scholarly journals Myxosporea (Myxozoa, Cnidaria) Lack DNA Cytosine Methylation

2020 ◽  
Author(s):  
Ryan Kyger ◽  
Agusto Luzuriaga-Neira ◽  
Thomas Layman ◽  
Tatiana Orli Milkewitz Sandberg ◽  
Devika Singh ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Cytosine Methylation ◽  
Bisulfite Sequencing ◽  
Regulatory Mechanism ◽  
Regulation Of Gene Expression ◽  
Biological Processes ◽  
Free Living ◽  
Genome Bisulfite Sequencing ◽  
History Of ◽  
Dna Cytosine Methylation

Abstract DNA cytosine methylation is central to many biological processes, including regulation of gene expression, cellular differentiation, and development. This DNA modification is conserved across animals, having been found in representatives of sponges, ctenophores, cnidarians, and bilaterians, and with very few known instances of secondary loss in animals. Myxozoans are a group of microscopic, obligate endoparasitic cnidarians that have lost many genes over the course of their evolution from free-living ancestors. Here, we investigated the evolution of the key enzymes involved in DNA cytosine methylation in 29 cnidarians and found that these enzymes were lost in an ancestor of Myxosporea (the most speciose class of Myxozoa). Additionally, using whole-genome bisulfite sequencing, we confirmed that the genomes of two distant species of myxosporeans, Ceratonova shasta and Henneguya salminicola, completely lack DNA cytosine methylation. Our results add a notable and novel taxonomic group, the Myxosporea, to the very short list of animal taxa lacking DNA cytosine methylation, further illuminating the complex evolutionary history of this epigenetic regulatory mechanism.

scholarly journals Experience-dependent neuroplasticity of the developing hypothalamus: integrative epigenomic approaches

2017 ◽  
Author(s):  
Annie Vogel Ciernia ◽  
Benjamin I. Laufer ◽  
Keith W. Dunaway ◽  
Charles E. Mordaunt ◽  
Rochelle L. Coulson ◽  
...  
Keyword(s):  
Maternal Care ◽  
Cytosine Methylation ◽  
Bisulfite Sequencing ◽  
Mammalian Brain ◽  
Phenotypic Change ◽  
Rna Seq ◽  
Stress Response Genes ◽  
Rearing Conditions ◽  
Genome Bisulfite Sequencing ◽  
Dna Cytosine Methylation

AbstractBackgroundMaternal care during early-life plays a crucial role in the sculpting of the mammalian brain. Augmented maternal care during the first postnatal week promotes life-long stress resilience and improved memory compared with the outcome of routine rearing conditions. Recent evidence suggests that this potent phenotypic change commences with altered synaptic connectivity of stress sensitive hypothalamic neurons. However, the epigenomic basis of the long-lived consequences is not well understood.MethodsHere, we employed whole-genome bisulfite sequencing (WGBS), RNA-sequencing (RNA-seq), and a multiplex microRNA (miRNA) assay to examine the effects of augmented maternal care on DNA cytosine methylation, gene expression, and miRNA expression.ResultsA significant decrease in global DNA methylation was observed in offspring hypothalamus following a week of augmented maternal care, corresponding to differential methylation and expression of thousands of genes. Differentially methylated and expressed genes were enriched for functions in neurotransmission, neurodevelopment, protein synthesis, and oxidative phosphorylation, as well as known stress response genes. Twenty prioritized genes with three lines of evidence (methylation, expression, and altered miRNA target) were identified as highly relevant to the stress resiliency phenotype.ConclusionsThis combined unbiased approach enabled the discovery of novel genes and gene pathways that advance our understanding of the central epigenomic mechanisms underlying the profound effects of maternal care on the developing brain.

scholarly journals Dnmt3a and Dnmt3b-Decommissioned Fetal Enhancers are Linked to Kidney Disease

