TY  - JOUR
AU  - Karamysheva, Tatyana
AU  - Romanenko, Svetlana
AU  - Makunin, Alexey
AU  - Rajičić, Marija
AU  - Bogdanov, Alexey
AU  - Trifonov, Vladimir
AU  - Blagojević, Jelena
AU  - Vujošević, Mladen
AU  - Orishchenko, Konstantin
AU  - Rubtsov, Nikolay
PY  - 2021
UR  - http://www.ncbi.nlm.nih.gov/pubmed/34359988
UR  - http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC8305704
UR  - https://www.mdpi.com/2073-4409/10/7/1819
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/4453
AB  - The gene composition, function and evolution of B-chromosomes (Bs) have been actively discussed in recent years. However, the additional genomic elements are still enigmatic. One of Bs mysteries is their spatial organization in the interphase nucleus. It is known that heterochromatic compartments are not randomly localized in a nucleus. The purpose of this work was to study the organization and three-dimensional spatial arrangement of Bs in the interphase nucleus. Using microdissection of Bs and autosome centromeric heterochromatic regions of the yellow-necked mouse (Apodemus flavicollis) we obtained DNA probes for further two-dimensional (2D)- and three-dimensional (3D)- fluorescence in situ hybridization (FISH) studies. Simultaneous in situ hybridization of obtained here B-specific DNA probes and autosomal C-positive pericentromeric region-specific probes further corroborated the previously stated hypothesis about the pseudoautosomal origin of the additional chromosomes of this species. Analysis of the spatial organization of the Bs demonstrated the peripheral location of B-specific chromatin within the interphase nucleus and feasible contact with the nuclear envelope (similarly to pericentromeric regions of autosomes and sex chromosomes). It is assumed that such interaction is essential for the regulation of nuclear architecture. It also points out that Bs may follow the same mechanism as sex chromosomes to avoid a meiotic checkpoint.
T2  - Cells
T1  - New Data on Organization and Spatial Localization of B-Chromosomes in Cell Nuclei of the Yellow-Necked Mouse Apodemus flavicollis
IS  - 7
VL  - 10
DO  - 10.3390/cells10071819
SP  - 1819
ER  - 

@article{
author = "Karamysheva, Tatyana and Romanenko, Svetlana and Makunin, Alexey and Rajičić, Marija and Bogdanov, Alexey and Trifonov, Vladimir and Blagojević, Jelena and Vujošević, Mladen and Orishchenko, Konstantin and Rubtsov, Nikolay",
year = "2021",
abstract = "The gene composition, function and evolution of B-chromosomes (Bs) have been actively discussed in recent years. However, the additional genomic elements are still enigmatic. One of Bs mysteries is their spatial organization in the interphase nucleus. It is known that heterochromatic compartments are not randomly localized in a nucleus. The purpose of this work was to study the organization and three-dimensional spatial arrangement of Bs in the interphase nucleus. Using microdissection of Bs and autosome centromeric heterochromatic regions of the yellow-necked mouse (Apodemus flavicollis) we obtained DNA probes for further two-dimensional (2D)- and three-dimensional (3D)- fluorescence in situ hybridization (FISH) studies. Simultaneous in situ hybridization of obtained here B-specific DNA probes and autosomal C-positive pericentromeric region-specific probes further corroborated the previously stated hypothesis about the pseudoautosomal origin of the additional chromosomes of this species. Analysis of the spatial organization of the Bs demonstrated the peripheral location of B-specific chromatin within the interphase nucleus and feasible contact with the nuclear envelope (similarly to pericentromeric regions of autosomes and sex chromosomes). It is assumed that such interaction is essential for the regulation of nuclear architecture. It also points out that Bs may follow the same mechanism as sex chromosomes to avoid a meiotic checkpoint.",
journal = "Cells",
title = "New Data on Organization and Spatial Localization of B-Chromosomes in Cell Nuclei of the Yellow-Necked Mouse Apodemus flavicollis",
number = "7",
volume = "10",
doi = "10.3390/cells10071819",
pages = "1819"
}

