Brain-specific small RNA during development and ageing of mice

Pur alpha protein implicated in dendritic RNA transport interacts with ribosomes in neuronal cytoplasm

We have previously reported that pur alpha, known to be a regulator of DNA replication and transcription, links neural BC1 RNA to microtubules via dendrite-targeting RNA motifs. Here we demonstrate the subcellular localization of pur proteins within the brain. Pur proteins were detected in neurons but not in glia. Immunohistochemical staining was prominent in perikarya and proximal dendrites and also extended into primary dendritic processes, but no significant signals were detected in the distal regions of dendrite. When homogenates of mouse brain were fractionated, pur alpha was most concentrated in the microsomal pellet. Consistently, pur alpha co-fractionated with free polysomes as well as with membrane-bound polysomes and the association with polysomes was mediated by binding ribosomal subunits. Levels of ribosomes with pur alpha progressively increased during postnatal development of the brain.

Identification of a negative regulatory DNA element for neuronal BC1 RNA expression by RNA polymerase III

BC1 RNA is a neuronal cell-specific RNA polymerase III (Pol III) transcript. The BC1 RNA gene has plural types of Pol III promoters, in addition to which an E-box sequence (E2 site) acts as a transcriptional activator, which is recognized by a brain-specific protein(s). Using an in vitro transcription system, we found that the upstream region of the BC1 RNA gene contained a sequence that interfered with the activity of the E-box element in a distance-independent manner. A tandem repeat within this sequence, which was weakly homologous with the neuron-restrictive silencer element (NRSE) found in the Pol II system, was recognized by a brain nuclear protein. Consistently, the transcriptional activity increased by deleting the tandem repeat sequence. We called this BC1 RNA-repressing element BCRE. The DNA-binding specificities of BCRE-binding protein differed from that of NRSE-binding protein (NRSF). A similar protein with an ability to bind to BCRE was also found in liver and kidney. Furthermore, the glutamate analog kainic acid increased the DNA-binding of both E2 site-binding protein and BCRE-binding protein, and then the levels of BC1 RNA also increased transiently. Our results suggested that both positive and negative regulatory elements contribute to neuronal BC1 RNA expression.

The dendritic translocation of translin protein in the form of BC1 RNA protein particles in developing rat hippocampal neurons in primary culture

Neural BC1 RNA is distributed in neuronal dendrites as ribonucleoprotein particles (RNP). Our previous studies indicated the presence of Translin in BC1 RNPs, which is a translational repressor and links a subset of mRNAs to microtubules. In this study, we confirmed that Translin associates with BC1 RNP and we used immunocytochemical methods to examine the subcellular distribution of Translin in developing hippocampal cells in primary cultures. Translin was detected in both the nuclei and cytoplasm of neurons, whereas in glial cells it was localized in the nuclei. Consistent with the reported developmental time course of BC1 RNA expression and dendritic delivery the translocation of Translin to the neuronal dendrites appeared to correlate with neuronal development and differentiation events such as the onset of synaptogenesis in culture. These observations suggest that BC1 RNP or Translin itself may be relevant to the dendritic translation of mRNAs in response to transsynaptic activity.

An E-box sequence acts as a transcriptional activator for BC1 RNA expression by RNA polymerase III in the brain

BC1 RNA is a small cytoplasmic RNA that is transcribed by RNA polymerase III (Pol III) in the rodent nervous system. In addition to essential intragenic promoter elements for Pol III, the BC1 RNA gene has five E-box sequences (CANNTG) in its 5' flanking region. Deletion analysis using an in vitro transcription system revealed that the region containing the E2 site (CAATTG) was necessary for effective transcription of BC1 RNA. A construct with point mutations within the E2 site showed reduced transcriptional activity. Furthermore, DNaseT I protection and gel retardation assays demonstrated that the E2 site was recognized specifically by a brain nuclear protein(s). These results suggest that the upstream E-box sequence and its binding protein may be involved in the regulation by Pol III of preferential BC1 RNA expression in the brain.

