RNA transcription eukaryotic

A ribozyme activity that led to RNA-modifications that are analogous to the 5 -5 pyrophosphate caps of eukaryotic RNA transcripts was selected by Huang and Yarns [84]. Actually the author s intention was to isolate ribozymes which catalyze the formation of a mixed anhydride between an amino acid carboxylate and a 5 -terminal phosphate of an RNA, an activity that is chemically analogous to the activation of amino acids by ATP catalyzed by aminoacyl tRNA synthetases. However, while the selected ribozymes did... 

Figure 11-4. Splicing of a eukaryotic RNA transcript. A hypothetical hnRNA with two exons (EI and E2) and a single, large intron (I) is shown. Splicing can be divided into two main reactions initial attack of ribose near an A residue within the intron on the splice donor followed by attack of the newly available 3 end of exon I (EI) on the 5 end of exon 2 (E2) with coincident release of the intron. Special sequences surround the splice donor and acceptor sites. All steps occur within the spliceosome complex.

The absence of a nuclear membrane is a characteristic of bacteria that has a profound effect on transcription. Bacterial transcripts are processed rapidly, and their 5 ends often enter ribosomes and are directing protein synthesis, while the 3 ends of the genes are still being transcribed. In contrast, most eukaryotic RNA transcripts must be processed and transported out of the nucleus before they can function. As consequence, many aspects of the control of transcription differ between prokaryotes and eukaryotes. 

Fig. 17-5 Steps involved in the transcription and processing of a eukaryotic RNA transcript into mRNA.

There are close parallels between prokaryotic and eukaryotic RNA transcriptions. Transcription proceeds in four steps (Figure 13.12), namely ... 

Prokaryotic and eukaryotic RNA transcriptions show strong parallels though there are several important differences. A major distinction between prokaryotes and eukaryotes is the move from one prokaryotic enzyme that can faithfully transcribe DNA into RNA to three eukaryotic RNA polymerases. The eukaryotic RNA transcripts are precursors (e.g. pre-mRNA, pre-rRNA and pre-tRNA), which undergo processing to form respective mature RNAs. Furthermore, eukaryotic mRNAs are polyadenylated. A database for mammalian mRNA polyadenylation is available at PolyA DB (http // polya.umdnj.edu/polyadb). The eukaryotic transcription is tightly regulated and various proteins/factors known as transcription factors (TF) are involved in the eukaryotic transcription. The classification of transcription factors can be found at TRANFAC (http //transfac.gbf.de/TRANFAC/cl/cl.html). 

Alternative splicing The splicing of a eukaryotic RNA transcript in different ways, to include or exclude certain exons from the final mRNA. 

Figure 37-9. The eukaryotic basal transcription complex. Formation of the basal transcription complex begins when TFIID binds to the TATA box. It directs the assembly of several other components by protein-DNA and protein-protein interactions. The entire complex spans DNA from position -30 to +30 relative to the initiation site (+1, marked by bent arrow). The atomic level, x-ray-derived structures of RNA polymerase II alone and ofTBP bound to TATA promoter DNA in the presence of either TFIIB or TFIIA have all been solved at 3 A resolution. The structure of TFIID complexes have been determined by electron microscopy at 30 A resolution. Thus, the molecular structures of the transcription machinery are beginning to be elucidated. Much of this structural information is consistent with the models presented here.

In eukaryotes, general transcription factors must bind to the promoter to allow RNA polymerase II to bind and form the initiation complex at the start site for transcription. General manscription factors are common to most genes. The general transcription factor TFIID (the TATA fector) must bind to the TATA box before RNA polymerase II can bind. Other examples delude SP-1 and NF-.l that modulate basal transcription of many genes. 

C. Eukaryotic transcription is more complex than in prokaryotes, mainly in terms of the nature of the RNA polymerases, the assembly of the pre-initiation complex, and the need for processing eukaryotic RNAs. 

Eick, D., Wedel,A. and Heumann, H. From initiation to elongation comparison of transcription by prokaryotic and eukaryotic RNA polymerases (1994) Trends Gen. 10, 292-296... 

