Lab Publications in International Journals (from 1998)

Serdobova IM, Kramerov DA. (1998) Short Retroposons of the B2 Superfamily: Evolution and Application for the Study of Rodent Phylogeny. Journal of Molecular Evolution, 46, 202-214. [PDF]

Borodulina OR, Kramerov DA. (1999)  Wide Distribution of Short Interspersed Elements among Eukaryotic Genomes. FEBS Letters, 457: 409-413. [PDF]

Kramerov D, Vassetzky N, Serdobova I. (1999) The Evolutionary Position of Dormice (Gliridae) in Rodentia Determined by a Novel Short Retroposon. Molecular Biology and Evolution, 16: 715-717. [PDF]

Fedorov AN, Fedorova LV, Grechko VV, Ryabinin DM, Sheremet'eva VA, Bannikova AA, Lomov AA, Ryskov AP, Darevsky IS. (1999) Variable and Invariable DNA Repeat Characters Revealed by Taxonprint Approach Are Useful for Molecular Systematics.  Journal of Molecular Evolution, 48: 69-76. [PDF]

Kramerov DA, Vassetzky NS. (2001) Structure and Origin of a Novel Dimeric Retroposon B1-dID. Journal of Molecular Evolution, 52: 137-143. [PDF]

Borodulina OR, Kramerov DA. (2001) Short Interspersed Elements (SINEs) from Insectivores. Two Classes of Mammalian SINEs Distinguished by A-rich Tail Structure. Mammalian Genome, 12: 779-786. [PDF]

Gogolevskaya IK, Makarova JA, Gause LN, Kulichkova VA, Konstantinova IM, Kramerov DA. (2002). U87 RNA, a novel C/D box small nucleolar RNA from mammalian cells. Gene.  292, 199-204. [PDF]

Gogolevskaya IK, Kramerov DA. (2002) Evolutionary History of 4.5SI RNA and Indication That It Is Functional. Journal of Molecular Evolution, 54: 354-364. [PDF]

Vassetzky NS, Kramerov DA. (2002). CAN–A Pan-Carnivore SINE Family. Mammalian Genome, 13: 50-57. [PDF]

Bannikova AA, Bulatova NS, Krysanov EY, Kramerov DA. (2003) DNA Polymorphism within Sorex araneus and Two Congeneric Species as Inferred from Inter-SINE-PCR. Mammalia, 68: 263-274. 

Vassetzky NS, Ten OA, Kramerov DA. (2003) B1 and Related SINEs in Mammalian Genomes. Gene, 319: 149-160. [PDF]

Ciobanu D, Grechko VV, Darevsky IS, Kramerov DA. (2004). New Satellite DNA in Lacerta s. str. Lizards (Sauria: Lacertidae): Evolutionary Pathways and Phylogenetic Impact. Journal of Experimental Zoology. Part B. Molecular and Developmental Evolution. 302: 505-516. [PDF]

Bannikova AA, Lavrenchenko LA, Kramerov DA. (2005). Phylogenetic Relationships between Afrotropical and Palaearctic Crocidura Species Inferred from Inter-SINE-PCR. Biochemical Systematics and Ecology, 33: 45-49. [PDF]

Kramerov DA, Vassetzky NS. (2005). Short Retroposons in Eukaryotic Genomes. International Review of Cytology, 247: 165-221. [PDF]

Matveev VA, Kruskop SV, Kramerov DA. (2005). Revalidation of Myotis petax Hollister, 1912 and Its New Status in Connection with M. daubentonii (Kuhl, 1817) (Vespertilionidae, Chiroptera). Acta Chiropterologica, 7: 23-37. [PDF]

Gogolevskaya IK, Koval AP, Kramerov DA.  Evolutionary History of 4.5SH RNA. Molecular Biology and Evolution. 2005, 22: 1546-1554. [PDF]

Makarova JA, Kramerov DA. (2005). Noncoding RNA of U87 Host Gene Is Associated with Ribosomes and Is Relatively Resistant to Nonsense-Mediated Decay. Gene, 2005, 363: 51-60. [PDF]

