scholarly journals Tandem repeats in the CpG islands of imprinted genes

Genomics ◽  
2006 ◽  
Vol 88 (3) ◽  
pp. 323-332 ◽  
Author(s):  
Barbara Hutter ◽  
Volkhard Helms ◽  
Martina Paulsen
Keyword(s):  
Tandem Repeats ◽  
Cpg Islands ◽  
Imprinted Genes

scholarly journals Genetic conflict, genomic imprinting and establishment of the epigenotype in relation to growth

Reproduction ◽  
2001 ◽  
pp. 185-193 ◽  
Author(s):  
T Moore
Keyword(s):  
Genomic Imprinting ◽  
Parental Investment ◽  
Tandem Repeats ◽  
Cpg Islands ◽  
Subsequent Development ◽  
Imprinted Genes ◽  
Growth Disorders ◽  
Genetic Loci ◽  
Mammalian Embryo ◽  
Genetic Conflict

Genomic imprinting is the process that differentially modifies the parental alleles at certain genetic loci in the parental germlines. Such modifications of DNA and chromatin are somatically heritable and cause unequal expression of the parental alleles during subsequent development. In mammals, imprinted genes encode a relatively small number of functionally heterogeneous proteins. Nevertheless, imprinted genes exert important effects, primarily on fetal development, and their deregulation is implicated in a variety of pathologies including sporadic, inherited and induced growth disorders. Imprinted loci show several unusual structural and functional characteristics that may be related to mechanistic aspects of mono-allelic expression or to modes of evolution of imprinted genetic loci. Typically, imprinted genes are clustered in certain genomic regions and have relatively reduced intronic DNA content relative to non-imprinted genes. In addition, their regulatory regions frequently contain a combination of features including tandem repeats associated with differentially methylated CpG islands and overlapping transcription of coding or non-coding RNAs. The evolution of imprinting can be understood as the stable outcome of sexual selection acting differently on the parental alleles of genes that influence parental investment in offspring. Consistent with this explanation, imprinted genes are expressed predominantly during embryonic and postnatal development in mammals and in the developing endosperm of plants, and maternal or paternal expression at imprinted loci is associated with reduced or increased parental investment, respectively. Such selective forces have implications for understanding mechanistic aspects of genome reprogramming in the early mammalian embryo.

scholarly journals A First-Stage Approximation to Identify New Imprinted Genes through Sequence Analysis of Its Coding Regions

2009 ◽  
Vol 2009 ◽  
pp. 1-7 ◽  
Author(s):  
Elias Daura-Oller ◽  
Maria Cabré ◽  
Miguel A. Montero ◽  
José L. Paternáin ◽  
Antoni Romeu
Keyword(s):  
Tandem Repeats ◽  
Cpg Islands ◽  
Imprinted Genes ◽  
Coding Region ◽  
Training Set ◽  
Principle Components Analysis ◽  
Coding Regions ◽  
Gene Coding ◽  
Components Analysis ◽  
Simple Repeats

In the present study, a positive training set of 30 known human imprinted gene coding regions are compared with a set of 72 randomly sampled human nonimprinted gene coding regions (negative training set) to identify genomic features common to human imprinted genes. The most important feature of the present work is its ability to use multivariate analysis to look at variation, at coding region DNA level, among imprinted and non-imprinted genes. There is a force affecting genomic parameters that appears through the use of the appropriate multivariate methods (principle components analysis (PCA) and quadratic discriminant analysis (QDA) to analyse quantitative genomic data. We show that variables, such as CG content, [bp]% CpG islands, [bp]% Large Tandem Repeats, and [bp]% Simple Repeats, are able to distinguish coding regions of human imprinted genes.

scholarly journals Transposons, Tandem Repeats, and the Silencing of Imprinted Genes

2004 ◽  
Vol 69 (0) ◽  
pp. 371-380 ◽  
Author(s):  
R. MARTIENSSEN ◽  
Z. LIPPMAN ◽  
B. MAY ◽  
M. RONEMUS ◽  
M. VAUGHN
Keyword(s):  
Tandem Repeats ◽  
Imprinted Genes

scholarly journals Inference of cell-type specific imprinted regulatory elements and genes during human neuronal differentiation

2021 ◽  
Author(s):  
Dan Liang ◽  
Nil Aygün ◽  
Nana Matoba ◽  
Folami Ideraabdullah ◽  
Michael I Love ◽  
...  
Keyword(s):  
Gene Expression ◽  
Neural Progenitor Cells ◽  
Association Studies ◽  
Cpg Islands ◽  
Uniparental Disomy ◽  
Cell Types ◽  
Regulatory Elements ◽  
Imprinted Genes ◽  
Specific Cell ◽  
Cell Type

