Beyond mRNA: The role of non-coding RNAs in normal and aberrant hematopoiesis

Abstract

The role of non-coding Ribonucleic Acids (ncRNAs) in biology is currently an area of intense focus. Hematopoiesis requires rapidly changing regulatory molecules to guide appropriate differentiation and ncRNA are well suited for this. It is not surprising that virtually all aspects of hematopoiesis have roles for ncRNAs assigned to them and doubtlessly much more await characterization. Stem cell maintenance, lymphoid, myeloid and erythroid differentiation are all regulated by various ncRNAs, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and various transposable elements within the genome. As our understanding of the many and complex ncRNA roles continues to grow, new discoveries are challenging the existing classification schemes. In this review we briefly overview the broad categories of ncRNAs and discuss a few examples regulating normal and aberrant hematopoiesis.

Figure 1. miRNA Biogenesis

miRNA genes are transcribed by RNA polymerase II into pri-miRNA and then processed into pre-miRNA by the microprocessor complex, consisting of DGR8 and Drosha. Following exportin 5-mediated nuclear export to the cytoplasm, the Dicer complex generates mature miRNA duplexes which can associated with the RNA-induced silencing complex (RISC). Once associated with RISC the passenger strand is degraded leaving the guide miRNA to interact with the target mRNA.

Figure 2. piRNA biogenesis (adapted from Ku and Lin 2014 [133])

PIWI proteins and piRNAs regulate the expression of genes and transposons at both transcriptional and post-transcriptional levels. 1) Sense and antisense piRNA precursor transcripts are transcribed from piRNA clusters in the nucleus. 2) piRNA precursor transcripts are exported to the cytoplasm and processed by the primary biogenesis pathway to generate mature sense piRNAs. 3) mature piRNAs consisting of the 5′ end of the precursor then associate with PIWI proteins to enter the secondary piRNA pathway. 4) The PIWI:piRNA complexes then associate with the complementary sequence in unprocessed precursor piRNA (or transposons and protein-coding transcripts) and mediate cleavage. The resulting cleaved 5′ end of the piRNA precursors is taken up by another PIWI protein and the precursor (or transposon or protein-coding transcript) is silenced. This process is known as the ping-pong cycle. PIWI:piRNA complexes interact with polysomes, mRNA cap-binding complex (CBC), P-body components and piRNAs are mapped to the 3′UTR of mRNAs. The PIWI-piRNA complexes can enter the nucleus and regulate gene transcription through epigenetic mechanisms including heterochromatin formation and DNA methylation.

Figure 3. The Roles of lncRNA in mRNA Processing and Post-transcriptional Regulation

Within the nucleus, lncRNA modulates mRNA processing in one of two ways. 1) Binding mRNA at regions overlapping exon:intron boundaries. Antisense transcript can generate the complimentary sequence required. 2) lncRNA can recruit mRNA editing enzymes, such as adenosine deaminase (ADAR), to complementary mRNA sequences. In the cytoplasm, lncRNA regulates post-transcriptional events through at least four distinct mechanisms. 3) Recruitment of post-transcriptional machinery to mRNA due to possession of sequence specific domains, such as SIN EB2 repeat elements that have affinity for ribosomes. 4) lncRNA that contain Alu repeat elements associate with Alu elements in the 3′UTR of mRNA which recruits Staufen to induce a pathway leading to mRNA decay. 5) Linear or circular lncRNAs can serve as molecular sponges to sequester miRNAs from their target sequences. 6) lncRNAs can mask sequences in mRNA that would serve as targets for miRNAs bound to RNA-induced silencing complex (RISC).

Figure 4. Transposon mechanisms

Class 1 transposons utilize an RNA intermendiate. The RNA is transcribed by host machinery and then reverse-transcribed and integrated elsewhere into the genome by enzymes encoded by the retrotransposon itself (autonomous retrotransposons), or encoded by another retrotransposon (parasitic or non-autonomous retrotransposons). Class II transposable elements move within the genome by a “cut-and-paste’ mechanism with no RNA intermediate.