scholarly journals Distinct Responses of Arabidopsis Telomeres and Transposable Elements to Zebularine Exposure

2021 ◽  
Vol 22 (1) ◽  
pp. 468
Author(s):  
Klára Konečná ◽  
Pavla Polanská Sováková ◽  
Karin Anteková ◽  
Jiří Fajkus ◽  
Miloslava Fojtová
Keyword(s):  
Transposable Elements ◽  
Transcriptional Activation ◽  
Genome Stability ◽  
Cytosine Methylation ◽  
Individual Variability ◽  
Correlated Response ◽  
Telomere Shortening ◽  
Treatment Changes ◽  
Telomere Homeostasis ◽  
Genomic Regions

Involvement of epigenetic mechanisms in the regulation of telomeres and transposable elements (TEs), genomic regions with the protective and potentially detrimental function, respectively, has been frequently studied. Here, we analyzed telomere lengths in Arabidopsis thaliana plants of Columbia, Landsberg erecta and Wassilevskija ecotypes exposed repeatedly to the hypomethylation drug zebularine during germination. Shorter telomeres were detected in plants growing from seedlings germinated in the presence of zebularine with a progression in telomeric phenotype across generations, relatively high inter-individual variability, and diverse responses among ecotypes. Interestingly, the extent of telomere shortening in zebularine Columbia and Wassilevskija plants corresponded to the transcriptional activation of TEs, suggesting a correlated response of these genomic elements to the zebularine treatment. Changes in lengths of telomeres and levels of TE transcripts in leaves were not always correlated with a hypomethylation of cytosines located in these regions, indicating a cytosine methylation-independent level of their regulation. These observations, including differences among ecotypes together with distinct dynamics of the reversal of the disruption of telomere homeostasis and TEs transcriptional activation, reflect a complex involvement of epigenetic processes in the regulation of crucial genomic regions. Our results further demonstrate the ability of plant cells to cope with these changes without a critical loss of the genome stability.

scholarly journals Pathway conversion enables a double-lock mechanism to maintain DNA methylation and genome stability

2021 ◽  
Vol 118 (35) ◽  
pp. e2107320118
Author(s):  
Li He ◽  
Cheng Zhao ◽  
Qingzhu Zhang ◽  
Gaurav Zinta ◽  
Dong Wang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Arabidopsis Thaliana ◽  
Transposable Elements ◽  
Genome Stability ◽  
First Generation ◽  
Genomic Stability ◽  
Genome Integrity ◽  
Chromatin Remodeler ◽  
Genomic Regions

The CMT2 and RNA-directed DNA methylation (RdDM) pathways have been proposed to separately maintain CHH methylation in specific regions of the Arabidopsis thaliana genome. Here, we show that dysfunction of the chromatin remodeler DDM1 causes hundreds of genomic regions to switch from CMT2 dependency to RdDM dependency in DNA methylation. These converted loci are enriched at the edge regions of long transposable elements (TEs). Furthermore, we found that dysfunction in both DDM1 and RdDM causes strong reactivation of TEs and a burst of TE transposition in the first generation of mutant plants, indicating that the DDM1 and RdDM pathways together are critical to maintaining TE repression and protecting genomic stability. Our findings reveal the existence of a pathway conversion–based backup mechanism to guarantee the maintenance of DNA methylation and genome integrity.

scholarly journals Telomere Biology and Human Phenotype

Cells ◽  
2019 ◽  
Vol 8 (1) ◽  
pp. 73 ◽  
Author(s):  
Kara Turner ◽  
Vimal Vasu ◽  
Darren Griffin
Keyword(s):  
Genome Stability ◽  
Telomere Shortening ◽  
Human Phenotype ◽  
Telomere Attrition ◽  
Age Related ◽  
Telomere Homeostasis ◽  
Telomere Biology ◽  
And Function

Telomeres are nucleoprotein structures that cap the end of each chromosome arm and function to maintain genome stability. The length of telomeres is known to shorten with each cell division and it is well-established that telomere attrition is related to replicative capacity in vitro. Moreover, telomere loss is also correlated with the process of aging in vivo. In this review, we discuss the mechanisms that lead to telomere shortening and summarise telomere homeostasis in humans throughout a lifetime. In addition, we discuss the available evidence that shows that telomere shortening is related to human aging and the onset of age-related disease.

scholarly journals Locus-specific chromatin profiling of evolutionarily young transposable elements

