scholarly journals Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Austin B. Mudd ◽  
Jessen V. Bredeson ◽  
Rachel Baum ◽  
Dirk Hockemeyer ◽  
Daniel S. Rokhsar
Keyword(s):  
Karyotype Evolution ◽  
Rapid Evolution ◽  
Three Dimensional ◽  
Interphase Nuclei ◽  
Chromatin Compaction ◽  
Show Evidence ◽  
Chromosome Fusions ◽  
Genome Assemblies ◽  
Muntiacus Muntjak ◽  
Muntiacus Reevesi

AbstractClosely related muntjac deer show striking karyotype differences. Here we describe chromosome-scale genome assemblies for Chinese and Indian muntjacs, Muntiacus reevesi (2n = 46) and Muntiacus muntjak vaginalis (2n = 6/7), and analyze their evolution and architecture. The genomes show extensive collinearity with each other and with other deer and cattle. We identified numerous fusion events unique to and shared by muntjacs relative to the cervid ancestor, confirming many cytogenetic observations with genome sequence. One of these M. muntjak fusions reversed an earlier fission in the cervid lineage. Comparative Hi-C analysis showed that the chromosome fusions on the M. muntjak lineage altered long-range, three-dimensional chromosome organization relative to M. reevesi in interphase nuclei including A/B compartment structure. This reshaping of multi-megabase contacts occurred without notable change in local chromatin compaction, even near fusion sites. A few genes involved in chromosome maintenance show evidence for rapid evolution, possibly associated with the dramatic changes in karyotype.

scholarly journals Muntjac chromosome evolution and architecture

2019 ◽  
Author(s):  
Austin B. Mudd ◽  
Jessen V. Bredeson ◽  
Rachel Baum ◽  
Dirk Hockemeyer ◽  
Daniel S. Rokhsar
Keyword(s):  
Chromosome Evolution ◽  
Common Ancestor ◽  
Karyotype Evolution ◽  
Karyotype Analysis ◽  
Rapid Evolution ◽  
Unique Case ◽  
Show Evidence ◽  
Genome Assemblies ◽  
Muntiacus Muntjak ◽  
Muntiacus Reevesi

AbstractDespite their recent divergence, muntjac deer show striking karyotype differences. Here we describe new chromosome-scale genome assemblies for the Chinese and Indian muntjacs, Muntiacus reevesi (2n=46) and Muntiacus muntjak (2n=6/7), and analyze their evolution and architecture. We identified six fusion events shared by both species relative to the cervid ancestor and therefore present in the muntjac common ancestor, six fusion events unique to the M. reevesi lineage, and twenty-six fusion events unique to the M. muntjak lineage. One of these M. muntjak fusions reverses an earlier fission in the cervid lineage. Although comparative Hi-C analysis revealed differences in long-range genome contacts and A/B compartment structures, we discovered widespread conservation of local chromatin contacts between the muntjacs, even near the fusion sites. A small number of genes involved in chromosome maintenance show evidence for rapid evolution, possibly associated with the dramatic changes in karyotype. Analysis of muntjac genomes reveals new insights into this unique case of rapid karyotype evolution and the resulting biological variation.

scholarly journals Bridging the Gap between Vertebrate Cytogenetics and Genomics with Single-Chromosome Sequencing (ChromSeq)

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 124
Author(s):  
Alessio Iannucci ◽  
Alexey I. Makunin ◽  
Artem P. Lisachov ◽  
Claudio Ciofi ◽  
Roscoe Stanyon ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Karyotype Evolution ◽  
Genomic Data ◽  
Anolis Carolinensis ◽  
Vertebrate Genome ◽  
Single Chromosome ◽  
Sequencing Technologies ◽  
Novel Approaches ◽  
Genome Assemblies ◽  
Generation Sequencing

The study of vertebrate genome evolution is currently facing a revolution, brought about by next generation sequencing technologies that allow researchers to produce nearly complete and error-free genome assemblies. Novel approaches however do not always provide a direct link with information on vertebrate genome evolution gained from cytogenetic approaches. It is useful to preserve and link cytogenetic data with novel genomic discoveries. Sequencing of DNA from single isolated chromosomes (ChromSeq) is an elegant approach to determine the chromosome content and assign genome assemblies to chromosomes, thus bridging the gap between cytogenetics and genomics. The aim of this paper is to describe how ChromSeq can support the study of vertebrate genome evolution and how it can help link cytogenetic and genomic data. We show key examples of ChromSeq application in the refinement of vertebrate genome assemblies and in the study of vertebrate chromosome and karyotype evolution. We also provide a general overview of the approach and a concrete example of genome refinement using this method in the species Anolis carolinensis.

scholarly journals Donkey genome and insight into the imprinting of fast karyotype evolution

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Jinlong Huang ◽  
Yiping Zhao ◽  
Dongyi Bai ◽  
Wunierfu Shiraigol ◽  
Bei Li ◽  
...  
Keyword(s):  
Target Genes ◽  
Karyotype Evolution ◽  
De Novo ◽  
Cycle Phase ◽  
Satellite Sequences ◽  
Chromatid Segregation ◽  
Karyotypic Instability ◽  
Wild Ass ◽  
Genome Assemblies ◽  
Insight Into

