Stable accumulation of a rat truncated repeat transcript in Xenopus oocytes

In vivo transcription of a cloned prosimian primate SINE sequence

SINE transcription was studied by introducing a galago Monomer family member (gal39), into the mouse Ltk- cell line. Cells transiently transfected with gal39 produce gal39-specific RNA polymerase III-directed transcripts. In permanent cell lines gal39 expression was largely shut off. Genomic environment, copy number and tandem repetition of integrated SINE sequences influenced whether or not RNA polymerase III-directed gal39 transcripts were detectable. These transcripts differ in length from the observed endogenous transcript in cultured galago cells which hybridizes to this repetitive DNA family.

Cell-specific expression of transfected brain identifier repetitive DNAs

To define the neural-specific expression of rat repetitive identifier (ID) DNA, we co-transfected an intron B subclone of the rat growth hormone (rGH) gene, containing a tandem array of two type 2 repeats and a single ID monomer, and a plasmid conferring neomycin resistance into human SK-N-MC neuroblastoma, HeLa epidermal carcinoma, 293 kidney and 251 MG glioblastoma cells. Transcript analysis from both individual and pools of G418-resistant cells revealed that rGH intron B repeats were expressed only in SK-N-MC neuroblastoma cells as small, cytoplasmic RNAs of 85, 110, 155 and 180 bases. Primer-extension studies show these repetitive RNAs to contain a common 5' end that maps precisely to the beginning of the ID element and that type 2 transcripts are not stably expressed. However, ID DNA expression from two other transfected plasmids, each containing only the ID core sequence, was not restricted to the SK-N-MC cell line. These data show that the transfected rGH ID sequence is selectively expressed in a neural-specific manner resulting in BC-like RNAs, and furthermore, suggest that flanking DNA may play a role in cell-specific expression of certain repetitive DNA elements.

Expression of small cytoplasmic transcripts of the rat identifier element in vivo and in cultured cells

We examined the level of expression of small RNA transcripts hybridizing to a rodent repetitive DNA element, the identifier (ID) sequence, in a variety of cell types in vivo and in cultured mammalian cells. A 160-nucleotide (160n) cytoplasmic poly(A)+ RNA (BC1) appeared in late embryonic and early postnatal rat brain development, was enriched in the cerebral cortex, and appeared to be restricted to neural tissue and the anterior pituitary gland. A 110n RNA (BC2) was specifically enriched in brain, especially the postnatal cortex, but was detectable at low levels in peripheral tissues. A third, related 75n poly(A)- RNA (T3) was found in rat brain and at lower levels in peripheral tissues but was very abundant in the testes. The BC RNAs were found in a variety of rat cell lines, and their level of expression was dependent upon cell culture conditions. A rat ID probe detected BC-like RNAs in mouse brain but not liver and detected a 200n RNA in monkey brain but not liver at lower hybridization stringencies. These RNAs were expressed by mouse and primate cell lines. Thus, tissue-specific expression of small ID-sequence-related transcripts is conserved among mammals, but the tight regulation found in vivo is lost by cells in culture.

Expression of small cytoplasmic transcripts of the rat identifier element in vivo and in cultured cells

We examined the level of expression of small RNA transcripts hybridizing to a rodent repetitive DNA element, the identifier (ID) sequence, in a variety of cell types in vivo and in cultured mammalian cells. A 160-nucleotide (160n) cytoplasmic poly(A)+ RNA (BC1) appeared in late embryonic and early postnatal rat brain development, was enriched in the cerebral cortex, and appeared to be restricted to neural tissue and the anterior pituitary gland. A 110n RNA (BC2) was specifically enriched in brain, especially the postnatal cortex, but was detectable at low levels in peripheral tissues. A third, related 75n poly(A)- RNA (T3) was found in rat brain and at lower levels in peripheral tissues but was very abundant in the testes. The BC RNAs were found in a variety of rat cell lines, and their level of expression was dependent upon cell culture conditions. A rat ID probe detected BC-like RNAs in mouse brain but not liver and detected a 200n RNA in monkey brain but not liver at lower hybridization stringencies. These RNAs were expressed by mouse and primate cell lines. Thus, tissue-specific expression of small ID-sequence-related transcripts is conserved among mammals, but the tight regulation found in vivo is lost by cells in culture.

Neural BC1 RNA: cDNA clones reveal nonrepetitive sequence content

BC1 is a small developmentally regulated RNA that is prevalent in nervous tissue. In order to determine if BC1 RNA represents the transcriptional by-product of various repetitive brain identifier (ID) elements or the independent transcript of a single or a few genes, we compared the sequences of a population of cDNA clones derived from in vitro C-tailed BC1 RNA. Each of 10 randomly selected clones revealed a 5' domain that was identical in sequence to the ID element, followed by an internal region of poly(A). In 8 of the clones, we found an identical, nonrepetitive sequence domain located at the 3' end of each molecule. An oligonucleotide of 30 residues complementary to this section identified only BC1 RNA in blot-hybridization analysis. Our results strongly suggest that BC1 RNA is transcribed specifically from the BC1 gene(s) and is not a highly heterogeneous population of ID-containing RNA polymerase III transcripts. Moreover, the availability of a unique BC1 RNA sequence will facilitate studies on tissue- and stage-specific gene regulation and will help in clarifying the role of this small RNA in the brain.