2020 ◽  
Vol 31 (4) ◽  
pp. 765-782
Author(s):  
Yuting Guan ◽  
Hongbo Liu ◽  
Ziyuan Ma ◽  
Szu-Yuan Li ◽  
Jihwan Park ◽  
...  
Keyword(s):  
Kidney Disease ◽  
Dna Methyltransferase ◽  
Cytosine Methylation ◽  
Bisulfite Sequencing ◽  
Kidney Development ◽  
Epigenetic Mark ◽  
Whole Genome ◽  
Whole Genome Bisulfite Sequencing ◽  
Genome Bisulfite Sequencing ◽  
Tubule Cells

BackgroundCytosine methylation is an epigenetic mark that dictates cell fate and response to stimuli. The timing and establishment of methylation logic during kidney development remains unknown. DNA methyltransferase 3a and 3b are the enzymes capable of establishing de novo methylation.MethodsWe generated mice with genetic deletion of Dnmt3a and Dnmt3b in nephron progenitor cells (Six2CreDnmt3a/3b) and kidney tubule cells (KspCreDnmt3a/3b). We characterized KspCreDnmt3a/3b mice at baseline and after injury. Unbiased omics profiling, such as whole genome bisulfite sequencing, reduced representation bisulfite sequencing and RNA sequencing were performed on whole-kidney samples and isolated renal tubule cells.ResultsKspCreDnmt3a/3b mice showed no obvious morphologic and functional alterations at baseline. Knockout animals exhibited increased resistance to cisplatin-induced kidney injury, but not to folic acid–induced fibrosis. Whole-genome bisulfite sequencing indicated that Dnmt3a and Dnmt3b play an important role in methylation of gene regulatory regions that act as fetal-specific enhancers in the developing kidney but are decommissioned in the mature kidney. Loss of Dnmt3a and Dnmt3b resulted in failure to silence developmental genes. We also found that fetal-enhancer regions methylated by Dnmt3a and Dnmt3b were enriched for kidney disease genetic risk loci. Methylation patterns of kidneys from patients with CKD showed defects similar to those in mice with Dnmt3a and Dnmt3b deletion.ConclusionsOur results indicate a potential locus-specific convergence of genetic, epigenetic, and developmental elements in kidney disease development.

scholarly journals The miR-302/367 cluster: a comprehensive update on its evolution and functions

Open Biology ◽  
2015 ◽  
Vol 5 (12) ◽  
pp. 150138 ◽  
Author(s):  
Zeqian Gao ◽  
Xueliang Zhu ◽  
Yongxi Dou
Keyword(s):  
Evolutionary History ◽  
Regulation Of Gene Expression ◽  
Embryonic Stem ◽  
Signalling Pathways ◽  
Transcriptional Level ◽  
Biological Processes ◽  
Related Protein ◽  
Non Coding Rnas ◽  
Cycle Regulation ◽  
Fine Tune

microRNAs are a subclass of small non-coding RNAs that fine-tune the regulation of gene expression at the post-transcriptional level. The miR-302/367 cluster, generally consisting of five members, miR-367, miR-302d, miR-302a, miR-302c and miR-302b, is ubiquitously distributed in vertebrates and occupies an intragenic cluster located in the gene La-related protein 7 ( LARP7 ). The cluster was demonstrated to play an important role in diverse biological processes, such as the pluripotency of human embryonic stem cells (hESCs), self-renewal and reprogramming. This paper provides an overview of the mir-302/367 cluster, discusses our current understanding of the cluster's evolutionary history and transcriptional regulation and reviews the literature surrounding the cluster's roles in cell cycle regulation, epigenetic regulation and different cellular signalling pathways.

scholarly journals Lifetime genealogical divergence within plants leads to epigenetic mosaicism in the long lived shrub Lavandula latifolia (Lamiaceae)

2020 ◽  
Author(s):  
Carlos M. Herrera ◽  
Pilar Bazaga ◽  
Ricardo Pérez ◽  
Conchita Alonso
Keyword(s):  
Dna Methylation ◽  
Cytosine Methylation ◽  
Fragment Length Polymorphism ◽  
Global Dna Methylation ◽  
Epigenetic Variation ◽  
Methylation State ◽  
Plant Parts ◽  
History Of ◽  
Lavandula Latifolia ◽  
Dna Cytosine Methylation

