Chromatin‐associated noncoding RNAs in development and inheritance

Abstract

Noncoding RNAs (ncRNAs) have emerged as crucial players in chromatin regulation. Their diversity allows them to partake in the regulation of numerous cellular processes across species. During development, long and short ncRNAs act in conjunction with each other where long ncRNAs (lncRNAs) are best understood in establishing appropriate gene expression patterns, while short ncRNAs (sRNAs) are known to establish constitutive heterochromatin and suppress mobile elements. Additionally, increasing evidence demonstrates roles of sRNAs in several typically lncRNA-mediated processes such as dosage compensation, indicating a complex regulatory network of noncoding RNAs. Together, various ncRNAs establish many mitotically heritable epigenetic marks during development. Additionally, they participate in mechanisms that regulate maintenance of these epigenetic marks during the lifespan of the organism. Interestingly, some epigenetic traits are transmitted to the next generation(s) via paramutations or transgenerational inheritance mediated by sRNAs. In this review, we give an overview of the various functions and regulations of ncRNAs and the mechanisms they employ in the establishment and maintenance of epigenetic marks and multi-generational transmission of epigenetic traits. WIREs RNA 2017, 8:e1435. doi: 10.1002/wrna.1435 For further resources related to this article, please visit the WIREs website.

Transcriptomic Analysis of Potential “lncRNA–mRNA” Interactions in Liver of the Marine Teleost Cynoglossus semilaevis Fed Diets With Different DHA/EPA Ratios

“…The co-expression and co-localization relationship of “LNC_000285– baz2a ” indicated that the lncRNA LNC_000285 probably mediated the regulatory effects of dietary DHA/EPA on gene expression through promoting heterochromatin formation. Inducing heterochromatin formation and suppressing mobile elements were major mechanisms of transcription-regulating effects of non-coding RNAs (Cusanelli and Chartrand, 2015; Meller et al, 2015; Acharya et al, 2017; da Rocha and Heard, 2017; Oliva-Rico and Herrera, 2017). In human pancreatic ductal adenocarcinoma, the lncRNA HOTAIR contributed in the silence of MicroRNA-34a by enchancer of zeste homolog 2 through induction of heterochromatin formation (Li et al, 2016).…”

The chromatin-associated RNAs in gene regulation and cancer

“…The X-inactivation center (XIC) that can be transcribed to lncRNA Xist is essential and necessary during inactivation [58]. Previous studies have shown that many Xist RNAs might coat the X-chromosome in cis, consequently interacting with approximately 1000 genes directly and leading to transcriptional repression [59]. However, the latest research suggests that interaction with only approximately 50 locally confined foci on the inactive X-chromosome by approximately 100 Xist RNAs which trigger more than 1000 genes to become inactive [60].…”

Genome-wide analysis and functional annotation of chromatin-enriched noncoding RNAs in rice during somatic cell regeneration

“…lncRNA-directed processes also function in dosage compensation in Drosophila, where the localization of the histone acetyltransferase MOF to the male X chromosome is dependent on roX ncRNAs [ 15 ]. Moreover, recent findings suggest that ncRNAs are integral components of chromatin [ 12 , 13 ] that play an important role in the higher-order chromatin structure of pericentric heterochromatin by organizing heterochromatic components [ 16 , 17 ]. In plants, lncRNAs have been reported to interact with chromatin remodelers [ 18 ].…”