Transposable element-derived sequences in vertebrate development

Abstract

Transposable elements (TEs) are major components of all vertebrate genomes that can cause deleterious insertions and genomic instability. However, depending on the specific genomic context of their insertion site, TE sequences can sometimes get positively selected, leading to what are called “exaptation” events. TE sequence exaptation constitutes an important source of novelties for gene, genome and organism evolution, giving rise to new regulatory sequences, protein-coding exons/genes and non-coding RNAs, which can play various roles beneficial to the host. In this review, we focus on the development of vertebrates, which present many derived traits such as bones, adaptive immunity and a complex brain. We illustrate how TE-derived sequences have given rise to developmental innovations in vertebrates and how they thereby contributed to the evolutionary success of this lineage.

Retrotransposons as Drivers of Mammalian Brain Evolution

“…An impressive body of studies in the last two decades have addressed the role that retrotransposons played in mammalian, and particularly in human, evolution by facilitating the appearance of genomic novelties. As new evidence accumulated, authoritative reviews were published at various times, covering in great detail the genomic impact and the different emerging aspects of retrotransposons [ 6 , 8 , 13 , 37 , 38 , 52 , 54 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 , 76 , 77 , 78 ]. In a nutshell, it is thought that retrotransposons contributed to the generation of genomic novelties in two main ways: (i) indirectly, through the promotion of genomic rearrangements; and (ii) directly, through exaptation of retrotransposon-derived sequences.…”

ARID1A loss derepresses human endogenous retrovirus-H to modulate BRD4-dependent transcription

“…To validate these upregulated ERVs, we repeated the analysis with another independent RNA-seq dataset (GSE50760) of CRC tissues, and identified 17 ERVs that showed consistent upregulation. Specific activation of ERVs is linked with pluoripotency in embryonic cells 6,20 . We compared the upregulated ERVs in CRC tissues with that observed in early embryos and ESCs, and pinpointed two elements, HERVH-int and LTR7Y, that constitute a full-legth HERVH (Fig.…”

“…The majority of them has lost the ability to transpose during evolution and had long been regarded as functionless repetitive DNA. Recent studies however have begun to reveal that TEs are an abundant source of many regulatory sequences 2,3,5,6 , such as microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) [7][8][9][10][11][12] , and that TEs are co-opted to serve important functions including transcriptional regulation, chromatin organization and 3D compartmentalization, especially during early embryogenesis and in embryonic stem cells (ESCs) 6,[13][14][15][16][17][18][19][20][21][22][23] .…”

DeepGRP: engineering a software tool for predicting genomic repetitive elements using Recurrent Neural Networks with attention

“…A more recent approach to repeat annotation is based on profile Hidden Markov Models (pHMMs). The open access database Dfam [ 28 ] provides a large collection of multiple sequence alignments of families of repetitive sequences and pHMMs derived from these. Sequences are annotated based on hits of the pHMMs in the sequences.…”

“…The hits are computed using the HMMER software [ 29 ]. As Dfam provides a comprehensive collection of repetitive elements of high quality, is freely available and easy to use, it is likely to become the state of the art for repetitive element annotation in the near future [ 28 ].…”