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16Journal of Siberian Federal University. Biology 2018 11(1): 60-74
УДК 577.21; 577.29
Functional Insights
into Genic Neighbourhood Organization of Helitron Transposons in Bos taurus Genomes
Anna V. Babii*a, Svetlana N. Koval'chuka, Tat'iana T. Glazkoab, Valerii I. Glazkoab and Gleb I. Kosovskiia
aFederal State Budget Scientific Institution Center of Experimental Embryology and Reproductive Biotechnologies bld. 4, 12 Kostyakova Str., Moscow, 127422, Russia bRussian State Agrarian University -Moscow Timiryazev Agricultural Academy 49 Timiryazevskaya Str., Moscow, 127550, Russia
Received 05.08.2016, received in revised form 08.08.2016, accepted 27.12.2016, published online 24.01.2017 Transposable elements (TEs) represent well-known factors of genomic variability and evolution. TEs are important providers of regulatory elements that are able to significantly influence the architecture and expression of the host genome. Currently, of a special interest are the DNA transposons helitrons. They are supposed to be involved in horizontal transfer of genetic material between distant taxa and to dramatically impact the host genomes via phenomena of exon-shuffling and gene capture. Thereby, and due to their high level of polymorphism and relatively high frequency in the eukaryotic genomes, helitrons can be used as "anchors" for genome scanning of different breeds of farm animals aimed at revealing their "gene pool standards". Currently, there are no comprehensive studies dedicated to helitrons and their interaction and impact on host genomic landscape in cattle (Bos taurus). Earlier we showed the possibility of using the 3 '-end consensus sequence of Heligloria helitrons for estimation of consolidation of different cattle breeds via multilocus genotyping. In the present study, in order to investigate the context features of the DNA regions flanked by the inverted repeats of Heligloria helitrons fragments in Bos taurus genomes, we pyrosequenced such fragments (of about 550 bp in length) from three cattle breeds and analyzed the functional implications of the identified genes. Thus, here we provide an insight into the functional organization of the genic neighbourhood of helitron transposons in the genomes of different Bos taurus breeds and an attempt to understand possible consequences of such distribution of helitrons on these genomes.
Keywords: Bos taurus, helitrons, genes, genome, functions, breeds.
© Siberian Federal University. All rights reserved Corresponding author E-mail address: anna.babii@yahoo.com
*
Citation: Babii A.V., Koval'chuk S.N., Glazko T.T., Glazko V.I., Kosovskii G.I. Functional insights into genic neighbourhood organization of helitron transposons in Bos taurus genomes. J. Sib. Fed. Univ. Biol., 2018, 11(1), 60-74. DOI: 10.17516/19971389-0003.
Функциональное исследование организации генного окружения транспозонов хелитронов в геномах Bos taurus
А.В. Бабий'1, С.Н. Ковальчука, Т.Т. Глазкоаб, В.И. Глазкоаб, Г.Ю. Косовский3
аЦентр экспериментальной эмбриологии и репродуктивных биотехнологий
Россия, 127422, Москва, ул. Костякова, 12, стр. 4 бРоссийский государственный аграрный университет -
МСХА им. К.А. Тимирязева Россия, 127550, Москва, ул. Тимирязевская, 49
Мобильные элементы (МЭ) являются хорошо известными факторами геномной изменчивости и эволюции. Будучи важными источниками регуляторных элементов, МЭ способны оказывать существенное влияние на архитектуру и экспрессию генома хозяина. В настоящее время особый интерес вызывает исследование ДНК транспозонов хелитронов. Предполагается, что хелитроны вовлечены в горизонтальный перенос генетического материала между удаленными таксонами и способны значительно повлиять на геном хозяина за счет механизмов перетасовки экзонов (exon-shuffling) и «захвата» генов (gene capture). Благодаря этому и в связи с высоким уровнем полиморфизма и относительно высокой плотностью в геномах эукариот, хелитроны могут быть использованы в качестве «якорей» для геномного сканирования различных пород сельскохозяйственных животных с целью выявления их генофондного стандарта. В настоящее время не существует комплексных исследований, посвященных хелитронам и их взаимодействию и влиянию на геномный ландшафт крупного рогатого скота (Bos taurus). Ранее нами была показана возможность использования консенсусной последовательности 3-конца хелитронов семейства Heligloria для полилокусного генотипирования (геномного сканирования) с целью оценки консолидированности разных пород крупного рогатого скота. В настоящем исследовании для изучения контекстных особенностей участков ДНК, фланкированных инвертированными повторами фрагментов хелитронов Heligloria, были секвенированы подобные геномные участки (около 550 п.н.), принадлежащие трем породам крупного рогатого скота, и проанализированы функциональные особенности выявленных генов. Таким образом, в данной работе представлена функциональная организация генного окружения транспозонов хелитронов в геномах разных пород Bos taurus и обсуждается возможное влияние подобного распределения хелитронов на геномы исследованных групп животных.
