Roles of Long Non-coding RNAs in X-Chromosome Inactivation

Exon Mapping in Long Noncoding RNAs Using Digital Filters

“… 6 The Xist lncRNA has been found to be essential in X-chromosome inactivation during female eutherian mammalian development. 11 However, it is to be noted that the functions/involvement of lncRNAs is not limited to the ones mentioned here. The same lncRNA can be implicated more than one disease/function.…”

Transposable elements, contributors in the evolution of organisms (from an arms race to a source of raw materials)

“…However, the specific integrations of TEs with certain patterns of insertion preferences in the genomes indicate that the evolutionary events of TEs and their insertions occurred before the emergence of eukaryotic groups [ 15 , 19 , 21 ]. For example, cis-regulatory elements in the genome contain specific integrations of TEs in promoter regions, in sex-determination regions (SDRs) on XY.ZW and in X inactivation center (XIC) [ 19 , 21 , 22 , 23 , 24 ]. Theorizing, TEs were opted and inserted as ‘domesticated agents’ in the genome to serve cellular function beneficial to the host organism for example for adaptation in conflicts of evolutionary events [ 9 , 10 , 11 ].…”

“…They also influence the kind of mating system (e.g. self-crosses or out-crosses in plants), where Arabidopsis species is as an instance [ 19 , 24 , 31 ]. There is a dramatic variation in TE copy number and composition in different fish taxa, ranging from 55% in the zebrafish ( Danio rerio ) to only 6% in the green spotted pufferfish (Tetraodon nigroviridis).…”

“…Both processes are controlled by cis-acting master control regions evolutionary derived by TEs, X inactivation center (XIC), and imprinting control region (ICR), respectively ( Figure 3 ) [ 22 , 91 ]. In mammals, XIC makes a region ~500-kb encoding a cluster of lncRNAs including Xist and Tsix ( Figure 3 A) [ 24 , 91 ]. In mammals, imprinting of the gene clusters is controlled by ICRs, CpG-rich cis-regulatory elements (CpG islands) marked by DNA methylation most often on the maternal alleles .…”

“…There is a massive accumulation of L1-Alu pairs on the human X where functioning in dosage compensation. In the inactivation process, L1s are serving as ‘‘way stations’’ for the spread of the inactivation signal [ 24 , 105 ] and as Repeat Insertion Domains of LncRNA (RIDL) in Xist which promoting the spread of Xist along X, the agent of X-chromosome inactivation [ 17 , 22 , 24 ].…”