Karamysheva, T., Romanenko, S., Makunin, A., Rajičić, M., Bogdanov, A., Trifonov, V., Blagojević, J., Vujošević, M., Orishchenko, K.,& Rubtsov, N.. (2021). New Data on Organization and Spatial Localization of B-Chromosomes in Cell Nuclei of the Yellow-Necked Mouse Apodemus flavicollis. in Cells, 10(7), 1819.
https://doi.org/10.3390/cells10071819

Karamysheva T, Romanenko S, Makunin A, Rajičić M, Bogdanov A, Trifonov V, Blagojević J, Vujošević M, Orishchenko K, Rubtsov N. New Data on Organization and Spatial Localization of B-Chromosomes in Cell Nuclei of the Yellow-Necked Mouse Apodemus flavicollis. in Cells. 2021;10(7):1819.
doi:10.3390/cells10071819 .

Karamysheva, Tatyana, Romanenko, Svetlana, Makunin, Alexey, Rajičić, Marija, Bogdanov, Alexey, Trifonov, Vladimir, Blagojević, Jelena, Vujošević, Mladen, Orishchenko, Konstantin, Rubtsov, Nikolay, "New Data on Organization and Spatial Localization of B-Chromosomes in Cell Nuclei of the Yellow-Necked Mouse Apodemus flavicollis" in Cells, 10, no. 7 (2021):1819,
https://doi.org/10.3390/cells10071819 . .

TY  - JOUR
AU  - Makunin, Alexey I.
AU  - Rajičić, Marija
AU  - Karamysheva, Tatyana V.
AU  - Romanenko, Svetlana A.
AU  - Druzhkova, Anna S.
AU  - Blagojević, Jelena
AU  - Vujošević, Mladen
AU  - Rubtsov, Nikolay B.
AU  - Graphodatsky, Alexander S.
AU  - Trifonov, Vladimir A.
PY  - 2018
UR  - http://link.springer.com/10.1007/s00412-018-0662-0
UR  - http://www.ncbi.nlm.nih.gov/pubmed/29380046
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/2969
AB  - Supernumerary chromosomes sporadically arise in many eukaryotic species as a result of genomic rearrangements. If present in a substantial part of species population, those are called B chromosomes, or Bs. This is the case for 70 mammalian species, most of which are rodents. In humans, the most common types of extra chromosomes, sSMCs (small supernumerary marker chromosomes), are diagnosed in approximately 1 of 2000 postnatal cases. Due to low frequency in population, human sSMCs are not considered B chromosomes. Genetic content of both B-chromosomes and sSMCs in most cases remains understudied. Here, we apply microdissection of single chromosomes with subsequent low-pass sequencing on Ion Torrent PGM and Illumina MiSeq to identify unique and repetitive DNA sequences present in a single human sSMC and several B chromosomes in mice Apodemus flavicollis and Apodemus peninsulae. The pipeline for sequencing data analysis was made available in Galaxy interface as an addition to previously published command-line version. Human sSMC was attributed to the proximal part of chromosome 15 long arm, and breakpoints leading to its formation were located into satellite DNA arrays. Genetic content of Apodemus B chromosomes was species-specific, and minor alterations were observed in both species. Common features of Bs in these Apodemus species were satellite DNA and ERV enrichment, as well as the presence of the vaccinia-related kinase gene Vrk1. Understanding of the non-essential genome elements content provides important insights into genome evolution in general.
T2  - Chromosoma
T1  - Low-pass single-chromosome sequencing of human small supernumerary marker chromosomes (sSMCs) and Apodemus B chromosomes.
IS  - 3
VL  - 127
DO  - 10.1007/s00412-018-0662-0
SP  - 301
EP  - 311
ER  - 

