MDTE DB: A Database for MicroRNAs Derived from Transposable Element

Wei, Guanyun; Qin, Sheng; Li, Wenjuan; Chen, Liming; Ma, Fei

doi:10.1109/tcbb.2015.2511767

Cited by 34 publications

(60 citation statements)

References 49 publications

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“…As said, the information of transposable element was contained in the reference genome website. The use of TE databases might be biased because the database could be over-complicated due to entangled sources (Bao et al, 2015), complex mechanisms and pipelines (Wei et al, 2016), or inaccessible websites (Roberg-Perez et al, 2003; Wu and Lu, 2019).…”

Section: Methodsmentioning

confidence: 99%

Genome-wide transcriptome and translatome analyses reveal the role of protein extension and domestication in liver cancer oncogenesis

Wang

2021

Preprint

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One gene could be transcribed to different RNA isoforms, and then produce various forms of protein sequences. This mechanism largely diversifies the cellular pool and allows natural selection to select from a wider range of substrates. Most of the deleterious changes should be either purged or only be observed in patients with deficiencies or diseases. In the cancer field, the "intra-gene" changes between tumor and normal tissues such as the alternative splicing, stop codon read-through, or protein domestication could not be captured by differential expression analyses. In this work, we collected public transcriptome and translatome data from ten patients with liver cancer, and performed genome-wide comparison on the stop codon read-through and protein domestication events. Both events could diversify the proteome without changing the genome sequence. Surprisingly, we found that compared to normal tissues, the tumor tissues globally have significantly higher occurrence of stop codon read-through events. Similarly, the translation signals of non-coding repetitive elements (protein domestication) are elevated in tumor samples. These read-through and domestication events show limited overlapping across the ten patients, suggesting the randomness of the occurrence. It also indicates that these tumor-specific read-through and domestication events should be deleterious, and should be purged by natural selection if they are not collected timely. Our work manifests the role of protein extension and domestication in liver cancer oncogenesis, and adds new aspects to the cancer field.

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Section: Methodsmentioning

confidence: 99%

Genome-wide transcriptome and translatome analyses reveal the role of protein extension and domestication in liver cancer oncogenesis

Wang

2021

Preprint

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“…As said, the information of transposable element contained in the reference genome website. The use of TE databases might be biased because the database could be over-complicated due to entangled sources (Bao et al 2015), complex mechanisms and pipelines (Wei et al 2016), or inaccessible websites (Roberg-Perez et al 2003;Wu and Lu 2019).…”

Section: Data Availabilitymentioning

confidence: 99%

Genome-wide transcriptome and translatome analyses reveal the role of protein extension and domestication in liver cancer oncogenesis

Wang

2021

Mol Genet Genomics

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One gene could be transcribed to different RNA isoforms, and then produce various forms of protein sequences. This mechanism largely diversifies the cellular pool and allows natural selection to select from a wider range of substrates. In the cancer field, the isoform switches between tumor and normal tissues, such as the alternative splicing, stop codon read-through, or protein domestication, are significantly ignored by the traditional differential expression analyses. The intention of this work is to fill this gap. We collected public transcriptome and translatome data from ten patients with liver cancer, and performed genome-wide comparison on the stop codon read-through and protein domestication events. Both events diversify the proteome during long-term evolution. Surprisingly, we found that the tumor tissues globally have higher occurrence of stop codon read-through events as well as protein domestication events (translation signals of non-coding repetitive elements). These read-through and domestication events show limited overlapping across the ten patients, indicating the randomness of their occurrence and their deleterious nature. These tumor-specific events might have been purged by natural selection if they are not collected timely. Our work manifests the role of protein extension and domestication in liver cancer oncogenesis, adding new aspects to the cancer field.

