Long Interspersed Nuclear Elements 1 (LINE1): The chimeric transcript L1-MET and its involvement in cancer

2020 ◽  
Vol 241 ◽  
pp. 1-11
Author(s):  
Andrea Cervantes-Ayalc ◽  
Ruth Ruiz Esparza-Garrido ◽  
Miguel Ángel Velázquez-Flores
Keyword(s):  
Chimeric Transcript ◽  
Long Interspersed Nuclear Elements

Association of HERV-K and LINE-1 hypomethylation with reduced disease-free survival in melanoma patients

Epigenomics ◽  
2020 ◽  
Vol 12 (19) ◽  
pp. 1689-1706
Author(s):  
Maurizio Cardelli ◽  
Remco van Doorn ◽  
Lares Larcher ◽  
Michela Di Donato ◽  
Francesco Piacenza ◽  
...  
Keyword(s):  
Independent Predictor ◽  
Disease Free Survival ◽  
Endogenous Retrovirus ◽  
Human Endogenous Retrovirus ◽  
Free Survival ◽  
Melanocytic Lesions ◽  
Long Interspersed Nuclear Elements ◽  
Melanoma Patients ◽  
And Gender ◽  
Disease Free

Aim: To evaluate CpG methylation of long interspersed nuclear elements 1 (LINE-1) and human endogenous retrovirus K (HERV-K) retroelements as potential prognostic biomarkers in cutaneous melanoma. Materials & methods: Methylation of HERV-K and LINE-1 retroelements was assessed in resected melanoma tissues from 82 patients ranging in age from 14 to 88 years. In addition, nevi from eight patients were included for comparison with nonmalignant melanocytic lesions. Results: Methylation levels were lower in melanomas than in nevi. HERV-K and LINE-1 methylation were decreased in melanoma patients with clinical parameters associated with adverse prognosis, while they were independent of age and gender. Hypomethylation of HERV-K (but not LINE-1) was an independent predictor of reduced disease-free survival. Conclusion: HERV-K hypomethylation can be a potential independent biomarker of melanoma recurrence.

Breakpoint junctions of chromosome 9p deletions in two human glioma cell lines

1994 ◽  
Vol 14 (11) ◽  
pp. 7604-7610
Author(s):  
H M Pomykala ◽  
S K Bohlander ◽  
P L Broeker ◽  
O I Olopade ◽  
M O Díaz
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Lymphoblastic Leukemia ◽  
Repetitive Sequences ◽  
Leukemia Cell ◽  
Chromosome 9 ◽  
Breakpoint Junction ◽  
Leukemia Cell Lines ◽  
Long Interspersed Nuclear Elements

Interstitial deletions of the short arm of chromosome 9 are associated with glioma, acute lymphoblastic leukemia, melanoma, mesothelioma, lung cancer, and bladder cancer. The distal breakpoints of the deletions (in relation to the centromere) in 14 glioma and leukemia cell lines have been mapped within the 400 kb IFN gene cluster located at band 9p21. To obtain information about the mechanism of these deletions, we have isolated and analyzed the nucleotide sequences at the breakpoint junctions in two glioma-derived cell lines. The A1235 cell line has a complex rearrangement of chromosome 9, including a deletion and an inversion that results in two breakpoint junctions. Both breakpoints of the distal inversion junction occurred within AT-rich regions. In the A172 cell line, a tandem heptamer repeat was found on either side of the deletion breakpoint junction. The distal breakpoint occurred 5' of IFNA2; the 256 bp sequenced from the proximal side of the breakpoint revealed 95% homology to long interspersed nuclear elements. One- and two-base-pair overlaps were observed at these junctions. The possible role of sequence overlaps, and repetitive sequences, in the rearrangement is discussed.

scholarly journals Isolation and Characterization of a 1.7-kb Transposable Element from a Mutator Line of Maize

Genetics ◽  
1987 ◽  
Vol 117 (2) ◽  
pp. 297-307
Author(s):  
Loverine P Taylor ◽  
Virginia Walbot
Keyword(s):  
Direct Repeat ◽  
Repeat Sequence ◽  
Gene Probe ◽  
Gene Transcript ◽  
Chimeric Transcript ◽  
Purple Pigment ◽  
Isolation And Characterization ◽  
Internal Sequence ◽  
Normal Gene

ABSTRACT We have cloned and sequenced a 1.7-kb Mu element from a Mutator line of maize and compared its structure to Mu1, a 1.4-kb element. With the exception of a 385-bp block of DNA present in the 1.7-kb element, these transposable elements are structurally similar, sharing terminally inverted and internal direct repeated sequences. Derivation of 1.4-kb elements from the 1.7-kb class via deletion of internal sequence is suggested by the finding that a portion of the extra DNA in Mu1.7 is part of a truncated direct repeat sequence in the 1.4-kb element. An abundant poly(A)+ RNA homologous to a portion of this extra DNA is present in several tissues of both Mutator and non-Mutator lines. Analysis of transcripts from an unstable mutant bronze1 (bz) allele containing a Mu1.7 element inserted in an exon of the gene detects three species of poly(A)+ RNA that hybridize to a Bz1 (Bronze) gene probe: the largest contains the entire Mu1.7 element in the Bz1 gene transcript; another appears to be a spliced, chimeric transcript; the smallest is normal size Bz1 mRNA. The latter is most likely encoded by the normal-size alleles detected by Southern analysis of tissue expressing purple pigment, suggesting that normal gene function is restored by excision of the Mu1.7 element.

