Advances in transposable elements: from mechanisms to applications in mammalian genomics

Abstract

It has been 70 years since Barbara McClintock discovered transposable elements (TE), and the mechanistic studies and functional applications of transposable elements have been at the forefront of life science research. As an essential part of the genome, TEs have been discovered in most species of prokaryotes and eukaryotes, and the relative proportion of the total genetic sequence they comprise gradually increases with the expansion of the genome. In humans, TEs account for about 40% of the genome and are deeply involved in gene regulation, chromosome structure maintenance, inflammatory response, and the etiology of genetic and non-genetic diseases. In-depth functional studies of TEs in mammalian cells and the human body have led to a greater understanding of these fundamental biological processes. At the same time, as a potent mutagen and efficient genome editing tool, TEs have been transformed into biological tools critical for developing new techniques. By controlling the random insertion of TEs into the genome to change the phenotype in cells and model organisms, critical proteins of many diseases have been systematically identified. Exploiting the TE's highly efficient in vitro insertion activity has driven the development of cutting-edge sequencing technologies. Recently, a new technology combining CRISPR with TEs was reported, which provides a novel targeted insertion system to both academia and industry. We suggest that interrogating biological processes that generally depend on the actions of TEs with TEs-derived genetic tools is a very efficient strategy. For example, excessive activation of TEs is an essential factor in the occurrence of cancer in humans. As potent mutagens, TEs have also been used to unravel the key regulatory elements and mechanisms of carcinogenesis. Through this review, we aim to effectively combine the traditional views of TEs with recent research progress, systematically link the mechanistic discoveries of TEs with the technological developments of TE-based tools, and provide a comprehensive approach and understanding for researchers in different fields.

Keywords: RNA-guided transposition; aging; forward genetic screening; high throughput sequencing; immune response; transposable elements; tumor genetics.

FIGURE 1

Summary of replication mechanisms of Class I and Class II TE subtypes. (A) Simplified representations of major steps in the transposition cycles of LTR and ERV; (B) Simplified representations of major steps in the transposition cycles of Non-LTR (LINE); (C) Simplified representations of major steps in the transposition cycles of Non-LTR (SINE); (D) Simplified representations of major steps in the transposition cycles of DNA transposon (“cut-and-paste” model); (E) Simplified representations of major steps in the transposition cycles of DNA transposon (“Rolling circle” model). Abbreviations: LTR, long terminal repeats; ERV, Endogenous retroviruses; LINE, long interspersed nuclear elements; SINE, short interspersed nuclear elements; IN, integrase; PR, protease; RT, reverse transcriptase; Pol, polyprotein; UTR, untranslated regions; TIR, terminal inverted repeat.

FIGURE 2

Distribution of somatic retrotransposon insertions (data reanalyzed from ref36). (A) Distribution of somatic retrotransposon insertions of different classes across tumor types; (B) Distribution of somatic retrotransposon insertions of different tumorigenesis germ layers; (C) Distribution of somatic retrotransposon insertions of different tumorigenesis organ types. Retrotranspositions are counted by summing somatic retrotransposon insertions, transductions, and somatic pseudogene insertions.

FIGURE 3

PGBD5 induced chromosome rearrangements and childhood tumor formation. PGBD5 could recognize genomic PSS sequences and induce cell transformation through PAXX-meditated end-joining DNA repair.

FIGURE 4

The cytosolic DNA and RNA mediated cGAS-STING pathway in innate immunity under conditions of infection and TE accumulation. (A) The mechanisms of free DNA and RNA sensing exist in mammalian cells and induce inflammation through the cGAS-STING pathway. (B) TEs DNA sequences and RNA intermediates could accumulate in the cytoplasm under conditions in Aicardi–Goutières syndrome, and induce cGAS-STING pathway and inflammation. Abbreviations: dsDNA, double-stranded DNA; dsRNA, double-stranded RNA; ssDNA, single-stranded DNA; ssRNA, single-stranded RNA; cGAS, Cyclic GMP-AMP synthase; STING, Stimulator Of Interferon Response CGAMP Interactor.

FIGURE 5

Transposon tools for cancer genomic screening in mice. Transposon and transposase-based mouse lines for cancer genomic screening; SB-based transposon mouse lines include T2/Onc, T2/Onc2, and T2/Onc3 (a1, a2); SB and PB-based transposon mouse lines include ATP1, ATP2, ATP3, ITP1, and IT2 (b1-b5); PB based transposon mouse lines PB-SMARTs (c1 and c2).

FIGURE 6

Transposon tools for phenotype-driven screening in mice. (A) Breeding scheme of phenotype-driven screening; (B) Transposon design and mutagenesis ability for phenotype drive screening; (C) Transposon design for brain region randomly labeling.

FIGURE 7

ATAC-seq and ATAC-see overviews. (A) Tn5 prefers to bind and cut open chromatin and simultaneously ligates with adapters in the truncated DNA during an ATAC-seq; (B) Schematic of ATAC-see. An optimized bifunctional Tn5 transposon with fluorescent adaptors could be used to label open chromatin regions in fixed cells.

FIGURE 8

Schematic of LIANTI technology. LIANTI utilizes Tn5 transposase coupled to synthetic hairpin DNAs with T7 promoter to randomly dig the genome of a single cell into pieces.

FIGURE 9

Schematic of RNA-guided DNA insertion with CRISPR-associated transposases. (A) Sequence structure of the classic Tn7 transposon; (B) Sequence structure of Tn6677 from V. cholerae strain HE-45; (C) Sequence structure of CRISPR-associated transposase and transposon from cyanobacteria Scytonema hofmanni; (D) Model for RNA-guided DNA transposition of Tn6677; (E) Model for RNA-guided DNA transposition of shCAST.