Constitutive Heterochromatin in Eukaryotic Genomes: A Mine of Transposable Elements

Marsano, Renè Massimiliano; Dimitri, Patrizio

doi:10.3390/cells11050761

Cited by 20 publications

(25 citation statements)

References 153 publications

(183 reference statements)

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“…Based on our research findings, lncRNA has a close relationship with transposons [ 14 ] and transposons play important roles in many physiological processes, such as heterochromatin formation [ 16 ]. Differentially expressed TE families were screened in the results of the transcriptional analysis.…”

Section: Resultsmentioning

confidence: 99%

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Genome-Wide Identification of Long Noncoding RNA and Their Potential Interactors in ISWI Mutants

Zhang¹,

Zhang²,

Liang³

2022

IJMS

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Long non-coding RNAs (lncRNAs) have been identified as key regulators of gene expression and participate in many vital physiological processes. Chromatin remodeling, being an important epigenetic modification, has been identified in many biological activities as well. However, the regulatory mechanism of lncRNA in chromatin remodeling remains unclear. In order to characterize the genome-wide lncRNA expression and their potential interacting factors during this process in Drosophila, we investigated the expression pattern of lncRNAs and mRNAs based on the transcriptome analyses and found significant differences between lncRNAs and mRNAs. Then, we performed TSA-FISH experiments of candidate lncRNAs and their potential interactors that have different functions in Drosophila embryos to determine their expression pattern. In addition, we also analyzed the expression of transposable elements (TEs) and their interactors to explore their expression in ISWI mutants. Our results provide a new perspective for understanding the possible regulatory mechanism of lncRNAs and TEs as well as their targets in chromatin remodeling.

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Section: Resultsmentioning

confidence: 99%

“…This similarity can be explained because they evolutionarily derive from TEs. TEs are repetitive, movable genomic sequences with the ability to integrate into new sites in the genome [ 16 ]. Transposon activation is critical at different developmental stages [ 17 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification of Long Noncoding RNA and Their Potential Interactors in ISWI Mutants

Zhang¹,

Zhang²,

Liang³

2022

IJMS

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“…The heterochromatin corresponds to an important fraction of the genome and constitute large blocks near centromeres and telomeres chromosomes [ 39 ]. The enrichment of TES in heterochromatin regions has been now considered a general aspect of this fraction [ 40 ]. In this sense, the increase in Rex 3 retroelements after treatment also correlates with the increase in heterochromatin.…”

Section: Resultsmentioning

confidence: 99%

“…Heterochromatic regions are marked in the pericentromeric portions of chromosomes, conventional configuration for C-banding of tambaqui. For details, see references [ 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 ]. 2( a )-II–C-banding after exposition to trichlorfon to 30% LC 50–96 h -48 h (C1 = 0.261 mg/L).…”

Section: Figurementioning

confidence: 99%

A Perspective of Molecular Cytogenomics, Toxicology, and Epigenetics for the Increase of Heterochromatic Regions and Retrotransposable Elements in Tambaqui (Colossoma macropomum) Exposed to the Parasiticide Trichlorfon

Costa

Silva

Soares

et al. 2022

Animals

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Rex retroelements are the best-known transposable elements class and are broadly distributed through fish and also individual genomes, playing an important role in their evolutionary dynamics. Several agents can stress these elements; among them, there are some parasitic compounds such as the organochlorophosphate Trichlorfon. Consequently, knowing that the organochlorophosphate Trichlorfon is indiscriminately used as an antiparasitic in aquaculture, the current study aimed to analyze the effects of this compound on the activation of the Transposable Elements (TEs) Rex1, Rex3, and Rex6 and the structure of heterochromatin in the mitotic chromosomes of the tambaqui (Colossoma macropomum). For this, two concentrations of the pesticide were used: 30% (0.261 mg/L) and 50% (0.435 mg/L) of the recommended LC50–96 h concentration (0.87 mg/L) for this fish species. The results revealed a dispersed distribution for Rex1 and Rex6 retroelements. Rex3 showed an increase in both marking intensity and distribution, as well as enhanced chromosomal heterochromatinization. This probably happened by the mediation of epigenetic adaptive mechanisms, causing the retroelement mobilization to be repressed. However, this behavior was most evident when Trichlorfon concentrations and exposure times were the greatest, reflecting the genetic flexibility necessary for this species to successfully adapt to environmental changes.

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“…Interestingly, the number of LINE1 insertions is increased in the Neo3 sequence (File S5), in agreement with the view that L1 plays a role in regulating neocentromere activity (Chueh et al 2009). However, the LINE1 family is reported to have insertion site preference in regions of constitutive AT-rich heterochromatin (Acosta et al 2008;Marsano and Dimitri 2022;Waters et al 2004). Probably, the higher number of elements found in the sequenced Neo3 region is a consequence of this aspect.…”

Section: Discussionmentioning

confidence: 99%

Genome characterization and CRISPR-Cas9 editing of a human neocentromere

et al. 2022

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The maintenance of genome integrity is ensured by proper chromosome inheritance during mitotic and meiotic cell divisions. The chromosomal counterpart responsible for chromosome segregation to daughter cells is the centromere, at which the spindle apparatus attaches through the kinetochore. Although all mammalian centromeres are primarily composed of megabase-long repetitive sequences, satellite-free human neocentromeres have been described. Neocentromeres and evolutionary new centromeres have revolutionized traditional knowledge about centromeres. Over the past 20 years, insights have been gained into their organization, but in spite of these advancements, the mechanisms underlying their formation and evolution are still unclear. Today, through modern and increasingly accessible genome editing and long-read sequencing techniques, research in this area is undergoing a sudden acceleration. In this article, we describe the primary sequence of a previously described human chromosome 3 neocentromere and observe its possible evolution and repair results after a chromosome breakage induced through CRISPR-Cas9 technologies. Our data represent an exciting advancement in the field of centromere/neocentromere evolution and chromosome stability.

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Constitutive Heterochromatin in Eukaryotic Genomes: A Mine of Transposable Elements

Cited by 20 publications

References 153 publications

Genome-Wide Identification of Long Noncoding RNA and Their Potential Interactors in ISWI Mutants

Genome-Wide Identification of Long Noncoding RNA and Their Potential Interactors in ISWI Mutants

A Perspective of Molecular Cytogenomics, Toxicology, and Epigenetics for the Increase of Heterochromatic Regions and Retrotransposable Elements in Tambaqui (Colossoma macropomum) Exposed to the Parasiticide Trichlorfon

Genome characterization and CRISPR-Cas9 editing of a human neocentromere

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