Epigenetic gene regulation by noncoding RNAs

Functional noncoding RNAs have distinct roles in epigenetic gene regulation. Large RNAs have been shown to control gene expression from a single locus (Tsix RNA), from chromosomal regions (Air RNA), and from entire chromosomes (roX and Xist RNAs). These RNAs regulate genes in cis; although the Drosophila roX RNAs can also function in trans. The chromatin modifications mediated by these RNAs can increase or decrease gene expression. These results suggest that the primary role of RNA molecules in epigenetic gene regulation is to restrict chromatin modifications to particular regions of the genome. However, given that RNA has been shown to be at the catalytic core of other ribonucleoprotein complexes, it is also possible that RNA also plays a role in modulating changes in chromatin structure.     

RNA and RNA binding proteins participate in early stages of cell spreading through spreading initiation centers

Focal adhesions are specialized attachment and signaling centers that form at sites of cell-matrix contacts. We employed a quantitative mass spectrometry-based method called SILAC to identify and quantify proteins interacting in an attachment-dependent manner with focal adhesion proteins. Subsequent confocal microscopy revealed a previously undescribed structure, which we have termed a spreading initiation center (SIC), existing only in early stages of cell spreading. SICs contain focal adhesion markers, appear to be surrounded by an actin sheath, and, surprisingly, contain numerous RNA binding proteins, ribosomal RNA, and perhaps other RNAs. Interfering with the function of FUS/TLS, hnRNP K, and hnRNP E1 results in increased spreading. Spreading initiation centers are ribonucleoprotein complexes distinct from focal adhesions and demonstrate a role for RNA and RNA binding proteins in the initiation of cell spreading.     

Recent advances in RNA-protein interaction studies

Conclusions The RNA binding sites for several small proteins have been characterised. These sites include double helical regions with hairpins, bulged bases and internal loops. As seen in Flock House virus structure, some proteins may recognise phosphate backbone of the canonical A-form helix not in a sequence-specific manner. If sequence-specific base contacts are to be made, then the A-helic major groove must be widened. This can be accomplished by introducing bulges, internal loops and hairpin loops into double helical regions. In these cases proteins may recognise both distorted backbone conformations and read out base sequences in a widened major groove. Crystallographic studies on complexes of aminoacyl-tRNA synthetase and tRNA showed that even RNAs with stable tertiary fold undergo substantial structural changes upon binding to the synthetases. The structural variability of RNA as well as the ability of RNA to distort upon protein binding may be crucial in RNA-protein interactions.     

siRNA介导基因沉默的分子机器、作用模式和应用前景

siRNA(small interfering RNA)介导的基因沉默是细胞内监控寄生的遗传物质、沉默无用的信息模板和调节自然的时空转换的一种分子机制。它与体液免疫和细胞免疫一起形成了动物和人类机体中免疫系统的三大支柱,从不同水平上来对抗体内外有害物质的干扰和侵犯。现已清楚,大约22个核苷酸长的双链RNA能够通过不同途径,以序列特异的方式来高效地沉默含有同源序列的靶RNA分子。这一古老而又迷人的系统现已被公认为是鉴定基因功能、调控基因表达和改变基因表型的简单而有效的方法。可以预计,这一新颖的技术在不远的将来必将形成一条研究功能基因组学、探索信号通路和创造遗传缺陷模型的高速公路,并将开创一条预防和治疗人类疾病的新途径。     

Common ground: small RNA programming and chromatin modifications

Epigenetic mechanisms regulate genome structure and expression profiles in eukaryotes. RNA interference (RNAi) and other small RNA-based chromatin-modifying activities can act to reset the epigenetic landscape at defined chromatin domains. Centromeric heterochromatin assembly is a RNAi-dependent process in the fission yeast Schizosaccharomyces pombe, and provides a paradigm for detailed examination of such epigenetic processes. Here we review recent progress in understanding the mechanisms that underpin RNAi-mediated heterochromatin formation in S. pombe. We discuss recent analyses of the events that trigger RNAi and manipulations which uncouple RNAi and chromatin modification. Finally we provide an overview of similar molecular machineries across species where related small RNA pathways appear to drive the epigenetic reprogramming in germ cells and/or during early development in metazoans.