scholarly journals Evolution and function of genomic imprinting in plants

2015 ◽  
Vol 29 (24) ◽  
pp. 2517-2531 ◽  
Author(s):  
Jessica A. Rodrigues ◽  
Daniel Zilberman
Keyword(s):  
Genomic Imprinting ◽  
Histone Methylation ◽  
Biological Significance ◽  
Flowering Plants ◽  
Evolutionary Forces ◽  
Plant Genes ◽  
Epigenetic Phenomenon ◽  
Parent Of Origin ◽  
And Function ◽  
Genome Scale

Genomic imprinting, an inherently epigenetic phenomenon defined by parent of origin-dependent gene expression, is observed in mammals and flowering plants. Genome-scale surveys of imprinted expression and the underlying differential epigenetic marks have led to the discovery of hundreds of imprinted plant genes and confirmed DNA and histone methylation as key regulators of plant imprinting. However, the biological roles of the vast majority of imprinted plant genes are unknown, and the evolutionary forces shaping plant imprinting remain rather opaque. Here, we review the mechanisms of plant genomic imprinting and discuss theories of imprinting evolution and biological significance in light of recent findings.

Imprinted small RNA genes

2004 ◽  
Vol 385 (10) ◽  
pp. 905-911 ◽  
Author(s):  
Hervé Seitz ◽  
Hélène Royo ◽  
Shau-Ping Lin ◽  
Neil Youngson ◽  
Anne C. Ferguson-Smith ◽  
...  
Keyword(s):  
Genomic Imprinting ◽  
Gene Families ◽  
Evolutionary Significance ◽  
Microrna Gene ◽  
Non Coding Rna ◽  
Epigenetic Phenomenon ◽  
Parent Of Origin ◽  
Microrna Genes ◽  
Rna Genes

Abstract Genomic imprinting is an epigenetic phenomenon that results in differential expression of both alleles, depending on their parent of origin. We have recently identified many imprinted small non-coding RNA genes belonging to the C/D RNA and microRNA gene families, both of which are usually known to play key roles in post-transcriptional metabolism of specific genes (e.g. C/D RNAs guide ribose methylation of target RNAs while microRNAs elicit either translational repression or RNA interference). Although the functional and evolutionary significance of this association between C/D RNA genes, microRNA genes and genomic imprinting is still highly elusive, these observations provide a framework for further analysis of the potential role of small non-coding RNAs in epigenetic control.

scholarly journals Canonical and Non-canonical Genomic Imprinting in Rodents

2021 ◽  
Vol 9 ◽  
Author(s):  
Hisato Kobayashi
Keyword(s):  
Dna Methylation ◽  
Genomic Imprinting ◽  
Mouse Genome ◽  
Genetic Regulation ◽  
Imprinted Genes ◽  
Evolutionary Divergence ◽  
Chromatin Modifications ◽  
Allele Specific ◽  
Epigenetic Phenomenon ◽  
Parent Of Origin

Genomic imprinting is an epigenetic phenomenon that results in unequal expression of homologous maternal and paternal alleles. This process is initiated in the germline, and the parental epigenetic memories can be maintained following fertilization and induce further allele-specific transcription and chromatin modifications of single or multiple neighboring genes, known as imprinted genes. To date, more than 260 imprinted genes have been identified in the mouse genome, most of which are controlled by imprinted germline differentially methylated regions (gDMRs) that exhibit parent-of-origin specific DNA methylation, which is considered primary imprint. Recent studies provide evidence that a subset of gDMR-less, placenta-specific imprinted genes is controlled by maternal-derived histone modifications. To further understand DNA methylation-dependent (canonical) and -independent (non-canonical) imprints, this review summarizes the loci under the control of each type of imprinting in the mouse and compares them with the respective homologs in other rodents. Understanding epigenetic systems that differ among loci or species may provide new models for exploring genetic regulation and evolutionary divergence.

scholarly journals Paternally expressed imprinted genes establish postzygotic hybridization barriers in Arabidopsis thaliana

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Philip Wolff ◽  
Hua Jiang ◽  
Guifeng Wang ◽  
Juan Santos-González ◽  
Claudia Köhler
Keyword(s):  
Arabidopsis Thaliana ◽  
Differential Expression ◽  
Seed Development ◽  
Genomic Imprinting ◽  
Imprinted Genes ◽  
Functional Requirement ◽  
Functional Roles ◽  
Epigenetic Phenomenon ◽  
Parent Of Origin

Genomic imprinting is an epigenetic phenomenon causing parent-of-origin specific differential expression of maternally and paternally inherited alleles. While many imprinted genes have been identified in plants, the functional roles of most of them are unknown. In this study, we systematically examine the functional requirement of paternally expressed imprinted genes (PEGs) during seed development in Arabidopsis thaliana. While none of the 15 analyzed peg mutants has qualitative or quantitative abnormalities of seed development, we identify three PEGs that establish postzygotic hybridization barriers in the endosperm, revealing that PEGs have a major role as speciation genes in plants. Our work reveals that a subset of PEGs maintains functional roles in the inbreeding plant Arabidopsis that become evident upon deregulated expression.

