Antisense promoter of human L1 retrotransposon drives transcription of adjacent cellular genes.

In the human genome, retrotranspositionally competent long interspersed nuclear elements (L1Hs) are involved in the generation of processed pseudogenes and mobilization of unrelated sequences into existing genes. Transcription of each L1Hs is initiated from its internal promoter but may also be driven from the promoters of adjacent cellular genes. Here I show that a hitherto unknown L1Hs antisense promoter (ASP) drives the transcription of adjacent genes. The ASP is located in the L1Hs 5' untranslated region (5'UTR) and works in the opposite direction. Fifteen cDNAs, isolated from a human NTera2D1 cDNA library by a differential screening method, contained L1Hs 5'UTRs spliced to the sequences of known genes or non-proteincoding sequences. Four of these chimeric transcripts, selected for detailed analysis, were detected in total RNA of different cell lines. Their abundance accounted for roughly 1 to 500% of the transcripts of four known genes, suggesting a large variation in the efficiency of L1Hs ASP-driven transcription. ASP-directed transcription was also revealed from expressed sequence tag sequences and confirmed by using an RNA dot blot analysis. Nine of the 15 randomly selected genomic L1Hs 5'UTRs had ASP activities about 7- to 50-fold higher than background in transient transfection assays. ASP was assigned to the L1Hs 5'UTR between nucleotides 400 to 600 by deletion and mutation analysis. These results indicate that many L1Hs contain active ASPs which are capable of interfering with normal gene expression, and this type of transcriptional control may be widespread.

Alternate promoters and alternate splicing of human tenascin-X, a gene with 5' and 3' ends buried in other genes.

Tenascin-X (TN-X) is an extracellular matrix protein encoded by a large gene that overlaps the steroid 21-hydroxylase (P450c21) gene in the HLA locus on chromosome 6p21.3. This may be the most complex locus in the human genome identified to date, containing 13 overlapping transcription units in 160 kb of DNA. Previous studies determined the sequence of 39 TN-X exons, encoding a 12 kb open reading frame, but the promoter(s) of the gene had not been located. We identify the principal TN-X promoter and a previously unknown 5' untranslated exon that lies more than 10 kb upstream from the previously known exons. This promoter, which is substantially different from the promoter for TN-C, initiates transcription in human fetal adrenal and muscle, but expression in human NCI-H295 adrenocortical carcinoma cells is initiated by two other promoters lying further upstream. One of these is the same as the promoter for a recently identified Creb-related protein (Creb-rp), but transcripts initiated form this promoter in human adrenal NCI-H295 tumor cells are spliced differently from Creb-rp, and are largely retained in the nuclei of these cells. By analogy with the other two members of the tenascin family, TN-C and TN-R, it has been predicted that TN-X should undergo alternate splicing in its fibronectin-like domains. RACE cloning and RNase protection experiments reveal no such alternate splicing. The TN-X gene appears to be unique in having both its 5' and 3' ends buried in other genes.

Hybridization of the complementary mRNAs for P450c21 (steroid 21-hydroxylase) and tenascin-X is prevented by sequence-specific binding of nuclear proteins.

The CYP21 gene that encodes the steroid 21-hydroxylase, P450c21, is overlapped on the opposite strand of DNA by the TX-X gene encoding the extracellular matrix protein, tenascin-X. These transcripts contain perfectly complementary segments of 299 bases at their 3'-ends. As these genes are tandemly duplicated and are transcribed in the adrenal cortex, we investigated whether these self-complementary transcripts formed RNA-RNA hybrids in vivo. Formation of heterogeneous nuclear ribonucleoprotein complexes between nascent RNA transcripts and nuclear proteins might modulate such potential RNA-RNA interactions. Using a double RNase protection assay, we found that these RNAs form very small amounts of double-stranded RNA-RNA hybrids in adrenal cells in vivo. To understand why these mRNAs fail to hybridize in vivo, we studied the actions of nuclear proteins on the binding and annealing of their complementary regions in vitro. The nucleation of interstrand annealing was kinetically favored over binding and was efficiently promoted by nuclear extracts. However, RNA-RNA strand zippering was inhibited, suggesting that protein binding and/or stable RNA secondary structures contribute to discontiguous base pairing. Increasing concentrations of nuclear proteins increased the relative proportion of these RNAs in perfect RNase-resistant duplexes but reached only about 20% of the total available RNA strands at saturating concentrations of nuclear proteins. Preincubation of either of the two single-stranded RNAs with nuclear proteins strongly inhibited the nucleation step of annealing, whereas preincubation of both strands abolished the annealing. RNase footprinting of the wild type and mutagenized overlapping transcripts suggested that sequence-specific binding of nuclear proteins is limited to the 5'-half of each RNA strand. These results indicate that the transcription of complementary, opposite-strand RNAs is not a mechanism for the regulation of the abundance of adrenal P450c21 mRNA and suggest that nuclear proteins strongly interfere with interstrand RNA base pairing in vitro as well as in vivo.

A promoter within intron 35 of the human C4A gene initiates abundant adrenal-specific transcription of a 1 kb RNA: location of a cryptic CYP21 promoter element?

