TY  - JOUR
AU  - Rajičić, Marija
AU  - Makunin, Alexey
AU  - Adnađević, Tanja
AU  - Trifonov, Vladimir
AU  - Vujošević, Mladen
AU  - Blagojević, Jelena
PY  - 2022
UR  - https://www.mdpi.com/2075-1729/12/1/50
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/4764
AB  - B chromosomes (Bs) are highly polymorphic additional chromosomes in the genomes of many species. Due to the dispensability of Bs and the lack of noticeable phenotypic effects in their carriers, they were considered genetically inert for a long time. Recent studies on Bs in Apodemus flavicollis revealed their genetic composition, potential origin, and spatial organization in the interphase nucleus. Surprisingly, the genetic content of Bs in this species is preserved in all studied samples, even in geographically distinct populations, indicating its biological importance. Using RT-PCR we studied the transcription activity of three genes (Rraga, Haus6, and Cenpe) previously identified on Bs in A. flavicollis. We analysed mRNA isolated from spleen tissues of 34 animals harboring different numbers of Bs (0–3).The products of transcriptional activity of the analysed sequences differ in individuals with and without Bs. We recorded B-genes and/or genes from the standard genome in the presence of Bs, showing sex-dependent higher levels of transcriptional activity. Furthermore, the transcriptional activity of Cenpe varied with the age of the animals differently in the group with and without Bs. With aging, the amount of product was only found to significantly decrease in B carriers. The potential biological significance of all these differences is discussed in the paper.
PB  - Basel: MDPI
T2  - Life
T1  - B Chromosomes’ Sequences in Yellow-Necked Mice Apodemus flavicollis—Exploring the Transcription
IS  - 1
VL  - 12
DO  - 10.3390/life12010050
SP  - 50
ER  - 

@article{
author = "Rajičić, Marija and Makunin, Alexey and Adnađević, Tanja and Trifonov, Vladimir and Vujošević, Mladen and Blagojević, Jelena",
year = "2022",
abstract = "B chromosomes (Bs) are highly polymorphic additional chromosomes in the genomes of many species. Due to the dispensability of Bs and the lack of noticeable phenotypic effects in their carriers, they were considered genetically inert for a long time. Recent studies on Bs in Apodemus flavicollis revealed their genetic composition, potential origin, and spatial organization in the interphase nucleus. Surprisingly, the genetic content of Bs in this species is preserved in all studied samples, even in geographically distinct populations, indicating its biological importance. Using RT-PCR we studied the transcription activity of three genes (Rraga, Haus6, and Cenpe) previously identified on Bs in A. flavicollis. We analysed mRNA isolated from spleen tissues of 34 animals harboring different numbers of Bs (0–3).The products of transcriptional activity of the analysed sequences differ in individuals with and without Bs. We recorded B-genes and/or genes from the standard genome in the presence of Bs, showing sex-dependent higher levels of transcriptional activity. Furthermore, the transcriptional activity of Cenpe varied with the age of the animals differently in the group with and without Bs. With aging, the amount of product was only found to significantly decrease in B carriers. The potential biological significance of all these differences is discussed in the paper.",
publisher = "Basel: MDPI",
journal = "Life",
title = "B Chromosomes’ Sequences in Yellow-Necked Mice Apodemus flavicollis—Exploring the Transcription",
number = "1",
volume = "12",
doi = "10.3390/life12010050",
pages = "50"
}

Rajičić, M., Makunin, A., Adnađević, T., Trifonov, V., Vujošević, M.,& Blagojević, J.. (2022). B Chromosomes’ Sequences in Yellow-Necked Mice Apodemus flavicollis—Exploring the Transcription. in Life
Basel: MDPI., 12(1), 50.
https://doi.org/10.3390/life12010050

Rajičić M, Makunin A, Adnađević T, Trifonov V, Vujošević M, Blagojević J. B Chromosomes’ Sequences in Yellow-Necked Mice Apodemus flavicollis—Exploring the Transcription. in Life. 2022;12(1):50.
doi:10.3390/life12010050 .

Rajičić, Marija, Makunin, Alexey, Adnađević, Tanja, Trifonov, Vladimir, Vujošević, Mladen, Blagojević, Jelena, "B Chromosomes’ Sequences in Yellow-Necked Mice Apodemus flavicollis—Exploring the Transcription" in Life, 12, no. 1 (2022):50,
https://doi.org/10.3390/life12010050 . .

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 . .