Mutational analysis reveals that an array of GCAAG/CTTGC motifs between sprit promoter sequences for RNA polymerase III is essential for neural BC1 RNA transcription

BC1 RNA is expressed from an identifier (ID) sequence by RNA polymerase III (Pol III) and occurs in neural cells as a ribonucleoprotein particle (BC1 RNP). On the BC1 RNA gene, between the Pol III promoter A and B boxes, there is a region which contains short inverted repeats, including three GCAAG/CTTGC motifs. We found that a nuclear protein binds specifically to this region and, using an in vitro transcription system, demonstrated that point mutations within these motifs markedly inhibit BC1 RNA transcription. These results suggest that the GCAAG/CTTGC motif region and its binding protein may play a role in the transcription of BC1 RNA. Moreover, we demonstrated that transcription is repressed by a concomitant molar excess of BC1 RNA and that the BC1 RNA transcribed by this system forms an RNP with nuclear protein(s), suggesting some interaction of BC1 RNA with transcription factor(s).

Neural BC1 RNA in mouse skeletal muscle is a denervation-induced RNA whose expression is developmentally regulated

We detected neural BC1 RNA in mouse skeletal muscle. The level of BC1 RNA was high in the fetus, but it declined progressively to the adult level as development proceeded. These observations suggest that this RNA is involved in the prenatal development and differentiation of muscles. Although its developmental expression correlates with the fetal period of polyneuronal innervation, BC1 RNA does not seem to play a direct role(s) in synaptogenesis, since its expression was not restricted to the neuromuscular junction. We also demonstrated that the BC1 RNA level in adult muscle was elevated after denervation, suggesting that changes in the activity of muscles or neural factors caused by axotomy, or both may result in BC1 RNA upregulation.

Developmental change in subcellular location of Bp-1 protein with an ability to interact with both identifier sequence and its brain-specific transcript, BC-1 RNA

Identifier sequences are transcribed to generate a brain-specific BC-1 RNA present as a ribonucleoprotein particle in the dendrites and somata of neurons. This ribonucleoprotein particle contains an identifier sequence-binding protein (Bp-1 protein). We report here the purification of BC-1 RNA and demonstrate that Bp-1 protein interacts directly with the RNA. We also demonstrate an accumulation of Bp-1 protein in the nucleus of brain cells from mouse fetus and newborns that precedes the postnatal increase in BC-1 RNA. Cytoplasmic Bp-1 protein present in a complex with BC-1 RNA increases postnatally with a concomitant decrease in nuclear Bp-1 protein. These observations suggest that Bp-1 protein may play a role(s) in the synthesis and nuclear export of BC-1 RNA.

ID sequence-binding protein factors during development of mice

The ID repetitive sequence has been reported to be transcribed as small RNA in both a brain-specific and a developmental stage-specific manner. Several brain-specific proteins required for transcription, along with RNA polymerase III, may be involved in controlling the gene activity throughout development. We analyzed extracts from the brains and livers of mice in an electrophoretic mobility shift assay. Of ID sequence-binding proteins, we detected a protein factor(s) that interacts specifically with the region between two promoter sequences for RNA polymerase III. This protein factor seems to be relevant to postnatal accumulation of the small RNA transcripts of ID sequences, since its time course of expression is consistent with that of the synthesis of the small RNA during development. A penta-nucleotide direct repeat (GCAAG) and its inverted complement (CTTGC) are both present in that region and may be involved in the binding site for the protein factor. The biological significance of the binding site and interacting protein factor(s) is discussed.

ID sequence-binding protein factor complexed in ribonucleoprotein particles

We analyzed brain extracts from fetal or adult mice with a 32P-labeled 5'-half fragment of identifier (ID) sequence in a gel mobility shift assay. Upon digestion of extracts with RNase A prior to the binding reactions, a protein factor(s) that specifically binds to the fragment was shown to appreciably increase in amount with either of the extracts. Furthermore, the binding was competed with single-stranded ID sequences. These observations suggest that the protein factor is capable of interacting with either the genes or their small RNA transcripts.