Borodulina OR, Kramerov DA. (2005) PCR-Based Approach to SINE Isolation: Simple and Complex SINEs. Gene,  349: 197-205. [PDF]

Gogolevsky KP, Kramerov DA. (2006) Short Interspersed Elements (SINEs) of the Geomyoidea Supperfamily Rodents. Gene, 373: 67-74. [PDF]

Borodulina OR, Kramerov DA. (2006) t-SINE or Simple SINE? Can Be Both. Gene, 375: 111. [PDF]

Grechko VV, Ciobanu DG, Darevsky IS, Kosushkin SA, Kramerov DA. (2006). Molecular Evolution of Satellite DNA Repeats and Speciation of Lizards of the Genus Darevskia (Sauria: Lacertidae). Genome. 49:1297-1307. [PDF]

Bannikova AA, Lebedev VS, Kramerov DA, Zaitsev MV. (2006) Phylogeny and Systematics of the Crocidura suaveolens Species Group: Corroboration and Controversy between Nuclear and Mitochondrial DNA Markers. Mammalia. 70: 106-119. [PDF]

Veniaminova NA, Vassetzky NS, Kramerov DA. (2007). B1 SINEs in Different Rodent Families. Genomics, 2007, 89: 678-686. [PDF]

Gogolevsky K.P., Vassetzky N.S., Kramerov D.A. (2008). Bov-B-Mobilized SINEs in Vertebrate Genomes. Gene, 407: 75-85. [PDF]

Borodulina OR and Kramerov DA. (2008). Transcripts Synthesized by RNA Polymerase III Can Be Polyadenylated in AAUAAA-Dependent Manner. RNA, 14: 1865-1873. [PDF]

Gogolevsky K.P., Vassetzky N.S., Kramerov D.A. (2009). 5S rRNA-derived and tRNA-derived SINEs in Fruit Bats. Genomics, 93: 494-500. [PDF]

Koval AP, Kramerov DA. (2009). 5'-Flanking Sequences Can Dramatically Influence 4.5SH RNA Gene Transcription by RNA-Polymerase III. Gene, 446: 75-80. [PDF]

Makarova JA, Kramerov DA. (2009). Analysis of C/D box snoRNA genes in vertebrates: The number of copies decreases in placental mammals. Genomics, 94: 11-19. [PDF]

Gogolevskaya IK, Kramerov DA. (2010). 4.5SI RNA Genes and the Role of Their 5'-Flanking Sequences in the Gene Transcription. Gene, 451: 32-37. [PDF]

Gogolevskaya IK, Veniaminova NA, Kramerov DA. (2010). Nucleotide Sequences of B1 SINE and 4.5SI RNA Support a Close Relationship of Zokors to Blind Mole Rats (Spalacinae) and Bamboo Rats (Rhizomyinae). Gene, 460: 30-38. [PDF]

Kramerov DA, Vassetzky NS. (2011). Origin and evolution of SINEs in eukaryotic genomes. Heredity, 107: 487-495. [PDF]

Koval AP, Veniaminova NA, Kramerov DA. (2011). Additional box B of RNA polymerase III promoter in SINE B1 can be functional. Gene, 487: 113-117. [PDF]

Kramerov DA, Vassetzky NS. (2011). SINEs. Wiley Interdisciplinary Reviews. RNA, 2: 772-786. [PDF]

Makarova JA, Kramerov DA. (2011). SNOntology: Myriads of Novel SnoRNAs or Just a Mirage? BMC Genomics, 12: 543. [PDF]

Grechko VV, Kosushkin SA, Borodulina OR, Butaeva FG, Darevsky IS. (2011) Short interspersed elements (SINEs) of squamate reptiles (Squam1 and Squam2): structure and phylogenetic significance. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 316B: 212-226. [PDF]

Koval AP, Gogolevskaya IK, Tatosyan KA, Kramerov DA. (2012). Complementarity of end regions increases the lifetime of small RNAs in mammalian cells. PLoS One, 7(9): e44157. [PDF]

Vassetzky NS, Kramerov DA. (2013). SINEBase: a database and tool for SINE analysis. Nucleic Acids Research, 41: D83-D89. [PDF]