Genomic imprinting results in gene expression biased by parental chromosome of origin and occurs in genes with important roles during human brain development. However, the cell-type and temporal specificity of imprinting during human neurogenesis is generally unknown. By detecting within-donor allelic biases in chromatin accessibility and gene expression that are unrelated to cross-donor genotype, we inferred imprinting in both primary human neural progenitor cells (phNPCs) and their differentiated neuronal progeny from up to 85 donors. We identified 43/20 putatively imprinted regulatory elements (IREs) in neurons/progenitors, and 133/79 putatively imprinted genes in neurons/progenitors. Though 10 IREs and 42 genes were shared between neurons and progenitors, most imprinting was only detected within specific cell types. In addition to well-known imprinted genes and their promoters, we inferred novel IREs and imprinted genes. We found IREs overlapped with CpG islands more than non-imprinted regulatory elements. Consistent with DNA methylation-based regulation of imprinted expression, some putatively imprinted regulatory elements also overlapped with differentially methylated regions on the maternal germline. Finally, we identified a progenitor-specific putatively imprinted gene overlap with copy number variation that is associated with uniparental disomy-like phenotypes. Our results can therefore be useful in interpreting the function of variants identified in future parent-of-origin association studies.

scholarly journals Tandem Repeat Hypothesis in Imprinting: Deletion of a Conserved Direct Repeat Element Upstream of H19 Has No Effect on Imprinting in the Igf2-H19 Region

2004 ◽  
Vol 24 (13) ◽  
pp. 5650-5656 ◽  
Author(s):  
Annabelle Lewis ◽  
Kohzoh Mitsuya ◽  
Miguel Constancia ◽  
Wolf Reik
Keyword(s):  
Tandem Repeat ◽  
Tandem Repeats ◽  
Direct Repeat ◽  
Regulatory Elements ◽  
Repeat Element ◽  
Allelic Expression ◽  
Differentially Methylated Region ◽  
Paternal Allele ◽  
Imprinted Genes ◽  
Allele Specific

ABSTRACT Igf2 and H19 are reciprocally imprinted genes on mouse distal chromosome 7. They share several regulatory elements, including a differentially methylated region (DMR) upstream of H19 that is paternally methylated throughout development. The cis-acting sequence requirements for targeting DNA methylation to the DMR remain unknown; however, it has been suggested that direct tandem repeats near DMRs could be involved. Previous studies of the imprinted Rasgrf1 locus demonstrate indeed that a direct repeat element adjacent to a DMR is responsible for establishing paternal allele-specific methylation at the DMR and therefore allelic expression of the Rasgrf1 transcript. We identified a prominent and conserved direct tandem repeat 1 kb upstream of the H19 DMR and proposed that it played a similar role in imprinted regulation of H19. To test our hypothesis, we generated mice harboring a 1.7-kb targeted deletion of the direct repeat element and analyzed fetal growth, allelic expression, and methylation within the Igf2-H19 region. Surprisingly the deletion had no effect on imprinting. These results together with deletions of other repeats close to imprinted genes suggest that direct repeats may not be important for the targeting of methylation at the majority of imprinted loci and that the Rasgrf1 locus may be an exception to this rule.

scholarly journals A Genome-Wide Screen for Normally Methylated Human CpG Islands That Can Identify Novel Imprinted Genes

2002 ◽  
Vol 12 (4) ◽  
pp. 543-554 ◽  
Author(s):  
L. Z. Strichman-Almashanu ◽  
R. S. Lee ◽  
P. O. Onyango ◽  
E. Perlman ◽  
F. Flam ◽  
...  
Keyword(s):  
Cpg Islands ◽  
Imprinted Genes ◽  
Genome Wide ◽  
A Genome

scholarly journals Aberrant methylation of multiple imprinted genes in embryos of tamoxifen-treated male rats

Reproduction ◽  
2013 ◽  
Vol 146 (2) ◽  
pp. 155-168 ◽  
Author(s):  
Neelam A Kedia-Mokashi ◽  
Leena Kadam ◽  
Mandar Ankolkar ◽  
Kushaan Dumasia ◽  
N H Balasinor
Keyword(s):  
De Novo ◽  
Methylation Status ◽  
Cpg Islands ◽  
Transcript Level ◽  
Male Rats ◽  
Imprinted Genes ◽  
Aberrant Methylation ◽  
Aberrant Expression ◽  
Treated Male ◽  
Epigenetic Phenomenon

