Transcription of two classes of rat growth hormone gene-associated repetitive DNA: differences in activity and effects of tandem repeat structure

Coordinated posttranscriptional control of gene expression by modular elements including Alu-like repetitive sequences

We previously reported that in rat fibroblasts, accumulation of a set of mRNAs ("pIL genes") was modulated as a function of cell growth and transformation, at a posttranscriptional stage, and by a mechanism that depends on a short nucleotide sequence containing an ID repetitive element. In mouse fibroblasts, hybridization with rat pIL probes identified mRNAs with the same pattern of expression, which did not contain ID sequences but contained a different regulatory element, encompassing a repetitive sequence of the B1 family. Expression in mouse cells of a reporter beta-globin gene carrying this element inserted in its 3' noncoding region was growth- and transformation-dependent. The nucleotide sequences of two murine and of three rat pIL cDNAs showed clear similarities in the region immediately adjacent to the ID and B1 repeats. Both the repeat and the flanking sequence were required to confer on beta-globin constructs the pattern of expression characteristic of the pIL genes. The hypothesis is presented that repetitive sequences in the eukaryotic genome might be modular parts of complex regulatory elements ensuring the coordinated expression of various mRNA species.

Sequence organization of variant mouse 4.5 S RNA genes and pseudogenes

The rodent 4.5 S RNA is an RNA polymerase III product with a sequence related to the Alu family of interspersed repeated DNA. A previous study identified a tandem array of 4.2-kb repeating units that contain the 4.5 S RNA coding sequence as well as many short repetitive sequences. To understand the genomic organization of this gene family, we have isolated and characterized 4.5 S RNA sequences that are part of the tandem array as well as identified members that are not part of the array. One variant 4.5 S RNA gene family member exhibits length polymorphisms in its minisatellite sites relative to the single previously reported gene. The 4.5 S RNA sequences that are not part of the tandem array possess many of the features of processed pseudogenes and are found adjacent to other interspersed repeated elements. These findings suggest that the mouse 4.5 S RNA can behave as a retroposon, resulting in the accumulation of 4.5 S RNA-like elements at many sites in the genome.

Synthesis and processing of small B2 transcripts in mouse embryonal carcinoma cells

B2 genes are short repeated sequences which are transcribed by RNA polymerase III. Abundant transcripts accumulate in embryonic and transformed cells, but transcripts are rare or absent from normal differentiated cell types. During retinoic acid-induced differentiation of P19 embryonal carcinoma cells, an early transient increase in B2 RNA levels is followed by a rapid drop in expression. The marked changes in B2 RNA levels are most likely due to transcriptional modulation since B2 RNA stabilities are unaffected by differentiation. At least four short-lived B2 RNAs with apparent lengths of 150, 180, 240, and 500 nucleotides were characterized. The two larger RNAs are polyadenylated and are more stable in cells. A cDNA of a B2 gene was isolated which was over 99% identical to the consensus sequence. This B2 cDNA can be transcribed in human cells and yields at least two distinct transcripts. We propose a model for B2 RNA metabolism which describes transcription, posttranscriptional modification and processing, and nucleocytoplasmic transport.

Synthesis and processing of small B2 transcripts in mouse embryonal carcinoma cells

B2 genes are short repeated sequences which are transcribed by RNA polymerase III. Abundant transcripts accumulate in embryonic and transformed cells, but transcripts are rare or absent from normal differentiated cell types. During retinoic acid-induced differentiation of P19 embryonal carcinoma cells, an early transient increase in B2 RNA levels is followed by a rapid drop in expression. The marked changes in B2 RNA levels are most likely due to transcriptional modulation since B2 RNA stabilities are unaffected by differentiation. At least four short-lived B2 RNAs with apparent lengths of 150, 180, 240, and 500 nucleotides were characterized. The two larger RNAs are polyadenylated and are more stable in cells. A cDNA of a B2 gene was isolated which was over 99% identical to the consensus sequence. This B2 cDNA can be transcribed in human cells and yields at least two distinct transcripts. We propose a model for B2 RNA metabolism which describes transcription, posttranscriptional modification and processing, and nucleocytoplasmic transport.

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.

