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Title: DNA Binding of Centromere Protein C (CENPC) Is Stabilized by Single-Stranded RNA}
Article:
Abstract:
Centromeres are the attachment points between the genome and the cytoskeleton: centromeres bind to kinetochores, which in turn bind to spindles and move chromosomes. Paradoxically, the DNA sequence of centromeres has little or no role in perpetuating kinetochores. As such they are striking examples of genetic information being transmitted in a manner that is independent of DNA sequence( epigenetically). It has been found that RNA transcribed from centromeres remains bound within the kinetochore region, and this local population of RNA is thought to be part of the epigenetic marking system. Here we carried out a genetic and biochemical study of maize CENPC, a key inner kinetochore protein. We show that DNA binding is conferred by a localized region 122 amino acids long, and that the DNA-binding reaction is exquisitely sensitive to single-stranded RNA. Long, single-stranded nucleic acids strongly promote the binding of CENPC to DNA, and the types of RNAs that stabilize DNA binding match in size and character the RNAs present on kinetochores in vivo. Removal or replacement of the binding module with HIV integrase binding domain causes a partial delocalization of CENPC in vivo. The data suggest that centromeric RNA helps to recruit CENPC to the inner kinetochore by altering its DNA binding characteristics.
Introduction:
Centromeres are important features of the genome that connect chromosomes to spindles. The connection occurs through a large multifunctional kinetochore complex that binds DNA, binds microtubules, and regulates the timing of anaphase[1]–[4]. Most plant and animal genomes contain diagnostic repeats that can be used to identify centromere boundaries, but unlike in fungi[5],[6], these sequences are not always necessary for organizing a functional kinetochore[7]–[9]. How kinetochores are accurately replicated is unknown and generally described as epigenetic–meant in the broadest sense that it is not easily classified as genetic. Functional centromere domains are marked by a histone H3 variant known as Centromeric Histone H3( CENH3) that has received intensive scrutiny as an important epigenetic identifier of centromeres[5]. In the absence of CENH3, all other kinetochore proteins fail to localize and chromosomes cannot move on the spindle[10]–[13]. CENH3 is assembled relatively late in the cell cycle, as late as anaphase-G1[14]–[16], by specialized CENH3 nucleosome assembly factors such as Mis16 and Mis18[17]. In addition several proteins that require CENH3 for localization also serve to target new CENH3[18]–[20]. One such protein is Centromere protein C( CENPC), a DNA binding protein that has a key role in centromere recognition and maintenance[21]. Drosophila CENPC is required to target CENH3, but CENH3 is also required to target CENPC[20],[22]. These data suggest that kinetochore replication is a self reinforcing process whereby key inner kinetochore proteins such as CENPC work in concert with CENH3 to replicate the content and position of centromeres. In species such as maize, the available data suggest that centromeric DNA does not function to recruit kinetochores until it is combined with specific epigenetic marks. Maize centromere repeats are under-methylated[23] and transcribed to produce stable RNAs that remain tightly bound to chromatin[24]. The centromeric RNAs are 40–200 nt in length, transcribed from both strands, and maintained in the single stranded state. It was proposed that RNA may serve as a structural template to help recruit kinetochore proteins[24]–[26]. A recent study revealed that human centromeres contain similar RNAs and established that RNAse treatment delocalizes CENPC from mature kinetochores[27]. More recent data show that suppression of transcription over a single LINE element in a human neocentromere impairs the formation of a kinetochore complex[28]. These data support the view that RNA facilitates or stabilizes the association of kinetochore proteins with centromeric DNA and implicate CENPC as a primary target of this activity. CENPC is a highly divergent protein defined by a short 23 amino acids motif. Outside the defining motif lies the DNA binding region( s), which in animals appear to be distributed in several broad domains[29]–[31]. In plants, there is no evidence that CENPC binds to centromeric DNA beyond the presumption that CENPC is functionally conserved. In this regard we were encouraged by the sequence analysis of Talbert and colleagues[32] who found that a small region of CENPC has been repeatedly duplicated in the grasses. The authors suggested that the exon 9–12 duplicated region may bind to DNA. Here we use a combination of in vitro and in vivo studies to show that maize CENPC has both DNA-binding and RNA-binding capacities, that the DNA/RNA-binding domain is localized to the exon duplication region, and that the binding domain is required for efficient centromere localization. We further show that RNA directly facilitates the binding of CENPC to DNA in vitro, providing a biochemical mechanism for the involvement of RNA in centromere specification. We argue that CENPC and RNA are a part of the template that directs CENH3 to newly replicated centromere DNA.