scholarly journals Epigenetic modifications potentially controlling the allelic expression of imprinted genes in sunflower endosperm

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhichao Zhang ◽  
Shuai Yu ◽  
Jing Li ◽  
Yanbin Zhu ◽  
Siqi Jiang ◽  
...  
Keyword(s):  
Genomic Imprinting ◽  
Noncoding Rnas ◽  
Methylation Pattern ◽  
Flowering Plants ◽  
Imprinted Genes ◽  
Genome Wide ◽  
Allelic Gene ◽  
Potential Basis ◽  
Epigenetic Phenomenon ◽  
Global Patterns

Abstract Background Genomic imprinting is an epigenetic phenomenon mainly occurs in endosperm of flowering plants. Genome-wide identification of imprinted genes have been completed in several dicot Cruciferous plant and monocot crops. Results Here, we analyzed global patterns of allelic gene expression in developing endosperm of sunflower which belongs to the composite family. Totally, 691 imprinted loci candidates were identified in 12 day-after-pollination sunflower endosperm including 79 maternally expressed genes (MEG) and 596 paternally expressed genes (PEG), 6 maternally expressed noncoding RNAs (MNC) and 10 paternally expressed noncoding RNAs (PNC). And a clear clustering of imprinted genes throughout the rapeseed genome was identified. Generally, imprinting in sunflower is conserved within a species, but intraspecific variation also was detected. Limited loci in sunflower are imprinted in other several different species. The DNA methylation pattern around imprinted genes were investigated in embryo and endosperm tissues. In CG context, the imprinted genes were significantly associated with differential methylated regions exhibiting hypomethylation in endosperm and hypermethylation in embryo, which indicated that the maternal demethylation in CG context potentially induce the genomic imprinting in endosperm. Conclusion Our study would be helpful for understanding of genomic imprinting in plants and provide potential basis for further research in imprinting in sunflower.

UNIPARENTAL DISOMY: MECHANISMS AND CLINICAL CONSEQUENCES

2003 ◽  
Vol 14 (2) ◽  
pp. 155-175 ◽  
Author(s):  
LISA G SHAFFER
Keyword(s):  
Genomic Imprinting ◽  
Normal State ◽  
Diploid Number ◽  
Uniparental Disomy ◽  
Monoallelic Expression ◽  
Clinical Consequences ◽  
Epigenetic Phenomenon ◽  
Parent Of Origin

During gametogenesis in mammals, half of the parental chromosomes segregate to each gamete. Upon fertilization of two haploid gametes, the diploid number is restored (Figure 1A). Nondisjunction, malsegregation of the chromosomes during gametogenesis, can give rise to chromosomally unbalanced offspring (trisomies and monosomies) (Figure 1B). Genomic imprinting is an epigenetic phenomenon in which the activity of a gene is reversibly modified depending on the parent of origin. This leads to unequal, monoallelic expression of the maternal and paternal alleles of a diploid locus (Figure 1C). Thus, the normal state of an imprinted locus is an “imbalance”, not of chromosomes, but of the functional genetic content.

scholarly journals Vulnerability of individual fish to capture by trawling is influenced by capacity for anaerobic metabolism

2015 ◽  
Vol 282 (1813) ◽  
pp. 20150603 ◽  
Author(s):  
Shaun S. Killen ◽  
Julie J. H. Nati ◽  
Cory D. Suski
Keyword(s):  
Large Scale ◽  
Swimming Performance ◽  
Anaerobic Capacity ◽  
Standard Metabolic Rate ◽  
Metabolic Demand ◽  
Evolutionary Forces ◽  
Individual Fish ◽  
Fundamental Information ◽  
Behavioural Phenotypes ◽  
And Function

The harvest of animals by humans may constitute one of the strongest evolutionary forces affecting wild populations. Vulnerability to harvest varies among individuals within species according to behavioural phenotypes, but we lack fundamental information regarding the physiological mechanisms underlying harvest-induced selection. It is unknown, for example, what physiological traits make some individual fish more susceptible to capture by commercial fisheries. Active fishing methods such as trawling pursue fish during harvest attempts, causing fish to use both aerobic steady-state swimming and anaerobic burst-type swimming to evade capture. Using simulated trawling procedures with schools of wild minnows Phoxinus phoxinus , we investigate two key questions to the study of fisheries-induced evolution that have been impossible to address using large-scale trawls: (i) are some individuals within a fish shoal consistently more susceptible to capture by trawling than others?; and (ii) if so, is this related to individual differences in swimming performance and metabolism? Results provide the first evidence of repeatable variation in susceptibility to trawling that is strongly related to anaerobic capacity and swimming ability. Maximum aerobic swim speed was also negatively correlated with vulnerability to trawling. Standard metabolic rate was highest among fish that were least vulnerable to trawling, but this relationship probably arose through correlations with anaerobic capacity. These results indicate that vulnerability to trawling is linked to anaerobic swimming performance and metabolic demand, drawing parallels with factors influencing susceptibility to natural predators. Selection on these traits by fisheries could induce shifts in the fundamental physiological makeup and function of descendent populations.

