scholarly journals DNA Modification Patterns within the Transposable Elements of the Fig (Ficus carica L.) Genome

Plants ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 451
Author(s):  
Gabriele Usai ◽  
Alberto Vangelisti ◽  
Samuel Simoni ◽  
Tommaso Giordani ◽  
Lucia Natali ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Transcriptional Repression ◽  
Ficus Carica ◽  
Dna Modification ◽  
Coding Regions ◽  
Dna Base ◽  
Plant Phenotype ◽  
Functional Implications ◽  
Element Activity ◽  
High Quality Genome

Transposable element activity can be harmful to the host’s genome integrity, but it can also provide selective advantages. One strategy to cope with transposons is epigenetic control through DNA base modifications. We report the non-canonic DNA modification dynamics of fig (Ficus carica L.) by exploiting high-quality genome reference and related N4-methylcytosine (4mC) and N6-methyladenine (6mA) data. Overall, 1.49% of transposon nucleotides showed either 4mC or 6mA modifications: the 4mC/6mA ratio was similar in Class I and Class II transposons, with a prevalence of 4mC, which is comparable to coding genes. Different percentages of 4mC or 6mA were observed among LTR-retrotransposon lineages and sub-lineages. Furthermore, both the Copia and Gypsy retroelements showed higher modification rates in the LTR and coding regions compared with their neighbour regions. Finally, the unconventional methylation of retrotransposons is unrelated to the number of close genes, suggesting that the 4mC and 6mA frequency in LTR-retrotransposons should not be related to transcriptional repression in the adjacency of the element. In conclusion, this study highlighted unconventional DNA modification patterns in fig transposable elements. Further investigations will focus on functional implications, in regards to how modified retroelements affect the expression of neighbouring genes, and whether these epigenetic markers can spread from repeats to genes, shaping the plant phenotype.

Molecular polymorphism of cytoplasmic DNA in Ficus carica L.: Insights from non-coding regions of chloroplast DNA

2010 ◽  
Vol 125 (3) ◽  
pp. 512-517 ◽  
Author(s):  
Ghada Baraket ◽  
Ahmed Ben Abdelkrim ◽  
Olfa Saddoud ◽  
Khaled Chatti ◽  
Messaoud Mars ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Ficus Carica ◽  
Molecular Polymorphism ◽  
Coding Regions ◽  
Cytoplasmic Dna

scholarly journals N6-Methyladenine DNA Modification in Human Genome

2017 ◽  
Author(s):  
Chuan-Le Xiao ◽  
Song Zhu ◽  
Minghui He ◽  
De Chen ◽  
Qian Zhang ◽  
...  
Keyword(s):  
Human Genome ◽  
Genomic Dna ◽  
Human Cells ◽  
Human Diseases ◽  
Dna Modification ◽  
Down Regulation ◽  
Coding Regions

SummaryDNA N6-methyladenine (6mA) modification is the most prevalent DNA modification in prokaryotes, but whether it exists in human cells and whether it plays a role in human diseases remain enigmatic. Here, we showed that 6mA is extensively present in human genome, and we cataloged 881,240 6mA sites accounting for ∼0.051% of the total adenines. [G/C]AGG[C/T] was the most significantly associated motif with 6mA modification. 6mA sites were enriched in the coding regions and mark actively transcribed genes in human cells. We further found that DNA N6-methyladenine and N6-demethyladenine modification in human genome were mediated by methyltransferase N6AMT1 and demethylase ALKBH1, respectively. The abundance of 6mA was significantly lower in cancers, accompaning with decreased N6AMT1 and increased ALKBH1 levels, and down-regulation of 6mA modification levels promoted tumorigenesis. Collectively, our results demonstrate that DNA 6mA modification is extensively present in human cells and the decrease of genomic DNA 6mA promotes human tumorigenesis.

scholarly journals Differential Contributions of DNA-Binding Proteins to Polycomb Response Element Activity at the Drosophila giant Gene

Genetics ◽  
2020 ◽  
Vol 214 (3) ◽  
pp. 623-634
Author(s):  
Elnaz Ghotbi ◽  
Kristina Lackey ◽  
Vicki Wong ◽  
Katie T. Thompson ◽  
Evan G. Caston ◽  
...  
Keyword(s):  
Dna Binding ◽  
Dna Sequences ◽  
Transcriptional Repression ◽  
Binding Proteins ◽  
Target Genes ◽  
Dna Binding Proteins ◽  
Polycomb Group ◽  
Link Type ◽  
Element Activity

