Patterns in the genome

Bickmore, Wendy A.

doi:10.1038/s41437-019-0220-4

Cited by 7 publications

(12 citation statements)

References 50 publications

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“…In mammalian chromosomes, gene density differences are correlated with chromosome banding patterns as the R-bands (gene-rich) have higher gene densities than the G-bands (gene-poor) [ 156 ]. The R- and G-band regions of chromosomes are also interlinked with different aspects of nuclear organization and gene regulation [ 167 ]. Increased acetylation of the amino terminus of histone H4 is observed in transcriptionally active regions [ 168 , 169 , 170 ].…”

Section: Independent Recombination Frequency Between Macro- and Microchromosomes As A Driver To Change Chromosome Structurementioning

confidence: 99%

Why Do Some Vertebrates Have Microchromosomes?

Srikulnath

Ahmad

Singchat

et al. 2021

Cells

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With more than 70,000 living species, vertebrates have a huge impact on the field of biology and research, including karyotype evolution. One prominent aspect of many vertebrate karyotypes is the enigmatic occurrence of tiny and often cytogenetically indistinguishable microchromosomes, which possess distinctive features compared to macrochromosomes. Why certain vertebrate species carry these microchromosomes in some lineages while others do not, and how they evolve remain open questions. New studies have shown that microchromosomes exhibit certain unique characteristics of genome structure and organization, such as high gene densities, low heterochromatin levels, and high rates of recombination. Our review focuses on recent concepts to expand current knowledge on the dynamic nature of karyotype evolution in vertebrates, raising important questions regarding the evolutionary origins and ramifications of microchromosomes. We introduce the basic karyotypic features to clarify the size, shape, and morphology of macro- and microchromosomes and report their distribution across different lineages. Finally, we characterize the mechanisms of different evolutionary forces underlying the origin and evolution of microchromosomes.

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Section: Independent Recombination Frequency Between Macro- and Microchromosomes As A Driver To Change Chromosome Structurementioning

confidence: 99%

Why Do Some Vertebrates Have Microchromosomes?

Srikulnath

Ahmad

Singchat

et al. 2021

Cells

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“…The higher order chromatin structure is highly dynamic and is regulated by epigenetic processes of DNA methylation, histone modification, and chromatin remodeling, ensuring proper cellular processes such as DNA replication, RNA transcription, and DNA damage repair in response to developmental or physiological signals ( Dekker and Mirny, 2016 ; Hansen et al., 2018 ; Bickmore, 2019 ). Structural variations or chromosomal rearrangements affect 3D genome organization and gene expression.…”

Section: Toward Precise and Predictable 3d Genome Editing: From 1d Tomentioning

confidence: 99%

“…The 3D genomes in the nuclear space are thought to be assembled in a hierarchical manner composed of successive chromosomal territories, compartments or clustering regions, TADs or topological domains, and chromatin loops ( Dekker and Mirny, 2016 ; Dixon et al., 2016 ; Bickmore, 2019 ). Briefly, each interphase chromosome occupies a distinct territory.…”

Section: Toward Precise and Predictable 3d Genome Editing: From 1d Tomentioning

confidence: 99%

Toward precise CRISPR DNA fragment editing and predictable 3D genome engineering

Shou

2020

Journal of Molecular Cell Biology

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Ever since gene targeting or specific modification of genome sequences in mice was achieved in the early 1980s, the reverse genetic approach of precise editing of any genomic locus has greatly accelerated biomedical research and biotechnology development. In particular, the recent development of the CRISPR/Cas9 system has greatly expedited genetic dissection of three-dimensional (3D) genomes. CRISPR gene editing results from targeted genome cleavage by ectopic bacterial Cas9 nuclease followed by presumed random ligations via the host double-strand break (DSB) repair machineries. Recent studies revealed, however, that the CRISPR genome editing system is precise and predictable because of cohesive Cas9 cleavage of targeting DNA. Here, we synthesize the current understanding of CRISPR DNA fragment editing mechanisms and recent progress in predictable outcomes from precise genetic engineering of 3D genomes. Specifically, we first briefly describe historical genetic studies leading to CRISPR and 3D genome engineering. We then summarize different types of chromosomal rearrangements by DNA fragment editing. Finally, we review significant progress from precise one-dimensional (1D) gene editing toward predictable 3D genome engineering and synthetic biology. The exciting and rapid advances in this emerging field provide new opportunities and challenges to understand or digest 3D genomes.

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“…G-bands contain AT-rich DNA sequences and a concentration of the long interspersed nuclear element L1 (LINE1). In contrast, the early replicating T-/R-bands concentrate a high density of Alu sequences, a clustering of CpG islands, and, accordingly a gene-richness [35]. In line with those previous observations in LCLs, all but three (2q31, 4q21, and 5q13) 13 preferential EBV-IS were located at G-positive cytobands, of which eight were visualized on the gene poorest CpG regions of the human genome (1p31, 1q31, 3q26, 5q21, 7q21, 8q21, 12q21, and 13q21) [36].…”

Section: Pattern Of Integration Of Statistically Significant Ebv In T...mentioning

confidence: 91%

Non-Random Pattern of Integration for Epstein-Barr Virus with Preference for Gene-Poor Genomic Chromosomal Regions into the Genome of Burkitt Lymphoma Cell Lines

Janjetovic

Hinke

Balachandran

et al. 2022

Viruses

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Background: Epstein-Barr virus (EBV) is an oncogenic virus found in about 95% of endemic Burkitt lymphoma (BL) cases. In latently infected cells, EBV DNA is mostly maintained in episomal form, but it can also be integrated into the host genome, or both forms can coexist in the infected cells. Methods: In this study, we mapped the chromosomal integration sites of EBV (EBV-IS) into the genome of 21 EBV+ BL cell lines (BL-CL) using metaphase fluorescence in situ hybridization (FISH). The data were used to investigate the EBV-IS distribution pattern in BL-CL, its relation to the genome instability, and to assess its association to common fragile sites and episomes. Results: We detected a total of 459 EBV-IS integrated into multiple genome localizations with a preference for gene-poor chromosomes. We did not observe any preferential affinity of EBV to integrate into common and rare fragile sites or enrichment of EBV-IS at the chromosomal breakpoints of the BL-CL analyzed here, as other DNA viruses do. Conclusions: We identified a non-random integration pattern into 13 cytobands, of which eight overlap with the EBV-IS in EBV-transformed lymphoblastoid cell lines and with a preference for gene- and CpGs-poor G-positive cytobands. Moreover, it has been demonstrated that the episomal form of EBV interacts in a non-random manner with gene-poor and AT-rich regions in EBV+ cell lines, which may explain the observed affinity for G-positive cytobands in the EBV integration process. Our results provide new insights into the patterns of EBV integration in BL-CL at the chromosomal level, revealing an unexpected connection between the episomal and integrated forms of EBV.

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Patterns in the genome

Cited by 7 publications

References 50 publications

Why Do Some Vertebrates Have Microchromosomes?

Why Do Some Vertebrates Have Microchromosomes?

Toward precise CRISPR DNA fragment editing and predictable 3D genome engineering

Non-Random Pattern of Integration for Epstein-Barr Virus with Preference for Gene-Poor Genomic Chromosomal Regions into the Genome of Burkitt Lymphoma Cell Lines

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