Ключевые слова: Bos taurus, хелитроны, гены, геном, функции, породы.
Introduction
Transposable elements (TEs) or transposons represent well-known factors of genomic variability and evolution (Chenais et al., 2012). For a long time TEs had been recognized as major sources of non-coding or "junk" DNA with uncertain functions for the organism's genome. The current data on TEs abundance in the genomes of different taxa of prokaryotes and eukaryotes show a lack of correlation between the level of organism's evolution and the amount of transposons hosted in its genome. Despite being considered as genetic burden for the host genomes, today exhaustive research projects such as ENCODE (Encyclopedia of DNA Elements) are gathering reliable evidence towards the important role of transposons in environmental adaptation of organisms and disease. Due to their structural elements and ability to multiply, transpose and mutate, TEs become important mutators and providers of regulatory elements that are able to significantly influence the architecture and expression of the host genome (Rebollo et al., 2011).
Currently, of a special interest are the DNA transposons helitrons. Discovered in 2001 by computational analysis of whole genome sequences in plant genomes (Kapitonov, Jurka, 2001), the Helitron superfamily represents class II TEs that are hypothesized to replicate via a "rolling circle" mechanism (Kapitonov, Jurka, 2001; Kapitonov, Jurka, 2007). This mechanism involves a helitron-encoded Rep/Helicase, which is predicted to act both as HUH endonuclease and 5' to 3' helicase, and generation of a single-stranded DNA intermediate without any subsequent creation of target site duplications (Kapitonov, Jurka, 2001; Kapitonov, Jurka, 2007; Thomas, Pritham, 2015). The "rolling circle" mechanism of replication, typical for single-stranded DNA viruses or bacterial plasmids, has not been revealed in other known
DNA transposons that migrate through genomes via "cut-and-paste" transposition (Kapitonov, Jurka, 2001; Kapitonov, Jurka, 2007; Thomas, Pritham, 2015). Also, all known helitrons share in common several structural features: the 5' TC and 3' CTRR termini and a palindrome sequence (16 to 20 bp) upstream the 3'-end (Feschotte, Wessler, 2001; Kapitonov, Jurka, 2001).
First discovered in plants, helitrons have soon been shown to exist in many other eukaryotic genomes, including mammals (Thomas et al., 2010; Thomas et al., 2014). These DNA transposons are supposed to be involved in horizontal transfer of genetic material between distant taxa (Thomas et al., 2010; Guo et al., 2014; Thomas et al., 2014; Coates, 2015) and to impact the genome architecture of their host as "DNA shuttles" (Feschotte, Wessler, 2001) via their implication in processes of exon-shuffling and gene capture (Gupta et al., 2005).
Due to their relatively high frequency in the eukaryotic genomes that ranges from 1.6% in Arabidopsis thaliana (Xiong et al., 2014) to up to 5.8% in little brown bat (Myotis lucifugus) (Thomas et al., 2014) and even 6.6% in maize (Zea mays) (Xiong et al., 2014), their high level of polymorphism and their considerable implication in genomic rearrangements (Kapitonov, Jurka, 2001; Kapitonov, Jurka, 2007; Thomas, Pritham, 2015), helitrons become promising candidate markers of highly polymorphic genomic regions. One possible application of helitron fragments is their use as "anchors" for multilocus genotyping (genome scanning) aimed at revealing the "gene pool standards" of different breeds of farm animals. Currently, there are no comprehensive studies dedicated to helitrons and their interaction and impact on host genomic landscape in cattle (Bos taurus). Earlier we showed the possibility of using the 3'-end consensus sequence of Heligloria helitrons for estimation of consolidation of different
cattle breeds via multilocus genotyping (Babii et al., 2015). In the present study, in order to investigate the context features of the DNA regions flanked by the inverted repeats of Heligloria helitrons fragments in the Bos taurus genomes, we pyrosequenced such fragments (of about 550 bp in length) from three cattle breeds and analyzed the identified genes, based on the existing data on their functions. Thus, here we provide an insight into the organization of the genic neighbourhood of helitron transposons in the genomes of different Bos taurus breeds and an attempt to understand possible consequences of such distribution of helitrons on these genomes.