Polycomb-group (PcG) proteins are evolutionarily conserved epigenetic regulators whose primary function is to maintain the transcriptional repression of target genes. Recruitment of Drosophila melanogaster PcG proteins to target genes requires the presence of one or more Polycomb Response Elements (PREs). The functions or necessity for more than one PRE at a gene are not clear and individual PREs at some loci may have distinct regulatory roles. Various combinations of sequence-specific DNA-binding proteins are present at a given PRE, but only Pleiohomeotic (Pho) is present at all strong PREs. The giant (gt) locus has two PREs, a proximal PRE1 and a distal PRE2. During early embryonic development, Pho binds to PRE1 ∼30-min prior to stable binding to PRE2. This observation indicated a possible dependence of PRE2 on PRE1 for PcG recruitment; however, we find here that PRE2 recruits PcG proteins and maintains transcriptional repression independently of Pho binding to PRE1. Pho-like (Phol) is partially redundant with Pho during larval development and binds to the same DNA sequences in vitro. Although binding of Pho to PRE1 is dependent on the presence of consensus Pho-Phol-binding sites, Phol binding is less so and appears to play a minimal role in recruiting other PcG proteins to gt. Another PRE-binding protein, Sp1/Kruppel-like factor, is dependent on the presence of Pho for PRE1 binding. Further, we show that, in addition to silencing gene expression, PcG proteins dampen transcription of an active gene.

scholarly journals Detection of Abrin-Like and Prepropulchellin-Like Toxin Genes and Transcripts Using Whole Genome Sequencing and Full-Length Transcript Sequencing of Abrus precatorius

Toxins ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 691 ◽  
Author(s):  
Blake T. Hovde ◽  
Hajnalka E. Daligault ◽  
Erik R. Hanschen ◽  
Yuliya A. Kunde ◽  
Matthew B. Johnson ◽  
...  
Keyword(s):  
Leaf Tissue ◽  
Genomic Region ◽  
Full Length ◽  
Toxin Gene ◽  
Abrus Precatorius ◽  
Coding Regions ◽  
Leaf Transcriptome ◽  
Full Length Transcript ◽  
Toxin Gene Expression ◽  
High Quality Genome

The sequenced genome and the leaf transcriptome of a near relative of Abrus pulchellus and Abrus precatorius was analyzed to characterize the genetic basis of toxin gene expression. From the high-quality genome assembly, a total of 26 potential coding regions were identified that contain genes with abrin-like, pulchellin-like, and agglutinin-like homology, with full-length transcripts detected in leaf tissue for 9 of the 26 coding regions. All of the toxin-like genes were identified within only five isolated regions of the genome, with each region containing 1 to 16 gene variants within each genomic region (<1 Mbp). The Abrus precatorius cultivar sequenced here contains genes which encode for proteins that are homologous to certain abrin and prepropulchellin genes previously identified, and we observed substantial diversity of genes and predicted gene products in Abrus precatorius and previously characterized toxins. This suggests diverse toxin repertoires within Abrus, potentially the results of rapid toxin evolution.

scholarly journals Domestication of rice has reduced the occurrence of transposable elements within gene coding regions

BMC Genomics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Xukai Li ◽  
Kai Guo ◽  
Xiaobo Zhu ◽  
Peng Chen ◽  
Ying Li ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Coding Regions ◽  
Gene Coding

DNA methylation dynamics at transposable elements in mammals

2019 ◽  
Vol 63 (6) ◽  
pp. 677-689
Author(s):  
Natasha Jansz
Keyword(s):  
Dna Methylation ◽  
Transposable Elements ◽  
Transposable Element ◽  
Human Development ◽  
Developmental Regulation ◽  
Repetitive Sequences ◽  
Single Copy ◽  
Regulatory Sequences ◽  
Dynamic Regulation ◽  
Element Activity

Abstract Transposable elements dominate the mammalian genome, but their contribution to genetic and epigenetic regulation has been largely overlooked. This was in part due to technical limitations, which made the study of repetitive sequences at single copy resolution difficult. The advancement of next-generation sequencing assays in the last decade has greatly enhanced our understanding of transposable element function. In some instances, specific transposable elements are thought to have been co-opted into regulatory roles during both mouse and human development, while in disease such regulatory potential can contribute to malignancy. DNA methylation is arguably the best characterised regulator of transposable element activity. DNA methylation is associated with transposable element repression, and acts to limit their genotoxic potential. In specific developmental contexts, erasure of DNA methylation is associated with a burst of transposable element expression. Developmental regulation of DNA methylation enables transposon activation, ensuring their survival and propagation throughout the host genome, and also allows the host access to regulatory sequences encoded within the elements. Here I discuss DNA methylation at transposable elements, describing its function and dynamic regulation throughout murine and human development.

scholarly journals Hybrid decay: a transgenerational epigenetic decline in vigor and viability triggered in backcross populations of teosinte with maize

