Long-Range Heterogeneity at the 3′ Ends of Human mRNAs

Iseli, Christian; Stevenson, Brian J.; Souza, Sandro J. de; Samaia, H. B.; Camargo, Anamaria A.; Buetow, Kenneth H.; Strausberg, Robert L.; Simpson, Andrew J.G.; Bücher, Philipp; Jongeneel, C. Victor

doi:10.1101/gr.62002

Cited by 71 publications

(49 citation statements)

References 22 publications

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“…Bioinformatic studies indicate that cleavage site choice within a poly(A) site is inherently imprecise (Pauws et al 2001;Tian et al 2005). In addition to cleavage site heterogeneity, alternative selection among different poly(A) sites (that range over distances in the kilobase range) is observed within the majority of human pre-mRNAs (Iseli et al 2002;Tian et al 2005). The consequences of alternative poly(A) site choice may impact the protein coding capacity of the message, as well as its localization, translation efficiency, and stability (Edwalds-Gilbert et al 1997).…”

Section: A Need For Precision and Uniformitymentioning

confidence: 99%

Eukaryotic mRNA 3′ processing: a common means to different ends: Figure 1.

Gilmartin¹

2005

Genes Dev.

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In principle, the formation of the 3Ј end of a eukaryotic mRNA is a simple process. At a minimum, it involves the hydrolysis of a single phosphodiester bond in the nascent transcript. For one unique class of mRNAs, transcripts of the metazoan replication-dependent histone genes, this is indeed the only requirement. All other eukaryotic mRNAs require both cleavage and subsequent poly(A) addition to the newly generated 3Ј hydroxyl. Despite this apparent simplicity, and more than two decades of work, basic questions concerning the mechanisms of 3Ј-end formation for both classes of transcripts persist. The accumulated evidence indicates that the mechanisms by which the ends of histone and polyadenylated mRNA are formed are fundamentally distinct, both in the factors responsible for processing and the RNA sequence elements that direct their action (for review, see Marzluff 2005;Zhao et al. 1999a). The 3Ј processing of polyadenylated mRNAs requires a complex of over a dozen proteins, nearly all of which are conserved from yeast to humans. In contrast, the formation of the 3Ј ends of the metazoan replication-dependent histone transcripts not only requires a unique set of proteins, but an essential snRNA component as well. In both cases, the identity of the endonuclease has remained largely a matter of speculation.Two reports-one from Kolev and Steitz (2005) in this issue of Genes & Development, and the second from Dominski et al. (2005a) have revealed that the mechanisms of poly(A) site processing and histone 3Ј processing are not quite as unique as they appear. Surprisingly, the two processing machines share a common core of proteins that almost certainly includes the endonuclease. The most exciting aspect of these reports, however, is that they provide a fresh insight into the evolution of what had seemed to be needlessly redundant mechanisms for generating mRNA 3Ј ends. In essence, these reports indicate that the enzymatic machinery responsible for cleaving all nascent pre-mRNAs is likely to be identical; the differences lie in the elaborate mechanisms that have evolved to recruit this machinery to the two classes of transcripts. The driving forces responsible for the evolution of two distinct 3Ј processing complexes are likely to involve the conflicting pressures of posttranscriptional regulation: coordinate cell cycle control of the replication-dependent histone mRNAs versus the developmental and cell-type-specific regulation of alternative poly(A) site selection. Similarities among contrastsThe RNA sequence elements that direct the 3Ј processing of histone and polyadenylated mRNAs could hardly be more different (Fig. 1A). Three elements contribute to mammalian poly(A) site recognition, each of which is recognized by a distinct protein complex (Zhao et al. 1999a). The most well conserved element is the AAUAAA hexamer that generally resides between 10 and 30 nucleotides (nt) upstream of the cleavage site. This element is recognized by a five-subunit complex termed cleavage and polyadenylation specificity factor (CP...

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Section: A Need For Precision and Uniformitymentioning

confidence: 99%

Eukaryotic mRNA 3′ processing: a common means to different ends: Figure 1.

Gilmartin¹

2005

Genes Dev.

