Mobile Genomics: Tools and Techniques for Tackling Transposons

O'Neill, K., Brocks, D., Hammell, M. G. (March 2020) Mobile Genomics: Tools and Techniques for Tackling Transposons. Philos Trans R Soc Lond B Biol Sci, 375 (1795). ISSN 0962-8436

URL: https://pubmed.ncbi.nlm.nih.gov/32075565/
DOI: 10.1098/rstb.2019.0345

Abstract

Next-generation sequencing approaches have fundamentally changed the types of questions that can be asked about gene function and regulation. With the goal of approaching truly genome-wide quantifications of all the interaction partners and downstream effects of particular genes, these quantitative assays have allowed for an unprecedented level of detail in exploring biological interactions. However, many challenges remain in our ability to accurately describe and quantify the interactions that take place in those hard to reach and extremely repetitive regions of our genome comprised mostly of transposable elements (TEs). Tools dedicated to TE-derived sequences have lagged behind, making the inclusion of these sequences in genome-wide analyses difficult. Recent improvements, both computational and experimental, allow for the better inclusion of TE sequences in genomic assays and a renewed appreciation for the importance of TE biology. This review will discuss the recent improvements that have been made in the computational analysis of TE-derived sequences as well as the areas where such analysis still proves difficult. This article is part of a discussion meeting issue 'Crossroads between transposons and gene regulation'.

Item Type: Paper
Subjects: bioinformatics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA expression > transposable elements
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transposons
Investigative techniques and equipment > assays > whole genome sequencing
CSHL Authors:
Communities: CSHL labs > Hammell M. lab
CSHL Cancer Center Program > Cancer Genetics and Genomics Program
Depositing User: Adrian Gomez
Date: 30 March 2020
Date Deposited: 06 Apr 2020 16:16
Last Modified: 05 Nov 2020 19:15
PMCID: PMC7061981
Related URLs:
URI: https://repository.cshl.edu/id/eprint/39230

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