ognizant Communication Corporation

GENE EXPRESSION

ABSTRACTS
VOLUME 10, NUMBERS 1/2

Gene Expression, Vol. 10, pp. 3-16
1052-2166/02 $20.00 + .00
Copyright © 2002 Cognizant Comm. Corp.
Printed in the USA. All rights reserved.

Unconventional Rules of Small Nuclear RNA Transcription and Cap Modification in Trypanosomatids

Christian Tschudi1 and Elisabetta Ullu1,2

Departments of 1Internal Medicine and 2Cell Biology, Yale University School of Medicine, PO Box 208022, 333 Cedar Street, New Haven, CT 06520-8022

This review focuses on the spliced leader (SL) RNA and uridylic acid-rich small nuclear RNAs (U-snRNAs) involved in pre-mRNA processing in trypanosomatid protozoa, with particular emphasis on the mechanism of transcription and cap formation. The SL RNA plays a central role in mRNA biogenesis by providing the unique cap 4 structure to the 5´ end of all mRNAs by trans-splicing. The trimethylguanosine capped U-snRNAs, on the other hand, represent an unusual example among eukaryotic snRNAs in that they are transcribed by RNA polymerase III. This implies the existence of a distinctive mechanism for capping enzyme selection by the transcriptional machinery. Furthermore, the transcription units of U-snRNA genes offer yet another example of the variety of choices that have been established during eukaryotic evolution, namely that an upstream tRNA gene or tRNA-like gene provides extragenic promoter elements for a downstream small RNA gene.

Key words: Spliced leader RNA; trans-Splicing; Cap formation; Cap 4 structure; Trimethylguanosine cap; U-snRNAs; RNA polymerase III transcription; tRNA
genes

Address correspondence to Christian Tschudi, Department of Internal Medicine, Yale University School of Medicine, PO Box 208022, 333 Cedar Street, New Haven, CT 06520-8022. Tel: (203) 785-7332; Fax: (203) 785-3864; E-mail: christian.tschudi@yale.edu




Gene Expression, Vol. 10, pp. 7-39
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Copyright © 2002 Cognizant Comm. Corp.
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Small Nucleolar RNAs: Versatile trans-Acting Molecules of Ancient Evolutionary Origin

Michael P. Terns and Rebecca M. Terns

Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602

The small nucleolar RNAs (snoRNAs) are an abundant class of trans-acting RNAs that function in ribosome biogenesis in the eukaryotic nucleolus. Elegant work has revealed that most known snoRNAs guide modification of pre-ribosomal RNA (pre-rRNA) by base pairing near target sites. Other snoRNAs are involved in cleavage of pre-rRNA by mechanisms that have not yet been detailed. Moreover, our appreciation of the cellular roles of the snoRNAs is expanding with new evidence that snoRNAs also target modification of small nuclear RNAs and messenger RNAs. Many snoRNAs are produced by unorthodox modes of biogenesis including salvage from introns of pre-mRNAs. The recent discovery that homologs of snoRNAs as well as associated proteins exist in the domain Archaea indicates that the RNA-guided RNA modification system is of ancient evolutionary origin. In addition, it has become clear that the RNA component of vertebrate telomerase (an enzyme implicated in cancer and cellular senescence) is related to snoRNAs. During its evolution, vertebrate telomerase RNA appears to have co-opted a snoRNA domain that is essential for the function of telomerase RNA in vivo. The unique properties of snoRNAs are now being harnessed for basic research and therapeutic applications.

Key words: Small nucleolar RNA; Nucleolus; RNP; Telomerase; Archaea; RNA transport; Ribosome; RNA modification; RNA processing; Cajal body; Ribozyme

Address correspondence to Michael P. Terns, Department of Biochemistry and Molecular Biology, University of Georgia, Life Sciences Building, Athens, GA 30602. Tel: (706) 542-1896; Fax: (706) 542-1752; E-mail: mterns@bmb.uga.edu




Gene Expression, Vol. 10, pp. 41-57
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Copyright © 2002 Cognizant Comm. Corp.
Printed in the USA. All rights reserved.