2021 ◽  
Author(s):  
Darren Taylor ◽  
Robert Lowe ◽  
Claude Philippe ◽  
Kevin C. L. Cheng ◽  
Gael Cristofari ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Genome Stability ◽  
Specific Protein ◽  
Spatial Proximity ◽  
Sequencing Data ◽  
Mapping Tool ◽  
Specific Regulation ◽  
Chromatin Profiling ◽  
Interspersed Repeats ◽  
Genomic Regions

ABSTRACTDespite a vast expansion in the availability of epigenomic data, our knowledge of the chromatin landscape at interspersed repeats remains highly limited by difficulties in mapping short-read sequencing data to these regions. In particular, little is known about the locus-specific regulation of evolutionarily young transposable elements (TEs), which have been implicated in genome stability, gene regulation and innate immunity in a variety of developmental and disease contexts. Here we propose an approach for generating locus-specific protein-DNA binding profiles at interspersed repeats, which leverages information on the spatial proximity between repetitive and non-repetitive genomic regions. We demonstrate that the combination of HiChIP and a newly developed mapping tool (PAtChER) yields accurate protein enrichment profiles at individual repetitive loci. Using this approach, we reveal previously unappreciated variation in the epigenetic profiles of young TE loci in mouse and human cells. Insights gained using our method will be invaluable for dissecting the molecular determinants of TE regulation and their impact on the genome.

scholarly journals Low temperature triggers genome-wide hypermethylation of transposable elements and centromeres in maize

2019 ◽  
Author(s):  
Zeineb Achour ◽  
Johann Joets ◽  
Martine Leguilloux ◽  
Hélène Sellier ◽  
Jean-Philippe Pichon ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Transposable Elements ◽  
Transcriptional Activation ◽  
Gene Expression Regulation ◽  
Environmental Cues ◽  
Specific Response ◽  
Genome Wide ◽  
A Genome ◽  
Response To Stress ◽  
Context Specific

ABSTRACTCharacterizing the molecular processes developed by plants to respond to environmental cues is a major task to better understand local adaptation. DNA methylation is a chromatin mark involved in the transcriptional silencing of transposable elements (TEs) and gene expression regulation. While the molecular bases of DNA methylation regulation are now well described, involvement of DNA methylation in plant response to environmental cues remains poorly characterized. Here, using the TE-rich maize genome and analyzing methylome response to prolonged cold at the chromosome and feature scales, we investigate how genomic architecture affects methylome response to stress in a cold-sensitive genotype. Interestingly, we show that cold stress induces a genome-wide methylation increase through the hypermethylation of TE sequences and centromeres. Our work highlights a cytosine context-specific response of TE methylation that depends on TE types, chromosomal location and proximity to genes. The patterns observed can be explained by the parallel transcriptional activation of multiple DNA methylation pathways that methylate TEs in the various chromatin locations where they reside. Our results open new insights into the possible role of genome-wide DNA methylation in phenotypic response to stress.

scholarly journals Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Shujun Ou ◽  
Weija Su ◽  
Yi Liao ◽  
Kapeel Chougule ◽  
Jireh R. A. Agda ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Animal Species ◽  
Performance Metrics ◽  
De Novo ◽  
Terminal Inverted Repeat ◽  
Miniature Inverted Transposable Elements ◽  
Sensitivity Specificity ◽  
Genomic Regions ◽  
Assembly Algorithms ◽  
Eukaryotic Genomes

Abstract Background Sequencing technology and assembly algorithms have matured to the point that high-quality de novo assembly is possible for large, repetitive genomes. Current assemblies traverse transposable elements (TEs) and provide an opportunity for comprehensive annotation of TEs. Numerous methods exist for annotation of each class of TEs, but their relative performances have not been systematically compared. Moreover, a comprehensive pipeline is needed to produce a non-redundant library of TEs for species lacking this resource to generate whole-genome TE annotations. Results We benchmark existing programs based on a carefully curated library of rice TEs. We evaluate the performance of methods annotating long terminal repeat (LTR) retrotransposons, terminal inverted repeat (TIR) transposons, short TIR transposons known as miniature inverted transposable elements (MITEs), and Helitrons. Performance metrics include sensitivity, specificity, accuracy, precision, FDR, and F1. Using the most robust programs, we create a comprehensive pipeline called Extensive de-novo TE Annotator (EDTA) that produces a filtered non-redundant TE library for annotation of structurally intact and fragmented elements. EDTA also deconvolutes nested TE insertions frequently found in highly repetitive genomic regions. Using other model species with curated TE libraries (maize and Drosophila), EDTA is shown to be robust across both plant and animal species. Conclusions The benchmarking results and pipeline developed here will greatly facilitate TE annotation in eukaryotic genomes. These annotations will promote a much more in-depth understanding of the diversity and evolution of TEs at both intra- and inter-species levels. EDTA is open-source and freely available: https://github.com/oushujun/EDTA.

