open
Abstract
Falcons are diverse birds of cultural and economic importance. They have undergone major lineage-specific chromosomal rearrangements, resulting in greatly-reduced chromosome counts relative to other birds. Here, we use 10X Genomics linked reads to provide new high-contiguity genomes for two gyrfalcons, a saker falcon, a lanner falcon, three subspecies of peregrine falcons, and the common kestrel. Assisted by a transcriptome sequenced from 22 gyrfalcon tissues, we annotate these genomes for a variety of genomic features, estimate historical demography, and then investigate genomic equilibrium in the context of falcon-specific chromosomal rearrangements. We find that falcon genomes are not in AT-GC equilibrium with a bias in substitutions towards higher AT content; this bias is predominantly but not exclusively driven by hypermutability of CpG sites. Small indels and large structural variants were also biased towards insertions rather than deletions. Patterns of disequilibrium were linked to chromosomal rearrangements: falcons have lost GC content in regions that have fused to larger chromosomes from microchromosomes and gained GC content in regions of macrochromosomes that have translocated to microchromosomes. Inserted bases have accumulated on regions ancestrally belonging to microchromosomes, consistent with insertion-biased gene conversion. We also find an excess of interspersed repeats on regions of microchromosomes that have fused to macrochromosomes. Our results reveal that falcon genomes are in a state of flux. They further suggest that many of the key differences between microchromosomes and macrochromosomes are driven by differences in chromosome size, and indicate a clear role for recombination and biased-gene-conversion in determining genomic equilibrium.
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Affiliation(s)
- Justin J S Wilcox
- Center for Genomics & Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | | | - Jaime Samour
- Wildlife Management and Falcon Medicine and Breeding Consultancy, Abu Dhabi, United Arab Emirates
| | | | - Youssef Idaghdour
- Center for Genomics & Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
- Biology Program, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Stéphane Boissinot
- Center for Genomics & Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
- Biology Program, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
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6
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Nanodosimetric Calculations of Radiation-Induced DNA Damage in a New Nucleus Geometrical Model Based on the Isochore Theory. Int J Mol Sci 2022; 23:ijms23073770. [PMID: 35409128 PMCID: PMC8998209 DOI: 10.3390/ijms23073770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 11/16/2022] Open
Abstract
Double-strand breaks (DSBs) in nuclear DNA represents radiation-induced damage that has been identified as particularly deleterious. Calculating this damage using Monte Carlo track structure modeling could be a suitable indicator to better assess and anticipate the side-effects of radiation therapy. However, as already demonstrated in previous work, the geometrical description of the nucleus and the DNA content used in the simulation significantly influence damage calculations. Therefore, in order to obtain accurate results, this geometry must be as realistic as possible. In this study, a new geometrical model of an endothelial cell nucleus and DNA distribution according to the isochore theory are presented and used in a Monte Carlo simulation chain based on the Geant4-DNA toolkit. In this theory, heterochromatin and euchromatin compaction are distributed along the genome according to five different families (L1, L2, H1, H2, and H3). Each of these families is associated with a different hetero/euchromatin rate related to its compaction level. In order to compare the results with those obtained using a previous nuclear geometry, simulations were performed for protons with linear energy transfers (LETs) of 4.29 keV/µm, 19.51 keV/µm, and 43.25 keV/µm. The organization of the chromatin fibers at different compaction levels linked to isochore families increased the DSB yield by 6-10%, and it allowed the most affected part of the genome to be identified. These new results indicate that the genome core is more radiosensitive than the genome desert, with a 3-8% increase in damage depending on the LET. This work highlights the importance of using realistic distributions of chromatin compaction levels to calculate radio-induced damage using Monte Carlo simulation methods.
