A Long-Distance Relationship between RNAi and Polycomb

Induced Apoptosis Investigation in Wild-type and FLT3-ITD Acute Myeloid Leukemia Cells by Nanochannel Electroporation and Single-cell qRT-PCR

Nanochannel electroporation (NEP) was applied to deliver precise dosages of myeloid cell leukemia-1 (Mcl-1)-specific siRNA and molecular beacons to two types of acute myeloid leukemia (AML) cells, FMS-like tyrosine kinase-3 wild-type (WT) and internal tandem duplications (ITD) type at the single-cell level. NEP, together with single-cell quantitative reverse transcription PCR, led to an observation showing nearly 20-folds more Mcl-1 siRNA than MCL1 mRNA were required to induce cell death for both cell lines and patient blasts, i.e., ~8,800 siRNAs for ~500 ± 50 mRNAs in ITD cells and ~6,000 siRNAs for ~300 ± 50 mRNAs in WT cells. A time-lapse study revealed that >75% MCL1 mRNA was downregulated within 1 hour after delivery of a small amount of siRNA. However, additional siRNA was required to inhibit the newly transcribed mRNA for >12 hours until the cell lost its ability of self-protection recovery. A multidelivery strategy of low doses and short delivery interval, which require 77% less siRNA and has the potential of lower side effects and clinical cost, was as effective as a single high-dose siRNA delivery. Our method provides a viable analytical tool to investigate gene silencing at the single-cell level for oligonucleotide-based therapy.

Identification of the Drosophila X chromosome: The long and short of it

The different dose of X chromosomes in males and females produces a potentially fatal imbalance in X-linked gene products. This imbalance is addressed by dosage compensation, a process that modulates expression from an entire X chromosome in one sex. Dosage compensation acts on thousands of genes with disparate expression patterns. Both flies and mammals accomplish this with remarkable specificity by targeting epigenetic chromatin modifications to a single chromosome. Long noncoding RNAs that are expressed from the X chromosome are essential elements of the targeting mechanism in both lineages. We recently discovered that the siRNA pathway, as well as small RNA from satellite repeats that are strikingly enriched on the fly X chromosome, also promote X recognition. In this article we review the current understanding of X recognition in flies and discuss potential mechanisms by which the siRNA pathway, repetitive elements and long noncoding RNAs might cooperate to promote X recognition.

A view of nuclear Polycomb bodies

Polycomb group (PcG) proteins are concentrated in nuclear foci called PcG bodies. Although some of these foci are due to the tendency of PcG binding sites in the genome to occur in linear clusters, distant PcG sites can contact one another and in some cases congregate in the same PcG body when they are repressed. Experiments using transgenes containing PcG binding sites reveal that co-localization depends on the presence of insulator elements rather than of Polycomb Response Elements (PREs) and that it can occur also when the transgenes are in the active state. A model is proposed according to which insulator proteins mediate shuttling of PcG target genes between PcG bodies when repressed to transcription factories when transcriptionally active.

Stable transmission of reversible modifications: maintenance of epigenetic information through the cell cycle

Even though every cell in a multicellular organism contains the same genes, the differing spatiotemporal expression of these genes determines the eventual phenotype of a cell. This means that each cell type contains a specific epigenetic program that needs to be replicated through cell divisions, along with the genome, in order to maintain cell identity. The stable inheritance of these programs throughout the cell cycle relies on several epigenetic mechanisms. In this review, DNA methylation and histone methylation by specific histone lysine methyltransferases (KMT) and the Polycomb/Trithorax proteins are considered as the primary mediators of epigenetic inheritance. In addition, non-coding RNAs and nuclear organization are implicated in the stable transfer of epigenetic information. Although most epigenetic modifications are reversible in nature, they can be stably maintained by self-recruitment of modifying protein complexes or maintenance of these complexes or structures through the cell cycle.

X chromosome inactivation in the absence of Dicer

Dicer is central to the RNA interference (RNAi) pathway, because it is required for processing of double-stranded RNA (dsRNA) precursors into small RNA effector molecules. In principle, any long dsRNA could serve as a substrate for Dicer. The X inactive specific transcript (Xist) is an untranslated RNA that is required for dosage compensation in mammals. It coats and silences 1 of the 2 X chromosomes in female cells and initiates a chromosomewide change in chromatin structure that includes the recruitment of Polycomb proteins, but it is largely unknown how Xist RNA mediates these processes. To investigate a potential link between the RNAi pathway and X inactivation, we generated and analyzed Dicer-deficient embryonic stem (ES) cells. In the absence of Dicer, coating by Xist RNA, initiation of silencing, and recruitment of Polycomb proteins occur normally. Dicer ablation had modest effects on the steady-state levels of spliced Xist RNA. Together our data indicate that the RNAi machinery is not essential for the initiation of X inactivation.

