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Abstract
RNA is a crucial component of every living organism and is necessary for gene expression and its regulation in the cell. Mechanisms of RNA synthesis (especially mRNA synthesis) were a subject of extensive study for a long time. More recently, RNA degradation pathways began to be considered as equally important part of eukaryotic cell metabolism. These pathways have been studied intensely, and ample information accumulated about RNA degradation systems and their role in cell life. It is currently obvious that RNA decay is of no less importance as RNA synthesis and contributes to regulating the RNA level in the cell. The review considers the main RNA degradation enzymes, the decay pathways of various coding and non-coding RNAs, the mechanisms providing RNA quality control in the nucleus and cytoplasm, and certain structural elements responsible for RNA stability or short life in the cell.
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Affiliation(s)
- K A Tatosyan
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - I G Ustyantsev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - D A Kramerov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
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Ustyantsev IG, Tatosyan KA, Stasenko DV, Kochanova NY, Borodulina OR, Kramerov DA. [Polyadenylation of Sine Transcripts Generated by RNA Polymerase III Dramatically Prolongs Their Lifetime in Cells]. Mol Biol (Mosk) 2020; 54:78-86. [PMID: 32163391 DOI: 10.31857/s0026898419040165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 11/24/2022]
Abstract
Short Interspersed Elements (SINEs) are mobile genetic elements of higher eukaryotes, which originated during evolution from various tRNAs and less often from 5S rRNA and 7SL RNA. Similar to the genes of these RNAs, SINEs are transcribed by RNA polymerase III. The transcripts of some mammalian SINEs have an ability to undergo AAUAAA-dependent polyadenylation, which is unique for the RNA polymerase III transcripts. It is well known that this polyadenylation of many RNA polymerase II transcripts (e.g., mRNAs) increases their lifetime in the cell. The aim of this work is to examine whether the stability of SINE transcripts increases as a result of AAUAAA-dependent polyadenylation. HeLa cells were transfected with SINE DNA, both containing and not containing the polyadenylation signal (AATAAA). One day later, the transcription was inhibited by actinomycin D, and the decrease in the level of the SINE transcripts was monitored by northern hybridization. For all the eight studied SINEs, the half-life of nonpolyadenylated transcripts was 20-30 minutes, and for polyadenylated transcripts, this parameter exceeded 3 hours. Interestingly, the insertion of an additional 80-bp DNA fragment into the middle region of B2 SINE did not significantly reduce the stability of the polyadenylated transcripts. It is most likely that the increase in the lifetime of the polyadenylated SINE transcripts is due to the fact that the poly(A) tail interacts with the poly(A)-binding proteins (PABPs), thus protecting the RNA from degradation by the exonucleases acting from the 3'-end. The results make it possible to design SINE-based vectors intended for the expression of short noncoding RNAs, which are stable in a cell due to polyadenylation.
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Affiliation(s)
- I G Ustyantsev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - K A Tatosyan
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - D V Stasenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - N Y Kochanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - O R Borodulina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - D A Kramerov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia.,
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Ustyantsev IG, Tatosyan KA, Stasenko DV, Kochanova NY, Borodulina OR, Kramerov DA. Polyadenylation of Sine Transcripts Generated by RNA Polymerase III Dramatically Prolongs Their Lifetime in Cells. Mol Biol 2020. [DOI: 10.1134/s0026893319040150] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Tatosyan KA, Koval AP, Gogolevskaya IK, Kramerov DA. [4.5SI and 4.5SH RNAs: Expression in various rodent organs and abundance and distribution in the cell]. Mol Biol (Mosk) 2019; 51:142-149. [PMID: 28251977 DOI: 10.7868/s0026898417010177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 03/31/2016] [Indexed: 11/23/2022]
Abstract
Studying the structure, functions, and cell physiology of small RNAs remains important. The 4.5SI and 4.5SH small RNAs, which were among the first to be discovered and sequenced, share several features, i.e., they are both approximately 100 nt in size, are synthesized by RNA polymerase III, and are found only in rodents of several related families. Genes coding for these RNAs are evolutionarily related to short interspersed elements (SINEs). However, the two RNAs differ in nucleotide sequence, half-life in the cell, and the organization of their genes in the genome. Although the 4.5SI and 4.5SH RNAs have been identified more than three decades ago, several aspects of their metabolism in the cell are still poorly understood. The 4.5SI and 4.5SH RNA levels were measured in various organs of three rodent species (mouse, rat, and hamster). Both of the RNAs were found to occur at high levels, which were much the same in different organs in the case of the 4.5SI RNA and varied among organs in the case of the 4.5SH RNA. Both 4.5SI and 4.5SH RNAs demonstrated a predominantly nuclear localization with a detectable presence in the cytoplasm. The copy number per cell for the RNAs was estimated at 0.4-2.4 × 10^(6). A quantitative study for the 4.5SI and 4.5SH RNAs was performed for the first time and resolved a number of contradictions in data from other studies.
