Retrotransposon-associated long non-coding RNAs in mice and men

Abstract

Over a half of mammalian genomes is occupied by repetitive elements whose ability to provide functional sequences, move into new locations, and recombine underlies the so-called genome plasticity. At the same time, mobile elements exemplify selfish DNA, which is expanding in the genome at the expense of the host. The selfish generosity of mobile genetic elements is in the center of research interest as it offers insights into mechanisms underlying evolution and emergence of new genes. In terms of numbers, with over 20,000 in count, protein-coding genes make an outstanding >2 % minority. This number is exceeded by an ever-growing list of genes producing long non-coding RNAs (lncRNAs), which do not encode for proteins. LncRNAs are a dynamically evolving population of genes. While it is not yet clear what fraction of lncRNAs represents functionally important ones, their features imply that many lncRNAs emerge at random as new non-functional elements whose functionality is acquired through natural selection. Here, we explore the intersection of worlds of mobile genetic elements (particularly retrotransposons) and lncRNAs. In addition to summarizing essential features of mobile elements and lncRNAs, we focus on how retrotransposons contribute to lncRNA evolution, structure, and function in mammals.

Transcription of highly repetitive tandemly organized DNA in amphibians and birds: A historical overview and modern concepts

“…We propose that transcription on lateral loops often begins at adjacent active LTR promoters. Interestingly, activation of transcription from scattered LTR promoters in oocytes was recently shown in mammals, [65][66][67] thus implying evolutionary conservation of the transcription initiation mechanism during oogenesis.…”

Retrotransposons Manipulating Mammalian Skeletal Development in Chondrocytes

“…The mammalian genome contains two major classes of mobile genetic elements, and retrotransposons fall into the class 1 category [2]. Class 2 mobile genetic elements represent DNA transposons, which travel in the host genome by cutting and pasting themselves.…”

“…Class 2 mobile genetic elements represent DNA transposons, which travel in the host genome by cutting and pasting themselves. Although the human genome contains 294,000 copies of DNA transposon-associated elements, they are no longer active and are regarded as genetic fossils [2]. In contrast, class 1 mobile genetic elements include a number of active retrotransposons that are able to modify our genome structure.…”

“…For example, the number of protein-coding genes in the human genome turned out to be approximately 20,000 [1], which is comparable to, and even less than, that in the murine genome. Regarding the organization of the human genome, the area used for encoding those proteins is as much as 2%, whereas 55% of the whole genome is occupied by repetitive sequences [2]. Considering that primordial eukaryotic genomes are much smaller and contain much fewer repetitive elements, it is clear that the expansion of repetitive elements has played a critical role in the development of the human genome during the course of mammalian evolution.…”

“…Expansion of repetitive sequences can be achieved at the level of DNA replication. However, the contribution of such a process at a DNA level to human evolution seems to be limited, since most of the repetitive sequences in the human genome originate from mobile genetic elements entitled retrotransposons multiplying through the reverse-transcription process (Figure 1a) [2].…”