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Changing Directions in Pol III Transcription

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Changing Directions in Pol III Transcription Downloaded from genesdev.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press COMMENTARY Changing directions in Pol III transcription Approximately 8 years ago, our thinking about the orga- The U6 snRNA genes also contain what may be a 'ca- nization of promoter elements in DNA took a sudden nonical' RNA polymerase III box A promoter element, turn. The realization that initiation of transcription by previously shown to be important for the transcription RNA polymerase III relied upon intragenic sequences, of tRNA, adenovirus VA, and 5S RNA genes (reviewed and thus differed significantly from the paradigm then in Sharp et al. 1985). Remarkably, neither this element provided by prokaryotic RNA polymerases, raised many nor, for that matter, are any of the gene's internal se- questions about the origins of the various transcription quences required for transcription in vitro (Carbon et al. systems and why they might be so different. 1987; Das et al. 1988). Only when placed in competition These questions are slowly being answered. Compar- with other RNA Pol III transcribed genes does the box A isons of the structures of RNA polymerases of eu- internal sequence confer a transcriptional advantage to karyotes and of prokaryotes are revealing their con- the U6 snRNA gene (Carbon et al. 1987). Thus, we do served functional elements, indicating they have not yet know the extent to which U6 snRNA transcrip- common origins (for review, see Buhler et al. 1987). tion in vivo relies solely upon upstream elements, nor Concurrently, some of the ostensibly major differences are there insights into whether any of these elements between eukaryotic RNA polymerase II promoter ele- participate in the regulation of transcription. ments and prokaryotic promoters (notably, the impor- Findings analogous to these in several respects have tance of far upstream sequences) no longer appear to be been reported recently by groups studying transcription that distinctive (see Ptashne 1986). And now, an ever-in- initiation of the human 7SK and 7SL RNA genes. As creasing volume of information is dispelling the notion with the U6 snRNA genes, upstream sequences are re- that promoter elements recognized by any of the eukary- quired for transcription of both types of 7S RNA genes otic RNA polymerases are necessarily unique. (Ullu and Weiner 1985; Murphy et al. 1987). The 7SK In the February issue of Genes & Development, two genes also can rely solely upon upstream sequences for articles provide additional detail to what is known about transcription initiation in vitro. These upstream se- the mechanism of RNA polymerase III transcription ini- quences include a TATA motif. Although it is by no tiation, and raise interesting questions about whether means certain that this motif is a site of action of the the control of such transcription might not resemble RNA polymerase II transcription factor TFIID, its pres- that utilized by RNA polymerase II. Kunkel and Pe- ence and significance for 7SK RNA transcription is pro- derson (1988) report that transcription in vitro of human vocative. The 7SK RNA genes have no obvious internal U6 snRNA by an RNA polymerase III-like enzyme is de- sequence homologies with tRNA, VA, or 5S RNA genes, pendent upon sequence elements 43-67 nucleotides up- but firm proof that internal sequences are unimportant stream of the transcription start site. Furthermore, they for transcription in vivo has not yet been produced. report that transcription in vivo relies upon distal 5'- These studies of transcription initiation of the U6, flanking sequences, including a region containing the 7SK, and 7SL RNA genes strongly implicate usage of up- well-known 'octamer' motif (ATGCAAAT) that is re- stream elements, some of which are common to RNA quired for expression of immunoglobulin, histone, and Pol II transcribed genes. However, caution is warranted U2 snRNA genes (see Fletcher et al. 1987 for a recent before jumping to the conclusion that RNA polymerase discussion of the importance of this motif and its asso- II and RNA polymerase III can follow common paths to ciated binding protein). Kunkel and Pederson also report prospective initiation sites. The evidence that the U6, that the U2 snRNA gene promoter elements (which are 7SK, and 7SL genes are transcribed by 'bona fide' RNA utilized by RNA polymerase II) can in some instance re- polymerase III relies solely upon ~-amanitin insensi- place the naturally occurring U6 snRNA gene upstream tivity, the utilization of pol III termination signals, and elements. competition assays with 5S RNA genes (Kunkel et al. These data follow on the heels of experiments re- 1986; Carbon et al. 1987; Reddy et al. 1987; Das et al. ported by Bark et al. (1987) and by Carbon et al. (1987). 