Makarova JA, Maltseva DV, Galatenko VV, Abbasi A, Maximenko DG, Grigoriev AI, Tonevitsky AG, Northoff H. (2014). Exercise immunology meets MiRNAs. Exercise Immunology Review, 20: 135-164. [PDF]

Koval AP, Gogolevskaya IK, Tatosyan KA, Kramerov DA. (2015) A 5′–3′ terminal stem in small non-coding RNAs extends their lifetime. Gene, 555:464-468. [PDF]

Lazareva E, Lezzhov A, Vassetzky N, Solovyev A, Morozov S. (2015) Acquisition of Full-Length Viral Helicase Domains by Insect Retrotransposon-Encoded Polypeptides. Frontiers in Microbiology, 6: 1447. [PDF]

Tatosyan KA, Kramerov DA. (2016). Heat shock increases lifetime of a small RNA and induces its accumulation in cells. Gene, 587: 33-41. [PDF]

Borodulina OR, Golubchikova JS, Ustyantsev IG, Kramerov DA. (2016). Polyadenylation of RNA transcribed from mammalian SINEs by RNA polymerase III: Complex requirements for nucleotide sequences. Biochimica et Biophysica Acta - Gene Regulatory Mechanisms, 1859: 355-365. [PDF]

Lab Publications in Russian Journals (from 1998)

Kramerov DA. (1999) The Evidence of Close Phylogenetic Relationship between Gliridae and Sciuridae Families Based on the Study of Short Retroposon B1-dID. Doklady. Biological Sciences, 364: 277-280.

Vasetskii NS, Gogolevskaya IK, Borodulina OR, Kramerov DA. (1999) B1-dID–A New Short Retroposon from Rodents. Molecular Biology, 33: 520-527.

Gogolevskaia IK, Kramerov DA. (2000) Distribution of 4.5S1 RNA among Rodents and Its Conserved Nucleotide Sequence. Molecular Biology,
34: 11-17.

Grechko VV. (2002) Using Molecular DNA Markers in Phylogeny and Systematics. Russian Journal of Genetics, 38: 1013-1033. [PDF]

Bannikova AA, Matveev VA, Kramerov DA. (2002) Using Inter-SINE-PCR to Study Mammalian Phylogeny. Russian Journal of Genetics,  38: 853-864. [PDF]

Chiobanu D, Rudykh IA, Riabinina NL, Grechko VV, Kramerov DA, Darevsky IS. (2002) Reticulate Evolution of Parthenogenetic Species of the Lacertidae Rock Lizards: Inheritance of CLsat Tandem Repeats and Anonymous RAPD Markers. Molecular Biology, 36: 296-306. [PDF]

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. Doklady. Biochemistry and Biophysics, 2003, 392: 1-5. [PDF]

Bannikova AA, Kramerov DA, Vasilenko VN, Dzuev RI, Dolgov VA. (2003). DNA Polymorphism of Erinaceus Hedgehogs and E. concolor Taxon (Insectivora, Erinaceidae). Russian Journal of Zoology, 82: 70-80.

Makarova JA, Kramerov DA. (2005) Mammalian 87 Small Nucleolar RNA and Its Host Gene. Molecular Biology, 39: 665-663. [PDF]

Ten OA, Borodulina OR, Vassetsky NS, Oparina NIu, Kramerov DA. (2006) Repetitive Sequences of the Tree Shrew Genome (Mammalia, Scandentia). Molecular Biology, 40: 74-83. [PDF]

Kosushkin SA, Borodulina OR, Grechko VV, Kramerov DA. (2006) A New Family of Interspersed Repeats from Squamate Reptiles. Molecular Biology, 40: 378-382. [PDF]

Grechko VV, Fedorova LV, Riabinin DM, Riabinina NL, Chobanu DG, Kosushkin SA, Darevskii IS. (2006) Molecular Markers of Nuclear DNA in the Study of Evolution and Speciation Process in an Example of "Lacerta agilis Complex" (Sauria: Lacertidae). Molecular Biology, 40: 61-73. [PDF]

