Nascent RNA

Template binding RNA polymerase (RNAP) binds to DNA and locates a promoter (P) melts the two DNA strands to form a preinitiation complex (PIQ. (2) Chain initiation RNAP holoenzyme (core + one of multiple sigma factors) catalyzes the coupling of the first base (usually ATP or GTP) to a second ribonucleoside triphosphate to form a dinucleotide. (3) Chain elongation Successive residues are added to the 3 -OH terminus of the nascent RNA molecule. (4) Chain termination and release The completed RNA chain and RNAP are released from the template. The RNAP holoenzyme re-forms, finds a promoter, and the cycle is repeated. 

Berkhout B, Silverman RH, Jeang KT (1989) Tat trans-activates the human immunodeficiency virus through a nascent RNA target. CeU 59(2) 273-282... 

Boffa, L.C., Walker, J., Chen, T.A., Sterner, R., Mariani, M.R., and Allfrey, V.G. (1990) Factors effecting nucleosome structure in transcriptionally active chromatin. Histone acetylation, nascent RNA and inhibitors of RNA synthesis. Eur. J. Biochem. 194, 811-823. 

DNA, since proximity eflfects demand that the DNA or nascent RNA closest to the histones at the point of disruption will be the polyanion for which those histones will preferentially reassociate. Ten Heggeler-Bordier et al. [95] have verified these observations. They used immuno-electron microscopy to determine what happens to histones after transcription with T7 RNA polymerase of a multi-nucleosomal template and also observed transfer to the nascent RNA. In contrast, Kirov et al. [96] have reported that no histones displace during transcription with this polymerase. However, as described above, transcriptional efficiency and ultimately histone displacement is not efficient in very low ionic strength conditions. 

Nascent RNA. The initial transcripts of RNA, before any modification or processing. 

Fig. 3. A transcription bubble. The DNA double helix Is unwound and RNA polymerase then synthesizes an RNA copy of the DNA template strand. The nascent RNA transiently forms an RNA-DNA hybrid helix but then peels away from the DNA which Is subsequently rewound into a helix once more.

The bacterial RNA polymerase has a subunit composition of ap>3 a, the a subunit being involved in correct initiation of transcription. Appropriate regulatory protein binding to the promoter region permits correct RNA polymerase binding, double-stranded DNA (dsDNA) unwinding and correct initiation of transcription. The dsDNA unwinds and the nascent RNA forms a transient RNA-DNA hybrid in the transcription bubble of unwound DNA that moves down the DNA. 

Mironov AS, Gusarov I, Raflkov R, Lopez LE, Shatalin K, Kreneva RA, Perumov DA, Nudler E. Sensing small molecules by nascent RNA a mechanism to control transcription in bacteria. Cell 2002 111 747-756. 

RNA polymerase proceeds along the DNA template, transcribing one of its strands until it reaches a terminator sequence. This sequence encodes a termination signal, which in E. coli is a base-paired hairpin on the newly synthesized RNA molecule (Figure 5.28). This hairpin is formed by base pairing of self-complementary sequences that are rich in G and C. Nascent RNA spontaneously dissociates from RNA polymerase when this hairpin is followed by a string of U residues. 

Splicing is a facile complex operation that is carried out by spliceosomes, which are assemblies of proteins and small RNA molecules (Section 28.3.4). This enzymatic machinery recognizes signals in the nascent RNA that specify the splice sites. Introns nearly always begin with GU and end with an AG that is preceded by a pyrimidine-rich tract (Figure 5.35). This consensus sequence is part of the signal for splicing. 

DNA stores genetic information in a stable form that can be readily replicated. However, the expression of this genetic information requires its flow from DNA to RNA to protein, as was introduced in Chapter 5. The present chapter deals with how RNA is synthesized and spliced. We begin with transcription in Escherichia coli and focus on three questions What are the properties of promoters (the DNA sites at which RNA transcription is initiated), and how do the promoters function How do RNA polymerase, the DNA template, and the nascent RNA chain interact with one another How is transcription terminated ... 

How does this combination hairpin-oligo(U) structure terminate transcription First, it seems likely that RNA polymerase pauses immediately after it has synthesized a stretch of RNA that folds into a hairpin. Furthermore, the RNA-DNA hybrid helix produced after the hairpin is unstable because its rU-dA base pairs are the weakest of the four kinds. Hence, the pause in transcription caused by the hairpin permits the weakly bound nascent RNA to dissociate from the DNA template and then from the enzyme. The solitary DNA template strand rejoins its partner to re-form the DNA duplex, and the transcription bubble closes. 

Figure 28.12. Mechanism For the Termination of Transcription hy p Protein. This protein is an ATP-dependent helicase that hinds the nascent RNA chain and pulls it away from RNA polymerase and the DNA template.

A second major difference between prokaryotes and eukaryotes is the extent of RNA processing. Although both prokaryotes and eukaryotes modify tRNA and rRNA, eukaryotes very extensively process nascent RNA destined to become mRNA. Primary transcripts (pre-mRNA molecules), the products of RNA polymerase action, acquire a cap at... 

Attenuation Is a Prokaryotic Mechanism for Regulating Transcription Through Modulation of Nascent RNA Secondary Structure... 

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