scholarly journals Intrinsic disorder in protein domains contributes to both organism complexity and clade-specific functions

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chao Gao ◽  
Chong Ma ◽  
Huqiang Wang ◽  
Haolin Zhong ◽  
Jiayin Zang ◽  
...  
Keyword(s):  
Biological Significance ◽  
Protein Domains ◽  
Functional Requirements ◽  
Post Translational Modification ◽  
Intrinsically Disordered ◽  
Genome Wide ◽  
Complex Functions ◽  
Disorder Degree ◽  
Functional Features ◽  
And Function

AbstractInterestingly, some protein domains are intrinsically disordered (abbreviated as IDD), and the disorder degree of same domains may differ in different contexts. However, the evolutionary causes and biological significance of these phenomena are unclear. Here, we address these issues by genome-wide analyses of the evolutionary and functional features of IDDs in 1,870 species across the three superkingdoms. As the result, there is a significant positive correlation between the proportion of IDDs and organism complexity with some interesting exceptions. These phenomena may be due to the high disorder of clade-specific domains and the different disorder degrees of the domains shared in different clades. The functions of IDDs are clade-specific and the higher proportion of post-translational modification sites may contribute to their complex functions. Compared with metazoans, fungi have more IDDs with a consecutive disorder region but a low disorder ratio, which reflects their different functional requirements. As for disorder variation, it’s greater for domains among different proteins than those within the same proteins. Some clade-specific ‘no-variation’ or ‘high-variation’ domains are involved in clade-specific functions. In sum, intrinsic domain disorder is related to both the organism complexity and clade-specific functions. These results deepen the understanding of the evolution and function of IDDs.

scholarly journals The Hippo Pathway: A Master Regulatory Network Important in Cancer

Cells ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1416
Author(s):  
Qiuping Liu ◽  
Xiaomeng Liu ◽  
Guanbin Song
Keyword(s):  
Metabolic Regulation ◽  
Human Cancer ◽  
Hippo Pathway ◽  
Tumor Development ◽  
Biological Significance ◽  
Cancer Development ◽  
Hippo Signaling ◽  
Complex Regulation ◽  
And Function ◽  
The Hippo Pathway

The Hippo pathway is pervasively activated and has been well recognized to play critical roles in human cancer. The deregulation of Hippo signaling involved in cancer development, progression, and resistance to cancer treatment have been confirmed in several human cancers. Its biological significance and deregulation in cancer have drawn increasing interest in the past few years. A fundamental understanding of the complexity of the Hippo pathway in cancer is crucial for improving future clinical interventions and therapy for cancers. In this review, we try to clarify the complex regulation and function of the Hippo signaling network in cancer development, including its role in signal transduction, metabolic regulation, and tumor development, as well as tumor therapies targeting the Hippo pathway.

TETRASPORE is required for male meiotic cytokinesis in Arabidopsis thaliana

Development ◽  
1997 ◽  
Vol 124 (13) ◽  
pp. 2645-2657 ◽  
Author(s):  
M. Spielman ◽  
D. Preuss ◽  
F.L. Li ◽  
W.E. Browne ◽  
R.J. Scott ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Pollen Development ◽  
Male Meiosis ◽  
Pollen Grain ◽  
Flowering Plants ◽  
External Wall ◽  
Normal Pollen ◽  
Wide Range ◽  
Asymmetric Divisions ◽  
And Function

In flowering plants, male meiosis occurs in the microsporocyte to produce four microspores, each of which develops into a pollen grain. Here we describe four mutant alleles of TETRASPORE (TES), a gene essential for microsporocyte cytokinesis in Arabidopsis thaliana. Following failure of male meiotic cytokinesis in tes mutants, all four microspore nuclei remain within the same cytoplasm, with some completing their developmental programmes to form functional pollen nuclei. Both of the mitotic divisions seen in normal pollen development take place in tes mutants, including the asymmetric division required for the differentiation of gametes; some tes grains perform multiple asymmetric divisions in the same cytoplasm. tes pollen shows a variety of abnormalities subsequent to the cytokinetic defect, including fusion of nuclei, formation of ectopic internal walls, and disruptions to external wall patterning. In addition, ovules fertilized by tes pollen often abort, possibly because of excess paternal genomes in the endosperm. Thus tes mutants not only reveal a gene specific to male meiosis, but aid investigation of a wide range of processes in pollen development and function.

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