Abstract
Genomic repeats have been intensely studied as regulatory elements controlling gene transcription, splicing and genome architecture. Our understanding of the role of the repetitive RNA such as the RNA coming from genomic repeats, or repetitive sequences embedded in mRNA/lncRNAs, in nuclear and cellular functions is instead still limited. In this review we discuss evidence supporting the multifaceted roles of repetitive RNA and RNA binding proteins in nuclear organization, gene regulation, and in the formation of dynamic membrane-less aggregates. We hope that our review will further stimulate research in the consolidating field of repetitive RNA biology.
Highlights
Our understanding of the role of the repetitive RNA such as the RNA coming from genomic repeats, or repetitive sequences embedded in mRNA/long non-coding RNA (lncRNA), in nuclear and cellular functions is instead still limited
These regions always express at least one lncRNA, whose expression PoO generally inversely correlates with the parent of origin of the expressed allele of the neighboring genes, i.e., expression of the paternal lncRNA will result in the expression of the maternal cluster protein coding genes (Royo and Cavaillé, 2008)
MALAT1 associates with actively transcribed genes in the periphery of nuclear speckles and dozens of RNAbinding proteins (RBP), and these findings suggest that it could act as a scaffold mediating those interactions
Summary
Repetitive caRNAs are transcribed from repetitive DNA sequences such as DNA-containing genomic repeats, fragments of genomic repeats or repeated motifs such as simple repeats (Biscotti et al, 2015). It is believed that repetitive sequences make up at least half of the human genome, with some estimates placing it at two thirds (de Koning et al, 2011) Such sequences were once labeled the “dark matter” of the genome or “junk DNA,” but it is becoming more and more clear that they instead play critical roles in regulating gene expression at different levels (Statello et al, 2021). They can be classified in two broad categories: low complexity, consisting of adjacent sequences repeated in tandem, and interspersed repeats, complex sequences generally capable of being transcribed and sometimes translated. In the paragraphs we will briefly examine the role of medium repetitive RNAs (such tandem and interspersed) in the establishment and maintenance of the two heterochromatin and the euchromatin states
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