ISSN 0026-8933, Molecular Biology, 2006, Vol. 40, No. 4, pp. 528–540. © Pleiades Publishing, Inc., 2006. Original Russian Text © R.N. Kotelnikov, S.G. Shpiz, A.I. Kalmykova, V.A. Gvozdev, 2006, published in Molekulyarnaya Biologiya, 2006, Vol. 40, No. 4, pp. 595–608. 528 INTRODUCTION RNA interference (RNAi) is the most important recent discovery in molecular biology, changing the views of gene expression regulation in eukaryotic cells. RNAi is based on the inhibition of gene expression by short RNAs, varying from 20 to 27 nt. Not only does RNAi regulate the expression of genes at the translation levels, mRNA degradation, and transcription [1], but it is also capable of directing programmed genome rear- rangements [2]. Gene silencing via RNAi is highly spe- cific, because short RNAs find homologous nucleotide sequences in their targets, e.g., in mRNA. RNAi speci- ficity is taken advantage of in functional genomics, which is aimed at identifying the functions of particular proteins. Related experimental techniques have been described in many reviews (e.g., see [3]). Initially the term RNAi was applied to gene silencing by exoge- nous (artificially introduced) double-stranded RNAs (dsRNAs) with a homologous nucleotide sequence. It has been found that RNAi is due to small interfering RNAs (siRNAs), which result from the processing of exogenous dsRNA. Natural RNAi caused by endoge- nous dsRNA was first described in Drosophila [4]. Endogenous dsRNA and siRNA arise, in particular, via a symmetrical transcription of repetitive genomic sequences, including mobile genetic elements. That is why RNAi is capable of inhibiting their expression and transposition [5]. The discovery of RNAi changed the view of small RNAs’ role in suppressing mRNA translation. A new system that regulates gene expression was revealed: this system is based on microRNAs (miRNAs) that are generated from hairpin-forming transcripts. The mechanisms sustaining the function and generation of siRNA and miRNA from extended dsRNA or the dou- ble-stranded region of hairpin RNA proved to be highly similar in some cases. Moreover, the same pro- teins were found to mediate RNA silencing depending on different short RNAs. Hence, RNAi is considered here as gene silencing with siRNA and miRNA. Note that RNAi inhibits gene expression causing a loss of function. In some cases, e.g., where dsRNA results from transcription of centromeric repeats, RNAi ensures the function of the corresponding genome regions by inducing their heterochromatization (com- paction), which is essential for chromosome segrega- tion during cell division [6]. Thus, a functional analy- sis demonstrates that RNAi, operating at various lev- els of gene expression, is important for the development and cell differentiation in eukaryotes. Many reviews have considered the role of RNAi in the conserved eukaryotic silencing system, whose rudi- ments are detectable in archaebacteria. Here we focus on the structure of RNA-binding domains found in RNAi proteins. The results of relevant studies have helped to elucidate mechanisms sustaining the func- tion of such proteins and regulating their activity. The processing of siRNA and pre-miRNA precur- sors along with the effects of short RNAs on gene expression are illustrated in Fig. 1. The mechanisms of gene silencing with short RNAs have been described in many reviews [7–11], including those in Russian [3, 12–14]. To trigger the RNAi pathway, endonuclease Dicer cleaves dsRNA into 21- to 24-bp duplexes, containing 2-nt overhangs at the 3' ends and phosphates at the 5' ends (Fig. 1). These siRNAs are incorporated into an effector RNA-induced silencing complex (RISC) RNA-Binding Proteins in RNA Interference R. N. Kotelnikov a , S. G. Shpiz a, b , A. I. Kalmykova a , and V. A. Gvozdev a, b a Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182 Russia; e-mail: gvozdev@img.ras.ru, kotelnikov@img.ras.ru b Moscow State University, Moscow, 119899 Russia Received February 6, 2006 Abstract—Short RNAs (21–27 nt) silence genes that contain homologous nucleotide sequences; this is known as RNA silencing. This review considers the generation of short RNAs from their precursors: double-stranded RNAs, capable of inducing RNA interference, and hairpin RNAs, whose processing yields microRNAs, as well as the properties of RNA-binding domains that were initially identified in proteins operating in RNA interfer- ence. The interactions between these domains and known RNA-binding modules within proteins involved in RNA interference and microRNA generation are described. DOI: 10.1134/S0026893306040054 Key words: RNA interference, RNA silencing, short RNAs, domains UDC 577.21