Silencing of Transposable Elements Mediated by 5-mC and Compensation of the Heterochromatin Content by Presence of B Chromosomes in Astyanax scabripinnis

The way in which transcriptional activity overcomes the physical DNA structure and gene regulation mechanisms involves complex processes that are not yet fully understood. Modifications in the cytosine-guanine sequence of DNA by 5-mC are preferentially located in heterochromatic regions and are related to gene silencing. Herein, we investigate evidence of epigenetic regulation related to the B chromosome model and transposable elements in A. scabripinnis. Indirect immunofluorescence using anti-5-mC to mark methylated regions was employed along with quantitative ELISA to determine the total genomic DNA methylation level. 5-mC signals were dispersed in the chromosomes of both females and males, with preferential accumulation in the B chromosome. In addition to the heterochromatic methylated regions, our results suggest that methylation is associated with transposable elements (LINE and Tc1-Mariner). Heterochromatin content was measured based on the C-band length in relation to the size of chromosome 1. The B chromosome in A. scabripinnis comprises heterochromatin located in the pericentromeric region of both arms of this isochromosome. In this context, individuals with B chromosomes should have an increased heterochromatin content when compared to individuals that do not. Although, both heterochromatin content and genome methylation showed no significant differences between sexes or in relation to the occurrence of B chromosomes. Our evidence suggests that the B chromosome can have a compensation effect on the heterochromatin content and that methylation possibly operates to silence TEs in A. scabripinnis. This represents a sui generis compensation and gene activity buffering mechanism.

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Methylation-Mediated Transcriptional Silencing in Euchromatin by Methyl-CpG Binding Protein MBD1 Isoforms

Molecular and Cellular Biology ◽

10.1128/mcb.19.9.6415 ◽

1999 ◽

Vol 19 (9) ◽

pp. 6415-6426 ◽

Cited By ~ 131

Author(s):

Naoyuki Fujita ◽

Shin-ichiro Takebayashi ◽

Katsuzumi Okumura ◽

Shinichi Kudo ◽

Tsutomu Chiba ◽

...

Keyword(s):

Dna Methylation ◽

Transcriptional Repression ◽

Mammalian Cells ◽

Fluorescent Protein ◽

Cpg Islands ◽

Transcriptional Silencing ◽

Pericentromeric Region ◽

Chromosome 1 ◽

Reverse Transcription Pcr ◽

Genome Methylation

ABSTRACT DNA methylation of promoter-associated CpG islands is involved in the transcriptional repression of vertebrate genes. To investigate the mechanisms underlying gene inactivation by DNA methylation, we characterized a human MBD1 protein, one of the components of MeCP1, which possesses a methyl-CpG binding domain (MBD) and cysteine-rich (CXXC) domains. Four novel MBD1 isoforms (MBD1v1, MBD1v2, MBD1v3, and MBD1v4) were identified by the reverse transcription-PCR method. We found that these transcripts were alternatively spliced in the region of CXXC domains and the C terminus. Green fluorescent protein-fused MBD1 was localized to multiple foci on the human genome, mostly in the euchromatin regions, and particularly concentrated in the pericentromeric region of chromosome 1. Both the MBD sequence and genome methylation were required for proper localization of the MBD1 protein. We further investigated whether MBD1 isoforms are responsible for transcriptional repression of human genes. A bacterially expressed MBD1 protein bound preferentially to methylated DNA fragments containing CpG islands from the tumor suppressor genes p16,VHL, and E-cadherin and from an imprintedSNRPN gene. All MBD1 isoforms inhibited promoter activities of these genes via methylation. Interestingly, MBD1 isoforms v1 and v2 containing three CXXC domains also suppressed unmethylated promoter activities in mammalian cells. These effects were further manifested inDrosophila melanogaster cells, which lack genome methylation. Sp1-activated transcription of methylated p16and SNRPN promoters was inhibited by all of the MBD1 isoforms, whereas the isoforms v1 and v2 reduced Sp1-activated transcription from unmethylated promoters as well. These findings suggested that the MBD1 isoforms have different roles in methylation-mediated transcriptional silencing in euchromatin.

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B Chromosome Variants of the Grasshopper Xyleus discoideus angulatus Are Potentially Derived from Pericentromeric DNA

Cytogenetic and Genome Research ◽

10.1159/000480036 ◽

2017 ◽

Vol 152 (4) ◽

pp. 213-221 ◽

Cited By ~ 5

Author(s):

Andrezza C.S. Bernardino ◽

Diogo C. Cabral-de-Mello ◽

Carolina B. Machado ◽

Octavio M. Palacios-Gimenez ◽

Neide Santos ◽

...

