Transposable elements in human cancers by genome-wide EST alignment

Abstract

Transposable elements may affect coding sequences, splicing patterns, and transcriptional regulation of human genes. Particles of the transposable elements have been detected in several tissues and tumors. Here, we report genome-wide analysis of gene expression regulated by transposable elements in human cancers. We adopted an analysis pipeline for screening methods to detect cancerspecific expression from expressed human sequences. We developed a database (TECESdb) for understanding the mechanism of cancer development in relation to transposable elements. A total of 999 genes fused with transposable elements were found to be cancer-related in our analysis of the EST database. According to GO (Gene Ontology) analysis, the majority of the 999 cancer-specific genes have functional association with gene receptor, DNA binding, and kinase activity. Our data could contribute greatly to our understanding of human cancers in relation to transposable elements.

Cooperation and conflict in cancer: An evolutionary perspective

“…28 A causal link between MGEs and carcinogenesis has also been identified as MGE activity may cause genome damage, 12,31,32,33 dysregulation of genome replication or cell cycling, disruption of cooperative cellular behaviour and eventually neoplasia. 34,35,36,37,38 In a recent whole-genome analysis of RNA transcripts using digital gene expression analysis, an increase in satellite repeat marker expression was identified in pancreatic (human and mouse), prostate, lung, kidney and ovarian tumours. 39,40 Of the satellite regions expressed in tumours, MGEs, including LINE-1 (the most abundant MGE in the human genome) were highly enriched.…”

“…Some MGEs are truly 'selfish' elements. Their reproduction within the genome is deleterious to the rest of the host genome 34 just like any other host-parasite relationship. In the case of MGE fitness, overexpression increases reproduction and underexpression increases viability.…”

An alternative approach to medical genetics based on modern evolutionary biology. Part 4: HERVs in cancer

“…35 Other researchers have linked HERV-related sequences, such as LINE-1s, SINES and Alus to a variety of cancers, 36 including oesophageal adenocarcinoma. 37 It is too early to confirm any putative role of HERVs and products in such associations, but one study has reported a possible mechanism of HERV-induced malignancy.…”

“…HERV-H has been found in leukaemia and various cancer cell lines as well as cancers of the lung, stomach, intestine, bone marrow, bladder, prostate and cervix, 22, 23, 24, 25 HERV-K with melanoma, seminomas, the blood of leukaemia patients, teratocarcinomas and breast cancer lines, 26, 27, 28, 29, 30, 31, 32, 33, 34 and HERV-E in prostate carcinoma 35 . Other researchers have linked HERV-related sequences, such as LINE-1s, SINES and Alus to a variety of cancers, 36 including oesophageal adenocarcinoma 37 . It is too early to confirm any putative role of HERVs and products in such associations, but one study has reported a possible mechanism of HERV-induced malignancy.…”

Απομόνωση και ανάλυση γονιδίων της οικογένειας HSP90 στο είδος Mytilus galloprovincialis (Lamark 1819)

“…Ένας τρόπος που τα µεταθετά στοιχεία επηρεάζουν τη µεταγραφή των γονιδίων είναι µε την εισαγωγή τους τόσο σε εξόνια όσο και ιντρόνια και τη δηµιουργία πρόωρων θέσεων τερµατισµού, µε αποτέλεσµα να λαµβάνει χώρα εναλλακτική συρραφή εξονίων και ιντρονίων και παραγωγή εναλλακτικών, ηµιτελών, συνήθως µεταγραφηµάτων-πρωτεϊνών (Davis et al 1998, Talamas et al 2006, Kim et al 2007. Επιπρόσθετα, δευτεροταγείς δοµές RNA επηρεάζουν την εναλλακτική συρραφή εξονίων-ιντρονίων (alternative splicing), καθώς µπορεί να εµπλέκονται στην αναγνώριση των θέσεων αποκοπής-συρραφής (Shepard & Hertel 2008).…”