2019 ◽  
Author(s):  
Wei Xue ◽  
Sarah N. Anderson ◽  
Xufeng Wang ◽  
Liyan Yang ◽  
Peter A. Crisp ◽  
...  
Keyword(s):  
Transposable Elements ◽  
De Novo ◽  
Genome Instability ◽  
Sequence Similarity ◽  
Hybrid Incompatibility ◽  
Advanced Backcross ◽  
Genome Wide ◽  
Normal Maize ◽  
Plant Phenotype ◽  
Backcross Populations

ABSTRACTIn the course of generating populations of maize with teosinte chromosomal introgressions, an unusual sickly plant phenotype was noted in individuals from crosses with two teosinte accessions collected near Valle de Bravo, Mexico. The plants of these Bravo teosinte accessions appear phenotypically normal themselves and the F1plants appear similar to typical maize x teosinte F1s. However, upon backcrossing to maize, the BC1and subsequent generations display a number of detrimental characteristics including shorter stature, reduced seed set and abnormal floral structures. This phenomenon is observed in all BC individuals and there is no chromosomal segment linked to the sickly plant phenotype in advanced backcross generations. Once the sickly phenotype appears in a lineage, normal plants are never again recovered by continued backcrossing to the normal maize parent. Whole-genome shotgun sequencing reveals a small number of genomic sequences, some with homology to transposable elements, that have increased in copy number in the backcross populations. Transcriptome analysis of seedlings, which do not have striking phenotypic abnormalities, identified segments of 18 maize genes that exhibit increased expression in sickly plants. Ade novoassembly of transcripts present in plants exhibiting the sickly phenotype identified a set of 59 up-regulated novel transcripts. These transcripts include some examples with sequence similarity to transposable elements and other sequences present in the recurrent maize parent (W22) genome as well as novel sequences not present in the W22 genome. Genome-wide profiles of gene expression, DNA methylation and sRNAs are similar between sickly plants and normal controls, although a few up-regulated transcripts and transposable elements are associated with altered sRNA or methylation profiles. This study documents hybrid incompatibility and genome instability triggered by the backcrossing of Bravo teosinte with maize. We name this phenomenon “hybrid decay” and present ideas on the mechanism that may underlie it.

scholarly journals Highly contiguous assemblies of 101 drosophilid genomes

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Bernard Y Kim ◽  
Jeremy Wang ◽  
Danny E Miller ◽  
Olga Barmina ◽  
Emily Kay Delaney ◽  
...  
Keyword(s):  
High Quality ◽  
Coding Regions ◽  
Public Resource ◽  
Oxford Nanopore ◽  
Starting Point ◽  
Long Read ◽  
Species Groups ◽  
Genome Assemblies ◽  
High Quality Genome ◽  
Laboratory Protocol

Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long-read sequencing allow high-quality genome assemblies for tens or even hundreds of species to be efficiently generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of genome assemblies for 101 lines of 93 drosophilid species encompassing 14 species groups and 35 sub-groups. The genomes are highly contiguous and complete, with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. We show that Nanopore-based assemblies are highly accurate in coding regions, particularly with respect to coding insertions and deletions. These assemblies, along with a detailed laboratory protocol and assembly pipelines, are released as a public resource and will serve as a starting point for addressing broad questions of genetics, ecology, and evolution at the scale of hundreds of species.

scholarly journals What Can Domesticated Genes Tell Us about the Intron Gain in Mammals?

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Dušan Kordiš ◽  
Janez Kokošar
Keyword(s):  
Transposable Elements ◽  
De Novo ◽  
Single Copy ◽  
Intron Gain ◽  
Current Understanding ◽  
Dna Transposons ◽  
Coding Regions ◽  
Positional Bias ◽  
Ideal System

Domesticated genes, originating from retroelements or from DNA-transposons, constitute an ideal system for testing the hypothesis on the absence of intron gain in mammals. Since single-copy domesticated genes originated from the intronless multicopy transposable elements, the ancestral intron state for domesticated genes is zero. A phylogenomic approach has been used to analyse all domesticated genes in mammals and chordates that originated from the coding parts of transposable elements. A significant amount of intron gain was found only in domesticated genes of placental mammals, where more than 70 cases were identified. De novo gained introns show clear positional bias, since they are distributed mainly in 5′ UTR and coding regions, while 3′ UTR introns are very rare. In the coding regions of some domesticated genes up to 8 de novo gained introns have been found. Surprisingly, the majority of intron gains have occurred in the ancestor of placental mammals. Domesticated genes could constitute an excellent system on which to analyse the mechanisms of intron gain. This paper summarizes the current understanding of intron gain in mammals.

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