Processing of the primary transcript for the rat growth hormone gene in vivo

Processing of the rat growth hormone (rGH) gene primary transcript and the effects of thyroid and glucocorticoid hormones on rGH pre-mRNA levels have been studied using subcloned radiolabeled DNA fragments from each of the four introns of this gene as probes. Blot-hybridization analysis of poly(A)+RNA from GC cells, GH3 cells, and normal pituitary gland indicates that processing of intron sequences from the precursor transcript takes place in a qualitatively similar fashion in each of these cell types. The data indicate that, in general, those introns closest to the termini of the primary transcript are removed first followed by removal of the internal introns. The suggested order of removal is IA, ID, IC, and IB. This process is unaffected qualitatively by thyroid or glucocorticoid hormones, both of which increase the rate of transcription of the gene. In addition to the primary transcript and the partially processed intermediate transcripts, GC and GH3 cells were found to contain a heterogenous group of intron-containing polyadenylated rGH gene transcripts which cannot be accounted for by any combination of intron deletions. These transcripts could arise either from internal start sites in the gene, premature termination of transcription, or inefficient processing of rGH mRNA precursors in the transformed cells. Thyroid hormone rapidly increases the levels of intron C-containing transcripts with kinetics that parallel the binding of thyroid hormone receptor to nuclei, but does not alter the ratio of primary to partially processed transcripts. These data suggest that most of the stimulatory activity of this hormone is due to effects on rGH gene transcription and not on pre-mRNA processing.(ABSTRACT TRUNCATED AT 250 WORDS)

Nucleotide sequence and transcription of a rat tRNA(Phe) gene and a neighboring Alu-like element

A bacteriophage gamma Ch4A clone containing a 22-kb rat DNA insert was isolated and found to contain a solitary tRNA(Phe)GAA gene and, 436 bp downstream of it, an Alu-like element. The nucleotide sequence of a 1141-bp DNA fragment containing these genes was determined. The rat tRNA(Phe)GAA gene, with the exception of an additional A in the extra arm, has a sequence identical to that of a rabbit liver tRNA(Phe). The Alu-like element belongs to the rodent B2 family of short interspersed repetitive nucleotide sequences. This repetitive element, B2Phe, is flanked by 12-bp direct repeats, contains an internal split promoter (block A and block B) for RNA polymerase III and is devoid of an A-rich segment at the 3' end. Like other members of the B2 family, the B2Phe element presents 64% sequence homology with rat serine tRNA and contains a serine (GCT) anticodon. Both tRNA(Phe)GAA gene and B2Phe element were found to be transcriptionally active in HeLa cell and Xenopus oocyte nuclear extracts. The tRNA(Phe) gene transcripts were processed during the course of transcription to form mature-size tRNA(Phe). The transcription efficiency of the B2Phe element was found to be an order of magnitude higher than that of the tRNA(Phe) gene. Competition experiments demonstrate that the B2Phe DNA can form a more stable transcription complex than the tRNA(Phe) gene and compete with it for binding of transcription factors.

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.

Selective transcription and DNase I protection of the rat prolactin gene by GH3 pituitary cell-free extracts

Prolactin (PRL) is a member of the growth hormone gene family that is specifically expressed in the lactotroph cells of the anterior pituitary. Whole cell extracts have been prepared from cultured GH3 rat pituitary tumor cells to study lactotroph-specific expression of the rat PRL (rPRL) gene in an in vitro transcription assay. The human alpha 1-globin and Rous sarcoma virus promoters efficiently initiate transcription in both HeLa and GH3 cell extracts, whereas the rPRL promoter containing 425 base pairs of 5' flanking DNA is active only in GH3 pituitary cell-free extracts. Transcription of the rPRL gene was reconstituted in HeLa cell extracts by the addition of GH3 cell extracts. DNase I digestion of the rPRL promoter reveals two protected regions centered at positions -55 (I) and -160 (III) that are GH3 cell-specific and rPRL promoter-selective. These "footprints" overlie a highly conserved 8-base-pair motif, CCTGATAATA. By contrast, footprint II at position -125 is common to both HeLa and GH3 cell extracts and overlies a 15-base-pair sequence found in all members of the growth hormone gene family. Thus, GH3 pituitary cell-free extracts selectively transcribe the rPRL gene and contain cell-specific factors that directly interact with the rPRL promoter. These studies provide useful assays to further identify, purify, and characterize pituitary-specific transcription factors and to address the biochemical mechanisms involved in rPRL gene expression.

Differential ability of various plasmid DNAs to sequester inhibitors of RNA polymerase III transcription

Deletion mutants of the Drosophila tRNA(Arg) gene that lack A-box promoter sequences are not transcribed in several cell-free systems; however, they are actively expressed in vivo in Xenopus oocytes (Sharp et al., 1983a). We show that two A-box deletion mutants of the tRNA(Arg) gene can be transcribed by a HeLa cell-free transcription system if it is preincubated with various DNAs, indicating that an inhibitor is responsible for the lack of mutant tRNA gene transcription. Optimal mutant transcription rescue, and presumably optimal binding of inhibitor, is facilitated by the presence of an active RNA polymerase II promoter in the preincubating DNA. Plasmid DNAs containing RNA polymerase III or weak RNA polymerase II promoters are of intermediate rescue efficiency, and pBR322 DNA is least efficient. Competition studies indicate that the stability of the inhibitor-DNA complex formed initially is apparently increased if the preincubating DNA contains an active RNA polymerase II promoter. Thus, HeLa whole-cell lysates contain a specific inhibitor(s) of RNA polymerase III transcription that primarily affects weakened RNA polymerase III promoters (e.g., A-box deletion mutants) and binds preferentially to DNAs containing an active RNA polymerase II promoter. Yet this apparent sequestration of inhibitor by Class II templates does not appear to inhibit their subsequent transcription by RNA polymerase II. These data raise the possibility that there may be interactions between the RNA polymerase II and III transcription machinery.