1988). Studies with purified RNA polymerases and tran- The latter group reports that the Xenopus tropicalis U6 scription factors, together with more extensive competi- snRNA gene relies upon at least three 5'-flanking ele- tion analyses, are required to establish solidly that it is ments for transcription in vivo. Two of these are the the same RNA polymerase III holoenzyme that tran- same as the human U6 snRNA proximal and distal ele- scribes these genes as transcribes tRNA, VA, and 5S ments studied by Kunkel and Pederson, and the third is a RNA genes. TATA motif close to the transcription initiation start Transcription of Xenopus 5S RNA genes requires site. These three motifs are present in all known U6 RNA polymerase III, TFIIIA, TFIIIB, and one or more snRNA genes and remarkably resemble promoter ele- proteins collectively called TFIIIC. TFIIIA binds the 5S ments utilized by RNA polymerase II. RNA gene intemal control region and helps recruit GENES & DEVELOPMENT 2:373-375 91988 by Cold Spring Harbor Laboratory ISSN 0890-9369/88 $1.00 373 Downloaded from genesdev.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press Folk TFIIIB and TFIIIC to a stable transcription complex contain an activity that strips transcription complexes (Shastry et al. 1982; Lassar et al. 1983; Setzer and Brown from oocyte 5S RNA genes. Presumably this activity 1985). Heretofore, much attention has been paid to (which fractionates with ribosomes through several TFIIIA, largely because it was readily purified. It was the steps) recognizes some aspect of the TFIIIC/TFIIIA/DNA first eukaryotic transcription factor to be characterized, structure assembled near the 5' end of the internal con- and it is the prototypical zinc-finger domain DNA trol region. How this activity succeeds in removing a binding protein (Rhodes and Klug 1987). complex that is exceedingly stable in vitro to high ionic Following fertilization of Xenopus oocytes, a remark- strength (Setzer and Brown 1985; Carey et al. 1986; Jahn able developmental program ensues. As part of this pro- et al. 1987), and to the transit of multiple RNA poly- gram, transcription of a vast excess of oocyte 5S RNA merases (Wolffe et al. 1986) is certainly not clear. genes is repressed while transcription of a relatively Apart from the few base changes in the 5S RNA in- small number of somatic 5S RNA genes is activated. ternal control region, the only sequence differences be- The severalfold lower affinity of TFIIIA for a subclass of tween the Xenopus laevis major somatic and oocyte 5S oocyte 5S RNA genes compared to the major somatic 5S RNA genes occur in the spacer regions. Heretofore, RNA genes has been suggested to be the cause of the these spacer regions have not been viewed to be of major preferential inactivation of all the oocyte genes (Brown significance, for in a germinal vesicle transcription and Schlissel 1985). It is now apparent that this explana- system they have little effect upon transcription initia- tion does not suffice, and additional factors must be in- tion (Wormington et al. 1981). However, that upstream voked to explain the transcriptional switch. sequences can be important for 5S RNA transcription In the February issue of Genes & Development, has been documented with genes from Bombyx and McConkey and Bogenhagen (1988) demonstrate that Neurospora. These, as well as the 5S RNA genes of Dip- TFIIIA binds equally well to the Xenopus major class of tera, contain conserved upstream sequence elements re- oocyte 5S RNA genes as to the somatic 5S RNA genes. sembling the RNA polymerase II TATA motif (Morton Thus, everything else being equal, the first step in the and Sprague 1984; Rubacha et al. 1984; Selker et al. formation of a stable transcription complex, the associa- 1986; Garcia et al. 1987). Exploration of the importance tion of TFIIIA with 5S DNA, should occur equally well of these sequences and of the spacer regions in Xenopus on these genes in vivo. However, everything else does 5S RNA genes in appropriate transcription systems may not appear to be equal, for in a transcription system de- shed new light upon the assembly of transcription com- rived from mature oocytes, the oocyte 5S RNA genes are plexes and the developmentally regulated expression of transcribed in vitro at only a few percent of the rate of 5S RNA synthesis in Xenopus. the somatic genes. These results confirm similar results Perusal of these reports and of much accumulating ev- recently reported by Peck et al. (1987) and by Millstein idence that tRNA synthesis is modulated, and in some et al. (1987). instances absolutely dependent upon 5'-flanking se- If a difference in TFIIIA affinity is not the cause of the quences (I have not mentioned this evidence for lack of transcriptional switch between somatic and oocyte space), makes it clear that there is still much to be genes, then what is? These genes differ from each other leamed about the initiation of transcription by RNA by a few nucleotide substitutions near the 5' end of the polymerase III.
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