Grechko VV, Bannikova AA, Kosushkin SA, Riabinina NL, Milto KD, Darevsky IS, Kramerov DA. (2007) Molecular-Genetic Diversification of Lizard Complex D. raddei (Sauria: Lacertidae): Early Stages of Speciation. Molecular Biology, 41: 839-851. [PDF]

Veniaminova NA, Gogolevsky KP, Vassetsky NS, Kramerov DA. (2007) Comparative Analysis of Copy Number of ID and B1 Short Retroposons in Rodent Genomes. Molecular Biology, 41: 1081-1084. [PDF]

Veniaminova NA, Vassetsky NS, Lavrechenko LA, Popov SV, Kramerov DA. (2007) Phylogeny of the Order Rodentia Inferred from Structural Analysis of Short Retrotransposon B1. Russian Journal of Genetics, 43: 916-929. [PDF]

Makarova JA, Kramerov DA. (2007a) Small nucleolar RNAs.Molecular Biology, 41: 246-259. [PDF]

Makarova JA, Kramerov DA. (2007b) Small nucleolar RNA genes. Russian Journal of Genetics, 43: 149-158. [PDF]

Makarova JA, Kramerov DA. (2007c) Noncoding RNAs. Biochemistry (Moscow), 72: 1427-1448. [PDF]

Ryabinina NL, Bannikova AA, Sheremet’eva VA, Chikobava MG, Lapin BA, Kramerov DA. (2008) Analysis of DNA of Higher Primates Using Inter-SINE PCR. Russian Journal of Genetics, 44: 315-322. [PDF]

Kramerov DA, Vasetskii NS. (2009) Short interspersed repetitive sequences as a phylogenetic tool. Molecular Biology, 43: 735-746. [PDF]

Brandler OV, Lyapunova EA, Bannikova AA, Kramerov DA. (2010) Phylogeny and systematics of marmots (Marmota, Sciuridae, Rodentia) inferred from inter-SINE PCR data. Russian Journal of Genetics, 46: 283-292. [PDF]

Makarova JA, Kramerov DA. (2010) Small nucleolar RNAs and their genes in vertebrates. Russian Journal of Genetics, 46: 1052-1054. [PDF]

Makarova JA, Ivanova SM, Tonevitsky AG, Grigoriev AI (2013) New functions of small nucleolar RNAs. Biochemistry (Moscow), 78: 638-650. [PDF]

Kosushkin SA, Grechko VV. (2013) Molecular genetic relationships and some issues of systematics of rock lizards of the genus Darevskia (Squamata: Lacertidae) based on locus analysis of SINE-type repeats (Squam1). Russian Journal of Genetics, 49: 857-869. [PDF]

Tatosyan KA, Koval AP, Gogolevskaya IK, Kramerov DA. (2017). 4.5SI and 4.5SH RNAs: Expression in Various Rodent Organs and Abundance and Distribution in the Cell. Molecular Biology, 51: 122-129. [PDF]


Deininger PL, Jolly DJ, Rubin CM, Friedmann T, Schmid CW. (1981) Base Sequence Studies of 300 Nucleotide Renatured Repeated Human DNA Clones. Journal of Molecuar Biology, 151: 17-33.

Gilbert N. and Labuda D. (2000) Evolutionary Inventions and Continuity of CORE-SINEs in Mammals. Journal of Molecular Biology, 298: 365-377.

Grechko VV, Fedorova LV, Fedorov AN, Slobodyanyuk SY, Ryabinin DM, Melnikova MH, Bannikova AA, Lomov AA, Sheremet’eva VA, Gorshkov VA, Sevostyanova GA, Semenova SK, Ryskov AP, Mednikov BM, Darevsky IS. (1997) Restriction Endonuclease Analysis of Highly Repetitive DNA as a Phylogenetic Tool. Journal of Molecular Evolution, 45: 332–336. [PDF]

Harada F, Kato N. (1980) Nucleotide Sequences of 4.5S RNAs Associated with Poly(A)-Conaining RNAs of Mouse and Hamster Cells. Nucleic Acids Research, 8: 1273-1285.