Genomic imprinting is an epigenetic phenomenon known to regulate fetal growth and development. Studies from our laboratory have demonstrated that treatment of adult male rats with tamoxifen increased postimplantation loss around mid gestation. Further studies demonstrated the aberrant expression of transcripts of several imprinted genes in the resorbing embryos at days 11 and 13 of gestation including IGF2. In addition, decreased methylation at theIgf2–H19imprint control region was observed in spermatozoa and in resorbing embryos sired by tamoxifen-treated males. In this study, methylation analysis of the imprinted genes, which were found to be differentially expressed, was done using EpiTYPER in the spermatozoa of tamoxifen-treated rats and in postimplantation embryos sired by tamoxifen-treated rats. Differentially methylated regions (DMRs) for most imprinted genes have not been identified in the rats. Hence, initial experiments were performed to identify the putative DMRs in the genes selected for the study. Increased methylation at CpG islands present in the putative DMRs of a number of imprinted genes was observed in the resorbing embryos sired by tamoxifen-treated male rats. This increase in methylation is associated with the downregulation of most of these genes at the transcript level in resorbing embryos. No change in the methylation status of these genes was observed in spermatozoa. These observations suggest that a deregulation of mechanisms protecting unmethylated alleles from a wave ofde novomethylation occurs following implantation.

scholarly journals Characterization of gene promoters in pig: conservative elements, regulatory motifs and evolutionary trend

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7204
Author(s):  
Kai Wei ◽  
Lei Ma ◽  
Tingting Zhang
Keyword(s):  
Tandem Repeats ◽  
Evolutionary Dynamics ◽  
Cpg Islands ◽  
Gene Promoter ◽  
Evolutionary Process ◽  
Upstream Sequence ◽  
Evolutionary Trend ◽  
Gene Promoters ◽  
Promoter Regions ◽  
Regulatory Motifs

It is vital to understand the conservation and evolution of gene promoter sequences in order to understand environmental adaptation. The level of promoter conservation varies greatly between housekeeping (HK) and tissue-specific (TS) genes, denoting differences in the strength of the evolutionary constraints. Here, we analyzed promoter conservation and evolution to exploit differential regulation between HK and TS genes. The analysis of conserved elements showed CpG islands, short tandem repeats and G-quadruplex sequences are highly enriched in HK promoters relative to TS promoters. In addition, the type and density of regulatory motifs in TS promoters are much higher than HK promoters, indicating that TS genes show more complex regulatory patterns than HK genes. Moreover, the evolutionary dynamics of promoters showed similar evolutionary trend to coding sequences. HK promoters suffer more stringent selective pressure in the long-term evolutionary process. HK genes tend to show increased upstream sequence conservation due to stringent selection pressures acting on the promoter regions. The specificity of TS gene expression may be due to complex regulatory motifs acting in different tissues or conditions. The results from this study can be used to deepen our understanding of adaptive evolution.

scholarly journals Identification of porcine imprinted genes involved in skeletal muscle development by high-throughput sequencing

2020 ◽  
Author(s):  
Xinhua Hou ◽  
Zishuai Wang ◽  
Ligang Wang ◽  
Fuping Zhao ◽  
Xin Liu ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Cell Proliferation ◽  
Muscle Development ◽  
High Throughput Sequencing ◽  
Cpg Islands ◽  
Meat Production ◽  
Imprinted Genes ◽  
Skeletal Muscle Development ◽  
Mammalian Development ◽  
Imprinted Gene

Abstract Background Imprinted genes—exhibiting parent-specific transcription—play essential roles in the process of mammalian development and growth. To further understand the imprinted genes involved in skeletal muscle development, DNA-seq and RNA-seq were used to explore the characteristics of imprinted genes involved in skeletal muscle development from porcine reciprocal crosses. Results A total of 211 paternally and 417 maternally imprinted genes were obtained in this study. Of the candidate imprinted genes, 50 paternally and 112 maternally imprinted genes possessed cytosine and guanine dinucleotide (CpG) islands in their promoters that may have regulated the imprinted gene expression. Imprint-related motifs were predicted and PBX1 motifs may mediate the expression of imprinted genes in the process of skeletal-muscle development. Functional analysis showed that a maternally imprinted gene of EPHB1 was involved in skeletal muscle cell proliferation. Imprinted genes involved in the biological processes of cell proliferation, differentiation and fusion were also analyzed. More maternally imprinted genes, including ADRA1D, E2F1, FBXO40, GHRH and WNT5A, were involved in skeletal muscle development than paternally imprinted genes. Conclusions Skeletal muscle development is crucial for meat production. This study identified 628 porcine imprinted genes in skeletal muscle and revealed their functional role in skeletal muscle development. Our findings should further assist with the potential use of imprinted genes in pig breeding.

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