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Affiliation(s)
- K A Tatosyan
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - A P Koval
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - I K Gogolevskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - D A Kramerov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia.,
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Tatosyan KA, Koval AP, Kramerov DA. [Small Noncoding 4.5SH and 4.5SI RNAs and Their Binding to Proteins]. Mol Biol (Mosk) 2018; 52:1038-1044. [PMID: 30633246 DOI: 10.1134/s0026898418060162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 05/22/2018] [Indexed: 06/09/2023]
Abstract
The functions of small noncoding RNAs 4.5SH and 4.5SI found in murine-like rodents are unclear. These RNAs synthesized by RNA polymerase III are widely expressed in rodent organs and tissues. Using crosslinking assays, it was shown that approximately half of all 4.5SI and 4.5SH RNA molecules were bound to proteins provisionally called X and Y, respectively. An immunoprecipitation experiment showed that both these RNAs were associated with the La protein, which did not crosslink to them. The termini of 4.5SI RNA form a long duplex stem, which makes the molecule more stable than 4.5SH RNA. Modification of the 5'-end sequence destructing the stem of 4.5SI RNA altered its protein-binding properties; after the 3'-end sequence was changed to the complementary, both the stem structure and the RNA binding to protein X were restored. Presumably, this protein plays a role in increasing the half-life of 4.5SI RNA.
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Affiliation(s)
- K A Tatosyan
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - A P Koval
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - D A Kramerov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
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Ustyantsev IG, Golubchikova JS, Borodulina OR, Kramerov DA. [Canonical and noncanonical RNA polyadenylation]. Mol Biol (Mosk) 2017; 51:262-273. [PMID: 28537233 DOI: 10.7868/s0026898417010189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/03/2016] [Indexed: 11/23/2022]
Abstract
Polyadenylation is the non-template addition of adenosine nucleotides at the 3'-end of RNA, which occurs after transcription and generates a poly(A) tail up to 250-300 nucleotides long. In the first section of our review, we consider the classical process of mRNA 3'-terminus formation, which involves the cleavage of the transcript synthesized by RNA polymerase II and the associated poly(A) tail synthesis by canonical polyadenylate polymerase. Nucleotide sequences needed for mRNA cleavage and poly(A) tail synthesis, in particular the AAUAAA polyadenylation signal, as well as numerous proteins and their complexes involved in mRNA cleavage and polyadenylation, is described in detail. The significance of the poly(A) tail for prolonging mRNA lifetime and stimulating their translation is discussed. Data presented in the second section demonstrate that RNA transcribed by RNA polymerase III from certain SINEs (Short Interspersed Elements) can undergo AAUAAA-dependent polyadenylation. The structural and functional features of RNA polymerase III determine the unusual character of polyadenylation of RNAs synthesized by this enzyme. The history of recent developments in this area of study have been described in greater detail, in particular the discovery of AAUAAA-dependent polyadenylation of RNA synthesized by RNA polymerase III, which has not been discussed previously. Data on AAUAAA-independent polyadenylation catalyzed by noncanonical TRAMP poly(A)-polymerases (Trf4 and Trf5) have been presented in the third section. These enzymes promote rapid degradation of RNAs by adding a short poly(A) tail to them. This mechanism enables the recognition, poly(A)-marking, and elimination of incorrectly folded noncoding transcripts (e.g. ribosomal and transfer RNAs).