FIGURE 26-8 Common sequences in promoters recognized by eukaryotic RNA polymerase II. The TATA box is the major assembly point for the proteins of the preinitiation complexes of Pol II. The DNA is unwound at the initiator sequence (Inr), and the transcription start site is usually within or very near this sequence. In the Inr consensus sequence shown here, N represents any nucleotide Y, a pyrimidine nucleotide. Many additional sequences serve as binding sites for a wide variety of proteins that affect the activity of Pol II. These sequences are important in regulating Pol II promoters and vary greatly in type and... 

Most eukaryotic mRNA transcripts produce only one mature mRNA and one corresponding polypeptide, but some can be processed in more than one way to produce different mRNAs and thus different polypeptides. The primary transcript contains molecular signals for all the alternative processing pathways, and the pathway favored in a given cell is determined by processing factors, RNA-binding proteins that promote one particular path. 

RNA Posttranscriptional Processing Predict the likely effects of a mutation in the sequence (5 )AAUAAA in a eukaryotic mRNA transcript. 

The sequences of eukaryotic promoters are more variable than their prokaryotic counterparts (see Fig. 26-8). The three eukaryotic RNA polymerases usually require an array of general transcription factors in order to bind to a promoter. Yet, as with prokaryotic gene expression, the basal level of transcription is determined by the effect of promoter sequences on the function of RNA polymerase and its associated transcription factors. 

As already noted, eukaryotic RNA polymerases have little or no intrinsic affinity for their promoters initiation of transcription is almost always dependent on the action of multiple activator proteins. One important reason for the apparent predominance of positive regulation seems obvious the storage of DNA within chromatin effectively renders most promoters inaccessible, so genes are normally silent in the absence of other regulation. The structure of chromatin affects access to some promoters more than others, but repressors that... 

The structure of RNA polymerase, the signals that control transcription, and the varieties of modification that RNA transcripts can undergo dffer among organisms, and particularly from prokaryotes to eukaryotes. Therefore, in this chapter, the discussions of prokaryotic and eukaryotic transcription are presented separately. 

A. Eukaryotic general transcription factors bound to the promoter. CTF, SP1, and TFIID are general transcription factors. B. Enhancer stimulation of RNA polymerase II. 

Removal of introns Maturation of eukaryotic mRNA usually involves the removal of RNA sequences, which do not code for protein (introns, or intervening sequences) from the primary tran script. The remaining coding sequences, the exons, are spliced together to form the mature mRNA. The molecular machine that accomplishes these tasks is known as the spliceosome. [Note A few eukaryotic primary transcripts contain no introns. Others con tain a few introns, whereas some, such as the primary transcripts for the a-chains of collagen, contain more than fifty intervening sequences that must be removed before mature mRNA is ready for translation.]... 

Nearly all of the RNA of the cell is synthesized (transcribed) in the nucleus, according to the instructions encoded in the DNA. Some of the RNA then moves out of the nucleus into the cytoplasm where it functions in protein synthesis and in some other ways. Many eukaryotic genes consist of several sequences that may be separated in the DNA of a chromosome by intervening sequences of hundreds or thousands of base pairs. The long RNA transcripts made from these split genes must be cut and spliced in the nucleus to form the correct messenger RNA molecules which are then sent out to the ribosomes in the cytoplasm. 

The eukaryotic RNA polymerases are not inhibited by rifamycin, but RNA polymerases II and III are completely inhibited by the mushroom poison a-amanitin (see Box 28-B). Inhibitors of DNA gyrase (Chapter 27) also interfere with transcription as do chain terminators such as cordycepin (3 -deoxyadenosine) and related nucleosides. 

Formation of the initiation complex for transcription for the three major classes of eukaryotic RNA polymerase Poll, PolII, and PolIII. Each polymerase consists of many subunits (not shown). In addition to the firmly bound subunits, a number of protein factors, called transcription factors (TFs), only associate with the polymerases at the initiation site for transcription. For all three polymerases some of... 

In eukaryotes most transcription takes place in the nucleus. Three nuclear RNA polymerases, I, II and III, are responsible for the synthesis of rRNA, mRNA, and small RNA transcripts, respectively. The polymerases contain more subunits than in E. coli, and other proteins must bind at the initiation sites or near the... 

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