Epigenetic mosaicism is a possible source of within-plant phenotypic heterogeneity, yet its frequency and developmental origin remain unexplored. This study examines whether the extant epigenetic heterogeneity within long-lived Lavandula latifolia (Lamiaceae) shrubs reflects recent epigenetic modifications experienced independently by different plant parts or, alternatively, it is the cumulative outcome of a steady lifetime process. Leaf samples from different architectural modules were collected from three L. latifolia plants and characterized epigenetically by global DNA cytosine methylation and methylation state of methylation-sensitive amplified fragment length polymorphism markers (MS-AFLP). Epigenetic characteristics of modules were then assembled with information on the branching history of plants. Methods borrowed from phylogenetic research were used to assess genealogical signal of extant epigenetic variation and reconstruct within-plant genealogical trajectory of epigenetic traits. Plants were epigenetically heterogeneous, as shown by differences among modules in global DNA methylation and variation in the methylation states of 6-8% of MS-AFLP markers. All epigenetic features exhibited significant genealogical signal within plants. Events of epigenetic divergence occurred throughout the lifespan of individuals and were subsequently propagated by branch divisions. Internal epigenetic diversification of L. latifolia individuals took place steadily during their development, a process which eventually led to persistent epigenetic mosaicism.

scholarly journals Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Dayana E. Salas-Leiva ◽  
Eelco C. Tromer ◽  
Bruce A. Curtis ◽  
Jon Jerlström-Hultqvist ◽  
Martin Kolisko ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Origin Recognition Complex ◽  
Common Ancestor ◽  
Genomic Analysis ◽  
Free Living ◽  
A Genome ◽  
History Of ◽  
Eukaryotic Dna ◽  
Comparative Genomics Analysis ◽  
Dna Processing

AbstractCells replicate and segregate their DNA with precision. Previous studies showed that these regulated cell-cycle processes were present in the last eukaryotic common ancestor and that their core molecular parts are conserved across eukaryotes. However, some metamonad parasites have secondarily lost components of the DNA processing and segregation apparatuses. To clarify the evolutionary history of these systems in these unusual eukaryotes, we generated a genome assembly for the free-living metamonad Carpediemonas membranifera and carried out a comparative genomics analysis. Here, we show that parasitic and free-living metamonads harbor an incomplete set of proteins for processing and segregating DNA. Unexpectedly, Carpediemonas species are further streamlined, lacking the origin recognition complex, Cdc6 and most structural kinetochore subunits. Carpediemonas species are thus the first known eukaryotes that appear to lack this suite of conserved complexes, suggesting that they likely rely on yet-to-be-discovered or alternative mechanisms to carry out these fundamental processes.

scholarly journals Whole-genome bisulfite sequencing in systemic sclerosis provides novel targets to understand disease pathogenesis

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Tianyuan Lu ◽  
Kathleen Oros Klein ◽  
Inés Colmegna ◽  
Maximilien Lora ◽  
Celia M. T. Greenwood ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Genetic Variation ◽  
Systemic Sclerosis ◽  
Cytosine Methylation ◽  
Bisulfite Sequencing ◽  
Whole Genome ◽  
Disease Pathogenesis ◽  
Whole Genome Bisulfite Sequencing ◽  
Genome Wide ◽  
Genome Bisulfite Sequencing

