scholarly journals Get Out and Stay Out: New Insights Into DNA Methylation Reprogramming in Mammals

2021 ◽  
Vol 8 ◽  
Author(s):  
Maxim V. C. Greenberg
Keyword(s):  
Dna Methylation ◽  
Transposable Elements ◽  
Early Embryogenesis ◽  
Pericentromeric Heterochromatin ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Impaired Function ◽  
Vulnerable Window

Vertebrate genomes are marked by notably high levels of 5-cytosine DNA methylation (5meC). The clearest function of DNA methylation among members of the subphylum is repression of potentially deleterious transposable elements (TEs). However, enrichment in the bodies of protein coding genes and pericentromeric heterochromatin indicate an important role for 5meC in those genomic compartments as well. Moreover, DNA methylation plays an important role in silencing of germline-specific genes. Impaired function of major components of DNA methylation machinery results in lethality in fish, amphibians and mammals. Despite such apparent importance, mammals exhibit a dramatic loss and regain of DNA methylation in early embryogenesis prior to implantation, and then again in the cells specified for the germline. In this minireview we will highlight recent studies that shine light on two major aspects of embryonic DNA methylation reprogramming: (1) The mechanism of DNA methylation loss after fertilization and (2) the protection of discrete loci from ectopic DNA methylation deposition during reestablishment. Finally, we will conclude with some extrapolations for the evolutionary underpinnings of such extraordinary events that seemingly put the genome under unnecessary risk during a particularly vulnerable window of development.

scholarly journals DNA methylation patterns of protein-coding genes and long non-coding RNAs in males with schizophrenia

2015 ◽  
Vol 12 (5) ◽  
pp. 6568-6576 ◽  
Author(s):  
QI LIAO ◽  
YUNLIANG WANG ◽  
JIA CHENG ◽  
DONGJUN DAI ◽  
XINGYU ZHOU ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Non Coding Rnas ◽  
Methylation Patterns

scholarly journals Identification of the expressome by machine learning on omics data

2019 ◽  
Vol 116 (36) ◽  
pp. 18119-18125 ◽  
Author(s):  
Ryan C. Sartor ◽  
Jaclyn Noshay ◽  
Nathan M. Springer ◽  
Steven P. Briggs
Keyword(s):  
Machine Learning ◽  
Dna Methylation ◽  
Inbred Lines ◽  
Training Data ◽  
Gene Body ◽  
Gene Body Methylation ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Methylation Patterns

Accurate annotation of plant genomes remains complex due to the presence of many pseudogenes arising from whole-genome duplication-generated redundancy or the capture and movement of gene fragments by transposable elements. Machine learning on genome-wide epigenetic marks, informed by transcriptomic and proteomic training data, could be used to improve annotations through classification of all putative protein-coding genes as either constitutively silent or able to be expressed. Expressed genes were subclassified as able to express both mRNAs and proteins or only RNAs, and CG gene body methylation was associated only with the former subclass. More than 60,000 protein-coding genes have been annotated in the reference genome of maize inbred B73. About two-thirds of these genes are transcribed and are designated the filtered gene set (FGS). Classification of genes by our trained random forest algorithm was accurate and relied only on histone modifications or DNA methylation patterns within the gene body; promoter methylation was unimportant. Other inbred lines are known to transcribe significantly different sets of genes, indicating that the FGS is specific to B73. We accurately classified the sets of transcribed genes in additional inbred lines, arising from inbred-specific DNA methylation patterns. This approach highlights the potential of using chromatin information to improve annotations of functional genes.

scholarly journals HSF2 Co-regulates Protein-coding and Long Non-coding RNA Genes Specific to Black Tissues of the Black Chicken, Yeonsan Ogye

2017 ◽  
Author(s):  
Hyosun Hong ◽  
Han-Ha Chai ◽  
Kyoungwoo Nam ◽  
Dajeong Lim ◽  
Kyung-Tai Lee ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Entire Body ◽  
Specific Expression ◽  
Protein Coding ◽  
Tissue Specific ◽  
Tissue Specific Expression ◽  
Protein Coding Genes ◽  
Non Coding Rna ◽  
Black Coloring ◽  
Long Non Coding Rna

AbstractThe Yeonsan Ogye (Ogye) is a rare Korean domestic chicken breed, the entire body of which, including its feathers and skin, has a unique black coloring. Although some protein-coding genes related to this unique feature have been examined, non-coding elements have not been globally investigated. In this study, high-throughput RNA sequencing and DNA methylation sequencing were performed to dissect the expression landscape of 14,264 Ogye protein-coding and 6900 long non-coding RNA (lncRNA) genes along with DNA methylation landscape in twenty different Ogye tissues. About 75% of Ogye lncRNAs showed tissue-specific expression whereas about 45% of protein-coding genes did. For some genes, the tissue-specific expression levels were inversely correlated with DNA methylation levels in their promoters. About 39% of the tissue-specific lncRNAs displayed functional association with proximal or distal protein-coding genes. In particular, heat shock transcription factor 2 (HSF2)-associated lncRNAs were discovered to be functionally linked to protein-coding genes that are specifically expressed in black skin tissues, tended to be more syntenically conserved in mammals, and were differentially expressed in black tissues relative to white tissues. Our results not only facilitate understanding how the non-coding genome regulates unique phenotypes but also should be of use for future genomic breeding of chickens.

scholarly journals Non-Coding Transcriptome Maps across Twenty Tissues of the Korean Black Chicken, Yeonsan Ogye

2018 ◽  
Vol 19 (8) ◽  
pp. 2359
Author(s):  
Hyosun Hong ◽  
Han-Ha Chai ◽  
Kyoungwoo Nam ◽  
Dajeong Lim ◽  
Kyung-Tai Lee ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Entire Body ◽  
Specific Expression ◽  
Protein Coding ◽  
Tissue Specific ◽  
Tissue Specific Expression ◽  
Protein Coding Genes ◽  
Black Skin ◽  
Black Coloring ◽  
Transcriptome Expression