Kapitonov VV, Jurka J. (2003) A Novel Class of SINE Elements Derived from 5S rRNA. Molecular Biology and Evolution, 20: 694-702.

Kramerov DA, Grigoryan AA, Ryskov AP, Georgiev GP. (1979) Long Double-Stranded Sequences (dsRNA-B) of Nuclear pre-mRNA Consist of a Few Highly Abundant Classes of Sequences: Evidence from DNA Cloning Experiments. Nucleic Acids Research, 6: 697-713. [PDF]

Kramerov DA, Lekakh IV, Samarina OP, Ryskov AP (1982). The Sequences Homologous to Major Interspersed Repeats B1 and B2 of Mouse Genome Are Present in mRNA and Small Cytoplasmic poly(A)+ RNA. Nucleic Acids Research, 10: 7477-7491. [PDF]

Kramerov DA, Tillib SV, Ryskov AP, Georgiev GP. (1985) Nucleotide Sequence of Small Polyadenylated B2 RNA. Nucleic Acids Research, 13: 6423-6437. [PDF]

Kramerov DA, Tillib SV, Shumyatsky GP, Georgiev GP. (1990) The Most Abundant Nascent Poly(A)+ RNAs Are Transcribed by RNA Polymerase III in Murine Tumor Cells. Nucleic Acids Research, 18: 4499-4506. [PDF]

Krayev AS, Kramerov DA, Skryabin KG, Ryskov AP, Bayev AA, Georgiev GP. (1980) The Nucleotide Sequence of the Ubiquitous Repetitive DNA Sequence B1 Complementary to the Most Abundant Class of Mouse Fold-Back RNA. Nucleic Acids Research, 8: 1201-1215. [PDF]

Krayev AS, Markusheva TV, Kramerov DA, Ryskov AP, Skryabin KG, Bayev AA, Georgiev GP. (1982) Ubiquitous Transposon-Like Repeats B1 and B2 of the Mouse Genome: B2 Sequencing. Nucleic Acids Research, 10: 7461-7475. [PDF]

Nishihara H, Terai Y, Okada N. (2002) Characterization of Novel Alu- and tRNA-Related SINEs from the Tree Shrew and Evolutionary Implications of Their Origins. Molecular Biology and Evolution, 19: 1964-1972.

Nishihara H, Smit AF, Okada N. (2006) Functional Noncoding Sequences Derived from SINEs in the Mammalian Genome. Genome Research, 16: 864-874.

Ohshima K and Okada N. (2005) SINEs and LINEs: Symbionts of Eukaryotic Genomes with a Common Tail. Cytogenetic and Genome Research, 110: 475-490.

Okada N and Hamada M. (1997) The 3' Ends of tRNA-Derived SINEs Originated from the 3' Ends of LINEs: A New Example from the Bovine Genome. Journal of Molecular Evolution, 44 suppl 1: S52-S56.

Ro-Choi TS, Reddy R, Henning D, Takano T, Taylor C, Busch H. (1972) Nucleotide Sequence of 4.5S RNA I of Novikoff Hepatoma Cell Nuclei.  Journal of Biological Chemistry, 247: 3205-3222.

Rubin CM, Houck CM, Deininger PL, Friedmann T, Schmid CW. (1980) Partial Nucleotide Sequence of the 300-Nucleotide Interspersed Repeated Human DNA Sequences. Nature, 284: 372-374.

Schoeniger, L. O., and W. R. Jelinek. (1986) 4.5S RNA Is Encoded by Hundreds of Tandemly Linked Genes, Has a Short Half-Life, and Is Hydrogen Bonded in Vivo to Poly(A)-Terminated RNAs in the Cytoplasm of Cultured Mouse Cells. Molecular and Cell Biology, 6: 1508-1519.

Ullu E, Tschudi C. (1984) Alu Sequences are Processed 7SL RNA Genes. Nature, 312: 171-172.

Zietkiewicz E, Richer C, Sinnett D, Labuda D. (1998) Monophyletic Origin of Alu Elements in Primates. Journal of Molecular Evolution, 47: 172-182.


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