Nonrandom integration of human U4 RNA pseudogenes

Secondary structure of 7SK and 7-2 small RNAs. Possible origin of some 7SK pseudogenes from cDNA formed through self-priming by 7SK RNA

Pseudogenes having homology to small RNAs, like 7SL, 7SK, 6S, 4.5S, U1, U2, and U3 RNAs, are abundant and dispersed in the genomes of higher eukaryotes [reviewed in Weiner et al. (1986) Annu. Rev. Biochem. 55, 631-661]. To understand better the possible origin of these pseudogenes, we studied the abilities of cytoplasmic 7SL, 7SK, and nucleolar 7-2 RNAs to self-prime and result in the synthesis of cDNAs. When rat 7SK RNA was used as substrate, a 294-nucleotide-long cDNA was synthesized in vitro by reverse transcriptase, indicating that the 3' end of 7SK RNA can act in a self-priming manner to generate 7SK cDNA. When 7-2 RNA was used as a substrate, a cDNA of approximately 235 nucleotides was observed; 7SL RNA did not act as a self-primer. Earlier studies have shown that DNAs homologous to 7SK RNA are represented by a moderately reiterated family in the mammalian genomes and many of these sequences were found to be truncated 7SK pseudogenes [Murphy et al. (1984) J. Mol. Biol. 177, 575-590]. In this study, one 7SK clone from the rat genome was characterized by sequencing. This clone contained 243 base pairs homologous to the 5' end of 7SK RNA, and was flanked by direct repeats. These data suggest that, as previously proposed for some U3 pseudogenes [Bernstein et al. (1983) Cell 32, 461-472], one mechanism for the generation of truncated 7SK pseudogenes may be the integration of self-primed reverse transcripts of 7SK RNA at random genomic sites.

Nucleotide sequence and organization of full length human U4 RNA pseudogenes

Two loci encoding human U4 RNA, designated U4/7 and U4/14, have been isolated and sequenced. Both are pseudogenes in that their sequences do not match any identified human U4 RNA species perfectly. The U4/7 locus harbours a full-length pseudogene of 144 bp with eight base substitutions in the structural region. This pseudogene might be derived from a hitherto unidentified human U4 RNA gene. The second locus, U4/14, has a complex structure; the structural sequence of a U4 gene has apparently been integrated into an Alu sequence.

Mouse U3-RNA-processed pseudogenes are nonrandomly integrated into genomic DNA. Implications for the process of retrogene formation

We have characterized three mouse U3-RNA-processed pseudogenes. Together with previous analyses of mouse functional genes and of rat genes and pseudogenes, these data provide some insights into the processes of U3 retrogene formation during the evolution of rodents. All the mouse retrogenes correspond to a full-length U3B-coding sequence with a 3'-poly(A) tail and are precisely flanked by a pair of direct repeats, in agreement with formation through an RNA intermediate followed by insertion at staggered nicks in the genome. All the rodents U3 retrogenes identified so far are produced from a U3B-RNA form, with two of them (one for each rodent) formed from a 3'-elongated U3-RNA precursor, pointing to the particular susceptibility of RNA precursors forms to serve as templates for retrogene formation. Rodent full-length U3 retrogenes are not inserted randomly in the genome but are systematically found in a context of simple sequences, prone to slipped-strand mispairings and likely to favour the appearance of single-stranded DNA. Moreover their flanking repeats share not only the same size (15 bp) but also common sequence features (which extend to vicinal upstream nucleotides) suggesting that common mechanisms, specific to this class of retrogenes, have been involved in their formation. For the first time, a model accounting for the generation of full-length cDNA copies from nonpolyadenylated RNA templates is proposed. Rodent U3 retrogenes appear to be of rather recent origin (posterior to the mouse/rat divergence) and some of them could have undergone subsequent genetic exchanges with the functional genes.

Fragments of rDNA within the Chinese hamster genome

We report the isolation and partial characterization of distinct EcoRI fragments of the Chinese hamster genome which contain regions complementary to a 1-kb portion of the mature 18 S ribosomal RNA molecule. This previously undescribed 18 S rDNA-like region, which we have termed a "fragment of ribosomal DNA" (frDNA), has been shown by sequence analysis to correspond to a region extending 1 kb upstream from the 3' terminus of the mature 18 S rRNA. Within the five frDNA-containing clones described here, no other region of the ribosomal RNA cistron was detected, making it unlikely that these are polymorphic forms of the ribosomal DNA repeat. The 18 S rDNA-complementary region appears to be flanked by an imperfect direct repeat, which could have been the result of the retroinsertion of a fragment of ribosomal RNA. Directly adjacent to the 18 S rDNA-like region we have identified nonribosomal sequences which appear common to all of the frDNA-containing clones we examined. At least eight different-sized EcoRI fragments contain frDNAs and the abundance of the frDNAs appears to be of the order of 30 per genome. The occurrence of multiple copies of this ribosomal-nonribosomal chimera suggests that, once formed, the chimera was duplicated within the genome.