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7
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Li W, Almirantis Y, Provata A. Revisiting the neutral dynamics derived limiting guanine-cytosine content using human de novo point mutation data. Meta Gene 2022. [DOI: 10.1016/j.mgene.2021.100994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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8
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Loskutov IG, Gnutikov AA, Blinova EV, Rodionov AV. The Origin and Resource Potential of Wild and Cultivated Species of the Genus of Oats (Avena L.). RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421060065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Simón D, Cristina J, Musto H. Nucleotide Composition and Codon Usage Across Viruses and Their Respective Hosts. Front Microbiol 2021; 12:646300. [PMID: 34262534 PMCID: PMC8274242 DOI: 10.3389/fmicb.2021.646300] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 06/04/2021] [Indexed: 11/13/2022] Open
Abstract
The genetic material of the three domains of life (Bacteria, Archaea, and Eukaryota) is always double-stranded DNA, and their GC content (molar content of guanine plus cytosine) varies between ≈ 13% and ≈ 75%. Nucleotide composition is the simplest way of characterizing genomes. Despite this simplicity, it has several implications. Indeed, it is the main factor that determines, among other features, dinucleotide frequencies, repeated short DNA sequences, and codon and amino acid usage. Which forces drive this strong variation is still a matter of controversy. For rather obvious reasons, most of the studies concerning this huge variation and its consequences, have been done in free-living organisms. However, no recent comprehensive study of all known viruses has been done (that is, concerning all available sequences). Viruses, by far the most abundant biological entities on Earth, are the causative agents of many diseases. An overview of these entities is important also because their genetic material is not always double-stranded DNA: indeed, certain viruses have as genetic material single-stranded DNA, double-stranded RNA, single-stranded RNA, and/or retro-transcribing. Therefore, one may wonder if what we have learned about the evolution of GC content and its implications in prokaryotes and eukaryotes also applies to viruses. In this contribution, we attempt to describe compositional properties of ∼ 10,000 viral species: base composition (globally and according to Baltimore classification), correlations among non-coding regions and the three codon positions, and the relationship of the nucleotide frequencies and codon usage of viruses with the same feature of their hosts. This allowed us to determine how the base composition of phages strongly correlate with the value of their respective hosts, while eukaryotic viruses do not (with fungi and protists as exceptions). Finally, we discuss some of these results concerning codon usage: reinforcing previous results, we found that phages and hosts exhibit moderate to high correlations, while for eukaryotes and their viruses the correlations are weak or do not exist.
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Affiliation(s)
- Diego Simón
- Laboratorio de Genómica Evolutiva, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.,Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la Republica, Montevideo, Uruguay.,Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Juan Cristina
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la Republica, Montevideo, Uruguay
| | - Héctor Musto
- Laboratorio de Genómica Evolutiva, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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10
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Cai Z, He Y, Liu S, Xue Y, Quan H, Zhang L, Gao YQ. Hierarchical dinucleotide distribution in genome along evolution and its effect on chromatin packing. Life Sci Alliance 2021; 4:4/8/e202101028. [PMID: 34168075 PMCID: PMC8321668 DOI: 10.26508/lsa.202101028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 11/29/2022] Open
Abstract
It describes how hierarchical CpG distribution on the genomes of species change in the evolution and the correlation with the chromatin structure. Dinucleotide densities and their distribution patterns vary significantly among species. Previous studies revealed that CpG is susceptible to methylation, enriched at topologically associating domain boundaries and its distribution along the genome correlates with chromatin compartmentalization. However, the multi-scale organizations of CpG in the linear genome, their role in chromatin organization, and how they change along the evolution are only partially understood. By comparing the CpG distribution at different genomic length scales, we quantify the difference between the CpG distributions of different species and evaluate how the hierarchical uneven CpG distribution appears in evolution. The clustering of species based on the CpG distribution is consistent with the phylogenetic tree. Interestingly, we found the CpG distribution and chromatin structure to be correlated in many different length scales, especially for mammals and avians, consistent with the mosaic CpG distribution in the genomes of these species.