Keyword(s):

Repetitive Dna ◽

Evolutionary Dynamics ◽

Chromosome Evolution ◽

Pericentromeric Region ◽

B Chromosome ◽

B Chromosomes ◽

Different Populations ◽

B Chromosome Evolution ◽

Shed Light

B chromosomes, extra elements present in the karyotypes of some eukaryote species, have been described in the grasshopper Xyleus discoideus angulatus. Although some studies have proposed an autosomal origin of the B chromosome in X. d. angulatus, little is known about its repetitive DNA composition and evolutionary dynamics. The aim of the present work was to shed light on the B chromosome evolution in X. d. angulatus by cytogenetic analysis of 27 populations from Pernambuco and Ceará states (Brazil). The frequency of B chromosomes in the different populations was determined, and chromosome measurements and fluorescence in situ hybridization (FISH) with C0t-DNA and telomeric and B chromosome sequences were performed in cells from B-carrying individuals. The results revealed variations in B chromosome prevalence among the populations and showed that some B chromosomes were smaller in certain populations. FISH produced similar patterns for the C0t-DNA probe in all hybridized individuals, whereas telomeric and B chromosome probes, obtained by microdissection, exhibited variations in their distribution. These results indicate the presence of 3 morphotypes of B chromosomes in X. d. angulatus, with variation in repetitive DNA composition during their evolution. In this species, B chromosomes have an intraspecific origin and probably arose from the pericentromeric region of A chromosomes.

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Structural and Functional Analysis of Transposable Elements Focusing on B Chromosomes of the Cichlid Fish Astatotilapia latifasciata

10.20944/preprints201803.0145.v1 ◽

2018 ◽

Author(s):

Rafael Coan ◽

Cesar Martins

Keyword(s):

Transposable Elements ◽

Repetitive Sequences ◽

Chromosome Complement ◽

Cichlid Fish ◽

B Chromosome ◽

B Chromosomes ◽

Sequencing Data ◽

Taxonomic Groups ◽

African Cichlids

B chromosomes (B) are supernumerary elements found in many taxonomic groups. Most B chromosomes are rich in heterochromatin and composed of abundant repetitive sequences, especially transposable elements (TEs). Bs origin is generally linked to the A chromosome complement (A). The first report of a B chromosome in African cichlids was on Astatotilapia latifasciata, which can harbor 0, 1 or 2 B chromosomes. Classical cytogenetics studies found high TE content on the species B chromosome. In this study, we aim to understand TE composition and expression on A. latifasciata genome and its relation to the B chromosome. We use bioinformatics analysis to explore TEs genome organization and also their composition on the B chromosome. Bioinformatics findings were validated by fluorescent in situ hybridization (FISH) and real-time PCR (qPCR). A. latifasciata has a TE content similar to other cichlid fishes and several expanded elements on its B chromosome. With RNA sequencing data (RNA-seq) we showed that all major TE classes are transcribed in brain, muscle and male/female gonads. The evaluation of TE expression between B- and B+ individuals showed that few elements have differential expression among groups and expanded B elements were not highly transcribed. Putative silencing mechanisms may the acting on the B chromosome of A. latifasciata to prevent adverse consequences of repeat transcription and mobilization in the genome.

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Repetitive DNA landscape in essential A and supernumerary B chromosomes of Festuca pratensis Huds

Scientific Reports ◽

10.1038/s41598-019-56383-1 ◽

2019 ◽

Vol 9 (1) ◽

Author(s):

Rahman Ebrahimzadegan ◽

Andreas Houben ◽

Ghader Mirzaghaderi

Keyword(s):

Repetitive Sequences ◽

Nuclear Genome ◽

B Chromosome ◽

B Chromosomes ◽

Festuca Pratensis ◽

Ltr Retrotransposons ◽

Chromosome Identification ◽

Satellite Repeats ◽

Low Pass ◽

Illumina Sequence

AbstractHere, we characterized the basic properties of repetitive sequences in essential A and supernumerary B chromosomes of Festuca pratensis Huds. This was performed by comparative analysis of low-pass Illumina sequence reads of B chromosome lacking (−B) and B chromosome containing (+B) individuals of F. pratensis. 61% of the nuclear genome is composed of repetitive sequences. 43.1% of the genome are transposons of which DNA transposons and retrotransposons made up 2.3% and 40.8%, respectively. LTR retrotransposons are the most abundant mobile elements and contribute to 40.7% of the genome and divided into Ty3-gypsy and Ty1-copia super families with 32.97% and 7.78% of the genome, respectively. Eighteen different satellite repeats were identified making up 3.9% of the genome. Five satellite repeats were used as cytological markers for chromosome identification and genome analysis in the genus Festuca. Four satellite repeats were identified on B chromosomes among which Fp-Sat48 and Fp-Sat253 were specific to the B chromosome of F. pratensis.