Materials and Methods
Sample preparation and DNA pyrosequencing
The genomic regions of about 550 bp, flanked by the inverted repeats of 3'-end consensus sequence of Heligoria family of helitrons were previously obtained via multilocus genotyping by ISSR-PCR-like (inter-simple sequence repeat polymerase chain reaction) amplification (Babii et al., 2015) of 3 cattle breeds: the local beef Kalmyk breed (30 animals) and 2 factory-grown dairy breeds - the Ayrshire breed (15 animals) and the holsteinized Black-and-White cattle (15 animals). Briefly, the PCR samples were prepared using qPCRmix-HS (5x) mix (Evrogen, Russia) and the 3'-end of the Heligloria helitrons as a primer (5'-GCAACGCGTGGCCGG-3'). The ISSR-PCR-like amplification was run under optimized conditions (95 °C for 2 min; 94 °C for 15 sec, 56 °C for 15 sec, 72 °C for 2 min, 40 cycles; 72 °C for 2 min). Subsequently, the obtained amplicons were separated in ethidium bromide stained agarose gel (1.2%) for 120 min, and their length was determined using the DNA marker (O'Gene Ruler DNA Ladder mix 100-10 000 bp, Thermo Scientific, USA).
The amplicons of about 550 bp, obtained after the multilocus genotyping of the above-mentioned animals, were further purified from the agarose gel and prepared for DNA sequencing. For that purpose we used the 454 pyrosequencing technology (GS Junior from Roche, Switzerland) and the manufacturer's protocols for sample preparation and sequencing.
Sequence analysis
Only reliable sequences, in terms of their coverage (at least 10x), length (> 400 bp) and primer sequence at flanks (at least 10 primer nucleotides), were considered for further research. The selected DNA sequences were analyzed using the NCBI BLASTn tool (https://blast. ncbi.nlm.nih.gov/Blast.cgi) (NCBI Genomes (chromosome) database, Bos_taurus_UMD_3.1.1 reference genome, default parameters; cutoff -90% identity, E-value 0.0). We used NCBI's Gene database (for Bos taurus) to map the genomic regions - like untranslated regions (UTRs), exons or introns - flanked by the inverted sequences of 3'-end consensus of Heligloria helitrons, on the corresponding position within the genes. The identified genes were then functionally annotated, based on available information on their ontologies - in PANTHER Gene List Analysis tool (http://pantherdb.org/) and known functional implications - in UniProt (http://www.uniprot. org/) and GeneCards (http://www.genecards. org/) - for Homo sapiens as search species, as the corresponding data for the studied species Bos taurus are insufficient or missing.
Results and Discussion
Sequencing results - genes identified in the studied Bos taurus breeds
In the sequenced genomic regions, flanked by the inverted sequences of 3'-end of Heligloria helitrons from 3 studied cattle breeds, we identified sequence homology to 14 cattle genes.
According to our results, such fragments are differently distributed across the analyzed groups of cattle. For instance, DOCK5 and TMEM41A genes have been shown to be flanked by 3'-end helitron fragments in all 3 breeds (Table 1). In contrast, such fragments of the following genes were found in the sequences belonging to only one breed: SLC16A6 and PHC2 - in the representatives of Kalmyk breed; UBASH3A, NRG3, ARL4C, LOC784305 and BRD9 - in cows of Ayrshire breed; MYADML2, LOC61431 and LOC107131227 - in the analyzed population of holsteinized Black-and-White cattle (Table 1). Also, the helitrons flank the LOC100848239 gene in Kalmyk and holsteinized cattle and PTPRN2 gene in the representatives of the studied dairy breeds (Table 1).
Functional implications of the identified genes
In order to investigate the possible functional implications of the 14 genes identified above, we
first looked for the available gene ontology data. The results of PANTHER search showed that, generally, the identified genes represent proteins with nucleic acid binding, enzyme modulator and transporter activities, involved in diverse metabolic and cellular processes (Fig. 1). The details on ontologies of the identified genes are represented in Table 2.
