Although coding regions occupy less than 2% of the mammalian genome, a much larger portion of the genome is transcribed [1
]. The initial reports of this pervasive transcription generated some controversy regarding their biological relevance. However, several large scale analyses have since provided evidence that many noncoding transcripts are highly regulated and functional [6
In the past decade, there has been a profound shift in our understanding of the role of RNA molecules. They were once regarded as mere templates for generating proteins, but noncoding RNAs are emerging as highly versatile molecules that potentially function at every level of cellular regulation. The expanding catalogue of noncoding RNAs provides evidence that they are becoming as vast and varied as their protein-coding mRNA counterparts. Just as there are ubiquitously expressed housekeeping proteins, there are also housekeeping noncoding RNAs including, ribosomal, transfer, small nuclear and small nucleolar RNAs. On the other hand, regulatory noncoding RNAs generally show restricted patterns of expression during development and are frequently involved in regulating gene expression. Regulatory noncoding RNAs includes short RNAs (<200 nt) such as, small interfering RNAs, Piwi-associated RNAs, and of course, microRNAs. This review will focus on another class of regulatory noncoding RNAs, long noncoding RNAs (>200 nt), which have recently moved to the forefront of noncoding RNA research.
Long noncoding RNAs (lncRNAs), like mRNAs, can be capped, spliced and polyadenylated and fall into a variety of categories based on their genomic context as well as their functions. Some are located sense or antisense to other transcriptional units. Others are bidirectional, being transcribed near another gene from the opposite strand. LncRNAs can also be located within the intron of another transcript. Alternatively, intergenic noncoding RNAs lie between two genes or sets of genes. Functionally, lncRNAs have been shown to affect a wide range of cellular processes, including splicing [10
], localization [11
], transcription [12
], survival [13
], cell cycle [14
], migration [15
], metabolism [16
], and organization of cellular compartments [17
]. However, for the relatively small fraction of lncRNAs whose functions have been revealed, their predominant role seems to be the regulation of gene expression.
LncRNAs utilize a large arsenal of mechanisms to regulate gene expression. One well-studied mechanism is transcriptional interference, where the act of transcribing a lncRNA interferes with transcription initiation, elongation or termination of another sense or antisense gene [18
]. Some lncRNAs act as decoys, containing sequences that mimic transcription factor binding sites [16
] or miRNA target sites [19
] to titer these factors away from their primary targets thereby inhibiting their function. Other lncRNAs act as co-activators, binding to transcription factors and enhancing their transcriptional activity [12
]. LncRNAs can also affect transcription by binding to transcription factors and shuttling them into the cytoplasm to keep them away from their nuclear targets [11
]. Recent evidence also suggests that some lncRNAs may have enhancer-like function [22
], activating expression of nearby genes by an unknown mechanism.
Many lncRNAs interact with chromatin-modifying complexes to regulate gene expression. The idea that lncRNAs associate with chromatin-modifying complexes initially came from studies of X chromosome inactivation and genomic imprinting, but more recent global analyses have revealed that this may be a more universal characteristic of lncRNAs than originally anticipated. Almost 40% of large intergenic noncoding RNAs (lincRNAs) interact with chromatin-modifying complexes, such as the Polycomb Repressive Complex 2 (PRC2) and the CoREST/REST repressor complex [23
]. At least 24% of lincRNAs interact specifically with PRC2 [23
] and a recent study has identified thousands of additional lncRNAs that interact with PRC2 [24
], many of which are not intergenic RNAs. In addition, several lncRNAs have been shown to interact with the histone methyltransferase associated with the activating trithorax complex, MLL1 [25
], and the H3-K9 methyltransferase, G9a [27
]. While the functional relevance of these interactions is not yet well understood, several lncRNAs have also been shown to be required for targeting of these complexes to specific loci, either in cis
or in trans
, to regulate gene expression [27
]. Precisely how lncRNAs interact with chromatin-remodeling complexes and how they target specific genes is still largely unknown.
The predominant role of lncRNAs in regulating gene expression, combined with their strict spatiotemporal expression patterns, suggests that they may have a significant role in regulating key processes during development. Indeed, mechanistic evidence is accumulating for the role of lncRNAs in regulating differentiation and development, often epigenetically [32
]. In addition, numerous lncRNAs have been identified that are misregulated in cancer [35
]. However, the mechanisms of action of lncRNAs in tumor initiation and progression are largely unknown. In this review, we will discuss the role of lncRNAs during development and tumorigenesis, emphasizing what is currently known in the field of mammary gland biology.