scholarly journals Novel Genomic Regions Associated with Intramuscular Fatty Acid Composition in Rabbits

Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 2090
Author(s):  
Houda Laghouaouta ◽  
Bolívar Samuel Sosa-Madrid ◽  
Agostina Zubiri-Gaitán ◽  
Pilar Hernández ◽  
Agustín Blasco
Keyword(s):  
Fatty Acids ◽  
Fatty Acid Composition ◽  
Fatty Acid ◽  
Acid Composition ◽  
Correlated Response ◽  
A Genome ◽  
Genomic Variance ◽  
Genomic Regions ◽  
Imf Content ◽  
The Imf

Intramuscular fat (IMF) content and its composition affect the quality of meat. Selection for IMF generated a correlated response on its fatty acid composition. The increase of IMF content is associated with an increase of its saturated (SFA) and monounsaturated (MUFA) fatty acids, and consequently a decrease of polyunsaturated fatty acids (PUFA). We carried out a genome wide association study (GWAS) for IMF composition on two rabbit lines divergently selected for IMF content, using a Bayes B procedure. Association analyses were performed using 475 individuals and 90,235 Single Nucleotide Polymorphisms (SNPs). The main objectives were to identify genomic regions associated with the IMF composition and to generate a list of candidate genes. Genomic regions associated with the intramuscular fatty acid composition were spread across different rabbit chromosomes (OCU). An important region at 34.0–37.9 Mb on OCU1 was associated with C14:0, C16:0, SFA, and C18:2n6, explaining 3.5%, 11.2%, 11.3%, and 3.2% of the genomic variance, respectively. Another relevant genomic region was found to be associated at 46.0–48.9 Mb on OCU18, explaining up to 8% of the genomic variance of MUFA/SFA. The associated regions harbor several genes related to lipid metabolism, such as SCD, PLIN2, and ERLIN1. The main genomic regions associated with the fatty acids were not previously associated with IMF content in rabbits. Nonetheless, MTMR2 is the only gene that was associated with both the IMF content and composition in rabbits. Our study highlighted the polygenic nature of the fatty acids in rabbits and elucidated its genetic background.

scholarly journals Pwp1 regulates telomere length by stabilizing shelterin complex and maintaining histone H4K20 trimethylation

2019 ◽  
Vol 5 (1) ◽  
Author(s):  
Yangyang Yu ◽  
Wenwen Jia ◽  
Yao Lyu ◽  
Dingwen Su ◽  
Mingliang Bai ◽  
...  
Keyword(s):  
Telomere Length ◽  
Knockout Mice ◽  
Embryonic Stem ◽  
Telomere Maintenance ◽  
Reproductive Capacity ◽  
Mouse Development ◽  
Telomere Shortening ◽  
Shelterin Complex ◽  
Telomere Homeostasis ◽  
Novel Protein

Abstract Telomere maintenance is critical for chromosome stability. Here we report that periodic tryptophan protein 1 (PWP1) is involved in regulating telomere length homeostasis. Pwp1 appears to be essential for mouse development and embryonic stem cell (ESC) survival, as homozygous Pwp1-knockout mice and ESCs have never been obtained. Heterozygous Pwp1-knockout mice had shorter telomeres and decreased reproductive capacity. Pwp1 depletion induced rapid telomere shortening accompanied by reduced shelterin complex and increased DNA damage in telomeric regions. Mechanistically, PWP1 bound and stabilized the shelterin complex via its WD40 domains and regulated the overall level of H4K20me3. The rescue of telomere length in Pwp1-deficient cells by PWP1 overexpression depended on SUV4-20H2 co-expression and increased H4K20me3. Therefore, our study revealed a novel protein involved in telomere homeostasis in both mouse and human cells. This knowledge will improve our understanding of how chromatin structure and histone modifications are involved in maintaining telomere integrity.