Further, we looked for the information on these 14 genes in other databases, like GeneCards and UniProt (see Materials and Methods section) with regard to their known functions (in Homo sapiens as search species, due to the lack of data for the studied species Bos taurus). The findings allowed us to group the all 14 genes under study in 4 functional groups. Thereby, 4 genes (MYADML2, DOCK5, TMEM41A, UBASH3A) are involved in the immune system functioning, 5 genes (DLGAP2, PLCXD1, NRG3, PTPRN2, ARL4C) are components of the membrane signaling system, 2 genes (SLC16A6, ABCC4) allow the membrane transport, and 3 genes
Gene symbol Breed Breed "status"
SLC16A6 PHC2 Kalmyk Aborigine breed
MYADML2 LOC61431 LOC107131227 Holsteinized Black-and-White cattle Commercial dairy breed
UBASH3A NRG3 ARL4C LOC784305 BRD9 Ayrshire Commercial dairy breed
PTPRN2 Ayrshire Holsteinized Black-and-White cattle Commercial dairy breeds
LOC100848239 Kalmyk Aborigine breed
Holsteinized Black-and-White cattle Commercial dairy breed
DOCK5 TMEM41A Kalmyk Aborigine breed
Ayrshire Holsteinized Black-and-White cattle Commercial dairy breeds
Table 1. Genes identified in the sequenced genomic regions, flanked by the inverted sequences of 3'-end of Heligloria helitrons from two commercial dairy breeds of Ayrshire and holsteinized cattle and one local beef breed of Kalmyk cattle
Fig 1. Functional investigation of genes, identified in the sequenced genomic regions flanked by the inverted sequences of 3'-end of Heligloria helitrons, and their number, according to their ontological categories and protein class from PANTHER database: (a) Biological process; (b) Molecular function; (c) Cellular component; (d) Protein category
Table 2. Ontologies and protein class data extracted from PANTHER for the 14 genes, identified in the sequenced genomic regions flanked by the inverted repeats of 3'-end consensus sequence of Heligloria helitrons in the genomes of 3 studied cattle breeds. Data presented for Homo sapiens as search species
Gene PANTHER protein class PANTHER GO-Slim Biological process PANTHER GO-Slim Molecular function PANTHER GO-Slim Cellular component
1 2 3 4 5
UBASH3A None metabolic process (G0:0008152) None None
ZRSR2 ribonucleoprotein (PC00171) mRNA splicing, via spliceosome (G0:0008152) RNA binding (G0:0005488) ribonucleoprotein complex (G0:0032991)
PHC2 transcription factor (PC00218); chromatin/ chromatin-binding protein (PC00171) transcription from RNA polymerase II promoter (G0:0008152); cell cycle (G0:0044238); ectoderm development (G0:0006139); mesoderm development (G0:0016070); regulation of transcription from RNA polymerase II promoter (G0:0006351) sequence-specific DNA binding transcription factor activity (G0:0001071); sequence-specific DNA binding transcription factor activity (G0:0003700); chromatin binding (G0:0005488) None
ABCC4 ATP-binding cassette (ABC) transporter (PC00227) immune system process (G0:0002376); metabolic process (G0:0008152); response to toxic substance (G0:0050896); extracellular transport (GO:0009636) ATPase activity, coupled to transmembrane movement of substances (G0:0003824); transmembrane transporter activity (G0:0016787) None
DOCK5 guanyl-nucleotide exchange factor (PC00095) metabolic process (G0:0008152); cellular component movement (G0:0009987); cell communication (G0:0006928); intracellular protein transport (G0:0007154); phagocytosis (G0:0051179); regulation of catalytic activity (G0:0006810) catalytic activity (G0:0003824); protein binding (G0:0005488); small GTPase regulator activity (G0:0005515); guanyl-nucleotide exchange factor activity (G0:0030234) None
1 2 3 4 5
NRG3 growth factor (PC00207); membrane-bound signaling molecule (PC00112); kinase activator (PC00152) cell communication (GO: 0009987); single-multicellular organism process (GO: 0007154); system development (G0:0032501); response to stimulus (G0:0044707); regulation of biological process (G0:0032502) protein binding (GO:0005488) extracellular region (GO:0005576)
ARL4C small GTPase (PC00095) metabolic process (GO: 0008152); cell communication (GO:0009987); intracellular protein transport (GO: 0007154); vesicle-mediated transport (GO:0051179) GTPase activity (GO:0003824); protein binding (GO:0016787) None
SLC16A6 Transporter (PC00227) cellular process (GO:0009987); anion transport (GO:0051179) transmembrane transporter activity (GO:0005215) plasma membrane (GO:0016020); integral to membrane (GO:0005886); cell part (GO:0016021)
TMEM41A None None None None
PLCXD1 None None None None
MYADML2 None None None None
DLGAP2 transmembrane receptor regulatory/ adaptor protein (PC00226) neurological system process (GO:0032501) None None
BRD9 chromatin/ chromatin-binding protein (PC00171) None nucleic acid binding (GO:0005488); chromatin binding (GO:0003676) None
PTPRN2 receptor (PC00197); protein phosphatase (PC00181); protein phosphatase (PC00195) cellular protein modification process (GO: 0008152); cell communication (GO: 0044238) phosphoprotein phosphatase activity (GO:0003824); phosphoprotein phosphatase activity (GO:0016787); receptor activity (GO:0016788) cytoplasm (GO:0044464)
(BRD9, PHC2, ZRSR2) regulate transcription (Table 3). Here we have determined differences in localization of helitron 3'-end identity sequence in the 3 studied cattle breeds. Given this fact, we can expect that identification of such differences in different breeds and inbred groups may help control the dynamics of genetic structures, as well as reveal the "gene pool standards" of breeds and inbred groups and predict the reproduction of animals with desired phenotypes.