Abstract Background Systemic sclerosis (SSc) is a rare autoimmune connective tissue disease whose pathogenesis remains incompletely understood. Increasing evidence suggests that both genetic susceptibilities and changes in DNA methylation influence pivotal biological pathways and thereby contribute to the disease. The role of DNA methylation in SSc has not been fully elucidated, because existing investigations of DNA methylation predominantly focused on nucleotide CpGs within restricted genic regions, and were performed on samples containing mixed cell types. Methods We performed whole-genome bisulfite sequencing on purified CD4+ T lymphocytes from nine SSc patients and nine controls in a pilot study, and then profiled genome-wide cytosine methylation as well as genetic variations. We adopted robust statistical methods to identify differentially methylated genomic regions (DMRs). We then examined pathway enrichment associated with genes located in these DMRs. We also tested whether changes in CpG methylation were associated with adjacent genetic variation. Results We profiled DNA methylation at more than three million CpG dinucleotides genome-wide. We identified 599 DMRs associated with 340 genes, among which 54 genes exhibited further associations with adjacent genetic variation. We also found these genes were associated with pathways and functions that are known to be abnormal in SSc, including Wnt/β-catenin signaling pathway, skin lesion formation and progression, and angiogenesis. Conclusion The CD4+ T cell DNA cytosine methylation landscape in SSc involves crucial genes in disease pathogenesis. Some of the methylation patterns are also associated with genetic variation. These findings provide essential foundations for future studies of epigenetic regulation and genome-epigenome interaction in SSc.

scholarly journals Coral symbiotic algae calcifyex hospitein partnership with bacteria

2015 ◽  
Vol 112 (19) ◽  
pp. 6158-6163 ◽  
Author(s):  
Jörg C. Frommlet ◽  
Maria L. Sousa ◽  
Artur Alves ◽  
Sandra I. Vieira ◽  
David J. Suggett ◽  
...  
Keyword(s):  
Life History ◽  
Coral Reef ◽  
Evolutionary History ◽  
Central Importance ◽  
Free Living ◽  
Algal Communities ◽  
Symbiotic Algae ◽  
Coral Reef Ecosystems ◽  
History Of

Dinoflagellates of the genusSymbiodiniumare commonly recognized as invertebrate endosymbionts that are of central importance for the functioning of coral reef ecosystems. However, the endosymbiotic phase withinSymbiodiniumlife history is inherently tied to a more cryptic free-living (ex hospite) phase that remains largely unexplored. Here we show that free-livingSymbiodiniumspp. in culture commonly form calcifying bacterial–algal communities that produce aragonitic spherulites and encase the dinoflagellates as endolithic cells. This process is driven bySymbiodiniumphotosynthesis but occurs only in partnership with bacteria. Our findings not only place dinoflagellates on the map of microbial–algal organomineralization processes but also point toward an endolithic phase in theSymbiodiniumlife history, a phenomenon that may provide new perspectives on the biology and ecology ofSymbiodiniumspp. and the evolutionary history of the coral–dinoflagellate symbiosis.

scholarly journals Ultra-deep whole genome bisulfite sequencing reveals a single methylation hotspot in human brain mitochondrial DNA

2021 ◽  
Author(s):  
Romain Guitton ◽  
Christian Dölle ◽  
Guido Alves ◽  
Ole-Bjørn Tysnes ◽  
Gonzalo S. Nido ◽  
...  
Keyword(s):  
Gene Expression ◽  
Parkinson’S Disease ◽  
Mitochondrial Dna ◽  
Prefrontal Cortex ◽  
Cytosine Methylation ◽  
Bisulfite Sequencing ◽  
Whole Genome ◽  
Whole Genome Bisulfite Sequencing ◽  
Genome Bisulfite Sequencing ◽  
Low Levels