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Affiliation(s)
- I G Ustyantsev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - J S Golubchikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - O R Borodulina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - D A Kramerov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia.,
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Tatosyan KA, Koval AP, Gogolevskaya IK, Kramerov DA. 4.5SI and 4.5SH RNAs: Expression in various rodent organs and abundance and distribution in the cell. Mol Biol 2017. [DOI: 10.1134/s0026893317010174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ryabinina NL, Bannikova AA, Sheremet’eva VA, Chikobava MG, Lapin BA, Kramerov DA. Analysis of DNA of higher primates using inter-SINE PCR. RUSS J GENET+ 2011. [DOI: 10.1134/s1022795408030046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Makarova IA, Kramerov DA. [Small nucleolar RNAs and their genes in vertebrates]. Genetika 2010; 46:1185-1187. [PMID: 21061614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Genes of box C/D small nucleolar RNAs (snoRNAs) were searched for in the genomes of members of all classes of vertebrates that do not belong to placental mammals. A tendency for an increase in the number of copies of snoRNA genes was observed in such vertebrates. This trend was most pronounced in anamnia (amphibians and fish). Box C mutations were found in 14 snoRNAs in all gene copies among all species studied. The role of the described events is discussed.
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Makarova JA, Kramerov DA. Small nucleolar RNAs and their genes in vertebrates. RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410090097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Brandler OV, Lyapunova EA, Bannikova AA, Kramerov DA. Phylogeny and systematics of marmots (Marmota, Sciuridae, Rodentia) inferred from inter-SINE PCR data. RUSS J GENET+ 2010. [DOI: 10.1134/s102279541003004x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Brandler OV, Liapunova EA, Bannikova AA, Kramerov DA. [Phylogeny and systematics of marmots inferred from inter-SINE PCR data]. Genetika 2010; 46:321-331. [PMID: 20391776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Phylogenetic and taxonomic relationships in the genus Marmota were examined using inter-SINE PCR. The primers used were complementary to the consensus sequences of two short retroposons, MIR and B1-dID. The results suggest long-term genetic isolation of Nearctic and Palearctic marmots, but do not support subgeneric subdivision because of relatively low genetic differences between the marmot groups. Confirmation was received for the isolation of bobak and camtschatica, but not the caudata intrageneric species groups. Based on comparison of the mitochondrial and nuclear genome differences, the possibility of ancient hybridization between M. menzbieri and M. caudata was recognized. Species independence of M kastschenkoi within the suggested superspecies of M. baibacina was supported.
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Kramerov DA, Vasetskiĭ NS. [Short interspersed repetitive sequences (SINEs) and their use as a phylogenetic tool]. Mol Biol (Mosk) 2009; 43:795-806. [PMID: 19899627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The data on one of the most common repetitive elements of eukaryotic genomes, short interspersed elements (SINEs), are reviewed. Their structure, origin, and functioning in the genome are discussed. The variation and abundance of these neutral genomic markers makes them a convenient and reliable tool for phylogenetic analysis. The main methods of such analysis are presented, and the potential and limitations of this approach are discussed using specific examples.