Helitron insertions and their impact on gene expression
It is a well-known fact that insertions of TEs are able to greatly alter the gene structure and expression (Chénais et al., 2012). Such changes are available in the case of helitron transposons, as well, as there have been described many examples of how these DNA transposons can impact the gene integrity and function (Thomas, Pritham, 2015). It has been shown that helitron insertions can take place at different sites with corresponding consequences. Insertion in the promoter can disrupt the gene transcription (Gupta et al., 2005) or even provide a de novo promoter (Miller et al., 1995), while integration of helitrons upstream can enhance transcription (Inagaki et al., 2009). Integration of helitrons in the 5' UTR determines the diversification of the transcripts (Han et al., 2013), while their positioning in the 3' UTR can cause loss of function, due to disruption of polyadenylation (Tsukamoto et al., 2010). Helitrons are also able to jump into introns, thus disrupting or altering splicing (Barbaglia et al., 2012), or "capture" exons and other structural elements from different genes, creating chimeric transcripts (Lai et al., 2005; Barbaglia et al., 2012; Grabudzija et al., 2016). Besides, one possible consequence of gene capture by helitrons is the implication in host gene regulation by generation of small RNAs, which
target both the helitron and the parental gene (Li et al., 2013). Moreover, helitrons are able to promote the generation of protogene families through gene capture at RNA level (Thomas et al., 2014). In our study we were able to locate the DNA fragments, flanked by the inverted sequences of 3'-end of Heligloria helitrons in the genomes of the studied cattle breeds, on Bos taurus reference genome (Table 4). According to our results, in most of the cases the helitron-captured gene fragments are located in intronic regions. There are also gene regions, flanked by 3'-end of helitrons, that match the positions like 5' UTRs neighbouring exons or parts of exons and introns altogether (Table 4).
The dramatic changes triggered by transpositional activity of helitrons (Thomas et al., 2014), the link between the activity of transposable elements and occurrence of copy number variations (CNVs) and the fact that CNVs overlap with cattle genes involved in immune response and milk production (da Silva et al., 2016; Xu et al., 2016), particularly, are consistent with our findings on proximity of localization of the inverted repeats of helitron identity sequences (consensus sequence of 3'-end) and the corresponding functional groups of genes (Table 3). Findings are of a particular interest, given the fact that the cattle genome differs considerably from other mammalian genomes, including human, by the increased number of innate immunity gene families (Elsik et al., 2009). It is worth noting that preferable helitron localization in introns (Table 4) may indicate at the phenomenon of purifying selection, which prevents keeping of these transposons in gene coding regions. Given the fact that we have identified interbreed differences in helitron localization even in closely related breeds, like Ayrshire and holsteinized cattle, indicates at intense involvement of helitrons in complicate processes of genomic variability.