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Spatial organization of fibroblast and spermatocyte nuclei with different B-chromosome content in Korean field mouse, Apodemus peninsulae (Rodentia, Muridae)

Genome ◽

10.1139/gen-2017-0029 ◽

2017 ◽

Vol 60 (10) ◽

pp. 815-824 ◽

Cited By ~ 4

Author(s):

Tatyana V. Karamysheva ◽

Anna A. Torgasheva ◽

Yaroslav R. Yefremov ◽

Anton G. Bogomolov ◽

Thomas Liehr ◽

...

Keyword(s):

Laser Scanning ◽

Spatial Organization ◽

Constitutive Heterochromatin ◽

B Chromosome ◽

B Chromosomes ◽

Laser Scanning Microscopy ◽

Field Mouse ◽

Apodemus Peninsulae ◽

Basic Set ◽

Korean Field Mouse

Korean field mouse (Apodemus peninsulae) shows a wide variation in the number of B chromosomes composed of constitutive heterochromatin. For this reason, it provides a good model to study the influence of the number of centromeres and amount of heterochromatin on spatial organization of interphase nuclei. We analyzed the three-dimensional organization of fibroblast and spermatocyte nuclei of the field mice carrying a different number of B chromosomes using laser scanning microscopy and 3D fluorescence in situ hybridization. We detected a co-localization of the B chromosomes with constitutive heterochromatin of the chromosomes of the basic set. We showed a non-random distribution of B chromosomes in the spermatocyte nuclei. Unpaired B chromosomes showed a tendency to occur in the compartment formed by the unpaired part of the XY bivalent.

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B Chromosomes in Populations of Mammals Revisited

Genes ◽

10.3390/genes9100487 ◽

2018 ◽

Vol 9 (10) ◽

pp. 487 ◽

Cited By ~ 11

Author(s):

Mladen Vujošević ◽

Marija Rajičić ◽

Jelena Blagojević

Keyword(s):

Mammalian Species ◽

B Chromosome ◽

Molecular Techniques ◽

B Chromosomes ◽

General View ◽

Protein Coding ◽

Host Parasite Interactions ◽

Quantitative Characteristics ◽

Host Parasite

The study of B chromosomes (Bs) started more than a century ago, while their presence in mammals dates since 1965. As the past two decades have seen huge progress in application of molecular techniques, we decided to throw a glance on new data on Bs in mammals and to review them. We listed 85 mammals with Bs that make 1.94% of karyotypically studied species. Contrary to general view, a typical B chromosome in mammals appears both as sub- or metacentric that is the same size as small chromosomes of standard complement. Both karyotypically stable and unstable species possess Bs. The presence of Bs in certain species influences the cell division, the degree of recombination, the development, a number of quantitative characteristics, the host-parasite interactions and their behaviour. There is at least some data on molecular structure of Bs recorded in nearly a quarter of species. Nevertheless, a more detailed molecular composition of Bs presently known for six mammalian species, confirms the presence of protein coding genes, and the transcriptional activity for some of them. Therefore, the idea that Bs are inert is outdated, but the role of Bs is yet to be determined. The maintenance of Bs is obviously not the same for all species, so the current models must be adapted while bearing in mind that Bs are not inactive as it was once thought.

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Transmission rate variation among three B chromosome variants in the fish Prochilodus lineatus (Characiformes, Prochilodontidae)

Anais da Academia Brasileira de Ciências ◽

10.1590/0001-3765201387611 ◽

2013 ◽

Vol 85 (4) ◽

pp. 1371-1377 ◽

Cited By ~ 3

Author(s):

MANOLO PENITENTE ◽

TATIANA A. VOLTOLIN ◽

JOSE A. SENHORINI ◽

JEHUD BORTOLOZZI ◽

FAUSTO FORESTI ◽

...

Keyword(s):

Transmission Rate ◽

B Chromosome ◽

B Chromosomes ◽

Rate Variation ◽

Parental Line ◽

Prochilodus Lineatus ◽

Extinction Process ◽

Cytogenetic Studies ◽

Acrocentric Chromosomes ◽

Interesting System

Cytogenetic studies were developed in Prochilodus lineatus (Valenciennes 1836), describing an interesting system of small supernumerary chromosomes. The purpose of this work is to study the frequency and morphology of B chromosomes in individuals from the parental line and the inheritance patterns of these elements in individuals obtained from controlled crosses in the species P. lineatus. The transmission rate of B chromosomes revealed a kB=0.388 for the acrocentric type, a kB=0.507 for the metacentric type and a kB=0.526 for the submetacentric type. The obtained results raise hypothesis that B-acrocentric chromosomes are involved in an extinction process in this species, while the metacentric and submetacentric supernumerary elements comprises a neutral mechanism and follows a Mendelian transmission rate.