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Riabinina NL, Bannikova AA, Sheremet'eva VA, Chikobava MG, Lapin BA, Kramerov DA. [Analysis of DNA of higher primates using inter-SINE PCR]. Genetika 2008; 44:315-322. [PMID: 18664134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Two types (MIR and Alu) of short interspersed repeated DNA sequences (SINEs) were used for analysis of genetic relationships among higher primates, and for detection of polymorphism in human genomic DNA. The DNA regions located between the neighboring copies of these SINEs were amplified in polymerase chain reaction with primers complementary to the MIR and Alu consensus sequences (inter-SINE PCR). Comparison of the sets of amplified DNA fragments for different species or individuals provides evaluation of the relationships among them. Using inter-MIR PCR technique, the relationships among the higher primates of the infraorder Catarrhini reported elsewhere were confirmed, pointing to the efficiency of the method for phylogenetic studies. No human DNA polymorphism was revealed with the help of inter-MIR PCR. This polymorphism was detected by means of inter-Alu PCR, which is probably associated with the continuing amplification of Alu elements in human genome.
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Veniaminova NA, Gogolevsky KP, Vassetzky NS, Kramerov DA. Comparative analysis of the copy number of ID and B1 short retroposons in rodent genomes. Mol Biol 2007. [DOI: 10.1134/s0026893307060155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Veniaminova NA, Gogolevskiĭ KP, Vasetskiĭ NS, Kramerov DA. [Comparative analysis of copy number of ID and B1 short retroposons in rodent genomes]. Mol Biol (Mosk) 2007; 41:1081-1084. [PMID: 18318126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
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Grechko VV, Bannikova AA, Kosushkin SA, Ryabinina NL, Milto KD, Darevsky IS, Kramerov DA. Molecular genetic diversification of the lizard complex Darevskia raddei (Sauria: Lacertidae): Early stages of speciation. Mol Biol 2007. [DOI: 10.1134/s0026893307050093] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Grechko VV, Bannikova AA, Kosushkin SA, Riabinina NL, Mil'to KD, Darevskiĭĭ IS, Kramerov DA. [Molecular-genetic diversification of lizard complex D. raddei (Sauria: Lacertidae): early stages of speciation]. Mol Biol (Mosk) 2007; 41:839-851. [PMID: 18240566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A number of populations of genus Darevskia lizards were studied using inter-SINE-PCR (IS-PCR). The number and size of PCR-amplified spacers of genomic DNA flanked by SINE-type repeats were compared in 17 populations of the D. raddei species complex along with several other species from the same genus. Nei and Li's (D(NL)) genetic distances between populations were unequivocal. Individual differences among D. r. nairensis sample specimens and between the samples fall into a range of less than 0.1. Individual variability intra each of the D. r. raddei samples--into a range of 0.1-0.2, but the inter samples differences in this subspecies depends on its geographic localizations. Thus the differences between 10 samples from Armenia and Karabach fall into a range of 0.2-0.3, but between all these and two samples from Talysh (Azerbajdzhan)--of 0.3-0.4. At the same time, the variability between both known subspecies (D. r. raddei and D. r. nairensis) reaches the same values. The differences between "good" species D. raddei and D. rudis were about 0.60-0.7. It may be supposed that D. r. raddei is currently undergoing the speciation process. The population of lizards from Turkey which is considered to be close to D. raddei by some researchers and to D. rudis by others is, according to our molecular data, more closely related to the latter species. The difference of homogeneity between other populations was revealed by comparison of the DNL values. Possible phylogeographic pathways of Darevskia species distribution based on the molecular data were proposed.
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Veniaminova NA, Vasetskiĭ NS, Lavrechenko LA, Popov SV, Kramerov DA. [Phylogeny of the order Rodentia inferred from structural analysis of short retrotransposon B1]. Genetika 2007; 43:916-29. [PMID: 17899810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
A large-scale study of short retroposon (SINE) B1 has been conducted in the genome of rodents from most of the known families of this mammalian order. The B1 nucleotide sequences of rodents from different families exhibited a number of characteristic features including substitutions, deletions, and tandem duplications. Comparing the distribution of these features among the rodent families, the currently discussed phylogenetic relationships were tested. The results of analysis indicated (1) an early divergence of Sciuridae and related families (Aplodontidae and Gliridae) from the other rodents; (2) a possible subsequent divergence of beavers (Castoridae); (3) a monophyletic origin of the group Hystricognathi, which includes several families, such as porcupines (Hystricidae) and guinea pigs (Caviidae); (4) a possible monophyletic origin of the group formed by the remaining families, including six families of mouselike rodents (Myodonta). Various approaches to the use of short retroposons for phylogenetic studies are discussed.