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Affiliation(s)
- Zhicheng Cai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Biomedical Pioneering Innovation Center, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Yueying He
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Biomedical Pioneering Innovation Center, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Sirui Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Biomedical Pioneering Innovation Center, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Yue Xue
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Biomedical Pioneering Innovation Center, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Hui Quan
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Biomedical Pioneering Innovation Center, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Ling Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Biomedical Pioneering Innovation Center, Peking University, Beijing, China
| | - Yi Qin Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China .,Biomedical Pioneering Innovation Center, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
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11
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Paulson JR, Hudson DF, Cisneros-Soberanis F, Earnshaw WC. Mitotic chromosomes. Semin Cell Dev Biol 2021; 117:7-29. [PMID: 33836947 PMCID: PMC8406421 DOI: 10.1016/j.semcdb.2021.03.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/23/2021] [Accepted: 03/23/2021] [Indexed: 01/25/2023]
Abstract
Our understanding of the structure and function of mitotic chromosomes has come a long way since these iconic objects were first recognized more than 140 years ago, though many details remain to be elucidated. In this chapter, we start with the early history of chromosome studies and then describe the path that led to our current understanding of the formation and structure of mitotic chromosomes. We also discuss some of the remaining questions. It is now well established that each mitotic chromatid consists of a central organizing region containing a so-called "chromosome scaffold" from which loops of DNA project radially. Only a few key non-histone proteins and protein complexes are required to form the chromosome: topoisomerase IIα, cohesin, condensin I and condensin II, and the chromokinesin KIF4A. These proteins are concentrated along the axis of the chromatid. Condensins I and II are primarily responsible for shaping the chromosome and the scaffold, and they produce the loops of DNA by an ATP-dependent process known as loop extrusion. Modelling of Hi-C data suggests that condensin II adopts a spiral staircase arrangement with an extruded loop extending out from each step in a roughly helical pattern. Condensin I then forms loops nested within these larger condensin II loops, thereby giving rise to the final compaction of the mitotic chromosome in a process that requires Topo IIα.
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Affiliation(s)
- James R Paulson
- Department of Chemistry, University of Wisconsin Oshkosh, 800 Algoma Boulevard, Oshkosh, WI 54901, USA.
| | - Damien F Hudson
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Fernanda Cisneros-Soberanis
- Wellcome Trust Centre for Cell Biology, ICB, University of Edinburgh, Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - William C Earnshaw
- Wellcome Trust Centre for Cell Biology, ICB, University of Edinburgh, Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK.
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12
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Adapting Biased Gene Conversion theory to account for intensive GC-content deterioration in the human genome by novel mutations. PLoS One 2020; 15:e0232167. [PMID: 32353016 PMCID: PMC7192473 DOI: 10.1371/journal.pone.0232167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 04/09/2020] [Indexed: 12/23/2022] Open
Abstract
We examined seventy million well-characterized human mutations, and their impact on G+C-compositional dynamics, in order to understand the formation and maintenance of major genomic nucleotide sequence patterns. Among novel mutations, those that change a strong (S) base pair G:C/C:G to a weak (W) pair A:T/T:A occur at nearly twice the frequency of the opposite mutations. Such imbalance puts strong downward pressure on overall GC-content. However, along protracted paths to fixation, S→W mutations are much less likely to propagate than W→S mutations. The magnitude of relative propagation disadvantages for S→W mutations is inexplicable by any currently-accepted model. This fact forced us to re-examine the quantitative features of Biased Gene Conversion (BGC) theory. Revised parameters of BGC that, per average individual, convert 7–14 W base pairs into S pairs, would account for the S-content turnover differences between new and old mutations, and make BGC an instrumental force for nucleotide dynamics and evolution. BGC should thus be considered seriously in both theories and biomedical practice. In particular, BGC should be taken into account during allele imputations, where missing SNP alleles are computationally predicted based on the information about several neighboring alleles. Finally, we analyzed the effect of neighboring nucleotide context on the mutation frequencies, dynamics, and GC-composition turnover. For this purpose, we examined genomic regions having extremely biased nucleotide compositions (enriched for S-, W-, purine/pyrimidine strand asymmetry, or AC/GT-strand asymmetry). It was found that point mutations in these regions preferentially degrade the nucleotide inhomogeneities, decreasing the sequence biases. Degradation of sequence bias is highest for novel mutations, and considerably lower for older mutations (those widespread across populations). Besides BGC, there may be additional, still uncharacterized molecular mechanisms that either preserve genomic regions with biased nucleotide compositions from mutational degradation or fail to degrade such inhomogeneities in specific chromosomal regions.