Abstract The donkey, like the horse, is a promising model for exploring karyotypic instability. We report the de novo whole-genome assemblies of the donkey and the Asiatic wild ass. Our results reflect the distinct characteristics of donkeys, including more effective energy metabolism and better immunity than horses. The donkey shows a steady demographic trajectory. We detected abundant satellite sequences in some inactive centromere regions but not in neocentromere regions, while ribosomal RNAs frequently emerged in neocentromere regions but not in the obsolete centromere regions. Expanded miRNA families and five newly discovered miRNA target genes involved in meiosis may be associated with fast karyotype evolution. APC/C, controlling sister chromatid segregation, cytokinesis and the establishment of the G1 cell cycle phase were identified by analysis of miRNA targets and rapidly evolving genes.

Three-dimensional reconstruction of the chromatin bodies in the nuclei of mature erythrocytes from the newt Triturus cristatus: the number of nuclear envelope-attachment sites

1979 ◽  
Vol 35 (1) ◽  
pp. 59-66
Author(s):  
A.B. Murray ◽  
H.G. Davies
Keyword(s):  
Nuclear Envelope ◽  
Three Dimensional ◽  
Interphase Nuclei ◽  
Interphase Chromosome ◽  
Triturus Cristatus ◽  
3 Dimensional ◽  
Attachment Sites ◽  
Chromatin Body ◽  
Dimensional Reconstruction ◽  
Discrete Site

The arrangement of the chromatin bodies in the interphase nuclei of 6 erythrocytes has been investigated by means of 3-dimensional reconstruction from electron micrographs of serial sections. When the borders of chromatin bodies are marked on the surface of each model, discrete areas of chromatin in contact with the nuclear envelope are revealed. The number of these areas in approximately equal to the number of chromosomes in the diploid set. The data suggest that each chromatin body corresponds to a condensed interphase chromosome and that each chromosome is attached to one discrete site on the nuclear envelope. The data are insufficient to show whether or not the condensed chromosomes are arranged in any orderly pattern in these nuclei.

scholarly journals New insight into 3-D mesoscale eddy properties from CMEMS operational models in the western Mediterranean

Ocean Science ◽  
2019 ◽  
Vol 15 (4) ◽  
pp. 1111-1131 ◽  
Author(s):  
Evan Mason ◽  
Simón Ruiz ◽  
Romain Bourdalle-Badie ◽  
Guillaume Reffray ◽  
Marcos García-Sotillo ◽  
...  
Keyword(s):  
Composite Structures ◽  
Global Analysis ◽  
Rapid Evolution ◽  
Mesoscale Eddy ◽  
Three Dimensional ◽  
Western Mediterranean ◽  
Alboran Sea ◽  
Western Mediterranean Sea ◽  
Common Domain ◽  
Alborán Sea

Abstract. Rapid evolution of operational ocean forecasting systems is driven by advances in numerics and data assimilation schemes, and increase of in situ and satellite observations. The Copernicus Marine Service (CMEMS) is a major provider of operational products that are made available through an online catalogue. The service includes global and regional forecasts in near-real-time and reanalysis modes. Here, we apply an eddy tracker to daily sea surface height (SSH) fields from three such reanalysis products from the CMEMS catalogue, with the objective to evaluate their performance in terms of their eddy properties and three-dimensional composite structures over the 2013–2016 period. The products are (i) the Global Analysis Forecast, (ii) the Mediterranean Analysis Forecast and (iii) the Iberia–Biscay–Ireland Analysis Forecast. The common domain between these reanalyses is the western Mediterranean Sea (WMED) between the Strait of Gibraltar and Sardinia. This is a complex region with strong density gradients, especially in the Alboran Sea in the west where Atlantic and Mediterranean waters compete. Surface eddy property maps over the WMED of eddy radii, amplitudes and nonlinearity are consistent between the models, as well as with gridded altimetric data that serve as a reference. Mean 3-D eddy composites are shown only for three subregions in the Alboran Sea. These are mostly consistent between the models, with minor differences being attributed to details of the respective model configurations. This information can be informative for the ongoing development of these CMEMS operational modeling systems. The mesoscale data provided here may be of interest to CMEMS users and in the future could be a useful addition to a more diverse CMEMS catalogue.

