Non-linear sequence similarity between the Xist and Rsx long noncoding RNAs suggests shared functions of tandem repeat domains

Abstract

The marsupial inactive X chromosome expresses a long noncoding RNA (lncRNA) called Rsx that has been proposed to be the functional analogue of eutherian Xist. Despite the possibility that Xist and Rsx encode related functions, the two lncRNAs harbor no linear sequence similarity.However, both lncRNAs harbor domains of tandemly repeated sequence. In Xist, these repeat domains are known to be critical for function. Using k-mer based comparison, we show that the repeat domains of Xist and Rsx unexpectedly partition into two major clusters that each harbor substantial levels of non-linear sequence similarity. Xist Repeats B, C and D were most similar to each other and to Rsx Repeat 1, whereas Xist Repeats A and E were most similar to each other and to Rsx Repeats 2, 3, and 4. Similarities at the level of k-mers corresponded to domain-specific enrichment of protein-binding motifs. Within individual domains, protein-binding motifs were often enriched to extreme levels. Our data support the hypothesis that Xist and Rsx encode similar functions through different spatial arrangements of functionally analogous protein-binding domains. We propose that the two clusters of repeat domains in Xist and Rsx function in part to cooperatively recruit PRC1 and PRC2 to chromatin. The physical manner in which these domains engage with protein cofactors may be just as critical to the function of the domains as the protein cofactors themselves. The general approaches we outline in this report should prove useful in the study of any set of RNAs.

Long non-coding RNAs: definitions, functions, challenges and recommendations

“…Many lncRNA exons are derived from transposable elements 187,391 . The most highly conserved sequences in Xist, which has been intensively studied, are its repeats 7 , whereas its unique sequences have evolved rapidly 392 , and many of its biological functions, including recruitment of gene-repressive complexes and gene silencing, are mediated through its modular repeat elements 142,186,388,[393][394][395][396][397][398][399] . Transposable element-derived sequences participate in many RNA-protein interactions 369,400,401 , which leads to the conclusion that repeat structures are common building blocks of lncRNAs 87,391,396 and essential components of their function 391 .…”

“…It is assumed, in our view reasonably, that generally lncRNAs will engage b, Modular structural domains in lncRNAs that fulfil a range of functions [372][373][374][375] , including targeting DNA, such as in the case of auxin-regulated promoter loop (APOLO) 61 ; binding other RNAs -for example, terminal differentiation-induced non-coding RNA (TINCR) 458 , potentially involving RNA-binding proteins such as Staufen 1; and recruitment of proteins -for example, pyrimidine-rich noncoding transcript (PNCTR) recruiting of pyrimidine tract-binding protein 1 (PTBP1) through special RNA motifs 369 and X-inactive-specific transcript (XIST) recruiting split ends homologue (SPEN) and Polycomb repressive complex 2 (PRC2), perhaps in concert, which is the subject of active exploration and debate 142,397,399,423,424,459 . Modular functional domains can be repeated within a lncRNA or in multiple different lncRNAs 7,87,186,369,388,391,[393][394][395][396][397][398][399][400][401] in multilateral interactions similarly to TERC and the telomerase complex 108 , and there is some evidence to support this assumption in cases such as XIST (Fig. 3b), but the assumption has not yet been rigorously tested.…”

The how and why of lncRNA function: An innate immune perspective

“…While sequence conservation does not constrain lncRNA genes, lncRNA function is found to be conserved across species when identifying motifs or structure. A great example of this phenomena is represented in the study of human maternally expressed gene 3 (MEG3), which utilized the computer program mfold and multiple ex vivo and in vitro chemical probing techniques to identify common motifs critical for retained function in orangutan, rat, mouse and pig [222,223]. Another study highlighting the marsupial Rsx lncRNA was initially found to have no linear sequence similarity with the lncRNA Xist.…”

Functional evolutionary convergence of long noncoding RNAs involved in embryonic development

“…However, lncRNAs with similar functions often lack linear sequence homology which implies lncRNA function cannot be readily assigned from their nucleotide sequence. K-mer based comparison methods have been demonstrated to be useful to find functionally related lncRNAs with different spatial arrangements of related sequence motifs, where a k-mer is defined as all possible combinations of a continuous sequence of nucleotides of a given length k. K-mer-based classification has been demonstrated to be a powerful approach to detect recurrent relationships between motif sequence and function in lncRNAs even in the lack of evolutionary conservation (Kirk et al, 2018; Sprague et al, 2019). Additionally, lncRNAs with the same secondary or tertiary structure can exert identical molecular functions despite divergent nucleotide sequences (Smith et al, 2013), thus analyzing structural equivalence could also help identify lncRNAs with evolutionary preserved mechanisms (Ponti et al, 2018).…”