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“…This proportion is identical to the observed frequency in human annotated mRNAs (Gautheret et al 1998). By EST analysis, alternative polyadenylation seems to occur in at least 29%-40% of genes (Gautheret et al 1998;Beaudoing et al 2000), and many more such variable polyadenylation events probably escape the analysis, due to long-range heterogeneity of the 3Ј ends (Iseli et al 2002).…”

Section: Classes Of Polyadenylation Sitesmentioning

confidence: 99%

“…For quality control, we did not consider the completeness of the UTR regions, because variability of the starting site (Suzuki et al 2001a,b), 5∼50 bp trimming of 5Ј ends in the reference cDNA clones generated by conventional methods (Gubler and Hoffman 1983) and variation of polyadenylation sites (Beaudoing et al 2000;Iseli et al 2002), which also suggest that public databases probably do not contain all of the existing full-length UTR variations.…”

Section: Gene Discovery By Sequencingmentioning

confidence: 99%

“…Similarly, the 3Ј CDS score considered positive the cDNA clones that showed alignment extending downstream to the annotated stop codon. The final analysis (Table 2) of 5Ј and 3Ј ends against a larger data set versus complete mouse CDS suggests that 89.1% and 96.5% of the protein-coding cDNAs are, respectfully, 5Ј and 3Ј intact in relationship to CDS, suggesting that ∼85.7 % of clones have both ends complete.For quality control, we did not consider the completeness of the UTR regions, because variability of the starting site (Suzuki et al 2001a,b), 5∼50 bp trimming of 5Ј ends in the reference cDNA clones generated by conventional methods (Gubler and Hoffman 1983) and variation of polyadenylation sites (Beaudoing et al 2000;Iseli et al 2002), which also suggest that public databases probably do not contain all of the existing full-length UTR variations. …”

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confidence: 99%

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Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia

Carninci¹,

Waki²,

Shiraki³

et al. 2003

Genome Res.

156

132

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We report the construction of the mouse full-length cDNA encyclopedia, the most extensive view of a complex transcriptome, on the basis of preparing and sequencing 246 libraries. Before cloning, cDNAs were enriched in full-length by Cap-Trapper, and in most cases, aggressively subtracted/normalized. We have produced 1,442,236 successful 3Ј-end sequences clustered into 171,144 groups, from which 60,770 clones were fully sequenced cDNAs Cold Spring Harbor Laboratory Press on May 10, 2018 -Published by genome.cshlp.org Downloaded from annotated in the FANTOM-2 annotation. We have also produced 547,149 5Ј end reads, which clustered into 124,258 groups. Altogether, these cDNAs were further grouped in 70,000 transcriptional units (TU), which represent the best coverage of a transcriptome so far. By monitoring the extent of normalization/subtraction, we define the tentative equivalent coverage (TEC), which was estimated to be equivalent to >12,000,000 ESTs derived from standard libraries. High coverage explains discrepancies between the very large numbers of clusters (and TUs) of this project, which also include non-protein-coding RNAs, and the lower gene number estimation of genome annotations. Altogether, 5Ј-end clusters identify regions that are potential promoters for 8637 known genes and 5Ј-end clusters suggest the presence of almost 63,000 transcriptional starting points. An estimate of the frequency of polyadenylation signals suggests that at least half of the singletons in the EST set represent real mRNAs. Clones accounting for about half of the predicted TUs await further sequencing. The continued high-discovery rate suggests that the task of transcriptome discovery is not yet complete.[Supplemental material available online at www.genome.org.]One of the primary goals of genome sequencing projects is to identify the genome sequences that are transcribed into functional mRNAs, so that full-length cDNAs can be isolated to allow further downstream biology, and functional and structural genomics. The limitations of a priori genome annotation dictate that the transcriptome needs to be identified experimentally via cDNA cloning and sequencing. Although expressed sequence tags (ESTs) (Adams et al. 1991(Adams et al. , 1995Hillier et al. 1996;Marra et al. 1999;Kargul et al. 2001) and ORESTES (Camargo et al. 2001) have been extremely valuable for new gene discovery, these approaches have not allowed highthroughput recovering of full-length cDNA clones nor definition of protein sequence derived from actual cDNA clones. To overcome such problems, we undertook from the year 1995, a strategic project aimed at the comprehensive collection of at least one full-length cDNA derived from each mouse gene, a strategy that is recently becoming useful in similar projects to collect full-length gene collections (Stapleton et al. 2002;Strausberg et al. 2002).Because of the limited processivity of reverse transcriptase and other limitations, standard cDNA libraries generally contain a majority of truncated transcripts. The introductio...