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“…Многие микроРНК человека происходят от РЭ как в эволюции, так и при непо- Анализ представленных в PubMed публикаций в отношении 94 микроРНК, уровень которых повышается при различных ЗНО [74], показал, что некоторые из них обладают онкогенными свойствами. Произошедшая от LINE1 miR-644a [77] подавляет экспрессию драйверов микроокружения (c-Myc, AR, BcL-x), резистентного к кастрации рака простаты [78]. От LINE1 возникла также miR-450b, уровень которой значительно повышается при колоректальном раке [79].…”

Section: онкогенные некодирующие рнк и рэunclassified

“…От LINE2a произошли онкогенная miR-31 (сверхэкспрессируется при плоскоклеточном раке пищевода [80]) и miR-31 (онкоген для рака поджелудочной железы и колоректального рака) [81]. Для miR-335, которая усиливает выработку MT1-MMP (membrane-type1 matrix METalloproteinase) в клетках фибросаркомы и глиобластомы [82], показано происхождение от SINE (MIR) [77]. Онкогенная miR-378a также возникла от SINE [83].…”

Section: онкогенные некодирующие рнк и рэunclassified

Influence of retroelements on oncogenes and tumor suppressors in carcinogenesis: A review

Мустафин

2021

J. Mod. Onco.

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Analysis of scientific literature data has revealed several ways in which retrotransposons, when activated, are involved in carcinogenesis. First, retroelements can encode oncogenic proteins. For example, the Np9 protein is translated from HERV-K endogenous retrovirus transcript. Second, retroelements are used as alternative promoters of protooncogenes. Accordingly, their activation contributes to the enhanced expression of oncogenes (e.g. CSF1R, IRF5, MET, RAB3IP, CHRM3). Third, retroelements are located in the introns of some genes, and upon their activation, they form chimeric transcripts, such as LTR2-FABP7, LTR-ALK, LTR-ERBB4, LINE1-MET, which have pronounced oncogenic activity. Fourth, retroelements are transposed into tumor suppressor genes (e.g. APC, NF1, MSH2, PTEN, RB1, TSC2, STK11, VHL) and inactivate them, which is associated with the presence of hot spots of insertional mutagenesis in them. As a result, the growth of tumors and the survival of their cells are stimulated. It is important to note that protein products of tumor suppressor genes, such as TP53, RB1, VHL, BRCA1, ATM, are characterized by the ability to inhibit the activity of retroelements. Accordingly, when even one oncosuppressive gene is inactivated, a kind of "vicious circle" can be triggered when the control of expression of retroelements is weakened. The latter, in turn, inactivate other tumor suppressors containing hot spots of insertional mutagenesis. This stimulates new pathways of carcinogenesis and the production of oncogenes associated with transposons. Thus, it is possible to explain in a new way the mechanisms of tumor formation in hereditary tumor syndromes. This is due to the fact that the weakening of the function of an oncosuppressor in a germinal heterozygous mutation may be sufficient to trigger a vicious circle involving retroelements, oncogenes and other oncosuppressors. Similar mechanisms are likely for sporadic malignant tumors. However, the initiating event in them can be the direct activation of transposons under the influence of stressors, chemical and physical carcinogens. In addition to the events described, activation of retroelements causes genomic instability, which contributes to complex genomic rearrangements often observed in malignant tumors. MicroRNAs and long noncoding RNAs, the sources of which are retroelements, also play an important role in the evolution of tumors. Their study is promising for the development of targeted therapy for neoplasms.

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MDTE DB: A Database for MicroRNAs Derived from Transposable Element

Cited by 34 publications

References 49 publications

Genome-wide transcriptome and translatome analyses reveal the role of protein extension and domestication in liver cancer oncogenesis

Genome-wide transcriptome and translatome analyses reveal the role of protein extension and domestication in liver cancer oncogenesis

Genome-wide transcriptome and translatome analyses reveal the role of protein extension and domestication in liver cancer oncogenesis

Influence of retroelements on oncogenes and tumor suppressors in carcinogenesis: A review

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