Browsing by Subject "retrotransposon"

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  • Kalendar, Ruslan; Raskina, Olga; Belyayev, Alexander; Schulman, Alan (2020)
    Retrotransposable elements are widely distributed and diverse in eukaryotes. Their copy number increases through reverse-transcription-mediated propagation, while they can be lost through recombinational processes, generating genomic rearrangements. We previously identified extensive, structurally uniform retrotransposon groups in which no member contains the gag, pol, or env internal domains. Because of the lack of protein-coding capacity, these groups are non-autonomous in replication, even if transcriptionally active. The Cassandra element belongs to the non-autonomous group called terminal-repeat retrotransposons in miniature (TRIM). It carries 5S RNA sequences with conserved RNA polymerase (pol) III promoters and terminators in its long terminal repeats (LTRs). Here, we identified multiple extended tandem arrays of Cassandra retrotransposons within different plant species, including ferns. At least 12 copies of repeated LTRs (as the tandem unit) and internal domain (as a spacer), giving a pattern that resembles the cellular 5S rRNA genes, were identified. Cytogenetic analysis revealed the specific chromosomal pattern of the Cassandra retrotransposon with prominent clustering at and around 5S rDNA loci. The secondary structure of the Cassandra retroelement RNA is predicted to form super-loops, in which the two LTRs are complementary to each other and can initiate local recombination, leading to the tandem arrays of Cassandra elements. The array structures are conserved for Cassandra retroelements of different species. We speculate that recombination events similar to those of 5S rRNA genes may explain the wide variation in Cassandra copy number. Likewise, the organization of 5S rRNA gene sequences is very variable in flowering plants; part of what is taken for 5S gene copy variation may be variation in Cassandra number. The role of the Cassandra 5S sequences remains to be established.
  • Sulo, Päivi (Helsingin yliopisto, 2019)
    Retrotransposons are genetic elements with the ability to make a copy of themselves and insert the copy into a new location in a genome. Most of the retrotransposons in the human genome are not transposition competent and the remaining copies are prevented from moving by epigenetics. However, some tumors experience abnormal retrotransposon activity resulting in many copies of retrotransposons inserted into new locations. Retrotransposons can be detected from sequenced genome data by bioinformatic tools. One of them is TraFiC, a tool designed to detect somatic retrotransposon insertions from tumor samples. In this Master’s thesis, I test TraFiC with 201 colorectal cancer tumors and one colorectal adenoma and develop tools to further analyze retrotransposon insertions. These tools are TraID, a pipeline to detect transductions, insertions with flanking sequence from source elements, and InSeqR, a pipeline to recreate the inserted sequence from known insertion sites. TraFiC detected 4744 somatic insertions and TraID detected 346 somatic transductions from the tumor samples. 80 % of the detected insertions were identified as true somatic insertions based on visual examination of a subset of the calls. 87 % of insertions detected by TraFiC and 82 % of the insertions detected by TraID had their insertion breakpoints and the sequence flanking them recreated by InSeqR. The detected insertions with their sequence form a reliable and comprehensive call set that can be used to create new knowledge of somatic retrotransposon insertions in colorectal cancer.
  • Ramakrishnan, Muthusamy; Satish, Lakkakula; Kalendar, Ruslan; Mathiyazhagan, Narayanan; Sabariswaran, Kandasamy; Sharma, Anket; Emamverdian, Abolghassem; Wei, Qiang; Zhou, Mingbing (2021)
    Plant development processes are regulated by epigenetic alterations that shape nuclear structure, gene expression, and phenotypic plasticity; these alterations can provide the plant with protection from environmental stresses. During plant growth and development, these processes play a significant role in regulating gene expression to remodel chromatin structure. These epigenetic alterations are mainly regulated by transposable elements (TEs) whose abundance in plant genomes results in their interaction with genomes. Thus, TEs are the main source of epigenetic changes and form a substantial part of the plant genome. Furthermore, TEs can be activated under stress conditions, and activated elements cause mutagenic effects and substantial genetic variability. This introduces novel gene functions and structural variation in the insertion sites and primarily contributes to epigenetic modifications. Altogether, these modifications indirectly or directly provide the ability to withstand environmental stresses. In recent years, many studies have shown that TE methylation plays a major role in the evolution of the plant genome through epigenetic process that regulate gene imprinting, thereby upholding genome stability. The induced genetic rearrangements and insertions of mobile genetic elements in regions of active euchromatin contribute to genome alteration, leading to genomic stress. These TE-mediated epigenetic modifications lead to phenotypic diversity, genetic variation, and environmental stress tolerance. Thus, TE methylation is essential for plant evolution and stress adaptation, and TEs hold a relevant military position in the plant genome. High-throughput techniques have greatly advanced the understanding of TE-mediated gene expression and its associations with genome methylation and suggest that controlled mobilization of TEs could be used for crop breeding. However, development application in this area has been limited, and an integrated view of TE function and subsequent processes is lacking. In this review, we explore the enormous diversity and likely functions of the TE repertoire in adaptive evolution and discuss some recent examples of how TEs impact gene expression in plant development and stress adaptation.