Complement component C4 is encoded by two nearly identical genes, C4A and C4B, that encode a C4 precursor that is proteolytically cleaved into the alpha, beta and gamma subunits of the mature protein. C4 is expressed primarily in liver and to a much lesser extent in immune cells. We have identified a unique 1 kb RNA transcript, termed Z, that arises from a cryptic promoter lying in the intron between exons 35 and 36 of the C4 gene. Primer extension, RNase protection, and 5' RACE experiments locate the cap site in intron 35, 55 bases upstream from exon 36. Northern blotting and RNase protection assays show that expression of this 1 kb Z RNA transcript is confined to the adrenal gland. Z RNA contains the same open reading frame as C4 which predicts a protein of 131 amino acids, but antisera to C4 do not interact with epitopes on this protein when it is synthesized by cell-free translation, hence the presence or absence of a Z protein in vivo could not be determined. Transfection of Z promoter/reporter constructs into human adrenal NCI-H295 cells shows that most if not all of the sequences required for high-level adrenal expression lie within 235 bases upstream from the cap site, but that this region is inactive when transfected into COS-1, JEG-3 and Hep-G2 cells, suggesting it contains an adrenal-specific element. The 222 bases upstream from the cap site are 75% identical in the human C4A and mouse Slp genes, and contain a potential binding site for steroidogenic factor 1 (SF-1), an orphan zinc-finger nuclear receptor. We propose that this region, like a nearby region in the mouse genome, functions as an upstream element of the P450c21 promoter, and may be a component of an adrenal-specific locus-control region.

Translation of the rat LINE bicistronic RNAs in vitro involves ribosomal reinitiation instead of frameshifting.

The genomic structure of the rat LINE (L1Rn) DNA element contains two overlapping open reading frames (ORFs) and apparently has a potential to code for a DNA/RNA-binding protein (in ORF1) and a reverse transcriptase (in ORF2). We have characterized a 1,630-bp L1Rn cDNA clone encompassing the overlapping ORFs and a 600-bp genomic fragment derived from a full-length L1Rn member and containing the beginning of ORF1. These DNAs were used to restore in part the ORF1-ORF2 organization of L1Rn after being cloned into the pSP65 vector under the control of SP6 polymerase promoter. To test whether L1Rn ORF1 and ORF2 are expressed as a fusion protein, a series of capped RNAs with progressive truncations containing one or both ORFs were prepared and translated in the rabbit reticulocyte lysate. Our analysis indicates that the expression of a putative reverse transcriptase-encoded L1Rn ORF2 in vitro is regulated by reinitiation or internal initiation of translation but not by ribosomal frameshifting.

Smart2, a cosmid vector with a phage lambda origin for both systematic chromosome walking and P-element-mediated gene transfer in Drosophila.

We describe a new phage-lambda-replicon-based cosmid vector suitable for both chromosome walking and P-element-mediated transformation in Drosophila. Its unique BamHI cloning site is flanked by the promoters for the SP6 and T7-encoded RNA polymerases, permitting the synthesis of probes complementary to the ends of the cloned inserts for library screening. The selectable marker is tet for bacterial cell transformation and neo for Drosophila transformation expressed under the control of the Drosophila hsp70 promoter.

Consecutive DNA terminator sequencing by using enzymatically generated primers.

An improved strategy for the dideoxy chain termination sequencing of M13 recombinant DNA using enzymatically generated primers is presented. It involves synchronous extension of the universal primer with the Klenow fragment of DNA polymerase I at an average rate of 200 deoxynucleoside triphosphates per minute to the immediate downstream region of a preselected restriction enzyme site. Subsequent cleavage with the restriction enzyme generates the short primers with homogeneous 5' ends which can be used for further sequencing. The next restriction sites are selected in the newly sequenced regions of DNA by means of a microcomputer. By repeating this primer extension-cleavage-sequencing strategy sequences altogether about 6 kb long from several recombinant single-stranded M13 DNAs have been determined by using twenty restriction enzymes with different specificities.

Reversible inhibition of butyrylcholinesterase with aromatic hydrocarbons.

Reversible inhibition of butyrylcholinesterase (acylcholine acylhydrolase, EC 3.1.1.8) with several aroma hydrocarbons was investigated and the results obtained were analyzed in terms of the hydrophobic interaction, making use of the solvent-water partition coefficients for the parameterization of the hydrophobic character of the ligand molecule. To obtain purely hydrophobic effects, the compounds incapable of specific solvation (hydrogen-bond formation) in water as well as in the hydrophobic phase were specially selected for the reaction series. Determination of the hydrophobic properties of the enzyme binding site allows further investigation into the other specificity-determining factors of the non-covalent complex formation step of butyrylcholinesterase-catalyzed reactions.

Structural analyses of E. coli 5S RNA fragments, their associates and complexes with proteins L18 and L25.

The structure of Escherichia coli 5S RNA fragments 1-41 and 42-120 has been studied by the read-off gel sequencing technique using S1 nuclease and cobra venom RNase as probes. Comparison of the digestion patterns with those of reassociated and intact 5S RNA suggests that the structure of both fragments is very similar to that of the corresponding regions in the intact molecule. Six different fragments obtained by partial digestion with T1 RNase and S1 nuclease have been used for reconstitution of 5S RNA, its certain structural regions and complexes with ribosomal proteins L18 and L25 recognizes the double-helix consisting of nucleotides 79-97 (i.e. prokaryotic stem), whereas a loop-region around position 40 (possible positions 39-47) is involved in the interaction with protein L18.

[Effect of pH on the cholinesterase hydrolysis of different substrates]. / Vliianie pH na gidroliz kholinesterazoi razlichnykh substratov.

The effect of pH on the kinetic constants of cholinesterase-catalyzed hydrolysis of isoamylacetate and acetylthiocholine was investigated. For the first substrate the rate-limiting step is the enzyme acetylation reaction, while the overall hydrolysis rate of the second substrate is limited by the deacetylation reaction. It was concluded that a basic group is involved in the deacetylation reaction and in the non-covalent binding step of both ionic and non-ionic substrates. An acidic group participates in the both reaction steps. It was suggested that protonation of the basic group leads to a conformational transition of the free enzyme and can also participate in the catalytic mechanism. The second basic group characterized by Ka3 can be the functional group of the enzyme anionic site. Taken together, the influence of pH on cholinesterase catalysis can be generalized by the overall reaction scheme.