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Sequence analysis of genomic clones containing the intact Dictyostelium transposable element DIRS-1 reveals that in five of six cases DIRS-1 has inserted into other DIRS-1 sequences. The nucleotide sequences just beyond the endpoints of the terminal repeats of five different genomic clones can be aligned with different regions of the internal nucleotide sequence of DIRS-1. In the three genomic clones which contain flanking sequences on both sides of the element, both flanking sequences are homologous with DIRS-1. In one of these clones, both extended flanking sequences represent the full 4.1-kilobase EcoRI fragment of DIRS-1, which has been interrupted by the insertion of an intact DIRS-1 element. There is no duplication or deletion (except possibly 1 base) of the DIRS-1 sequence upon insertion of a second DIRS-1 transposon. DIRS-1-into-DIRS-1 insertions can occur in either a colinear or inverted orientation with respect to the target sequence; the target sequence need not be an intact DIRS-1 element. We also describe a cDNA clone which could be derived by transcription of a sequence that resulted from a DIRS-1-into-DIRS-1 insertion and discuss its significance concerning the function of the heat-shock promoters found in the terminal repeats of DIRS-1 and in other DIRS-l-related sequences.DIRS-1 is a 4.7-kilobase (kb) repetitive and apparently transposable Dictyostelium discoideum DNA segment. Its expression is induced by cellular stresses such as heat shock, high cell density, and the initiation of development (3, 13). DIRS-1 consists of a 4.1-kb unique sequence flanked by ca. 330-base-pair (bp) inverted repeats. Partial DNA sequencing of DIRS-1 indicates that it encodes at least three long open reading frames and that it is transcribed into RNA which is polyadenylated and associated with polysomes ( The DIRS-1 terminal repeats contain heat-shock promoters which appear to be involved in its transcription. A highly conserved region of the terminal repeat contains a 14-nucleotide sequence that is nearly identical to the consensus heat-shock promoter sequence of Drosophila melanogaster (13; 13a). When introduced into Saccharomyces cerevisiae the DIRS-1 terminal repeat stimulates heat-shock-inducible transcription of adjacent sequences (2). The major DIRS-1 transcripts induced during heat shock and development in Dictyostelium species initiate within the terminal repeats ca. 210 bp from the heat-shock promoters (S. M. Cohen, J.

DIRS-1 is a Dictyostelium discoideum transposable element that contains heat shock promoter sequences in the inverted terminal repeats. We showed that transcription of a 4.5-kilobase polyadenylated RNA initiates at a discrete site within the left-terminal repeat of DIRS-1, downstream from heat shock promoter and TATA box sequences. This RNA represents a full-length transcript of DIRS-1. We describe a cDNA clone that contains the 4.1 kilobases of internal sequence of DIRS-1, a cDNA clone that spans the junction between the internal sequences and the right-terminal repeat, and a cDNA clone that appears to have been transcribed from a rearranged genomic copy of DIRS-1. A second DIRS-1 RNA, named El, is transcribed on the opposite strand of DIRS-1 from the 4.5-kilobase RNA and is under control of the heat shock promoter in the right-terminal repeat. El transcription initiates at multiple positions both within and downstream from the right-terminal repeat. The same transcriptional initiation sites are used during normal development and during heat shock, suggesting that in all cases DIRS-1 transcription is regulated by the heat shock promoters contained within the two terminal repeats.Dictyostelium intermediate repeat sequence 1 (DIRS-1) is a moderately repetitive and apparently transposable element with several unusual features (4,7,15). DIRS-1 consists of 4.1 kilobases (kb) of unique internal sequence flanked by inverted terminal repeats of unequal length, 332 and 360 base pairs (bp) (6, 23). There are about 40 copies of the intact DIRS-1 element interspersed throughout the Dictyostelium genome, as well as an additional 200 copies of related sequences (7). Different Dictyostelium strains have different sequences flanking some of their DIRS-1 elements, indicating that the element had transposed after these strains were separated (7, 15).Transcription of DIRS-1-related sequences results in the production of a heterogeneous population of polyadenylated cytoplasmic RNAs that are differentially expressed during development (7, 24; C. Zuker, Ph.D. thesis, Massachusetts Institute of Technology, Cambridge). DIRS-1 RNAs are present at very low levels in growing cells, begin to accumulate within the first hour after initiation of development, and reach their maximal level by 15 h. Transcription of DIRS-1-related RNAs is induced in vegetative cells subjected to stresses such as heat shock and high cell density (22).Examination of the DNA sequence of the DIRS-1 terminal repeats has led to the identification of a putative heat shock promoter sequence (22, 23) homologous to the Drosophila consensus heat shock promoter (13,14). Stress-induced transcription of DIRS-1-related RNAs is presumed to be directed by these sequences. Cappello et al. (5) showed that a cloned partial copy of DIRS-1 (pB41.6) directs transcription of a heat-shock-inducible RNA in yeasts and that heatinducible transcription of this RNA is dependent on the presence of the DIRS-1 terminal repeat. The isolated terminal repeat also directs heat-inducible transcrip...

DIRS-1 is a 4.7-kilobase-pair repetitive and apparently transposable Dictyostelium genetic element that is transcribed during differentiation or after heat shock. The terminal regions of DIRS-1 are inverted repeats of 330 base pairs. The repeats are highly conserved both within a given element as well as between different members of the family (<10% divergence). At the distal end of all left repeats is a 32-nucleotide sequence composed almost entirely of A and T residues. In addition to this 32-base A+T sequence, the distal region of all right repeats is extended by a 28-base-pair A+T-rich sequence that is identical in all copies. The sequences flanking each DIRS-1 sequence are completely dissimilar, and there appears to be no duplication of the genomic DNA sequence at the presumed point of DIRS-1 insertion. The terminal repeats can also be found interspersed in the genome independently of the complete element. In addition, the terminal repeats carry a 15-nucleotide sequence that greatly resembles the Drosophila consensus heat shock promoter and may be involved in the transcriptional induction of the DIRS-1 sequences. A common feature of most eukaryotic and prokaryotic transposable elements is the presence of terminally repeated sequences-either direct (copia, Ty-1, Tn9) or inverted (most bacterial transposon elements) (2-4). We report here that the terminal regions of the Dictyostelium DIRS-1 element are inverted repeats of 330 base pairs (bp); all of the repeats on the right side of the transposon are extended by an additional 28 bp rich in A and T residues. We also show that the repeats are found interspersed in the genome, independent of the complete element. We discuss the possible origins of such genomic fragments.DIRS-1 hybridizes to a large number of differently sized cytoplasmic polyadenylylated RNAs that accumulate in a coordinated fashion during development (5). These RNAs appear to be mRNAs as they are polyadenylylated and are specifically associated with polysomes (unpublished data). Most of the RNAs carrying sequences complementary to DIRS-1 are induced in response to heat shock or to other "stresses" which precede the initiation of development (5). Moreover, one of the many genomic fragments related to DIRS-1 (clone pB41-6) contains a 15-base sequence that resembles a Drosophila heat shock promoter (5) and directs the synthesis of a heat-inducible RNA when introduced into yeast (6). We demonstrate here that the heat shock promoter responsible for the thermal induction of pB41-6 is contained within the terminal repeats of DIRS-1.