Discussion:
Our observation that the delCENPC and IntCENPC constructs, which lack the natural DNA binding domain of maize CENPC, localize to kinetochores with 80% efficiency( Figure 5) suggests that initial targeting of CENPC occurs independently of DNA binding. From these data we infer that the role of the DNA binding domain is to reinforce and/or stabilize accurate localization once it occurs. The fact that single stranded RNA has a strong positive effect on DNA binding suggests that centromeric RNA serves as an epigenetic mark that mediates this final and most stable state of assembly. Therefore we propose that CENPC is first recruited to kinetochores by protein-protein contacts and then converted to a functional DNA binding protein by centromeric RNA( Figure 8). We emphasize that our interpretation relies heavily on in vitro experiments, and that our in vivo data are complicated by the presence of wild type CENPC in the transformed lines, which may have influenced the recruitment of introduced YFP-tagged proteins. Although our data show that DNA binding has a role in maize CENPC function, our experiments cannot be used to quantify how important DNA binding is; nor do our data establish with certainty that RNA facilitates DNA binding in vivo. Nevertheless our data provide the first plausible mechanistic explanation for a previously unexplained phenomenon. The role of RNA in CENPC function may be similar in principle to the well-understood roX1 and roX2 RNAs of Drosophila, which function to up-regulate genes on the male X chromosome[50]. roX RNAs bind to a small complex of MSL( male-specific lethal) proteins and change their binding specificity so that they interact with many sites along the X chromosome[50]. Without roX RNAs, the MSL complex loses its specificity and dosage compensation is lost. Similarly, most of the centromeric RNA in maize probably functions in trans; that is, it is unlikely that all RNA associated with centromeric DNA is encoded by the DNA directly beneath it. However it is also very probable that each centromere has the capacity to transcribe its own large population of RNA. The transcriptionally competent state of each centromere[23] can provide a renewable, effective cis-acting source of RNA for stabilizing CENPC at the inner kinetochore. In the larger view, the mode of centromere replication may revolve around that fact that two proteins can serve as place markers, CENH3 and CENPC, and that they have different temporal patterns of incorporation. CENH3 is assembled in a defined period( G2 in plants, G1 in animals), while CENPC is incorporated throughout the cell cycle[16]. If, as in Drosophila, the two proteins can target each other to the kinetochore[20],[22], then at least one of the place markers will be present on DNA at all times( Figure 8). While CENH3 appears to be a defining feature in all eukaryotes, any number of other kinetochore proteins could serve as the second marker and target CENH3 or its assembly factors. CENPC is currently the best candidate in plants, but it is conceivable that other known or unknown kinetochore proteins, such as the functional equivalent of mammalian CENP-I or CENP-H may have similar roles[16],[18],[19].
Here we address the issue of how genetic information is passed from one generation to the next without the involvement of specific DNA sequences . This type of inheritance is referred to as epigenetics . Centromeric sequences are highly variable and in many cases are not sufficient for centromere function . Rather , secondary features of the DNA , such as methylation or associated RNA molecules may serve to recruit key centromere binding proteins . Prior data from several species have established that single-stranded RNAs are surprisingly abundant on centromeric chromatin . Here we identified the DNA-binding domain of a key centromere binding protein in maize ( CENPC ) and showed that it requires single-stranded RNA to effectively bind DNA in vitro . When the DNA/RNA binding domain was deleted , the accuracy of CENPC targeting to centromeres was reduced but not abolished . The results bolster the view that centromere-bound RNA is one component of the epigenetic determination process that assures centromeres are stably inherited . In addition , our data suggest a general mechanism for how RNA can influence the binding of chromatin proteins to DNA .