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13
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Arhondakis S, Milanesi M, Castrignanò T, Gioiosa S, Valentini A, Chillemi G. Evidence of distinct gene functional patterns in GC-poor and GC-rich isochores in Bos taurus. Anim Genet 2020; 51:358-368. [PMID: 32069522 DOI: 10.1111/age.12917] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2020] [Indexed: 01/10/2023]
Abstract
Vertebrate genomes are mosaics of megabase-size DNA segments with a fairly homogeneous base composition, called isochores. They are divided into five families characterized by different guanine-cytosine (GC) levels and linked to several functional and structural properties. The increased availability of fully sequenced genomes allows the investigation of isochores in several species, assessing their level of conservation across vertebrate genomes. In this work, we characterized the isochores in Bos taurus using the ARS-UCD1.2 genome version. The comparison of our results with the well-studied human isochores and those of other mammals revealed a large conservation in isochore families, in number, average GC levels and gene density. Exceptions to the established increase in gene density with the increase in isochores (GC%) were observed for the following gene biotypes: tRNA, small nuclear RNA, small nucleolar RNA and pseudogenes that have their maximum number in H2 and H1 isochores. Subsequently, we assessed the ontology of all gene biotypes looking for functional classes that are statistically over- or under-represented in each isochore. Receptor activity and sensory perception pathways were significantly over-represented in L1 and L2 (GC-poor) isochores. This was also validated for the horse genome. Our analysis of housekeeping genes confirmed a preferential localization in GC-rich isochores, as reported in other species. Finally, we assessed the SNP distribution of a bovine high-density SNP chip across the isochores, finding a higher density in the GC-rich families, reflecting a potential bias in the chip, widely used for genetic selection and biodiversity studies.
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Affiliation(s)
- S Arhondakis
- Bioinformatics and Computational Science (BioCoS), Boniali 11-19, Chania, 73134, Crete, Greece
| | - M Milanesi
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University, 16050-680 R. Clóvis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clóvis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil
| | - T Castrignanò
- SCAI - Super Computing Applications and Innovation Department, CINECA, Rome, Italy
| | - S Gioiosa
- SCAI - Super Computing Applications and Innovation Department, CINECA, Rome, Italy
| | - A Valentini
- Department for Innovation in Biological, Agro-food and Forest Systems, DIBAF, University of Tuscia, via S. Camillo de Lellis s.n.c, 01100, Viterbo, Italy
| | - G Chillemi
- Department for Innovation in Biological, Agro-food and Forest Systems, DIBAF, University of Tuscia, via S. Camillo de Lellis s.n.c, 01100, Viterbo, Italy.,Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, IBIOM, CNR, Bari, Italy
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14
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Lemaire S, Fontrodona N, Aubé F, Claude JB, Polvèche H, Modolo L, Bourgeois CF, Mortreux F, Auboeuf D. Characterizing the interplay between gene nucleotide composition bias and splicing. Genome Biol 2019; 20:259. [PMID: 31783898 PMCID: PMC6883713 DOI: 10.1186/s13059-019-1869-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 10/28/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Nucleotide composition bias plays an important role in the 1D and 3D organization of the human genome. Here, we investigate the potential interplay between nucleotide composition bias and the regulation of exon recognition during splicing. RESULTS By analyzing dozens of RNA-seq datasets, we identify two groups of splicing factors that activate either about 3200 GC-rich exons or about 4000 AT-rich exons. We show that splicing factor-dependent GC-rich exons have predicted RNA secondary structures at 5' ss and are dependent on U1 snRNP-associated proteins. In contrast, splicing factor-dependent AT-rich exons have a large number of decoy branch points, SF1- or U2AF2-binding sites and are dependent on U2 snRNP-associated proteins. Nucleotide composition bias also influences local chromatin organization, with consequences for exon recognition during splicing. Interestingly, the GC content of exons correlates with that of their hosting genes, isochores, and topologically associated domains. CONCLUSIONS We propose that regional nucleotide composition bias over several dozens of kilobase pairs leaves a local footprint at the exon level and induces constraints during splicing that can be alleviated by local chromatin organization at the DNA level and recruitment of specific splicing factors at the RNA level. Therefore, nucleotide composition bias establishes a direct link between genome organization and local regulatory processes, like alternative splicing.