scholarly journals Silencing of Euchromatic Transposable Elements as a Consequence of Nuclear Lamina Dysfunction

Cells ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 625
Author(s):  
Valeria Cavaliere ◽  
Giovanna Lattanzi ◽  
Davide Andrenacci
Keyword(s):  
Transposable Elements ◽  
Genome Instability ◽  
Nuclear Periphery ◽  
Nuclear Lamina ◽  
Rna Degradation ◽  
Loss Of Function ◽  
Heterochromatin Formation ◽  
Repressive Effect ◽  
Regulatory Effects ◽  
Genomic Regions

Transposable elements (TEs) are mobile genomic sequences that are normally repressed to avoid proliferation and genome instability. Gene silencing mechanisms repress TEs by RNA degradation or heterochromatin formation. Heterochromatin maintenance is therefore important to keep TEs silent. Loss of heterochromatic domains has been linked to lamin mutations, which have also been associated with derepression of TEs. In fact, lamins are structural components of the nuclear lamina (NL), which is considered a pivotal structure in the maintenance of heterochromatin domains at the nuclear periphery in a silent state. Here, we show that a lethal phenotype associated with Lamin loss-of-function mutations is influenced by Drosophila gypsy retrotransposons located in euchromatic regions, suggesting that NL dysfunction has also effects on active TEs located in euchromatic loci. In fact, expression analysis of different long terminal repeat (LTR) retrotransposons and of one non-LTR retrotransposon located near active genes shows that Lamin inactivation determines the silencing of euchromatic TEs. Furthermore, we show that the silencing effect on euchromatic TEs spreads to the neighboring genomic regions, with a repressive effect on nearby genes. We propose that NL dysfunction may have opposed regulatory effects on TEs that depend on their localization in active or repressed regions of the genome.

scholarly journals In Vivo Titration of Mitomycin C Action by Four Escherichia coli Genomic Regions on Multicopy Plasmids

2001 ◽  
Vol 183 (7) ◽  
pp. 2259-2264 ◽  
Author(s):  
Yan Wei ◽  
Amy C. Vollmer ◽  
Robert A. LaRossa
Keyword(s):  
Escherichia Coli ◽  
Mitomycin C ◽  
Transcriptional Activation ◽  
Efflux Pump ◽  
Wild Type ◽  
Potent Inducer ◽  
E Coli ◽  
Genomic Regions

ABSTRACT Mitomycin C (MMC), a DNA-damaging agent, is a potent inducer of the bacterial SOS response; surprisingly, it has not been used to select resistant mutants from wild-type Escherichia coli. MMC resistance is caused by the presence of any of four distinctE. coli genes (mdfA, gyrl, rob, andsdiA) on high-copy-number vectors. mdfAencodes a membrane efflux pump whose overexpression results in broad-spectrum chemical resistance. The gyrI (also called sbmC) gene product inhibits DNA gyrase activity in vitro, while the rob protein appears to function in transcriptional activation of efflux pumps. SdiA is a transcriptional activator of ftsQAZ genes involved in cell division.

scholarly journals Methylation, Transcription, and Rearrangements of Transposable Elements in Synthetic Allopolyploids

2011 ◽  
Vol 2011 ◽  
pp. 1-7 ◽  
Author(s):  
Beery Yaakov ◽  
Khalil Kashkush
Keyword(s):  
Transposable Elements ◽  
Transcriptional Activation ◽  
Genome Structure ◽  
Biological Significance ◽  
Wheat Genome ◽  
Wheat Species ◽  
Noncoding Sequences ◽  
Genomic Stress ◽  
Underlying Mechanisms ◽  
Allohexaploid Wheat

Transposable elements (TEs) constitute over 90% of the wheat genome. It was suggested that “genomic stress” such as hybridity or polyploidy might activate transposons. Intensive investigations of various polyploid systems revealed that allopolyploidization event is associated with widespread changes in genome structure, methylation, and expression involving low- and high-copy, coding and noncoding sequences. Massive demethylation and transcriptional activation of TEs were also observed in newly formed allopolyploids. Massive proliferation, however, was reported for very limited number of TE families in various polyploidy systems. The aim of this review is to summarize the accumulated data on genetic and epigenetic dynamics of TEs, particularly in synthetic allotetraploid and allohexaploid wheat species. In addition, the underlying mechanisms and the potential biological significance of TE dynamics following allopolyploidization are discussed.

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