Shaping the Genome with Non-Coding RNAs

Abstract

The human genome must be tightly packaged in order to fit inside the nucleus of a cell. Genome organization is functional rather than random, which allows for the proper execution of gene expression programs and other biological processes. Recently, three-dimensional chromatin organization has emerged as an important transcriptional control mechanism. For example, enhancers were shown to regulate target genes by physically interacting with them regardless of their linear distance and even if located on different chromosomes. These chromatin contacts can be measured with the “chromosome conformation capture” (3C) technology and other 3C-related techniques. Given the recent innovation of 3C-derived approaches, it is not surprising that we still know very little about the structure of our genome at high-resolution. Even less well understood is whether there exist distinct types of chromatin contacts and importantly, what regulates them. A new form of regulation involving the expression of long non-coding RNAs (lncRNAs) was recently identified. lncRNAs are a very abundant class of non-coding RNAs that are often expressed in a tissue-specific manner. Although their different subcellular localizations point to their involvement in numerous cellular processes, it is clear that lncRNAs play an important role in regulating gene expression. How they control transcription however is mostly unknown. In this review, we provide an overview of known lncRNA transcription regulation activities. We also discuss potential mechanisms by which ncRNAs might exert three-dimensional transcriptional control and what recent studies have revealed about their role in shaping our genome.

5'-Serial Analysis of Gene Expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea

“…Some of these tags could be identified in both the Myc and S1-Pri libraries, implying that they did not occur spuriously (Figure 2). We speculate that they may represent TSS of non-coding RNAs (ncRNAs) with regulatory functions that control gene expression [27-29]. However, further analysis of these non-coding RNAs is beyond the scope of the present study.…”

From cells to chromatin: Capturing snapshots of genome organization with 5C technology

“…There remain a tremendous number of unanswered questions relating to high-resolution genome organization that include the number of different contacts, what mediates them and how they are regulated [16]. Moreover, three-dimensional chromatin structure itself could represent an important transcription regulation mechanism [17].…”

Synthesizing the role of epigenetics in the response and adaptation of species to climate change in freshwater ecosystems

“…These studies corroborate that epigenetic mechanisms indeed have an important evolutionary role. More precisely, some of these studies provide in vivo evidence that epigenetic mechanisms are capable of shaping the genome of organisms, allowing long-term adaptations of populations to environmental changes (Bernardi & Bernardi, 1986;Jablonka & Lamb, 2007;Wang, Crutchley, & Dostie, 2011…”