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Affiliation(s)
- Sébastien Lemaire
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France
| | - Nicolas Fontrodona
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France
| | - Fabien Aubé
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France
| | - Jean-Baptiste Claude
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France
| | | | - Laurent Modolo
- LBMC Biocomputing Center, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France
| | - Cyril F Bourgeois
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France
| | - Franck Mortreux
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France
| | - Didier Auboeuf
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France.
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15
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Liu S, Zhang L, Quan H, Tian H, Meng L, Yang L, Feng H, Gao YQ. From 1D sequence to 3D chromatin dynamics and cellular functions: a phase separation perspective. Nucleic Acids Res 2019; 46:9367-9383. [PMID: 30053116 PMCID: PMC6182157 DOI: 10.1093/nar/gky633] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/12/2018] [Indexed: 11/28/2022] Open
Abstract
The high-order chromatin structure plays a non-negligible role in gene regulation. However, the mechanism, especially the sequence dependence for the formation of varied chromatin structures in different cells remains to be elucidated. As the nucleotide distributions in human and mouse genomes are highly uneven, we identified CGI (CpG island) forest and prairie genomic domains based on CGI densities of a species, dividing the genome into two sequentially, epigenetically, and transcriptionally distinct regions. These two megabase-sized domains also spatially segregate to different extents in different cell types. Forests and prairies show enhanced segregation from each other in development, differentiation, and senescence, meanwhile the multi-scale forest-prairie spatial intermingling is cell-type specific and increases in differentiation, helping to define cell identity. We propose that the phase separation of the 1D mosaic sequence in space serves as a potential driving force, and together with cell type specific epigenetic marks and transcription factors, shapes the chromatin structure in different cell types. The mosaicity in genome of different species in terms of forests and prairies could relate to observations in their biological processes like development and aging. In this way, we provide a bottoms-up theory to explain the chromatin structural and epigenetic changes in different processes.
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Affiliation(s)
- Sirui Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ling Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Hui Quan
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Hao Tian
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Luming Meng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Lijiang Yang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Huajie Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yi Qin Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
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16
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Bohlin J, Pettersson JHO. Evolution of Genomic Base Composition: From Single Cell Microbes to Multicellular Animals. Comput Struct Biotechnol J 2019; 17:362-370. [PMID: 30949307 PMCID: PMC6429543 DOI: 10.1016/j.csbj.2019.03.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 01/07/2023] Open
Abstract
Whole genome sequencing (WGS) of thousands of microbial genomes has provided considerable insight into evolutionary mechanisms in the microbial world. While substantially fewer eukaryotic genomes are available for analyses the number is rapidly increasing. This mini-review summarizes broadly evolutionary dynamics of base composition in the different domains of life from the perspective of prokaryotes. Common and different evolutionary mechanisms influencing genomic base composition in eukaryotes and prokaryotes are discussed. The conclusion from the data currently available suggests that while there are similarities there are also striking differences in how genomic base composition has evolved within prokaryotes and eukaryotes. For instance, homologous recombination appears to increase GC content locally in eukaryotes due to a non-selective process termed GC-biased gene conversion (gBGC). For prokaryotes on the other hand, increase in genomic GC content seems to be driven by the environment and selection. We find that similar phenomena observed for some organisms in each respective domain may be caused by very different mechanisms: while gBGC and recombination rates appear to explain the negative correlation between GC3 (GC content based on the third codon nucleotides) and genome size in some eukaryotes uptake of AT rich DNA sequences is the main reason for a similar negative correlation observed in prokaryotes. We provide further examples that indicate that base composition in prokaryotes and eukaryotes have evolved under very different constraints.