Yeonsan Ogye is a rare Korean domestic chicken breed whose entire body, including feathers and skin, has a unique black coloring. Although some protein-coding genes related to this unique feature have been examined, non-coding elements have not been widely investigated. Thus, we evaluated coding and non-coding transcriptome expression and identified long non-coding RNAs functionally linked to protein-coding genes in Ogye. High-throughput RNA sequencing and DNA methylation sequencing were performed to profile the expression of 14,264 Ogye protein-coding and 6900 long non-coding RNA (lncRNA) genes and detect DNA methylation in 20 different tissues of an individual Ogye. Approximately 75% of Ogye lncRNAs and 45% of protein-coding genes showed tissue-specific expression. For some genes, tissue-specific expression levels were inversely correlated with DNA methylation levels in their promoters. Approximately 39% of tissue-specific lncRNAs displayed functional associations with proximal or distal protein-coding genes. Heat shock transcription factor 2-associated lncRNAs appeared to be functionally linked to protein-coding genes specifically expressed in black skin tissues, more syntenically conserved in mammals, and differentially expressed in black relative to in white tissues. Pending experimental validation, our findings increase the understanding of how the non-coding genome regulates unique phenotypes and can be used for future genomic breeding of chickens.

scholarly journals Selection on the protein-coding genes of the TBE1 family of transposable elements in the ciliates Oxytricha fallax and O. trifallax

1997 ◽  
Vol 14 (7) ◽  
pp. 696-706 ◽  
Author(s):  
D. J. Witherspoon ◽  
T. G. Doak ◽  
K. R. Williams ◽  
A. Seegmiller ◽  
J. Seger ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Protein Coding ◽  
Protein Coding Genes

scholarly journals Discovering subgenomes of octoploid strawberry with repetitive sequences

2020 ◽  
Author(s):  
Adam Session ◽  
Daniel Rokhsar
Keyword(s):  
Transposable Elements ◽  
Conventional Method ◽  
Phylogenetic Relationships ◽  
Repetitive Sequences ◽  
Its Sequence ◽  
Chromosomal Distribution ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Polyploid Genome ◽  
Complementary Strategy

AbstractAlthough its sequence was recently determined in a genomic tour de force,{Edger 2019} the ancestry of the cultivated octoploid strawberry Fragaria x ananassa remains controversial.{Liston 2020; Edger 2020} Polyploids that arise by hybridization generally have chromosome sets, or subgenomes, of distinct ancestry.{Stebbins 1947; Garsmeur 2014} The conventional method for partitioning a polyploid genome into its constituent subgenomes relies on establishing phylogenetic relationships between protein-coding genes of the polyploid and its extant diploid relatives,{Edger 2018-sub} but this approach has not led to a consensus for cultivated strawberry.{Liston 2020; Edger 2020} Here we resolve this controversy using a complementary strategy that focuses on the chromosomal distribution of transposable elements and depends only on the octoploid sequence itself.{Session 2016; Mitros 2020} Our method independently confirms the consensus that two of the four subgenomes derived from the diploid lineages of F. vesca and F. iinumae.{Tennessen 2014; Edger 2019} For the remaining two subgenomes, however, we find a statistically well-supported partitioning that differs from ref. {Edger 2019} and other work (reviewed in {Hardigan 2020}). We also provide evidence for a shared allohexaploid intermediate and suggest a neutral explanation for the “dominance” of the F. vesca-related subgenome.

scholarly journals Involvement of transposable elements in neurogenesis

2020 ◽  
Vol 24 (2) ◽  
pp. 209-218
Author(s):  
R. N. Mustafin ◽  
E. K. Khusnutdinova
Keyword(s):  
Stem Cells ◽  
Transposable Elements ◽  
Human Brain ◽  
Significant Activity ◽  
Protein Coding ◽  
Neuronal Stem Cells ◽  
Protein Coding Genes ◽  
Non Coding Rna ◽  
Long Non Coding Rna

The article is about the role of transposons in the regulation of functioning of neuronal stem cells and mature neurons of the human brain. Starting from the first division of the zygote, embryonic development is governed by regular activations of transposable elements, which are necessary for the sequential regulation of the expression of genes specific for each cell type. These processes include differentiation of neuronal stem cells, which requires the finest tuning of expression of neuron genes in various regions of the brain. Therefore, in the hippocampus, the center of human neurogenesis, the highest transposon activity has been identified, which causes somatic mosai cism of cells during the formation of specific brain structures. Similar data were obtained in studies on experimental animals. Mobile genetic elements are the most important sources of long non-coding RNAs that are coexpressed with important brain protein-coding genes. Significant activity of long non-coding RNA was detected in the hippocampus, which confirms the role of transposons in the regulation of brain function. MicroRNAs, many of which arise from transposon transcripts, also play an important role in regulating the differentiation of neuronal stem cells. Therefore, transposons, through their own processed transcripts, take an active part in the epigenetic regulation of differentiation of neurons. The global regulatory role of transposons in the human brain is due to the emergence of protein-coding genes in evolution by their exonization, duplication and domestication. These genes are involved in an epigenetic regulatory network with the participation of transposons, since they contain nucleotide sequences complementary to miRNA and long non-coding RNA formed from transposons. In the memory formation, the role of the exchange of virus-like mRNA with the help of the Arc protein of endogenous retroviruses HERV between neurons has been revealed. A possible mechanism for the implementation of this mechanism may be reverse transcription of mRNA and site-specific insertion into the genome with a regulatory effect on the genes involved in the memory.  

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