@article{
author = "Makunin, Alexey I. and Rajičić, Marija and Karamysheva, Tatyana V. and Romanenko, Svetlana A. and Druzhkova, Anna S. and Blagojević, Jelena and Vujošević, Mladen and Rubtsov, Nikolay B. and Graphodatsky, Alexander S. and Trifonov, Vladimir A.",
year = "2018",
abstract = "Supernumerary chromosomes sporadically arise in many eukaryotic species as a result of genomic rearrangements. If present in a substantial part of species population, those are called B chromosomes, or Bs. This is the case for 70 mammalian species, most of which are rodents. In humans, the most common types of extra chromosomes, sSMCs (small supernumerary marker chromosomes), are diagnosed in approximately 1 of 2000 postnatal cases. Due to low frequency in population, human sSMCs are not considered B chromosomes. Genetic content of both B-chromosomes and sSMCs in most cases remains understudied. Here, we apply microdissection of single chromosomes with subsequent low-pass sequencing on Ion Torrent PGM and Illumina MiSeq to identify unique and repetitive DNA sequences present in a single human sSMC and several B chromosomes in mice Apodemus flavicollis and Apodemus peninsulae. The pipeline for sequencing data analysis was made available in Galaxy interface as an addition to previously published command-line version. Human sSMC was attributed to the proximal part of chromosome 15 long arm, and breakpoints leading to its formation were located into satellite DNA arrays. Genetic content of Apodemus B chromosomes was species-specific, and minor alterations were observed in both species. Common features of Bs in these Apodemus species were satellite DNA and ERV enrichment, as well as the presence of the vaccinia-related kinase gene Vrk1. Understanding of the non-essential genome elements content provides important insights into genome evolution in general.",
journal = "Chromosoma",
title = "Low-pass single-chromosome sequencing of human small supernumerary marker chromosomes (sSMCs) and Apodemus B chromosomes.",
number = "3",
volume = "127",
doi = "10.1007/s00412-018-0662-0",
pages = "301-311"
}

Makunin, A. I., Rajičić, M., Karamysheva, T. V., Romanenko, S. A., Druzhkova, A. S., Blagojević, J., Vujošević, M., Rubtsov, N. B., Graphodatsky, A. S.,& Trifonov, V. A.. (2018). Low-pass single-chromosome sequencing of human small supernumerary marker chromosomes (sSMCs) and Apodemus B chromosomes.. in Chromosoma, 127(3), 301-311.
https://doi.org/10.1007/s00412-018-0662-0

Makunin AI, Rajičić M, Karamysheva TV, Romanenko SA, Druzhkova AS, Blagojević J, Vujošević M, Rubtsov NB, Graphodatsky AS, Trifonov VA. Low-pass single-chromosome sequencing of human small supernumerary marker chromosomes (sSMCs) and Apodemus B chromosomes.. in Chromosoma. 2018;127(3):301-311.
doi:10.1007/s00412-018-0662-0 .

Makunin, Alexey I., Rajičić, Marija, Karamysheva, Tatyana V., Romanenko, Svetlana A., Druzhkova, Anna S., Blagojević, Jelena, Vujošević, Mladen, Rubtsov, Nikolay B., Graphodatsky, Alexander S., Trifonov, Vladimir A., "Low-pass single-chromosome sequencing of human small supernumerary marker chromosomes (sSMCs) and Apodemus B chromosomes." in Chromosoma, 127, no. 3 (2018):301-311,
https://doi.org/10.1007/s00412-018-0662-0 . .

TY  - JOUR
AU  - Rajičić, Marija
AU  - Romanenko, Svetlana A.
AU  - Karamysheva, Tatyana V.
AU  - Blagojević, Jelena
AU  - Adnađević, Tanja
AU  - Budinski, Ivana
AU  - Bogdanov, Aleksey S.
AU  - Trifonov, Vladimir A.
AU  - Rubtsov, Nikolay B.
AU  - Vujošević, Mladen
PY  - 2017
UR  - http://dx.plos.org/10.1371/journal.pone.0172704
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/2624
AB  - B chromosomes (Bs) are known for more than hundred years but their origin, structure and pattern of evolution are not well understood. In the past few years new methodological approaches, involving isolation of Bs followed by whole DNA amplification, DNA probe generation, and fluorescent in situ hybridization (FISH) or the B chromosome DNA sequencing, has allowed detailed analysis of their origin and molecular structure in different species. In this study we explored the origin of Bs in the yellow-necked wood mouse, Apodemus flavicollis, using generation of microdissected DNA probes followed by FISH on metaphase chromosomes. Bs of A. flavicollis were successfully isolated and DNA was used as the template for B-specific probes for the first time. We revealed homology of DNA derived from the analyzed B chromosomes to the pericentromeric region (PR) of sex chromosomes and subtelomeric region of two pairs of small autosomes, but lower homology to the rest of the Y chromosome. Moreover, all analysed Bs had the same structure regardless of their number per individual or the great geographic distance between examined populations from the Balkan Peninsula (Serbia) and Eastern Europe (south region of Russia and central Belarus). Therefore, it was suggested that B chromosomes in A. flavicollis have a unique common origin from the PR of sex chromosomes, and/or similar evolutionary pattern.
T2  - PloS one
T1  - The origin of B chromosomes in yellow-necked mice (Apodemus flavicollis)—Break rules but keep playing the game
IS  - 3
VL  - 12
DO  - 10.1371/journal.pone.0172704
SP  - e0172704
EP  - e0172704
ER  - 