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“…The SNP present in the 3Ј flanking region (C1801G) falls outside the putative transcribed region, and the current gene annotation suggests it would not be present in the mRNA sequence where it could potentially influence mRNA transport and stability, a well-documented phenomenon. However a recent study (28) revealed that up to 50% of currently annotated genes use more distant polyadenylation signals with varying efficiencies that were not necessarily dependent on distance from the open reading frame. It is therefore possible that the use of an alternate polyadenylation signal further downstream would include the 3Ј flanking SNP in the mRNA strand, presenting a potential mechanism for the variant to influence mRNA transport and stability.…”

Section: Discussionmentioning

confidence: 99%

Genetic Variation in BEACON Influences Quantitative Variation in Metabolic Syndrome–Related Phenotypes

et al. 2004

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The BEACON gene (also known as UBL5) was identified as differentially expressed between lean and obese Psammomys obesus, a polygenic animal model of obesity, type 2 diabetes, and dyslipidemia. The human homologue of BEACON is located on chromosome 19p, a region likely to contain genes affecting metabolic syndrome-related quantitative traits as established by linkage studies. To assess whether the human BEACON gene may be involved in influencing these traits, we exhaustively analyzed the complete gene for genetic variation in 40 unrelated individuals and identified four variants (three novel). The two more common variants were tested for association with a number of quantitative metabolic syndrome-related traits in two large cohorts of unrelated individuals. Significant associations were found between these variants and fat mass (P ‫؍‬ 0.026), percentage of fat (P ‫؍‬ 0.001), and waistto-hip ratio (P ‫؍‬ 0.031). The same variants were also associated with total cholesterol (P ‫؍‬ 0.024), LDL cholesterol (P ‫؍‬ 0.019), triglycerides (P ‫؍‬ 0.006), and postglucose load insulin levels (P ‫؍‬ 0.018). Multivariate analysis of these correlated phenotypes also yielded a highly significant association (P ‫؍‬ 0.0004), suggesting that BEACON may influence phenotypic variation in metabolic syndrome-related traits. Diabetes 53: [2467][2468][2469][2470][2471][2472] 2004 T he last two decades have seen a substantial increase in the prevalence of type 2 diabetes and obesity that has been largely attributed to increased availability of energy, dense food, and reduced levels of physical activity (1). Many individuals with obesity and type 2 diabetes exhibit clustering of a number of other cardiovascular disease risk factors collectively called the metabolic syndrome, which in addition to glucose intolerance and central (upper-body) obesity, include hyperinsulinemia/insulin resistance, hypertension, and dyslipidemia (1).The pathophysiology and etiology of the components of the metabolic syndrome remain poorly understood, although there is strong evidence to indicate that genetic factors modulate an individual's predisposition for development of these conditions (2,3). Evidence from twin and adoption studies (4 -8) suggest that these genetic factors account for a substantial proportion of the variation in several underlying quantitative phenotypes of the metabolic syndrome including BMI, waist circumference, cholesterol, triglycerides, and glucose and insulin levels. Previously we have described (9 -11) a polygenic animal model of obesity, type 2 diabetes, and dyslipidemia and subsequently used this model to identify genes whose products are involved in metabolic pathways that influence the development of the metabolic syndrome. One of these genes, the BEACON gene, was discovered by differential display PCR analysis of hypothalamic RNA from lean and obese Psammomys obesus (12). BEACON encodes a 73-amino-acid protein whose expression level in the hypothalamus was found correlated with body fat content in P. obesus (12). Intracere...

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Long-Range Heterogeneity at the 3′ Ends of Human mRNAs

Cited by 71 publications

References 22 publications

Eukaryotic mRNA 3′ processing: a common means to different ends: Figure 1.

Eukaryotic mRNA 3′ processing: a common means to different ends: Figure 1.

Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia

Genetic Variation in BEACON Influences Quantitative Variation in Metabolic Syndrome–Related Phenotypes

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