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Veniaminova NA, Vassetzky NS, Lavrenchenko LA, Popov SV, Kramerov DA. Phylogeny of the order rodentia inferred from structural analysis of short retroposon B1. RUSS J GENET+ 2007. [DOI: 10.1134/s1022795407070071] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Makarova IA, Kramerov DA. [Small nucleolar RNAs]. Mol Biol (Mosk) 2007; 41:246-59. [PMID: 17514894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Small nucleolar RNAs (snoRNAs) are an abundant class of non-protein-coding RNAs. In association with proteins they perform two most frequent nucleotide modifications in rRNAs and some other cellular RNAs: 2'-O-ribose methylation and pseudouridylation. SnoRNAs also participate in pre-rRNA cleavage and telomerase functions. Most snoRNAs fall into two families, box C/D and H/ACA, distinguished by the presence of conserved sequence boxes. Although C/D and H/ACA snoRNP proteins contain homologous regions, the assembly of these RNPs significantly differ. In addition, snoRNAs include the RNA component of RNAses P and MRP. The structure and function of small RNPs from Cajal bodies (small organelles associated with nucleoli) similar to snoRNP are also discussed.
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Makarova JA, Kramerov DA. Small nucleolar RNA genes. RUSS J GENET+ 2007. [DOI: 10.1134/s1022795407020019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Makarova IA, Kramerov DA. [Small nucleolar RNA genes]. Genetika 2007; 43:149-58. [PMID: 17385312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Small nucleolar RNAs (snoRNAs) are one of the most numerous and well-studied groups of non-protein-coding RNAs. In complex with proteins, snoRNAs perform the two most common nucleotide modifications in rRNA: 2'-O-methylation of ribose and pseudouridylation. Although the modification mechanisms and shoRNA structures are highly conserved, the snoRNA genes are surprisingly diverse in organization. In addition to genes transcribed independently, there are genes that are in introns of other genes, form clusters transcribed from a common promoter, or cluster in introns. Interestingly. one type of gene organization usually prevails in different taxa. Vertebrate snoRNAs mostly originate from introns of protein-coding genes; a small group of snoRNAs are encoded by introns of genes for noncoding RNAs.
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Chernykh VB, Chukhrova AL, Beskorovainaya TS, Grishina EM, Sorokina TM, Shileiko LV, Gogolevsky PA, Kalugina AS, Morina GV, Togobetsky AS, Tanevsky VE, Zdanovsky VM, Gogolevskaya IK, Kramerov DA, Polyakov AV, Kurilo LF. Types of Y chromosome deletions and their frequency in infertile men. RUSS J GENET+ 2006. [DOI: 10.1134/s1022795406080138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Chernykh VB, Chukhrova AL, Beskorovaĭnaia TS, Grishina EM, Sorokina TM, Shileĭko LV, Gogolevskiĭ PA, Kalugina AS, Morina GV, Togobetskiĭ AS, Tanevskiĭ VE, Zdanovskiĭ VM, Gogolevskaia IK, Kramerov DA, Poliakov AV, Kurilo LF. [Types of Y chromosome deletions and their frequency in infertile men]. Genetika 2006; 42:1130-6. [PMID: 17025164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Deletions of Y chromosome AZF locus were analyzed during a large-scale andrological and genetic examination of 810 infertile men. The search for Yq microdeletions was carried out according to the standard EAA/EMQN guidelines. The breakpoints were mapped for the deletions in AZF locus. The Y chromosome macro- and microdeletions were detected in 61 (7.5%) infertile men. The frequencies of AZF deletions during azoospermia and severe oligozoospermia amounted to 12.2 and 8.1 %, respectively. On the whole, the frequencies of Yq microdeletions and the genophenotypic correlations characteristic of various AZF deletion types comply with the relevant published data. However, spermatozoids in the ejaculate sediment of men with completely deleted AZFa region or AZFb+c deletions (from solitary spermatozoids to several dozens) were detected for the first time. It was demonstrated that the breakpoints were localized between AZFa and AZFb regions proximally to AZFb+c microdeletions for the majority of cytogenetically detectable deletions in the Y chromosome long arm. This indicates that the mechanisms underlying Yq macro- and microdeletions are somewhat different. The issues related to the role of Y chromosome deletions in the origins of monosomy for X chromosome and X/XY mosaicism are discussed.