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Recovery of a telomere-truncated chromosome via a compensating translocation in maize

Genome ◽

10.1139/g10-108 ◽

2011 ◽

Vol 54 (3) ◽

pp. 184-195 ◽

Cited By ~ 9

Author(s):

Robert T. Gaeta ◽

Tatiana V. Danilova ◽

Changzeng Zhao ◽

Rick E. Masonbrink ◽

Morgan E. McCaw ◽

...

Keyword(s):

In Situ Hybridization ◽

Fluorescent In Situ Hybridization ◽

Transgene Expression ◽

De Novo ◽

Extra Chromosome ◽

Single Gene ◽

B Chromosomes ◽

Chromosome 1 ◽

Chromosome 6

Maize-engineered minichromosomes are easily recovered from telomere-truncated B chromosomes but are rarely recovered from A chromosomes. B chromosomes lack known genes, and their truncation products are tolerated and transmitted during meiosis. In contrast, deficiency gametes resulting from truncated A chromosomes prevent their transmission. We report here a de novo compensating translocation that permitted recovery of a large truncation of chromosome 1 in maize. The truncation (trunc-1) and translocation with chromosome 6 (super-6) occurred during telomere-mediated truncation experiments and were characterized using single-gene fluorescent in situ hybridization (FISH) probes. The truncation contained a transgene signal near the end of the broken chromosome and transmitted together with the compensating translocation as a heterozygote to approximately 41%–55% of progeny. Transmission as an addition chromosome occurred in ~15% of progeny. Neither chromosome transmitted through pollen. Transgene expression (Bar) cosegregated with trunc-1 transcriptionally and phenotypically. Meiosis in T1 plants revealed eight bivalents and one tetravalent chain composed of chromosome 1, trunc-1, chromosome 6, and super-6 in diplotene and diakinesis. Our data suggest that de novo compensating translocations allow recovery of truncated A chromosomes by compensating deficiency in female gametes and by affecting chromosome pairing and segregation. The truncated chromosome can be maintained as an extra chromosome or together with the super-6 as a heterozygote.

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Identification of a family of repeated sequences on the rye B chromosome

Genome ◽

10.1139/g90-137 ◽

1990 ◽

Vol 33 (6) ◽

pp. 908-913 ◽

Cited By ~ 62

Author(s):

Michael J. Sandery ◽

John W. Forster ◽

Richard Blunden ◽

R. Neil Jones

Keyword(s):

Secale Cereale ◽

Direct Evidence ◽

B Chromosome ◽

Repeat Sequence ◽

B Chromosomes ◽

Repeated Sequences ◽

Significant Heterogeneity ◽

Origin And Evolution ◽

The Family

A novel family of highly repeated sequences on the B chromosome of rye (Secale cereale) has been identified. The D1100 family has not been detected on the rye A chromosomes and shows little or no homology to any previously described repeat sequence in rye. In addition, different rye species, and different B chromosomes within the same species, show significant heterogeneity in the arrangement of the D1100 sequences. An EcoRI clone of a member of the family has been obtained. These results provide direct evidence for the organisation and nature of the B-chromosome DNA in rye, and they are discussed in relation to the origin and evolution of rye B chromosomes.Key words: B chromosome, Secale cereale, repeated sequences.

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MOSAICISM OF AN ABNORMALLY LONG B CHROMOSOME IN A BOY WITH PHYSICAL AND MENTAL RETARDATION

PEDIATRICS ◽

10.1542/peds.39.1.68 ◽

1967 ◽

Vol 39 (1) ◽

pp. 68-74

Author(s):

Lillian Y. F. Hsu ◽

Iris Nemhauser ◽

Hilda K. Bettmann ◽

Edna H. Sobel

Keyword(s):

Mental Retardation ◽

Short Stature ◽

Cell Line ◽

Normal Cell ◽

B Chromosome ◽

B Chromosomes ◽

Normal Cell Line

An 11-year-old boy with short stature, mental retardation, low-set ears, simian creases, unusual dermatoglyphic patterns, and bilateral dysplastic mid-phalanges of the fifth fingers was found to have mosaicism in both leukocyte and fibroblast (skin) cultures. The normal cell-line predominated and the second cell-line contained an abnormally long chromosome B. The autoradiographic studies suggest that the abnormally long chromosome may involve a No. 5 which contains a translocated on inserted segment of an unknown donor autosome. The possible mechanism for the occurrence of this abnormality is discussed. Nine other instances of abnormally long B chromosomes (with lengthened long arm due to translocation) are reviewed and compared.

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