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Biology
Special Issues
Role of LINE-1 Retrotransposition in Human Disease and Immune Modulation
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Role of LINE-1 Retrotransposition in Human Disease and Immune Modulation

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Immunology".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 1434

Special Issue Editors

Dr. Enrico Berrino

E-Mail Website
Guest Editor
Department of Medical Sciences, Università degli studi di Torino, Torino, Italy
Interests: genetics; genomics; cancer; breast carcinoma; DNAseq; RNAseq
Dr. Sara Erika Bellomo

E-Mail Website
Guest Editor
Department of Oncology, Università degli studi di Torino, Torino, Italy
Interests: genetics; genomics; cancer; bioinfomatics; DNAseq; RNAseq

Special Issue Information

Dear Colleagues,

Retrotransposons represent a huge section of the human genome, and, in particular, the long interspersed nuclear elements-1 (LINE-1) sequences are the most prevalent. Since these elements are usually silenced through DNA methylation in adult tissues, their role is still controverted. However, LINE-1 reactivation has been reported in several human diseases, such as autoimmune syndrome, neurodegenerative pathologies, and cancer. Moreover, recent discoveries suggested feedback between immune modulation and LINE-1 expression.

This Special Issue is devoted to all aspects of LINE-1 reactivation, focusing, in particular, on the following main topics: LINE-1 sequences as biomarkers and their roles in different diseases; the cross-link between LINE-1 and therapeutics related to these diseases; the relationship between LINE-1 and genetics/genomics; and the implementation of the role of LINE-1 in the immune system. Manuscripts are welcome from both preclinical and clinical projects, and, if interesting, also on topics outside of human beings.

Dr. Enrico Berrino
Dr. Sara Erika Bellomo
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biology is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • LINE-1
  • retrotransposons
  • methylation
  • biomarker
  • immune system
  • genetics

Published Papers (1 paper)

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Research

23 pages, 826 KiB  
Article
Improved LINE-1 Detection through Pattern Matching by Increasing Probe Length
by Juan O. López, Javier L. Quiñones and Emanuel D. Martínez
Biology 2024, 13(4), 236; https://doi.org/10.3390/biology13040236 - 2 Apr 2024
Viewed by 1022
Abstract
Long Interspersed Element-1 (LINE-1 or L1) is an autonomous transposable element that accounts for 17% of the human genome. Strong correlations between abnormal L1 expression and diseases, particularly cancer, have been documented by numerous studies. L1PD (LINE-1 Pattern Detection) had been previously created [...] Read more.
Long Interspersed Element-1 (LINE-1 or L1) is an autonomous transposable element that accounts for 17% of the human genome. Strong correlations between abnormal L1 expression and diseases, particularly cancer, have been documented by numerous studies. L1PD (LINE-1 Pattern Detection) had been previously created to detect L1s by using a fixed pre-determined set of 50-mer probes and a pattern-matching algorithm. L1PD uses a novel seed-and-pattern-match strategy as opposed to the well-known seed-and-extend strategy employed by other tools. This study discusses an improved version of L1PD that shows how increasing the size of the k-mer probes from 50 to 75 or to 100 yields better results, as evidenced by experiments showing higher precision and recall when compared to the 50-mers. The probe-generation process was updated and the corresponding software is now shared so that users may generate probes for other reference genomes (with certain limitations). Additionally, L1PD was applied to other non-human genomes, such as dogs, horses, and cows, to further validate the pattern-matching strategy. The improved version of L1PD proves to be an efficient and promising approach for L1 detection. Full article
(This article belongs to the Special Issue Role of LINE-1 Retrotransposition in Human Disease and Immune Modulation)
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