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Affiliation(s)
- Jon Bohlin
- Norwegian Institute of Public Health, Division of Infection Control and Environmental Health, Department of Infectious Disease Epidemiology and Modelling, Lovisenberggata 8, 0456 Oslo, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, PO-Box 222 Skøyen, N-0213 Oslo, Norway.,Norwegian University of Life Sciences, Faculty of Veterinary Sciences, Production Animal Clinical Sciences, Ullevålsveien 72, 0454 Oslo, Norway
| | - John H-O Pettersson
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School the University of Sydney, New South Wales 2006, Australia.,Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Public Health Agency of Sweden, Nobels vg 18, SE-171 82 Solna, Sweden
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17
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Lamolle G, Sabbia V, Musto H, Bernardi G. The short-sequence design of DNA and its involvement in the 3-D structure of the genome. Sci Rep 2018; 8:17820. [PMID: 30546029 PMCID: PMC6292894 DOI: 10.1038/s41598-018-35864-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/08/2018] [Indexed: 11/25/2022] Open
Abstract
Recent investigations have shown that isochores are characterized by a 3-D structure which is primarily responsible for the topology of chromatin domains. More precisely, an analysis of human chromosome 21 demonstrated that low-heterogeneity, GC-poor isochores are characterized by the presence of oligo-Adenines that are intrinsically stiff, curved and unfavorable for nucleosome binding. This leads to a structure of the corresponding chromatin domains, the Lamina Associated Domains, or LADs, which is well suited for interaction with the lamina. In contrast, the high-heterogeneity GC-rich isochores are in the form of compositional peaks and valleys characterized by increasing gradients of oligo-Guanines in the peaks and oligo-Adenines in the valleys that lead to increasing nucleosome depletions in the corresponding chromatin domains, the Topological Associating Domains, or TADs. These results encouraged us to investigate in detail the di- and tri-nucleotide profiles of 100 Kb segments of chromosome 21, as well as those of the di- to octa-Adenines and di- to octa-Guanines in some representative regions of the chromosome. The results obtained show that the 3-D structures of isochores and chromatin domains depend not only upon oligo-Adenines and oligo-Guanines but also, to a lower but definite extent, upon the majority of di- and tri-nucleotides. This conclusion has strong implications for the biological role of non-coding sequences.
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Affiliation(s)
- Guillermo Lamolle
- Laboratorio de Organización y Evolución del Genoma, Unidad Genómica Evolutiva, Facultad de Ciencias, Montevideo, Uruguay
| | - Victor Sabbia
- Laboratorio de Organización y Evolución del Genoma, Unidad Genómica Evolutiva, Facultad de Ciencias, Montevideo, Uruguay
| | - Héctor Musto
- Laboratorio de Organización y Evolución del Genoma, Unidad Genómica Evolutiva, Facultad de Ciencias, Montevideo, Uruguay
| | - Giorgio Bernardi
- Science Department, Roma Tre University, Viale Marconi 446, 00146, Rome, Italy.
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
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18
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GC content elevates mutation and recombination rates in the yeast Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2018; 115:E7109-E7118. [PMID: 29987035 PMCID: PMC6064992 DOI: 10.1073/pnas.1807334115] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The chromosomes of many eukaryotes have regions of high GC content interspersed with regions of low GC content. In the yeast Saccharomyces cerevisiae, high-GC regions are often associated with high levels of meiotic recombination. In this study, we constructed URA3 genes that differ substantially in their base composition [URA3-AT (31% GC), URA3-WT (43% GC), and URA3-GC (63% GC)] but encode proteins with the same amino acid sequence. The strain with URA3-GC had an approximately sevenfold elevated rate of ura3 mutations compared with the strains with URA3-WT or URA3-AT About half of these mutations were single-base substitutions and were dependent on the error-prone DNA polymerase ζ. About 30% were deletions or duplications between short (5-10 base) direct repeats resulting from DNA polymerase slippage. The URA3-GC gene also had elevated rates of meiotic and mitotic recombination relative to the URA3-AT or URA3-WT genes. Thus, base composition has a substantial effect on the basic parameters of genome stability and evolution.