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Bannikova AA, Bulatova NS, Kramerov DA. [Molecular variability in the commom shrew Sorex araneus L. from European Russia and Siberia inferred from the length polymorphism of DNA regions flanked by short interspersed elements (Inter-SINE PCR) and the relationships between the Moscow and Seliger chromosome races]. Genetika 2006; 42:737-47. [PMID: 16871777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Genetic exchange among chromosomal races of the common shrew Sorex araneus and the problem of reproductive barriers have been extensively studied by means of such molecular markers as mtDNA, microsatellites, and allozymes. In the present study, the interpopulation and interracial polymorphism in the common shrew was derived, using fingerprints generated by amplified DNA regions flanked by short interspersed repeats (SINEs)-interSINE PCR (IS-PCR). We used primers, complementary to consensus sequences of two short retroposons: mammalian element MIR and the SOR element from the genome of Sorex araneus. Genetic differentiation among eleven populations of the common shrew from eight chromosome races was estimated. The NP and MJ analyses, as well as multidimensional scaling showed that all samples examined grouped into two main clusters, corresponding to European Russia and Siberia. The bootstrap support of the European Russia cluster in the NJ and MP analyses was respectively 76 and 61%. The bootstrap index for the Siberian cluster was 100% in both analyses; the Tomsk race, included into this cluster, was separated with the bootstrap support of NJ/MP 92/95%.
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Bannikova AA, Bulatova NS, Kramerov DA. Molecular variability in the common shrew Sorex araneus L. from european russia and siberia inferred from the length polymorphism of DNA regions flanked by short interspersed elements (inter-SINE PCR) and the relationships between the moscow and seliger chromosome races. RUSS J GENET+ 2006. [DOI: 10.1134/s1022795406060020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Kosushkin SA, Borodulina OR, Grechko VV, Kramerov DA. [A new family of interspersed repeats from squamate reptiles]. Mol Biol (Mosk) 2006; 40:378-82. [PMID: 16637281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
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Ten OA, Borodulina OR, Vasetskiĭ NS, Oparina NI, Kramerov DA. [Repetitive sequences of the tree shrew genome (Mammalia, Scandentia)]. Mol Biol (Mosk) 2006; 40:74-83. [PMID: 16523694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Copies of two repetitive elements of the genome of common tree shrew (Tupaia glis) were cloned and sequenced. The first element, Tu III, is a approximately 260 bp long short interspersed element (SINE) with the 5'-end derived from glycine RNA. Tu III carries long polypurine- and polypyrimidine-rich tracts, which may contribute to the specific secondary structure of Tu III RNA. This SINE was also found in the genome of smooth-tailed tree shrew of another genus (Dendrogale). Tu III seems to be confined to the order Scandentia (tree shrews) since it was not found in DNA of other tested mammals. The second element Tu-SAT1 is a tandem repeat with a monomer length of 365 bp. Some properties of its nucleotide sequence suggest that Tu-SAT1 is a centromeric satellite.