ABSTRACTWhile DNA methylation is established as a major regulator of gene expression in the nucleus, the existence of mitochondrial DNA (mtDNA) methylation remains controversial. Here, we characterised the mtDNA methylation landscape in the prefrontal cortex of neurological healthy individuals (n=26) and patients with Parkinson’s disease (n=27), using a combination of whole genome bisulfite sequencing (WGBS) and bisulfite-independent methods. Accurate mtDNA mapping from WGBS data required alignment to an mtDNA reference only, to avoid misalignment to nuclear mitochondrial pseudogenes. Once correctly aligned, WGBS data provided ultra-deep mtDNA coverage (16,723±7,711), and revealed overall very low levels of cytosine methylation. The highest methylation levels (5.49±0.97%) were found on CpG position m.545, located in the heavy-strand promoter 1 region. The m.545 methylation was validated using a combination of methylation-sensitive DNA digestion and quantitative PCR analysis. We detected no association between mtDNA methylation profile and Parkinson’s disease. Interestingly, m.545 methylation correlated with the levels of mtDNA transcripts, suggesting a putative role in regulating mtDNA gene expression. In addition, we propose a robust framework for methylation analysis of mtDNA from WGBS data, which is less prone to false-positive findings due to misalignment of nuclear mitochondrial pseudogene sequences.Graphical abstract of the analyses and main findingsFresh-frozen brain tissue was obtained from the prefrontal cortex (Brodmann area 9) of 53 individuals, comprising 27 patients with idiopathic PD and 26 healthy controls. Tissue from the same samples was used in three different downstream analyses. WGBS was conducted on all 53 samples and the data were analysed using three different alignment strategies. Alignment against an mtDNA reference only was clearly superior as it gave the highest and most even depth of coverage. WGBS analysis revealed that mtDNA harbours very low levels of cytosine methylation, with the exception of the CpG position m.545 within the HSP1 region (lower right inset). The m.545 methylation was confirmed by bisulfite- and sequencing-independent methods, employing methylation-specific MspJI DNA digestion, followed by quantification with qPCR or fluorescent PCR and capillary electrophoresis. Finally, mtDNA transcript levels were determined by RT-qPCR and correlated to m.545 methylation levels, showing a positive association.

scholarly journals Deep ancestral introgression shapes evolutionary history of dragonflies and damselflies

2020 ◽  
Author(s):  
Anton Suvorov ◽  
Celine Scornavacca ◽  
M. Stanley Fujimoto ◽  
Paul Bodily ◽  
Mark Clement ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Biological Processes ◽  
Species Relationships ◽  
Phenotypic Characteristics ◽  
Tree Model ◽  
Environmental Pressures ◽  
Evolutionary Force ◽  
Extant Species ◽  
History Of ◽  
Strictly Binary Tree

SUMMARYIntrogression is arguably one of the most important biological processes in the evolution of groups of related species, affecting at least 10% of the extant species in the animal kingdom. Introgression reduces genetic divergence between species, and in some cases can be highly beneficial, facilitating rapid adaptation to ever-changing environmental pressures. Introgression also significantly impacts inference of phylogenetic species relationships where a strictly binary tree model cannot adequately explain reticulate net-like species relationships. Here we use phylogenomic approaches to understand patterns of introgression along the evolutionary history of a unique, non-model, relic insect system: dragonflies and damselflies (Odonata). We demonstrate that introgression is a pervasive evolutionary force across various taxonomic levels within Odonata. In particular, we show that the morphologically “intermediate” species of Anisozygoptera (one of the three primary suborders within Odonata besides Zygoptera and Anisoptera), which retain phenotypic characteristics of the other two suborders, experienced high levels of introgression probably coming from zygopteran genomes. Additionally, we found evidence for multiple cases of deep inter-familial ancestral introgression. However, weaker evidence of introgression was found within more recently diverged focal clades: Aeshnidae, Gomphidae+Petaluridae and Libellulidae.

scholarly journals Distribution and Evolutionary History of Sialic Acid Catabolism in the Phylum Actinobacteria

2022 ◽  
Author(s):  
Yisong Li ◽  
Ying Huang
Keyword(s):  
Sialic Acid ◽  
Evolutionary History ◽  
Sialic Acids ◽  
Free Living ◽  
Evolutionary Pathway ◽  
History Of

Sialic acids play essential roles in the physiology of humans and other metazoan animals, and microbial sialic acid catabolism (SAC) is one of the processes critical for pathogenesis. To date, microbial SAC is studied mainly in commensals and pathogens, while its distribution in free-living microbes and evolutionary pathway remain largely unexplored.

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