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Animals : an open access journal from MDPI2024; 14(13); 1982; doi: 10.3390/ani14131982

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

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 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.
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Publication Date: 2024-07-05 PubMed ID: 38998094PubMed Central: PMC11240701DOI: 10.3390/ani14131982Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article investigates the structure, evolution, and polyadenylation of the Ere variety of Short Interspersed Elements (SINEs)– a type of eukaryotic retrotransposon– in the genomes of ungulate species such as horses, rhinos, and tapirs. Various subfamilies of the Ere SINE were identified and studied.

Overview of the Research

  • This study delves into Short Interspersed Elements (SINEs) which are a type of eukaryotic retrotransposon transcribed by RNA polymerase III (pol III). The focus of the study was specifically on a category of SINEs known as T SINEs that are made prominent by containing a pol III terminator and an A-rich tail in their 3′-end, which allows for AAUAAA-dependent polyadenylation, a feature unique to pol III transcripts.
  • The authors explored the Ere SINE found in ungulates (hooved animals) like horses, rhinoceroses, and tapirs.

Exploration of SINEs in Perissodactyla

  • The researchers utilized bioinformatics analysis in their investigations and discovered approximately four million Ere copies within all three families of ungulates studied.
  • The Ere SINEs can be grouped into two major subfamilies named EreA and EreB. EreA is differentiated by an additional 60-bp sequence. The 3′-end of several EreA copies and all of the EreB copies show a 50-bp sequence that is labeled as a terminal domain or TD.
  • The Ere family can be further divided into four subfamilies based on the presence and count of TDs, which are EreA_0TD, EreA_1TD, EreB_1TD, and EreB_2TD.

Significance of the AATAAA Signal

  • The study revealed that only copies of the EreA_0TD subfamily can be linked to T SINEs as they contain the AATAAA signal and the TCTTT transcription terminator specific to T SINEs.
  • Moreover, the SINEs belonging to the EreA and EreB_2TD subfamilies are the ones that retained their retrotranspositional activity in recent equid and rhinoceros evolution.

Experiments and Insights

  • To understand the critical sequences for the polyadenylation of pol III transcripts in equine EreA_0TD, the research used targeted mutagenesis and HeLa cell transfection. They succeeded in recognizing two spots in the 3′ half of the EreA, referred to as the β and τ signals, critical for the polyadenylation process.
  • The researchers discussed the evolution of Ere SINEs, with particular emphasis on the emergence of T SINEs and polyadenylation signals in comparison to other T SINEs, thus providing insights into these elements’ origins and evolution.

Cite This Article

APA
Ustyantsev IG, Kosushkin SA, Borodulina OR, Vassetzky NS, Kramerov DA. (2024). Ere, a Family of Short Interspersed Elements in the Genomes of Odd-Toed Ungulates (Perissodactyla). Animals (Basel), 14(13), 1982. https://doi.org/10.3390/ani14131982

Publication

Animals : an open access journal from MDPI
ISSN: 2076-2615
NlmUniqueID: 101635614
Country: Switzerland
Language: English
Volume: 14
Issue: 13
PII: 1982

Researcher Affiliations

Ustyantsev, Ilia G
  • Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
Kosushkin, Sergey A
  • Laboratory of Eukaryotic Genome Evolution, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
Borodulina, Olga R
  • Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
Vassetzky, Nikita S
  • Laboratory of Eukaryotic Genome Evolution, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
Kramerov, Dmitri A
  • Laboratory of Eukaryotic Genome Evolution, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.

Grant Funding

  • 19-14-00327 / Russian Science Foundation
  • 075-15-2019-1660 / Ministry of Science and Higher Education of the Russian Federation

Conflict of Interest Statement

The authors declare no conflicts of interest.

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Citations

This article has been cited 1 times.
  1. Borodulina OR, Kosushkin SA, Ustyantsev IG, Vassetzky NS, Kramerov DA. Analysis of RNA Transcribed by RNA Polymerase III from B2 SINEs in Mouse Cells. Noncoding RNA 2025 May 14;11(3).
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