@article{
editor = "Houben, Andreas",
author = "Rajičić, Marija and Romanenko, Svetlana A. and Karamysheva, Tatyana V. and Blagojević, Jelena and Adnađević, Tanja and Budinski, Ivana and Bogdanov, Aleksey S. and Trifonov, Vladimir A. and Rubtsov, Nikolay B. and Vujošević, Mladen",
year = "2017",
abstract = "B chromosomes (Bs) are known for more than hundred years but their origin, structure and pattern of evolution are not well understood. In the past few years new methodological approaches, involving isolation of Bs followed by whole DNA amplification, DNA probe generation, and fluorescent in situ hybridization (FISH) or the B chromosome DNA sequencing, has allowed detailed analysis of their origin and molecular structure in different species. In this study we explored the origin of Bs in the yellow-necked wood mouse, Apodemus flavicollis, using generation of microdissected DNA probes followed by FISH on metaphase chromosomes. Bs of A. flavicollis were successfully isolated and DNA was used as the template for B-specific probes for the first time. We revealed homology of DNA derived from the analyzed B chromosomes to the pericentromeric region (PR) of sex chromosomes and subtelomeric region of two pairs of small autosomes, but lower homology to the rest of the Y chromosome. Moreover, all analysed Bs had the same structure regardless of their number per individual or the great geographic distance between examined populations from the Balkan Peninsula (Serbia) and Eastern Europe (south region of Russia and central Belarus). Therefore, it was suggested that B chromosomes in A. flavicollis have a unique common origin from the PR of sex chromosomes, and/or similar evolutionary pattern.",
journal = "PloS one",
title = "The origin of B chromosomes in yellow-necked mice (Apodemus flavicollis)—Break rules but keep playing the game",
number = "3",
volume = "12",
doi = "10.1371/journal.pone.0172704",
pages = "e0172704-e0172704"
}

Houben, A., Rajičić, M., Romanenko, S. A., Karamysheva, T. V., Blagojević, J., Adnađević, T., Budinski, I., Bogdanov, A. S., Trifonov, V. A., Rubtsov, N. B.,& Vujošević, M.. (2017). The origin of B chromosomes in yellow-necked mice (Apodemus flavicollis)—Break rules but keep playing the game. in PloS one, 12(3), e0172704-e0172704.
https://doi.org/10.1371/journal.pone.0172704

Houben A, Rajičić M, Romanenko SA, Karamysheva TV, Blagojević J, Adnađević T, Budinski I, Bogdanov AS, Trifonov VA, Rubtsov NB, Vujošević M. The origin of B chromosomes in yellow-necked mice (Apodemus flavicollis)—Break rules but keep playing the game. in PloS one. 2017;12(3):e0172704-e0172704.
doi:10.1371/journal.pone.0172704 .

Houben, Andreas, Rajičić, Marija, Romanenko, Svetlana A., Karamysheva, Tatyana V., Blagojević, Jelena, Adnađević, Tanja, Budinski, Ivana, Bogdanov, Aleksey S., Trifonov, Vladimir A., Rubtsov, Nikolay B., Vujošević, Mladen, "The origin of B chromosomes in yellow-necked mice (Apodemus flavicollis)—Break rules but keep playing the game" in PloS one, 12, no. 3 (2017):e0172704-e0172704,
https://doi.org/10.1371/journal.pone.0172704 . .