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.

Stable accumulation of a rat truncated repeat transcript in Xenopus oocytes

To define potential mechanisms of expression of middle-repetitive DNA, Xenopus oocytes were employed to examine the rat type 2 and truncated repeat (TR) elements contained in an intron and in the 3'-flanking region of the rat growth hormone gene. These repeats contain significant sequence and structural homology to tRNA genes and, thus, may represent tRNA pseudogenes. Transcripts from the type 2 elements do not accumulate in the cytosol and are found predominantly in the nucleus, whereas those from TR DNA are expressed in the cytosol of neural and pituitary tissues. In HeLa cell extracts, the rat growth hormone type 2 sequences initiate RNA polymerase III transcription resulting in multiple transcripts of 175-970 nucleotides; some of these also contain TR sequences that are present only as downstream structures since the rat growth hormone-TR DNA lacks promoter activity. In Xenopus oocytes the same template also results in multiple transcripts, but with time a single, homogeneous 73-base RNA preferentially accumulates. This RNA probably arises from larger repetitive DNA transcripts as assessed by the kinetics of its formation, its 5' terminus, and the injection of transcripts generated in HeLa cell-free extracts into the oocytes. Sequence analysis of the 73-base RNA suggests that it is a TR transcripts derived from the TR region with tRNA homology. Stable type 2 transcripts were not detected. Thus, type 2 elements are transcribed in the oocytes, but RNAs from them are degraded whereas discrete TR DNA transcripts can be derived from larger RNA molecules and can accumulate in the cytosol due to their preferential stability. These findings indicate that posttranscriptional control mechanisms can operate to direct differential expression of closely related repetitive DNAs and suggest that structures similar to tRNA contained within the TR sequences may allow them to accumulate preferentially in the cytoplasm.

A highly reiterated family of transcribed oligo(A)-terminated, interspersed DNA elements in the genome of Bombyx mori

A library of low Cot DNA (Cot is the molar concentration of DNA times the incubation time in seconds) from Bombyx mori was used to isolate five independent clones of highly reiterated sequences from the genome of this organism. Sequence analysis revealed that all five clones belong to a single family of repetitive DNA elements, which we have named Bm1, and whose reiteration frequency is approximately 2.3 X 10(4) copies per haploid genome. Probing of a Bombyx genomic library (in lambda phage) with a Bm1 clone reveals that this repetitive sequence is dispersed throughout the genome. The pattern of interspersion was confirmed by Southern blot mapping of a large (270 X 10(3) base-pairs) domain of the chorion locus of Bombyx, where at least 13 independent regions were found to hybridize to Bm1. Four additional Bm1 elements have been sequenced from a 4.8 X 10(3) base-pair genomic fragment containing an early chorion gene. Two of these four elements are bounded by short (4 to 12 base-pairs) direct repeats. The nine Bm1 elements which have been sequenced are greater than 88% homologous to each other, and tend to fall in at least two size classes (253 base-pairs and 450 base-pairs). Seven of the nine Bm1 elements have a short 6 to 10 base-pair oligo(A) sequence at the 3' end. A sequence of about 29 base-pairs at the 3' end, including the oligo(A), shows 86% homology to the equivalent 3'-terminal domain of human Alu family repetitive elements. A 129 base-pair domain at the 5' end of Bm1 shows 66% homology to a Drosophila valine transfer RNA gene; thus the 5' end of Bm1 may contain the split internal RNA polymerase III promoter that is characteristic of most transcribed tRNA-like retroposons. Dot-blot analysis of Bombyx RNA shows that Bm1 DNA is indeed transcribed, and that the transcripts are well-represented in the total RNA of an ovarian-derived permanent cell line and posterior silk glands early in the fifth instar, but are less abundant in the RNA of pupae or silk glands late in the fifth instar.

Analysis of repetitive sequence elements containing tRNA-like sequences

Several repetitive sequence elements from diverse species share extensive sequence homology with tRNA molecules. Analysis of the tRNA-like sequences within these elements suggest that they have originated from authentic tRNA sequences. Elements containing tRNA-like sequences can be divided into three distinct groups whose members share extensive sequence homology, have similar sequence organization and have unique species distribution. We suggest that these three groups represent independent examples of retroposon families that have originated from tRNAs.

Structure and transcription of eukaryotic tRNA genes

The availability of cloned tRNA genes and a variety of eukaryotic in vitro transcription systems allowed rapid progress during the past few years in the characterization of signals in the DNA-controlling gene transcription and in the processing of the precurser RNAs formed. This will be the subject matter discussed in this review.