scholarly journals The Conserved Chimeric Transcript UPGRADE2 Is Associated with Unreduced Pollen Formation and Is Exclusively Found in Apomictic Boechera Species

2013 ◽  
Vol 163 (4) ◽  
pp. 1640-1659 ◽  
Author(s):  
M. Mau ◽  
J. M. Corral ◽  
H. Vogel ◽  
M. Melzer ◽  
J. Fuchs ◽  
...  
Keyword(s):  
Chimeric Transcript ◽  
Unreduced Pollen ◽  
Pollen Formation

scholarly journals Transcriptome profiling identifies a recurrent CRYL1-IFT88 chimeric transcript in hepatocellular carcinoma

Oncotarget ◽  
2017 ◽  
Vol 8 (25) ◽  
pp. 40693-40704 ◽  
Author(s):  
Yi Huang ◽  
Jiaying Zheng ◽  
Dunyan Chen ◽  
Feng Li ◽  
Wenbing Wu ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Transcriptome Profiling ◽  
Chimeric Transcript

scholarly journals Analysis of Wheat Bread-Making Gene (wbm) Evolution and Occurrence in Triticale Collection Reveal Origin via Interspecific Introgression into Chromosome 7AL

Agronomy ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 854 ◽  
Author(s):  
Ilya Kirov ◽  
Andrey Pirsikov ◽  
Natalia Milyukova ◽  
Maxim Dudnikov ◽  
Maxim Kolenkov ◽  
...  
Keyword(s):  
Orthologous Gene ◽  
Wheat Breeding ◽  
Wheat Bread ◽  
Bread Making ◽  
Pcr Screening ◽  
Interspecific Introgression ◽  
Unknown Species ◽  
Long Interspersed Nuclear Elements ◽  
Modern Genomic ◽  
Gene Information

Bread-making quality is a crucial trait for wheat and triticale breeding. Several genes significantly influence these characteristics, including glutenin genes and the wheat bread-making (wbm) gene. World wheat collection screening showed that only a few percent of cultivars carry the valuable wbm variant, providing a useful source for wheat breeding. In contrast, no such analysis has been performed for triticale (wheat (AABB genome) × rye (RR) amphidiploid) collections. Despite the importance of the wbm gene, information about its origin and genomic organization is lacking. Here, using modern genomic resources available for wheat and its relatives, as well as PCR screening, we aimed to examine the evolution of the wbm gene and its appearance in the triticale genotype collection. Bioinformatics analysis revealed that the wheat Chinese Spring genome does not have the wbm gene but instead possesses the orthologous gene, called wbm-like located on chromosome 7A. The analysis of upstream and downstream regions revealed the insertion of LINE1 (Long Interspersed Nuclear Elements) retrotransposons and Mutator DNA transposon in close vicinity to wbm-like. Comparative analysis of the wbm-like region in wheat genotypes and closely related species showed low similarity between the wbm locus and other sequences, suggesting that wbm originated via introgression from unknown species. PCR markers were developed to distinguish wbm and wbm-like sequences, and triticale collection was screened resulting in the detection of three genotypes carrying wbm-specific introgression, providing a useful source for triticale breeding programs.

scholarly journals Long INterspersed nuclear Elements (LINEs) in brain and non-brain tissues of the rat

2018 ◽  
Vol 374 (1) ◽  
pp. 17-24 ◽  
Author(s):  
Gianfranco Giorgi ◽  
Marco Virgili ◽  
Barbara Monti ◽  
Brunella Del Re
Keyword(s):  
Long Interspersed Nuclear Elements ◽  
Brain Tissues

scholarly journals Evolution and diversity of transposable elements in fish genomes

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Feng Shao ◽  
Minjin Han ◽  
Zuogang Peng
Keyword(s):  
Species Diversity ◽  
Transposable Elements ◽  
Long Terminal Repeat ◽  
Genome Size ◽  
Fish Species ◽  
Significant Variation ◽  
Genomic Sequences ◽  
Fish Genome ◽  
Long Interspersed Nuclear Elements ◽  
Fish Species Diversity

Abstract Transposable elements (TEs) are genomic sequences that can move, multiply, and often form sizable fractions of vertebrate genomes. Fish belong to a unique group of vertebrates, since their karyotypes and genome sizes are more diverse and complex, with probably higher diversity and evolution specificity of TE. To investigate the characteristics of fish TEs, we compared the mobilomes of 39 species, and observed significant variation of TE content in fish (from 5% in pufferfish to 56% in zebrafish), along with a positive correlation between fish genome size and TE content. In different classification hierarchies, retrotransposons (class), long terminal repeat (order), as well as Helitron, Maverick, Kolobok, CMC, DIRS, P, I, L1, L2, and 5S (superfamily) were all positively correlated with fish genome size. Consistent with previous studies, our data suggested fish genomes to not always be dominated by DNA transposons; long interspersed nuclear elements are also prominent in many species. This study suggests CR1 distribution in fish genomes to be obviously regular, and provides new clues concerning important events in vertebrate evolution. Altogether, our results highlight the importance of TEs in the structure and evolution of fish genomes and suggest fish species diversity to parallel transposon content diversification.

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