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Grechko VV, Ciobanu DG, Darevsky IS, Kramerov DA. Satellite DNA of lizards of the genus Lacerta s. str. (the group L. agilis), the family Lacertidae. DOKL BIOCHEM BIOPHYS 2005; 400:44-7. [PMID: 15846982 DOI: 10.1007/s10628-005-0029-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- V V Grechko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
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Makarova IA, Kramerov DA. [Mammalian 87 small nucleolar RNA and its host gene]. Mol Biol (Mosk) 2005; 39:655-63. [PMID: 16083012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The vast majority of C/D box small nucleolar RNAs (snoRNAs) direct site-specific methylation of ribose in rRNA. New mammalian snoRNA U87 belongs to the C/D family and is involved in ribose methylation of guanylic acid residue (position 3468) in 28S rRNA. A host gene harboring the U87 snoRNA gene in its intron was described for rodents and humans. In humans it has three neighbouring transcription start sites whereas in rat there are many scattered start sites. The transcript of this gene possesses some characteristic features of an mRNA (splicing, polyadenylation and cytoplasmic localization) but lacks long open reading frames and the degree of its conservation is much less than that of other host gene mRNAs. Such low conservation is discussed in the context of functional significance of exonic sequences of the gene.
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Gogolevskaya IK, Gogolevskiy PA, Naydenova IE, Gnetetskaya VA, Konoplyannikov AG, Lebedeva EG, Krasnopolskaya KV, Kramerov DA, Kalugina AS, Kourtser MA. P▪2 Prenatal determination of the fetal ABO and RhD blood group in alloimmunized pregnant women. Reprod Biomed Online 2005. [DOI: 10.1016/s1472-6483(11)60324-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Ciobanu DG, Grechko VV, Kramerov DA, Darevsky IS. A new subfamily of the satellite DNA, CLsatIV, of the lizard Darevskia lindholmi (Sauria, Laceridae): structure and evolution. DOKL BIOCHEM BIOPHYS 2004; 392:263-7. [PMID: 15255199 DOI: 10.1023/a:1026190713714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- D G Ciobanu
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow, 119991 Russia
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Rudykh IA, Grechko VV, Chobanu DG, Kramerov DA, Darevskiĭ IS. [Satellite DNA restriction site variability as a molecular basis of taxonoprint method: evidence from the study of Caucasian rock lizards]. Genetika 2002; 38:1110-1114. [PMID: 12244695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The restriction site distribution in satellite DNA of 17 Caucasian rock lizard species of the genus Lacerta (Darevskia gen. nov.), (Squamata, Lacertidae) was analyzed. The distribution patterns were shown to reflect the degree of satellite DNA evolutionary divergence, which could be revealed by taxonprint method, i.e., through the analysis of genomic DNA with a set of restriction endonucleases and subsequent computer-aided treatment. Thus, the taxonprint method offers an opportunity to examine the satellite DNA divergence in closely related species and infer their phylogeny of the species studied without reserting to costly and labor-consuming procedures. This is the advantage of using this technique at the early stages of genomic DNA phylogenetic analysis for rapid and effective estimation of relationships between closely related species as well as in the cases when DNA cloning and sequencing are too expensive or not feasible.
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Affiliation(s)
- I A Rudykh
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia.
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Bannikova AA, Matveev VA, Kramerov DA. [Using inter-SINE-PCR to study mammalian phylogeny]. Genetika 2002; 38:853-864. [PMID: 12138785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Results of the use of the fingerprinting method related to short interspersed elements (SINEs), inter-SINE-PCR, in the study of phylogenetic and taxonomic relationship in mammals from orders Chiroptera (family Vespertilionidae) and Lipotyphla (family Erinaceidae) are reported. The inter-SINE-PCR method is based on the amplification of fragments situated between copies of SINEs, which are short retroposons spaced 100 to 1000 bp apart. Specifically selected primers were used, which are complementary to consensus sequences of two short retroposons: the mammalian interspersed repeat (MIR), which is typical of all mammals and some other vertebrates, was used in the cases of bats and Erinaceidae, and the ERI-1 element recently isolated from the genome of the Daurian hedgehog was used in the case of Erinaceidae. The results support the current view on phylogenetic relationship between hedgehogs belonging to genera Erinaceus, Hemiechinus, and Paraechinus (but not the genus Atelerix). In bats, the phylogenetic reconstruction revealed a statistically valid topology only at lower taxonomic levels, whereas the topology for the genus and supragenus ranks was unresolved and fan-shaped. The benefits and limitations of the inter-SINE-PCR method are discussed.
