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 LncRNAs and PRC2: Coupled Partners in Embryonic Stem Cells

Epigenomes ◽  
2019 ◽  
Vol 3 (3) ◽  
pp. 14 ◽  
Author(s):  
Alessandro Fiorenzano ◽  
Emilia Pascale ◽  
Eduardo Jorge Patriarca ◽  
Gabriella Minchiotti ◽  
Annalisa Fico
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Single Cell Analysis ◽  
Embryonic Stem ◽  
Epigenetic Landscape ◽  
Polycomb Repressive Complex 2 ◽  
Non Coding Rna ◽  
Long Non Coding Rna ◽  
Rna Genes

The power of embryonic stem cells (ESCs) lies in their ability to self-renew and differentiate. Behind these two unique capabilities is a fine-tuned molecular network that shapes the genetic, epigenetic, and epitranscriptomic ESC plasticity. Although RNA has been shown to be functionally important in only a small minority of long non-coding RNA genes, a growing body of evidence has highlighted the pivotal and intricate role of lncRNAs in chromatin remodeling. Due to their multifaceted nature, lncRNAs interact with DNA, RNA, and proteins, and are emerging as new modulators of extensive gene expression programs through their participation in ESC-specific regulatory circuitries. Here, we review the tight cooperation between lncRNAs and Polycomb repressive complex 2 (PRC2), which is intimately involved in determining and maintaining the ESC epigenetic landscape. The lncRNA-PRC2 partnership is fundamental in securing the fully pluripotent state of ESCs, which must be primed to differentiate properly. We also reflect on the advantages brought to this field of research by the advent of single-cell analysis.

scholarly journals PO-0958: Radiogenomics: role of non-coding RNA genes in increased radiotherapy sensitivity

2017 ◽  
Vol 123 ◽  
pp. S529-S530
Author(s):  
L. Duran-Lozano ◽  
V. Reyes ◽  
M. Mollà ◽  
M.J. Fuentes-Raspall ◽  
M. Altabas ◽  
...  
Keyword(s):  
Non Coding Rna ◽  
Rna Genes

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 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.

scholarly journals Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting

2021 ◽  
Vol 118 (29) ◽  
pp. e2104445118
Author(s):  
Jessica A. Rodrigues ◽  
Ping-Hung Hsieh ◽  
Deling Ruan ◽  
Toshiro Nishimura ◽  
Manoj K. Sharma ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Genomic Imprinting ◽  
Small Rnas ◽  
Imprinted Genes ◽  
Dna Hypomethylation ◽  
Transcription Start ◽  
Specific Expression ◽  
Parent Of Origin

Parent-of-origin–dependent gene expression in mammals and flowering plants results from differing chromatin imprints (genomic imprinting) between maternally and paternally inherited alleles. Imprinted gene expression in the endosperm of seeds is associated with localized hypomethylation of maternally but not paternally inherited DNA, with certain small RNAs also displaying parent-of-origin–specific expression. To understand the evolution of imprinting mechanisms in Oryza sativa (rice), we analyzed imprinting divergence among four cultivars that span both japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted genes are imprinted across cultivars and enriched for functions in chromatin and transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted genes display divergent imprinting. Analyses of DNA methylation and small RNAs revealed that endosperm-specific 24-nt small RNA–producing loci show weak RNA-directed DNA methylation, frequently overlap genes, and are imprinted four times more often than genes. However, imprinting divergence most often correlated with local DNA methylation epimutations (9 of 17 assessable loci), which were largely stable within subspecies. Small insertion/deletion events and transposable element insertions accompanied 4 of the 9 locally epimutated loci and associated with imprinting divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic variation occurred at key regulatory regions—the promoter and transcription start site of maternally biased genes, and the promoter and gene body of paternally biased genes. Our results reinforce models for the role of maternal-specific DNA hypomethylation in imprinting of both maternally and paternally biased genes, and highlight the role of transposition and epimutation in rice imprinting evolution.

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.

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.

Role of MicroRNA Genes miR-1000 and miR-375 in Forming Olfactory Conditional Memory in Drosophila melanogaster

MicroRNA ◽  
2020 ◽  
Vol 09 ◽  
Author(s):  
Sadniman Rahman ◽  
Chaity Modak ◽  
Mousumi Akter ◽  
Mohammad Shamimul Alam
Keyword(s):  
Learning And Memory ◽  
Short Term Memory ◽  
Memory Loss ◽  
Memory Formation ◽  
Neural Integration ◽  
Significant Difference ◽  
Locomotion Speed ◽  
Microrna Genes ◽  
With Memory

Background: Learning and memory is basic aspects in neurogenetics as most of the neurological disorders start with dementia or memory loss. Several genes associated with memory formation have been discovered. MicroRNA genes miR-1000 and miR-375 were reported to be associated with neural integration and glucose homeostasis in some insects and vertebrates. However, neuronal function of these genes is yet to be established in D. melanogaster. Objective: Possible role of miR-1000 and miR-375 in learning and memory formation in this fly has been explored in the present study. Methods: Both appetitive and aversive olfactory conditional learning were tested in the miR-1000 and miR-375 knockout (KO) strains and compared with wild one. Five days old third instar larvae were trained by allowing them to be associated with an odor with reward (fructose) or punishment (salt). Then, the larvae were tested to calculate their preferences to the odor trained with. Learning index (LI) values and larval locomotion speed were calculated for all strains. Results: No significant difference was observed for larval locomotion speed in mutant strains. Knockout strain of miR-1000 showed significant deficiency in both appetitive and aversive memory formation whereas miR-375 KO strain showed a significantly lower response only in appetitive one. Conclusion: The results of the present study indicate important role played by these two genes in forming short-term memory in D. melanogaster.

scholarly journals Role of Long Non-Coding RNA Polymorphisms in Cancer Chemotherapeutic Response

2021 ◽  
Vol 11 (6) ◽  
pp. 513
Author(s):  
Zheng Zhang ◽  
Meng Gu ◽  
Zhongze Gu ◽  
Yan-Ru Lou
Keyword(s):  
Molecular Mechanisms ◽  
Neurological Diseases ◽  
Cellular Processes ◽  
Dna And Rna ◽  
Chemotherapeutic Response ◽  
Non Coding Rna ◽  
Response To Chemotherapy ◽  
Personalized Oncology ◽  
Long Non Coding Rna

Genetic polymorphisms are defined as the presence of two or more different alleles in the same locus, with a frequency higher than 1% in the population. Since the discovery of long non-coding RNAs (lncRNAs), which refer to a non-coding RNA with a length of more than 200 nucleotides, their biological roles have been increasingly revealed in recent years. They regulate many cellular processes, from pluripotency to cancer. Interestingly, abnormal expression or dysfunction of lncRNAs is closely related to the occurrence of human diseases, including cancer and degenerative neurological diseases. Particularly, their polymorphisms have been found to be associated with altered drug response and/or drug toxicity in cancer treatment. However, molecular mechanisms are not yet fully elucidated, which are expected to be discovered by detailed studies of RNA–protein, RNA–DNA, and RNA–lipid interactions. In conclusion, lncRNAs polymorphisms may become biomarkers for predicting the response to chemotherapy in cancer patients. Here we review and discuss how gene polymorphisms of lncRNAs affect cancer chemotherapeutic response. This knowledge may pave the way to personalized oncology treatments.

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