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19
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Berná L, Rodriguez M, Chiribao ML, Parodi-Talice A, Pita S, Rijo G, Alvarez-Valin F, Robello C. Expanding an expanded genome: long-read sequencing of Trypanosoma cruzi. Microb Genom 2018; 4. [PMID: 29708484 PMCID: PMC5994713 DOI: 10.1099/mgen.0.000177] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Although the genome of Trypanosoma cruzi, the causative agent of Chagas disease, was first made available in 2005, with additional strains reported later, the intrinsic genome complexity of this parasite (the abundance of repetitive sequences and genes organized in tandem) has traditionally hindered high-quality genome assembly and annotation. This also limits diverse types of analyses that require high degrees of precision. Long reads generated by third-generation sequencing technologies are particularly suitable to address the challenges associated with T. cruzi’s genome since they permit direct determination of the full sequence of large clusters of repetitive sequences without collapsing them. This, in turn, not only allows accurate estimation of gene copy numbers but also circumvents assembly fragmentation. Here, we present the analysis of the genome sequences of two T. cruzi clones: the hybrid TCC (TcVI) and the non-hybrid Dm28c (TcI), determined by PacBio Single Molecular Real-Time (SMRT) technology. The improved assemblies herein obtained permitted us to accurately estimate gene copy numbers, abundance and distribution of repetitive sequences (including satellites and retroelements). We found that the genome of T. cruzi is composed of a ‘core compartment’ and a ‘disruptive compartment’ which exhibit opposite GC content and gene composition. Novel tandem and dispersed repetitive sequences were identified, including some located inside coding sequences. Additionally, homologous chromosomes were separately assembled, allowing us to retrieve haplotypes as separate contigs instead of a unique mosaic sequence. Finally, manual annotation of surface multigene families, mucins and trans-sialidases allows now a better overview of these complex groups of genes.
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Affiliation(s)
- Luisa Berná
- 1Laboratory of Host Pathogen Interactions-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Matias Rodriguez
- 2Sección Biomatemática - Unidad de Genómica Evolutiva, Facultad de Ciencias-UDELAR, Montevideo, Uruguay
| | - María Laura Chiribao
- 1Laboratory of Host Pathogen Interactions-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay.,3Departamento de Bioquímica, Facultad de Medicina-UDELAR, Montevideo, Uruguay
| | - Adriana Parodi-Talice
- 1Laboratory of Host Pathogen Interactions-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay.,4Sección Genética, Facultad de Ciencias-UDELAR, Montevideo, Uruguay
| | - Sebastián Pita
- 1Laboratory of Host Pathogen Interactions-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay.,4Sección Genética, Facultad de Ciencias-UDELAR, Montevideo, Uruguay
| | - Gastón Rijo
- 1Laboratory of Host Pathogen Interactions-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Fernando Alvarez-Valin
- 2Sección Biomatemática - Unidad de Genómica Evolutiva, Facultad de Ciencias-UDELAR, Montevideo, Uruguay
| | - Carlos Robello
- 1Laboratory of Host Pathogen Interactions-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay.,3Departamento de Bioquímica, Facultad de Medicina-UDELAR, Montevideo, Uruguay
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20
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Poulet-Benedetti J, Valton AL, Prioleau MN. [G-quadruplex: key controllers of human genome duplication]. Med Sci (Paris) 2017; 33:1063-1070. [PMID: 29261494 DOI: 10.1051/medsci/20173312013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The correct duplication of the human genome is under the control of a spatiotemporal program that determines where and when replication forks start. This regulation thus mainly operates on replication start sites named replication origins. During the S-phase, about 50 000 origins fire in one human cell. However, the normal or perturbed progression of replication forks also strongly impacts on replication. Recently, several studies have put forward the role of a noncanonical DNA structure, the G-quadruplex, in the control of genome duplication. In this review, we describe the major impact of this structure on starting points and on the progression of replication forks.
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Affiliation(s)
- Jérémy Poulet-Benedetti
- Institut Jacques Monod, CNRS UMR7592, université Paris Diderot, Équipe labellisée ARC (Association pour la recherche sur le cancer), 75013 Paris, France
| | - Anne-Laure Valton
- Howard Hughes Medical Institute, Program in systems biology, Department of biochemistry and molecular pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605-0103, États-Unis
| | - Marie-Noëlle Prioleau
- Institut Jacques Monod, CNRS UMR7592, université Paris Diderot, Équipe labellisée ARC (Association pour la recherche sur le cancer), 75013 Paris, France
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