Table 3. Genes identified in the sequenced genomic regions, flanked by the inverted sequences of 3'-end of Heligloria helitrons from 3 studied cattle breeds, and grouped according to their known functional implications
Gene symbol Gene name Protein accession Function reference (in H. sapiens) Breed
Immune system functioning
MYADML2 Myeloid-Associated Differentiation MarkerLike 2 NP_001070416 (König et al., 2008; Reversade et al., 2009; Aranda et al., 2011) Holsteinized Black-and-White cattle
D0CK5 Dedicator Of Cytokinesis 5 NP_001309739 (Sanders et al., 2009; El-Sayed Moustafa et al., 2012) Kalmyk Ayrshire Holsteinized Black-and-White cattle
TMEM41A Transmembrane Protein 41A NP_001068668 (Korfali et al., 2010) Kalmyk Ayrshire Holsteinized Black-and-White cattle
UBASH3A Ubiquitin Associated And SH3 Domain Containing A NP_001015599 (Diaz-Gallo et al., 2013; Cai et al., 2014; Liu et al., 2015) Ayrshire
Membrane signaling system
L0C100848239 (DLGAP2*) Disks large-associated protein 2-like XP_015324048 (Wu et al., 2013; Li et al., 2014) Kalmyk Holsteinized Black-and-White cattle
L0C61431 (PLCXD1*) PI-PLC X domain-containing protein 1 -like NP_001096774 (Tarpey et al., 2009) Holsteinized Black-and-White cattle
NRG3 Neuregulin 3 NP_001192407 (Yang et al., 2013; Tost et al., 2014; Wang et al., 2014) Ayrshire
PTPRN2 Protein Tyrosine Phosphatase, Receptor Type, N XP_010803008 (Wu et al., 2007; Ross, 2014; Sorokin et al., 2015) Ayrshire Holsteinized Black-and-White cattle
ARL4C ADP-Ribo sylation Factor-Like 4C NP_001095818 (Jacobs et al., 1999; Fujii et al., 2015) Ayrshire
Membrane transport
SLC16A6 Solute carrier family 16, member 6 NP_001179601 (Murakami et al., 2005; Halestrap, 2013) Kalmyk
L0C784305 (ABCC4*) Multidrug resistance-associated protein 4-like XP_005213957 (Borst et al., 2000) Ayrshire
Regulation of transcription
BRD9 Bromodomain Containing 9 NP_001180021 (Filippakopoulos et al., 2012; Flynn et al., 2015; Huang et al., 2015) Ayrshire
PHC2 Polyhomeotic Homolog 2 NP_001179837 (Wei et al., 2006) Kalmyk
L0C107131227 (ZRSR2*) U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 2-like XP_015317295 (Shen et al., 2010; Hong et al., 2015) Holsteinized Black-and-White cattle
* - Gene symbols of the corresponding orthologs in H. sapiens genome
Table 4. Genomic location of the DNA fragments, flanked by the inverted sequences of 3'-end of Heligloria helitrons in the genomes of the studied cattle breeds, and the corresponding "captured" gene regions (according to Bos taurus reference genome assembly Bos_taurus_UMD_3.1.1)
Gene Chromosome Accession Helitron-flanked sequence coordinates on chromosome "Captured" gene regions
From To
MYADML2 19 AC_000176 51562400 51562868 5' UTR-exon
DOCK5 8 AC_000165 73478005 73478485 Intron
TMEM41A 1 AC_000158 82285812 82286326 5' UTR-exon
UBASH3A 1 AC_000158 144296391 144296855 Intron
LOC100848239 21 AC_000178 59998461 59998944 Intron
LOC61431 X AC_000187 143661532 143662030 Exon-intron
NRG3 28 AC_000185 37251244 37251734 Intron
PTPRN2 4 AC_000161 119785732 119786262 Intron
ARL4C 3 AC_000160 114716061 114716524 Exon
SLC16A6 19 AC_000176 62492807 62493336 Intron
LOC784305 12 AC_000169 70524501 70524981 Intron
BRD9 20 AC_000177 71517715 71518191 Intron- exon-intron
PHC2 2 AC_000159 121218094 121218535 Exon-intron
LOC107131227 X AC_000187 143060449 143060948 Intron
Conclusion
In the current work we explored the localization of DNA tranposons helitrons in the genomes of 3 cattle breeds (one aborigine breed of Kalmyks and 2 commercial dairy breeds of Ayrshire and holsteinized Black-and-White cattle), provided an analysis of the preferential sites of insertion of helitrons within cattle genes and determined the functional implications of such genes. We determined that the greatest number of genes, identified in the sequenced genomic regions flanked by the inverted repeats of Heligloria helitrons in the genomes of the studied breeds, were involved in cell signaling systems and immune system functioning. Moreover, the results revealed that helitrons tend to flank different gene regions
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