Genome size evolution: patterns, mechanisms, and methodological advances

Jd, Bainard; Tr, Gregory

doi:10.1139/gen-2013-0170

Cited by 4 publications

(2 citation statements)

References 19 publications

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“…Like in the present study, previous studies in mammals have mainly related cell size to DNA content 41,46,49,67,68 , and while this parameter is strongly correlated to nuclear size in a range of organisms 1,49,[68][69][70][71] , it has been suggested that the physical size of the nuclei might also be important. Thus, in cytokinesis-defective yeast, nuclear size correlates to cell size independent of DNA content 72 , and the importance of nuclear size per se has also been discussed for cells in developing Xenopus embryos 73 .…”

Section: Discussionsupporting

confidence: 66%

Myonuclear content regulates cell size with similar scaling properties in mice and humans

et al. 2020

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Muscle fibers are the largest cells in the body, and one of its few syncytia. Individual cell sizes are variable and adaptable, but what governs cell size has been unclear. We find that muscle fibers are DNA scarce compared to other cells, and that the nuclear number (N) adheres to the relationship N = aVb where V is the cytoplasmic volume. N invariably scales sublinearly to V (b < 1), making larger cells even more DNA scarce. N scales linearly to cell surface in adult humans, in adult and developing mice, and in mice with genetically reduced N, but in the latter the relationship eventually fails when they reach adulthood with extremely large myonuclear domains. Another exception is denervation-atrophy where nuclei are not eliminated. In conclusion, scaling exponents are remarkably similar across species, developmental stages and experimental conditions, suggesting an underlying scaling law where DNA-content functions as a limiter of muscle cell size.

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Section: Discussionsupporting

confidence: 66%

Myonuclear content regulates cell size with similar scaling properties in mice and humans

et al. 2020

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“…However, substantial variability of DNA content per haploid genome (C-value) have been widely observed even among the closely related species from same genus [3] , which is thereby termed the C-value paradox. Scientific publications in eukaryotes on diversity patterns, evolutionary mechanisms and research methodologies in relation to genome size were recently summarized [11] . The traditional view suggests that more than 90% of human genome are nonfunctional and therefore regarded as “junk DNA”, whereas ENCODE project recently argued that up to 80% of genome sequences have functional roles [2] , [12] .…”

Section: Outlines Of Genome Architecturementioning

confidence: 99%

Well-characterized sequence features of eukaryote genomes and implications for ab initio gene prediction

Huang

Chen

Deng

2016

Computational and Structural Biotechnology Journal

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In silico analysis of DNA sequences is an important area of computational biology in the post-genomic era. Over the past two decades, computational approaches for ab initio prediction of gene structure from genome sequence alone have largely facilitated our understanding on a variety of biological questions. Although the computational prediction of protein-coding genes has already been well-established, we are also facing challenges to robustly find the non-coding RNA genes, such as miRNA and lncRNA. Two main aspects of ab initio gene prediction include the computed values for describing sequence features and used algorithm for training the discriminant function, and by which different combinations are employed into various bioinformatic tools. Herein, we briefly review these well-characterized sequence features in eukaryote genomes and applications to ab initio gene prediction. The main purpose of this article is to provide an overview to beginners who aim to develop the related bioinformatic tools.

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An Immune Effector System in the Protochordate Gut Sheds Light on Fundamental Aspects of Vertebrate Immunity

Liberti

Leigh

Santis

et al. 2015

Results and Problems in Cell Differentiation

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A variety of germline and somatic immune mechanisms have evolved in vertebrate and invertebrate species to detect a wide array of pathogenic invaders. The gut is a particularly significant site in terms of distinguishing pathogens from potentially beneficial microbes. Ciona intestinalis, a filter-feeding marine protochordate that is ancestral to the vertebrate form, possesses variable region-containing chitin-binding proteins (VCBPs), a family of innate immune receptors, which recognize bacteria through an immunoglobulin-type variable region. The manner in which VCBPs mediate immune recognition appears to be related to the development and bacterial colonization of the gut, and it is likely that these molecules are critical elements in achieving overall immune and physiological homeostasis.

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Genome size evolution: patterns, mechanisms, and methodological advances

Cited by 4 publications

References 19 publications

Myonuclear content regulates cell size with similar scaling properties in mice and humans

Myonuclear content regulates cell size with similar scaling properties in mice and humans

Well-characterized sequence features of eukaryote genomes and implications for ab initio gene prediction

An Immune Effector System in the Protochordate Gut Sheds Light on Fundamental Aspects of Vertebrate Immunity

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