La Protein and its Associated Small Nuclear and Nucleolar Precursor RNAs

Richard J. Maraia and Robert V. Intine

Laboratory of Molecular Growth Regulation, National Institute of Child Health & Human Development, National Institutes of Health, Bethesda, MD 20892

After transcription by RNA polymerase (pol) III, nascent Pol III transcripts pass through RNA processing, modification, and transport machineries as part of their posttranscriptional maturation process. The first factor to interact with Pol III transcripts is La protein, which binds principally via its conserved N-terminal domain (NTD), to the UUU-OH motif that results from transcription termination. This review includes a sequence Logo of the most conserved region of La and its refined modeling as an RNA recognition motif (RRM). La protects RNAs from 3´ exonucleolytic digestion and also contributes to their nuclear retention. The variety of modifications found on La-associated RNAs is reviewed in detail and considered in the contexts of how La may bind the termini of structured RNAs without interfering with recognition by modification enzymes, and its ability to chaperone RNAs through multiple parts of their maturation pathways. The CTD of human La recognizes the 5´ end region of nascent RNA in a manner that is sensitive to serine 366 phosphorylation. Although the CTD can control pre-tRNA cleavage by RNase P, a rate-limiting step in tRNASerUGA maturation, the extent to which it acts in the maturation pathway(s) of other transcripts is unknown but considered here. Evidence that a fraction of La resides in the nucleolus together with recent findings that several Pol III transcripts pass through the nucleolus is also reviewed. An imminent goal is to understand how the bipartite RNA binding, intracellular trafficking, and signal transduction activities of La are integrated with the maturation pathways of the various RNAs with which it associates.

Key words: tRNA processing; RNA modification; RNase P; RNA recognition motif (RRM); Protein structure modeling; Transcription; Nucleolus; Autoantigen; 5´-ppp; Walker A motif; Lhp1; Sla1

Address correspondence to Richard J. Maraia, Laboratory of Molecular Growth Regulation, National Institute of Child Health & Human Development, National Institutes of Health, Bethesda, MD 20892-2753. Tel: (301) 402-3567; Fax: (301) 480-6863; E-mail: maraiar@mail.nih.gov




Gene Expression, Vol. 10, pp. 59-78
1052-2166/02 $20.00 + .00
Copyright © 2002 Cognizant Comm. Corp.
Printed in the USA. All rights reserved.

The 3´ End Formation in Small RNAs

Karthika Perumal and Ram Reddy

Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030

Small RNAs are a major class of RNAs along with transfer RNAs, ribosomal RNAs, and messenger RNAs. They vary in size from less than 100 nucleotides to several thousand nucleotides and have been identified and characterized both in prokaryotes and eukaryotes. Small RNAs participate in a variety of cellular functions including regulating RNA synthesis, RNA processing, guiding modifications in RNA, and in transport of proteins. Small RNAs are generated by a series of posttranscriptional processing steps following transcription. While RNA 5´ end structure, 5´ cap formation, and RNA processing mechanisms have been fairly well characterized, the 3´ end processing is poorly understood. Recent data point to an emerging theme in small RNAs metabolism in which the 3´ end processing is mediated by the exosome, a large multienzyme complex. In addition to removal of nucleotides by the exosome, there is simultaneous rebuilding of the 3´ end of some small RNA by adenylation and/or uridylation. This review presents a picture of both degradative and rebuilding reactions operative on the 3´ end of some small RNA molecules in prokaryotes and eukaryotes.

Key words: Small RNAs; 3´ End formation; 3´ Adenylation; 3´ Uridylation

Address correspondence to Ram Reddy, Ph.D., Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030. Tel: (713) 798-7906; Fax: (713) 798-3145; E-mail: rreddy@bcm.tmc.edu




Gene Expression, Vol. 10, pp. 79-92
1052-2166/02 $20.00 + .00
Copyright © 2002 Cognizant Comm. Corp.
Printed in the USA. All rights reserved.

RNA-Protein Interactions That Regulate Pre-mRNA Splicing

Ravinder Singh

Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, CO 80309

Splicing of nuclear precursor messenger RNAs is an important and ubiquitous type of gene regulation in metazoans. Splicing joins the coding sequences called exons by removing the intervening noncoding sequences, introns, from primary transcripts. Alternative splicing generates an enormous repertoire of functional diversity by producing multiple RNAs and proteins from a single gene. In fact, recent genome sequences from several organisms suggest that splicing regulation is likely to provide an important source of functional diversity in more complex organisms. Because splice sites are short sequences at the ends of introns, the functional splice sites have to be distinguished from an excessively large number of sequences in the primary transcripts that resemble a splice site. Furthermore, alternative splice sites have to be correctly chosen at appropriate times. Thus, selection of proper splice sites remains a daunting biological problem. This review focuses on a few examples in which the molecular and biochemical basis for splice site selection is better understood.

Key words: RNA binding proteins; Splicing factors; Enhancers; Silencers; Small nuclear ribonucleoprotein; Alternative splicing; Exon definition; Polypyrimidine tract; Combinatorial control

Address correspondence to Dr. Ravinder Singh, Department of Molecular, Cellular and Developmental Biology, Campus Box 347, University of Colorado at Boulder, Boulder, CO 80309. Tel: (303) 492-8886; Fax: (303) 492-7744; E-mail: rsingh@colorado.edu