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Affiliation(s)
- A A Bannikova
- Department of Vertebrate Zoology, Lomonosov Moscow State University, Moscow, 119899 Russia
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Chobanu D, Rudykh IA, Riabinina NL, Grechko VV, Kramerov DA, Darevskiĭ IS. [Reticulate evolution of parthenogenetic species of the Lacertidae rock lizards: inheritance of CLsat tandem repeats and anonymous RAPD markers]. Mol Biol (Mosk) 2002; 36:296-306. [PMID: 11969091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The genetic relatedness of several bisexual and of four unisexual "Lacerta saxicola complex" lizards was studied, using monomer sequences of the complex-specific CLsat tandem repeats and anonymous RAPD markers. Genomes of parthenospecies were shown to include different satellite monomers. The structure of each such monomer is specific for a certain pair of bisexual species. This fact might be interpreted in favor of co-dominant inheritance of these markers in bisexual species hybridogenesis. This idea is supported by the results obtained with RAPD markers; i.e., unisexual species genomes include only the loci characteristic of certain bisexual species. At the same time, in neither case parthenospecies possess specific, autoapomorphic loci that were not present in this or that bisexual species.
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Affiliation(s)
- D Chobanu
- Institute of Genetics, Moldavian Academy of Sciences, Kishinev, 111120 Moldova
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Borodulina OR, Kramerov DA. Short interspersed elements (SINEs) from insectivores. Two classes of mammalian SINEs distinguished by A-rich tail structure. Mamm Genome 2001; 12:779-86. [PMID: 11668393 DOI: 10.1007/s003350020029] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2000] [Accepted: 05/31/2001] [Indexed: 10/28/2022]
Abstract
Four tRNA-related SINE families were isolated from the genome of the shrew Sorex araneus (SOR element), mole Mogera robusta (TAL element), and hedgehog Mesechinus dauuricus (ERI-1 and ERI-2 elements). Each of these SINEs families is specific for a single Insectivora family: SOR, for Soricidae (shrews); TAL, for Talpidae (moles and desmans); ERI-1 and ERI-2, for Erinaceidae (hedgehogs). There is a long polypyrimidine region (TC-motif) in TAL, ERI-1, and ERI-2 elements located immediately upstream of an A-rich tail with polyadenylation signals (AATAAA) and an RNA polymerase III terminator (T(4-6)) or TCT(3-4)). Ten out of 14 analyzed mammalian tRNA-related SINE families have an A-rich tail similar to that of TAL, ERI-1, and ERI-2 elements. These elements were assigned to class T+. The other four SINEs including SOR element have no polyadenylation signal and transcription terminator in their A-rich tail and were assigned to class T-. Class T+ SINEs occur only in mammals, and most of them have a long polypyrimidine region. Possible models of retroposition of class T+ and T- SINEs are discussed.
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Affiliation(s)
- O R Borodulina
- Laboratory of Eukaryotic Genome Evolution, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Str., Moscow, 119991 Russia
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Abstract
Here we describe a new short retroposon family of rodents. Like the primate Alu element consisting of two similar monomers, it is dimeric, but the left and right monomers are different and descend from B1 and ID short retroposons, respectively. Such elements (B1-dID) were found in the genomes of Gliridae, Sciuridae, Castoridae, Caviidae, and Hystricidae. Nucleotide sequences of this retroposon can be assigned to several structural variants. Phylogenetic analysis of B1-dID and related sequences suggests a possible scenario of B1-dID evolution in the context of rodent evolution.
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Affiliation(s)
- D A Kramerov
- Laboratory of Eukaryotic Genome Evolution, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow, 117984, Russia.
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