Cotransposition of a highly repetitive DNA element with flanking sequences in the genome of the midge Chironomus thummi

A family of highly repetitive DNA elements, the Cla-elements, is present in the genomes of the two sibling species Chironomus th. thummi and Ch. th. piger. These Cla-elements are organized in large tandem repetitive clusters as well as occurring as interspersed monomeric elements, in both subspecies. The analysis of a monomeric Cla-element and several kilobases of its flanking sequences from Ch. th. piger revealed that the short Cla-elements are cotransposed together with adjacent DNA. We found the same association of Cla-elements with specific flanking DNA in clones obtained from the rDNA of Ch. th. thummi and from nonribosomal Cla-DNA of Ch. th. piger. The Cla-element-flanking DNA is clearly also repetitive, but mainly of interspersed organization.

Evidence of sequences resembling avian retrovirus long terminal repeats flanking the trout protamine gene

Additional TATA boxes are present in the flanking regions of trout protamine genes. Their activity as promoters was assayed using an in vitro transcription system. These additional TATA boxes, together with polyadenylation signals that include the consensus AATAAA and CACTG sequences very close to the promoters, suggest that these sequences may be closely related to retroviral long terminal repeat (LTR) sequences. Other features of retroviral LTRs that are also present are short inverted repeats. The LTR-like sequences flanking the trout protamine gene show significant homology to the avian sarcoma virus LTR over a 40-bp region. The trout protamine gene falls into the relatively rare intronless class of eukaryotic genes. This suggests that the gene could have been derived from a processed gene introduced into the genome by reverse transcription of a mature mRNA. The protamine-mRNA-coding region is flanked by AACA... TGTT sequences, which might represent vestigial traces of past recombination events and whose presence supports the notion that the protamine gene sequence was of foreign origin. Recent attempts in this laboratory to transfer the protamine gene into mouse cells have resulted in a high frequency of deletions similar to those observed with constructs in which a retrovirus was used as a vector to transfect foreign DNA with promoters. The distribution of protamine genes in the animal kingdom is very sporadic, which suggests that protamine genes appeared relatively late in evolution. The nonuniform occurrence of the gene among lower vertebrates may have been the result of its horizontal transmission only to certain species, possibly by infection with retroviruses that acquired it from a different species.

Genes for human U4 small nuclear RNA

A study of human genes coding for U4 small nuclear RNA is presented. It is known from previous studies that mammalian cells contain three major U4 RNA species, designated U4A, U4B, and U4C (Krol and Branlant, 1981). A clone was isolated from a human DNA library which contained two transcriptionally active genes for U4 RNA. U4 transcription was sensitive to low concentrations of alpha-amanitin, inferring that U4 RNA is a product of RNA polymerase II or RNA polymerase II-like activity. One of the two genes contains a coding region which matches the sequence of U4C RNA perfectly. The coding region of the second gene resembles U4B RNA although there are two differences between the sequence of this gene and the U4B RNA sequence, suggesting that it may encode a minor, hitherto undetected U4 RNA species. The 5'-flanking regions of the two U4 genes contain several almost perfectly conserved sequence motifs. One is located between positions -50 and -60. This motif is present in equivalent positions in the two U4 genes as well as in human U1 and U2 genes. A second motif, which is 19 nucleotides (nt) long and centered around nt position -140, is present in the two U4 genes but absent from U2 RNA genes. A third highly conserved region, located between nt positions -210 and -250, is a putative enhancer element. It includes one copy of the so-called octanucleotide motif, previously identified as adjacent to the early SV40 promoter and immunoglobulin promoters. Another highly conserved sequence motif, CTCTGTGA, is located approximately one helical turn upstream from the octanucleotide motif in both U2 and U4 genes. The human genome appears to contain a family of U4 RNA genes comprising at least 100 copies.

U4 small nuclear RNA pseudogenes from rat genome have common truncated 3'-ends

Four U4 RNA pseudogenes were isolated and characterized from a rat genomic bank. The four pseudogenes contained sequences completely homologous to U4 RNA from nucleotides 1 to 67 and had common truncated 3'-ends. Three of the four pseudogenes were flanked by 14 to 18 nucleotide-long direct repeats. The structural features of these four U4 RNA pseudogenes are consistent with the hypothesis that these pseudogenes arose by RNA self-primed complementary DNA synthesis and integration into the genome (Van Arsdell et al., Cell 26:11-17, 1981).