Short Transcripts

The transactivation-responsive region (TAR) is located immediately downstream of the transcriptional start site in the HIV-1 LTR, encompassing nucleotides h-1 to h-59 (Berkhout et al. 1989 Muesing et al. 1987), and is reqnired for the function of the viral trans-activator protein Tat. In the absence of Tat (Fig. 5.2b), short transcripts... 

Fig. 3. Predicted alternative splicing in HPS (Hermansky-Pudlak Syndrome). The HPS polypeptide is a novel transmembrane protein that is likely to be a component of multiple cytoplasmic organelles and is apparently crucial for their normal development and function. We demonstrated an putative alternate transcript of the HPS gene. By RT-PCR, two transcripts were found in normal human brain, kidney, liver, lung, pancreas, and placenta. The short transcript (AA700609, length 302 bp) shows a deletion of 521 bp in the 3 UTR region of the HPS gene.

During formation of a mature, functional mRNA, the introns are removed and exons are spliced together. For short transcription units, RNA splicing usually follows cleavage and polyadenylation of the 3 end of the primary transcript, as depicted In Figure 12-2. However, for long transcription units... 

The short transcript AUCCGUACG would be derived from which of the following template DNA sequences (Note all sequences are written from 5 to 3 )... 

The two homologous repeats, each of 88 amino acids, at both ends of the TBP DNA-binding domain form two stmcturally very similar motifs. The two motifs each comprise an antiparallel p sheet of five strands and two helices (Figure 9.4). These two motifs are joined together by a short loop to make a 10-stranded p sheet which forms a saddle-shaped molecule. The loops that connect p strands 2 and 3 of each motif can be visualized as the stirmps of this molecular saddle. The underside of the saddle forms a concave surface built up by the central eight strands of the p sheet (see Figure 9.4a). Side chains from this side of the P sheet, as well as residues from the stirrups, form the DNA-binding site. No a helices are involved in the interaction area, in contrast to the situation in most other eucaryotic transcription factors (see below). 

The side of the p sheet that faces away from DNA is covered by two long a helices. One of these helices contains a number of basic residues from the middle segment of the polypeptide chain while the second helix is formed by the C-terminal residues. Residues from these two helices and from the short loop that joins the two motifs (red in Figure 9.4) are likely candidates for interactions with other subunits of the TFIID complex, and with specific transcription factors. 

E Transcription is the process by which RNA is produced to carry genetic information from the nucleus to the ribosomes. A short segment of the DNA double helix unwinds, and complementary ribonucleotides line up to pro-... 

DNA response elements are generally found a short distance upstream of promoters in selected genes. They are specific for selective transcription factors and... 

Recently, the related phenomenon of RNA interference (RNAi) has attracted much attention [5]. RNAi occurs when a short (generally 21 nucleotides in length) double-stranded RNA (dsRNA) catalyticaUy represses the translation of a fully complementary mRNA sequence. The process appears to proceed via a complex formed between the antisense RNA strand and a protein with RNase activity [6]. Upon binding to the target mRNA sequence, the ribonucleoprotein complex initiates cleavage of the mRNA transcript thus preventing translation of intact protein. After dissociation from the truncated mRNAs, the ribonucleoprotein complex is free to act on other intact mRNAs. Such small interfering RNAs (siRNAs) have... 

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