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5. Additional file 2 of New Ther1-derived SINE Squam3 in scaled reptiles

Author

Vassetzky, Nikita S., Kosushkin, Sergei A., Korchagin, Vitaly I., and Ryskov, Alexey P.

Subjects
behavioral disciplines and activities
Abstract

Additional file 2: Fig. S2. A. Alignment of Ther1/MIR subfamilies. B. Comparison of full-length consensus sequences of Squam3, tuaMIR and other CORE SINEs with tRNA- and L2-derived regions. The corresponding regions are indicated above the sequences. C. CORE domains of CORE SINEs in vertebrates. The characteristic Squam3 deletion is marked in amaranth (as in Fig. 1).

Published
2021
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7. Additional file 1 of New Ther1-derived SINE Squam3 in scaled reptiles

Author

Vassetzky, Nikita S., Kosushkin, Sergei A., Korchagin, Vitaly I., and Ryskov, Alexey P.

Abstract

Additional file 1: Fig. S1. Alignment of species-specific Squam3 sequences. Green, Squam3A; red, Squam3B; blue - Suam3C. Species designations are: Squam3EmA, Eublepharis macularius; Squam3GjA, Gekko japonicus; Squam3PpA, Paroedura picta; Squam3Vk, Varanus komodoensis; Squam3Ch, Crotalus horridus; Squam3Pt, Pseudonaja textilis; Squam3Cp, Crotalus pyrrhus; Squam3Pg, Pantherophis guttatus; Squam3Nn, Naja naja; Squam3Oh, Ophiophagus hannah; Squam3Pmc, Protobothrops mucrosquamatus; Squam3Ts, Thamnophis sirtalis; Squam3Hc, Hydrophis cyanocinctus; Squam3Te, Thamnophis elegans; Squam3Pf, Protobothrops flavoviridis; Squam3Po, Pantherophis obsoletus; Squam3Cv, Crotalus viridis; Squam3Hh, Hydrophis hardwickii; Squam3Tb, Thermophis baileyi; Squam3Vb, Vipera berus; Squam3Ej Emydocephalus ijimae; Squam3Hm, Hydrophis melanocephalus; Squam3Ll, Laticauda laticaudata; Squam3Lc, Laticauda colubrina; Squam3Ns, Notechis scutatus; Squam3Pr, Protobothrops mucrosquamatus; Squam3PbC, Python bivittatus; Squam3DvB, Darevskia valentini; Squam3LbB, Lacerta bilineata; Squam3LaB, Lacerta agilis; Squam3LvB, Lacerta viridis; Squam3PmB, Podarcis muralis; Squam3ZvB, Zootica vivipara; Squam3GjB, Gekko japonicus; Squam3PpB and Squam3PpB3, Paroedura picta; Squam3GjB3, Gekko japonicus; Squam3EmB, Eublepharis macularius; Squam3SmB, Salvator merianae.

Published
2021
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15. SINEs

Author

Kramerov, Dmitri A., primary and Vassetzky, Nikita S., additional

Published
2011
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23. Short Retroposons in Eukaryotic Genomes.

Author

Kramerov, Dimitri A. and Vassetzky, Nikita S.

Subjects
GENOMES
Abstract

An abstract of the article "Short Retroposons in Eukaryotic Genomes," by Dimitri A. Kramerov and Nikita S. Vassetzky is presented.

Published
2005
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24. Ere, a Family of Short Interspersed Elements in the Genomes of Odd-Toed Ungulates (Perissodactyla).

Author

Ustyantsev IG, Kosushkin SA, Borodulina OR, Vassetzky NS, and Kramerov DA

Abstract

Short Interspersed Elements (SINEs) are eukaryotic retrotransposons transcribed by RNA polymerase III (pol III). Many mammalian SINEs (T + SINEs) contain a polyadenylation signal (AATAAA), a pol III transcription terminator, and an A-rich tail in their 3'-end. The RNAs of such SINEs have the capacity for AAUAAA-dependent polyadenylation, which is unique to pol III-generated transcripts. The structure, evolution, and polyadenylation of the Ere SINE of ungulates (horses, rhinos, and tapirs) were investigated in this study. A bioinformatics analysis revealed the presence of up to ~4 × 10 5 Ere copies in representatives of all three families. These copies can be classified into two large subfamilies, EreA and EreB, the former distinguished by an additional 60 bp sequence. The 3'-end of numerous EreA and all EreB copies exhibit a 50 bp sequence designated as a terminal domain (TD). The Ere family can be further subdivided into subfamilies EreA_0TD, EreA_1TD, EreB_1TD, and EreB_2TD, depending on the presence and number of terminal domains (TDs). Only EreA_0TD copies can be assigned to T + SINEs as they contain the AATAAA signal and the TCTTT transcription terminator. The analysis of young Ere copies identified by comparison with related perissodactyl genomes revealed that EreA_0TD and, to a much lesser extent, EreB_2TD have retained retrotranspositional activity in the recent evolution of equids and rhinoceroses. The targeted mutagenesis and transfection of HeLa cells were used to identify sequences in equine EreA_0TD that are critical for the polyadenylation of its pol III transcripts. In addition to AATAAA and the transcription terminator, two sites in the 3' half of EreA, termed the β and τ signals, were found to be essential for this process. The evolution of Ere, with a particular focus on the emergence of T + SINEs, as well as the polyadenylation signals are discussed in comparison with other T + SINEs.

Published
2024
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