Components of the RNAi machinery that mediate long-distance chromosomal associations are dispensable for meiotic and early somatic homolog pairing in Drosophila melanogaster

Homolog pairing is indispensable for the proper segregation of chromosomes in meiosis but the mechanism by which homologs uniquely pair with each other is poorly understood. In Drosophila, somatic chromosomes also undergo full homolog pairing by an unknown mechanism. It has been recently demonstrated that both insulator function and somatic long-distance interactions between Polycomb response elements (PREs) are stabilized by the RNAi machinery in Drosophila. This suggests the possibility that long-distance pairing interactions between homologs, either during meiosis or in the soma, may be stabilized by a similar mechanism. To test this hypothesis, we have characterized meiotic and early somatic chromosome pairing of homologous chromosomes in flies that are mutant for various components of the RNAi machinery. Despite the identification of a novel role for the piRNA machinery in meiotic progression and synaptonemal complex (SC) assembly, we have found that the components of the RNAi machinery that mediate long-distance chromosomal interactions are dispensable for homologous chromosome pairing. Thus, there appears to be at least two mechanisms that bring homologous sequences together within the nucleus: those that act between dispersed homologous sequences and those that act to align and pair homologous chromosomes.

Facultative heterochromatin: is there a distinctive molecular signature?

The Latin word "facultas" literally means "opportunity." Facultative heterochromatin (fHC) then designates genomic regions in the nucleus of a eukaryotic cell that have the opportunity to adopt open or compact conformations within temporal and spatial contexts. This review focuses on the molecular and functional aspects of fHC that distinguish it from constitutive heterochromatin (cHC) and euchromatin (EC) and discusses various concepts regarding the regulation of fHC structure. We begin by revisiting the historical developments that gave rise to our current appreciation of fHC.

Dynamics and interplay of nuclear architecture, genome organization, and gene expression

The organization of the genome in the nucleus of a eukaryotic cell is fairly complex and dynamic. Various features of the nuclear architecture, including compartmentalization of molecular machines and the spatial arrangement of genomic sequences, help to carry out and regulate nuclear processes, such as DNA replication, DNA repair, gene transcription, RNA processing, and mRNA transport. Compartmentalized multiprotein complexes undergo extensive modifications or exchange of protein subunits, allowing for an exquisite dynamics of structural components and functional processes of the nucleus. The architecture of the interphase nucleus is linked to the spatial arrangement of genes and gene clusters, the structure of chromatin, and the accessibility of regulatory DNA elements. In this review, we discuss recent studies that have provided exciting insight into the interplay between nuclear architecture, genome organization, and gene expression.

A new paradigm for developmental biology

It is usually thought that the development of complex organisms is controlled by protein regulatory factors and morphogenetic signals exchanged between cells and differentiating tissues during ontogeny. However, it is now evident that the majority of all animal genomes is transcribed, apparently in a developmentally regulated manner, suggesting that these genomes largely encode RNA machines and that there may be a vast hidden layer of RNA regulatory transactions in the background. I propose that the epigenetic trajectories of differentiation and development are primarily programmed by feed-forward RNA regulatory networks and that most of the information required for multicellular development is embedded in these networks, with cell–cell signalling required to provide important positional information and to correct stochastic errors in the endogenous RNA-directed program.

Chromatin insulators

Active and silenced chromatin domains are often in close juxtaposition to one another, and enhancer and silencer elements operate over large distances to regulate the genes in these domains. The lack of promiscuity in the function of these elements suggests that active mechanisms exist to restrict their activity. Insulators are DNA elements that restrict the effects of long-range regulatory elements. Studies on different insulators from different organisms have identified common themes in their mode of action. Numerous insulators map to promoters of genes or have binding sites for transcription factors and like active chromatin hubs and silenced loci, insulators also cluster in the nucleus. These results bring into focus potential conserved mechanisms by which these elements might function in the nucleus.

Biology of Polycomb and Trithorax Group Proteins

Cellular phenotypes can be ascribed to different patterns of gene expression. Epigenetic mechanisms control the generation of different phenotypes from the same genotype. Thus differentiation is basically a process driven by changes in gene activity during development, often in response to transient factors or environmental stimuli. To keep the specific characteristics of cell types, tissue-specific gene expression patterns must be transmitted stably from one cell to the daughter cells, also in the absence of the early-acting determination factors. This heritability of patterns of active and inactive genes is enabled by epigenetic mechanisms that create a layer of information on top of the DNA sequence that ensures mitotic and sometimes also meiotic transmission of expression patterns. The proteins of the Polycomb and Trithorax group comprise such a cellular memory mechanism that preserves gene expression patterns through many rounds of cell division. This review provides an overview of the genetics and molecular biology of these maintenance proteins, concentrating mainly on mechanisms of Polycomb group-mediated repression.