Hydrogen-bond patterns in 1,4-dihydro-2,3-quinoxalinediones: ligands for the glycine modulatory site on the NMDA receptor

1996 ◽  
Vol 52 (3) ◽  
pp. 487-499 ◽  
Author(s):  
M. Kubicki ◽  
T. W. Kindopp ◽  
M. V. Capparelli ◽  
P. W. Codding
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Binding Site ◽  
Three Dimensional ◽  
Hydrogen Bonding Pattern ◽  
Wide Range ◽  
Show Evidence ◽  
Additional Hydrogen Bond ◽  
Hydrogen Bond Patterns ◽  
Solvent Molecules

The crystal structures of five 1,4-dihydro-2,3-quinoxalinediones, antagonists of the NMDA modulatory glycine binding site on the excitary amino acid (EAA) receptor complex, have been determined: (I) 6,7-dinitro-1,4-dihydro-2,3-quinoxalinedione (DNQX); (II) 5,7-dinitro-1,4-dihydro-2,3-quinoxalinedione (MNQX); (III) 6-nitro-1,4-dihydro-2,3-quinoxalinedione hydrate; (IV) 6,7-dichloro-1,4-dihydro-2,3-quinoxalinedione; (V) 5,7-dichloro-1,4-dihydro-2,3-quinoxalinedione dimethylformamide. The crystal structure of the most active compound (II) contains a unique intramolecular N—H...O(NO2) hydrogen bond, which may be important for activity, as semiempirical calculations show that this bond is stable over a wide range of dihedral angles between the planes of the molecule and of the nitro group. In the other compounds the intermolecular hydrogen bonds connect molecules into three-dimensional networks. In compounds (I), (III) and (IV) head-to-tail: π-stacking is found between molecules connected by a center of symmetry. The geometries of the hydrogen-bonded —NH—C=O fragments show evidence of π-cooperativity or resonance-assisted hydrogen bonding. Graph-set analysis of the hydrogen-bond patterns of quinoxalinedione derivatives shows a tendency to form two types of hydrogen-bonding motifs: a centrosymmetric dimeric ring and an infinite chain. Even though this pattern may be modified by the presence of additional hydrogen-bond acceptors and/or donors, as well as by solvent molecules, general similarities have been found. Comparison of all quinoxalinedione structures suggests that the hydrogen-bonding pattern necessary for the biological activity at the glycine binding site contains one donor and two acceptors.

scholarly journals Impact of Chromosome Fusions on 3D Genome Organization and Gene Expression in Budding Yeast

Genetics ◽  
2020 ◽  
Vol 214 (3) ◽  
pp. 651-667 ◽  
Author(s):  
Marco Di Stefano ◽  
Francesca Di Giovanni ◽  
Vasilisa Pozharskaia ◽  
Mercè Gomar-Alba ◽  
Davide Baù ◽  
...  
Keyword(s):  
Gene Expression ◽  
Budding Yeast ◽  
Nuclear Organization ◽  
Nuclear Periphery ◽  
Three Dimensional ◽  
Global Gene Expression ◽  
3D Genome ◽  
Expression Of Genes ◽  
Genome Wide ◽  
Chromosome Fusions

The three-dimensional (3D) organization of chromosomes can influence transcription. However, the frequency and magnitude of these effects remain debated. To determine how changes in chromosome positioning affect transcription across thousands of genes with minimal perturbation, we characterized nuclear organization and global gene expression in budding yeast containing chromosome fusions. We used computational modeling and single-cell imaging to determine chromosome positions, and integrated these data with genome-wide transcriptional profiles from RNA sequencing. We find that chromosome fusions dramatically alter 3D nuclear organization without leading to strong genome-wide changes in transcription. However, we observe a mild but significant and reproducible increase in the expression of genes displaced away from the periphery. The increase in transcription is inversely proportional to the propensity of a given locus to be at the nuclear periphery; for example, a 10% decrease in the propensity of a gene to reside at the nuclear envelope is accompanied by a 10% increase in gene expression. Modeling suggests that this is due to both deletion of telomeres and to displacement of genes relative to the nuclear periphery. These data suggest that basal transcriptional activity is sensitive to radial changes in gene position, and provide insight into the functional relevance of budding yeast chromosome-level 3D organization in gene expression.

scholarly journals Systematic Chromatin Architecture Analysis in Xenopus tropicalis Reveals Conserved Three-Dimensional Folding Principles of Vertebrate Genomes

2020 ◽  
Author(s):  
Longjian Niu ◽  
Wei Shen ◽  
Zhaoying Shi ◽  
Na He ◽  
Jing Wan ◽  
...  
Keyword(s):  
Binding Sites ◽  
Three Dimensional ◽  
Xenopus Tropicalis ◽  
Ctcf Binding ◽  
Interphase Nuclei ◽  
Chromosome Architecture ◽  
Topologically Associating Domains ◽  
Genome Activation ◽  
Zygotic Genome ◽  
Architecture Analysis

ABSTRACTMetazoan genomes are folded into 3D structures in interphase nuclei. However, the molecular mechanism remains unknown. Here, we show that topologically associating domains (TADs) form in two waves during Xenopus tropicalis embryogenesis, first at zygotic genome activation and then as the expression of CTCF and Rad21 is elevated. We also found TAD structures continually change for at least three times during development. Surprisingly, the directionality index is preferentially stronger on one side of TADs where orientation-biased CTCF and Rad21 binding are observed, a conserved pattern that is found in human cells as well. Depletion analysis revealed CTCF, Rad21, and RPB1, a component of RNAPII, are required for the establishment of TADs. Overall, our work shows that Xenopus is a powerful model for chromosome architecture analysis. Furthermore, our findings indicate that cohesin-mediated extrusion may anchor at orientation-biased CTCF binding sites, supporting a CTCF-anchored extrusion model as the mechanism for TAD establishment.

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