Insights from human/mouse genome comparisons

Pennacchio, Len A.

doi:10.1007/s00335-002-4001-1

Cited by 72 publications

(48 citation statements)

References 57 publications

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“…There appear to be only small differences in gene number due to gene duplication and loss and relatively few bona fide novel gene sequences (Pennacchio, 2003;Siepel et al, 2007). Similarly, in spite of the extreme anatomical differences between monocots such as rice (Oryza sativa) and eudicots such as Arabidopsis thaliana and their common ancestry more than 140 million years (MY) ago, comparisons of these distant angiosperm genomes suggest they too contain similar overall gene composition, intron-exon structures, and ;35,000 genes (Bennetzen et al, 2004;Tripathi and Sowdhamini, 2006;Schnable et al, 2009).…”

Section: What Is the Relationship Between Epigenetic Control And The mentioning

confidence: 99%

The Evolution of Epitype

Meagher

2010

Plant Cell

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The epitype of a single gene or entire genome is determined by cis-linked differences in chromatin structure. I explore the hypothesis that "epitype and associated phenotypes evolve by gene duplication, divergence, and subfunctionalization" parallel to models for the evolution of genotype. This hypothesis is dissected by considering the relationship between epigenetic control and phenotype, the phylogenetic evidence that epitype evolves from ancestral genes following gene duplication, and the possible evolutionary rates of change for different epitypes. Initial supporting arguments for this hypothesis are discussed based on conserved patterns of nucleosome phasing, DNA methylation, and histone variant H2AZ deposition that appear to contribute to the inheritance of epitype in plants and animals. However, patterns of histone modification in recent segmental chromosome duplications are not well conserved. A continued experimental examination of the link between gene phylogeny and epitype and the evolution of epigenetically determined phenotypes is needed to further explore this hypothesis.

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Section: What Is the Relationship Between Epigenetic Control And The mentioning

confidence: 99%

The Evolution of Epitype

Meagher

2010

Plant Cell

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“…Also, comparison between human and mouse genomes revealed enrichment of segmental duplications in regions of breaks of synteny, suggesting their involvement in evolutionary rearrangements (Probst et al 1999;Armengol et al 2003;Kent et al 2003;Pennacchio 2003;Pevzner and Tesler 2003). Recently, however, Bailey et al (2004) proposed that the association between small-scale segmental duplication and largescale genomic rearrangements is not causative.…”

Section: Genomic Rearrangements and Primate Evolutionmentioning

confidence: 99%

Serial segmental duplications during primate evolution result in complex human genome architecture

Stankiewicz¹,

Shaw²,

Withers³

et al. 2004

Genome Res.

100

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The human genome is particularly rich in low-copy repeats (LCRs) or segmental duplications (5%-10%), and this characteristic likely distinguishes us from lower mammals such as rodents. How and why the complex human genome architecture consisting of multiple LCRs has evolved remains an open question. Using molecular and computational analyses of human and primate genomic regions, we analyzed the structure and evolution of LCRs that resulted in complex architectural features of the human genome in proximal 17p. We found that multiple LCRs of different origins are situated adjacent to one another, whereas each LCR changed at different time points between >25 to 3-7 million years ago (Mya) during primate evolution. Evolutionary studies in primates suggested communication between the LCRs by gene conversion. The DNA transposable element MER1-Charlie3 and retroviral ERVL elements were identified at the breakpoint of the t(4;19) chromosome translocation in Gorilla gorilla, suggesting a potential role for transpositions in evolution of the primate genome. Thus, a series of consecutive segmental duplication events during primate evolution resulted in complex genome architecture in proximal 17p. Some of the more recent events led to the formation of novel genes that in human are expressed primarily in the brain. Our observations support the contention that serial segmental duplication events might have orchestrated primate evolution by the generation of novel fusion/fission genes as well as potentially by genomic inversions associated with decreased recombination rates facilitating gene divergence. The genome architecture resulting from the size, orientation, and arrangement of LCRs was shown to be responsible for genomic instability (Lupski 1998;Emanuel and Shaikh 2001;Stankiewicz and Lupski 2002a). Serving as substrates for nonallelic (or "ectopic") homologous recombination (NAHR), LCRs facilitate meiotic and potentially mitotic DNA rearrangements associated with several diseases that are referred to as genomic disorders. Genomic rearrangements can be responsible for Mendelian traits, contiguous gene syndromes, and whole-arm chromosome aberrations (Lupski 1998Stankiewicz and Lupski 2002a). During the last decade, substantial molecular data have emerged documenting that LCR-mediated NAHR is a major mechanism for human disease (Emanuel and Shaikh 2001;Stankiewicz and Lupski 2002a;Shaw and Lupski 2004).Several studies have shown that LCRs arose recently, apparently during primate evolution (Stankiewicz and Lupski 2002b). Recent data suggest that LCR-associated genome architecture does not represent simple segmental duplications but rather reflects complex rearrangements that are potentially the end product of multiple events (van Geel et al. 2002). These serial segmental duplications can result in a complex shuffling of genomic sequences (Babcock et al. 2003;.The gene-and LCR-rich human genomic region 17p11.2-p12 is rearranged in a variety of different constitutional, evolutionary, and cancer-associated structural chromoso...

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“…Mice in particular are a common model in hypothesis-driven cardiovascular research (Treuting et al, 2012) due to their short lifespan, their small size, the similarity of their well-decrypted genome with the human one and, most importantly, the possibility to induce genetic modifications (Pennacchio, 2003). Genetically or pharmacologically altered mouse models have provided insight into (amongst many other cardiovascular applications) abdominal aortic aneurysm (Trachet et al, 2014a,b), stable and unstable atherosclerotic plaque (Van der Donckt et al, 2014;De Wilde et al, 2015), diabetes (Reed and Herold, 2015), hypertrophy (Yamaguchi et al, 2007) and Marfan syndrome (Campens et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

A 1D model of the arterial circulation in mice

Aslanidou

Trachet

Reymond

et al. 2016

ALTEX

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SummaryAt a time of growing concern over the ethics of animal experimentation, mouse models are still an indispensable source of insight into the cardiovascular system and its most frequent pathologies. Nevertheless, reference data on the murine cardiovascular anatomy and physiology are lacking. In this work, we developed and validated an in silico, one dimensional model of the murine systemic arterial tree consisting of 85 arterial segments. Detailed aortic dimensions were obtained in vivo from contrast-enhanced micro-computed tomography in 3 male, C57BL/6J anesthetized mice and 3 male ApoE -/-mice, all 12-weeks old. Physiological input data were gathered from a wide range of literature data. The integrated form of the Navier-Stokes equations was solved numerically to yield pressures and flows throughout the arterial network. The resulting model predictions have been validated against invasive pressure waveforms and noninvasive velocity and diameter waveforms that were measured in vivo on an independent set of 47 mice. In conclusion, we present a validated one-dimensional model of the anesthetized murine cardiovascular system that can serve as a versatile tool in the field of preclinical cardiovascular research.

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Insights from human/mouse genome comparisons

Cited by 72 publications

References 57 publications

The Evolution of Epitype

The Evolution of Epitype

Serial segmental duplications during primate evolution result in complex human genome architecture

A 1D model of the arterial circulation in mice

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