RNAi in X inactivation: contrasting findings on the role of interference

microRNA-7 upregulates death receptor 5 and primes resistant brain tumors to caspase-mediated apoptosis

Background

MicroRNAs (miRs) are known to play a pivotal role in tumorigenesis, controlling cell proliferation and apoptosis. In this study, we investigated the potential of miR-7 to prime resistant tumor cells to apoptosis in glioblastoma (GBM).

Methods

We created constitutive and regulatable miR-7 expression vectors and utilized pharmacological inhibition of caspases and genetic loss of function to study the effect of forced expression of miR-7 on death receptor (DR) pathways in a cohort of GBM with established resistance to tumor necrosis factor apoptosis inducing ligand (TRAIL) and in patient-derived primary GBM stem cell (GSC) lines. We engineered adeno-associated virus (AAV)-miR-7 and stem cell (SC) releasing secretable (S)-TRAIL and utilized real time in vivo imaging and neuropathology to understand the effect of the combined treatment of AAV-miR-7 and SC-S-TRAIL in vitro and in mouse models of GBM from TRAIL-resistant GSC.

Results

We show that expression of miR-7 in GBM cells results in downregulation of epidermal growth factor receptor and phosphorylated Akt and activation of nuclear factor-kappaB signaling. This leads to an upregulation of DR5, ultimately priming resistant GBM cells to DR-ligand, TRAIL-induced apoptotic cell death. In vivo, a single administration of AAV-miR-7 significantly decreases tumor volumes, upregulates DR5, and enables SC-delivered S-TRAIL to eradicate GBM xenografts generated from patient-derived TRAIL-resistant GSC, significantly improving survival of mice.

Conclusions

This study identifies the unique role of miR-7 in linking cell proliferation to death pathways that can be targeted simultaneously to effectively eliminate GBM, thus presenting a promising strategy for treating GBM.

Post-transcriptional gene silencing, transcriptional gene silencing and human immunodeficiency virus

While human immunodeficiency virus 1 (HIV-1) infection is controlled through continuous, life-long use of a combination of drugs targeting different steps of the virus cycle, HIV-1 is never completely eradicated from the body. Despite decades of research there is still no effective vaccine to prevent HIV-1 infection. Therefore, the possibility of an RNA interference (RNAi)-based cure has become an increasingly explored approach. Endogenous gene expression is controlled at both, transcriptional and post-transcriptional levels by non-coding RNAs, which act through diverse molecular mechanisms including RNAi. RNAi has the potential to control the turning on/off of specific genes through transcriptional gene silencing (TGS), as well as fine-tuning their expression through post-transcriptional gene silencing (PTGS). In this review we will describe in detail the canonical RNAi pathways for PTGS and TGS, the relationship of TGS with other silencing mechanisms and will discuss a variety of approaches developed to suppress HIV-1 via manipulation of RNAi. We will briefly compare RNAi strategies against other approaches developed to target the virus, highlighting their potential to overcome the major obstacle to finding a cure, which is the specific targeting of the HIV-1 reservoir within latently infected cells.

Uncoupling of X-linked gene silencing from XIST binding by DICER1 and chromatin modulation on human inactive X chromosome

In mammals, X-inactivation process is achieved by the cis-spreading of long noncoding Xist RNA over one of the female X chromosomes. The Xist binding accumulates histones H3 methylation and H4 hypoacetylation required for X inactivation that leads to proper dosage compensation of the X-linked genes. Co-transcription of Tsix, an antisense copy of Xist, blocks the Xist coating on the Xi. In mice ES cells, an RNase III enzyme Dicer1 disrupts Xist binding and methylated H3K27me3 accumulation on the Xi. Later, multiple reports opposed these findings raising a question regarding the possible role of Dicer1 in murine X silencing. Here, we show that reduction of DICER1 in human female cells increases XIST transcripts without compromising the binding of the XIST and histone tail modifications on the Xi. Moreover, DICER1-depleted cells show differential upregulation of many human X-linked genes by binding different amounts of acetylated histone predominantly on their active promoter sites. Therefore, X-linked gene silencing, which is thought to be coupled with the accumulation of XIST and heterochromatin markers on Xi can be disrupted in DICER1 depleted human cells. These results suggest that DICER1 has no apparent effect on the recruitment of heterochromatic markers on the Xi but is required for inactivation of differentially regulated genes for the maintenance of proper dosage compensation in differentiated cells.

RNA-mediated silencing mechanisms in mammalian cells

Noncoding RNAs are a structural component of the nuclear scaffold and have been implicated in controlling gene expression. In mammals, long noncoding RNAs contribute to the regulation of imprinted gene expression, dosage compensation, development, and tumorigenesis. RNA is also a component of pericentric heterochromatin, and transcripts have been identified at the chromosomal telomeres. The functions of noncoding RNAs are likely diverse, and their underlying mechanisms are just beginning to be understood. Several noncoding RNAs interact with chromatin-modifying complexes and might have a role in targeting chromatin modifications to specific regions of the genome. This suggests a prominent function of RNA in establishing histone modification and DNA methylation patterns in development. Studies on model systems such as X inactivation, the regulation of the Hox clusters, and genomic imprinting have begun to shed light on the role of noncoding RNAs in chromosomal organization and regulation of gene expression. Well-studied examples of noncoding RNAs include Xist, Air, Kcnq1ot1, HOTAIR, and Tsix. Here, a concise review of noncoding RNA function in mammals is given, and the present understanding and future directions of the field are summarized.

Regulation of X-chromosome inactivation by the X-inactivation centre

X-chromosome inactivation (XCI) ensures dosage compensation in mammals and is a paradigm for allele-specific gene expression on a chromosome-wide scale. Important insights have been made into the developmental dynamics of this process. Recent studies have identified several cis- and trans-acting factors that regulate the initiation of XCI via the X-inactivation centre. Such studies have shed light on the relationship between XCI and pluripotency. They have also revealed the existence of dosage-dependent activators that trigger XCI when more than one X chromosome is present, as well as possible mechanisms underlying the monoallelic regulation of this process. The recent discovery of the plasticity of the inactive state during early development, or during cloning, and induced pluripotency have also contributed to the X chromosome becoming a gold standard in reprogramming studies.

The RNA infrastructure: an introduction to ncRNA networks

The RNA infrastructure connects RNA-based functions. With transcription-to-translation processing forming the core of the network, we can visualise how RNA-based regulation, cleavage and modification are the backbone of cellular function. The key to interpreting the RNA-infrastructure is in understanding how core RNAs (tRNA, mRNA and rRNA) and other ncRNAs operate in a spatial-temporal manner, moving around the nucleus, cytoplasm and organelles during processing, or in response to environmental cues. This chapter summarises the concept of the RNA-infrastructure, and highlights examples of RNA-based networking within prokaryotes and eukaryotes. It describes how transcription-to-translation processes are tightly connected, and explores some similarities and differences between prokaryotic and eukaryotic RNA networking.