The authors wish to note the following: ''We wish to add direct references to a stochastic model of DNA replication previously applied to the Xenopus laevis early embryonic divisions. That model was applied to molecular combing experiments on cellfree extracts from Xenopus laevis embryos.'' The additional references appear below. www.pnas.org/cgi

mRNA polyadenylation and pre-mRNA splicing are two essential steps for the maturation of most human mRNAs. Studies have shown that some genes generate mRNA variants involving both alternative polyadenylation and alternative splicing. Polyadenylation in introns can lead to conversion of an internal exon to a 3Ј terminal exon, which is termed composite terminal exon, or usage of a 3Ј terminal exon that is otherwise skipped, which is termed skipped terminal exon. Using cDNA/EST and genome sequences, we identified polyadenylation sites in introns for all currently known human genes. We found that ∼20% human genes have at least one intronic polyadenylation event that can potentially lead to mRNA variants, most of which encode different protein products. The conservation of human intronic poly(A) sites in mouse and rat genomes is lower than that of poly(A) sites in 3Ј-most exons. Quantitative analysis of a number of mRNA variants generated by intronic poly(A) sites suggests that the intronic polyadenylation activity can vary under different cellular conditions for most genes. Furthermore, we found that weak 5Ј splice site and large intron size are the determining factors controlling the usage of composite terminal exon poly(A) sites, whereas skipped terminal exon poly(A) sites tend to be associated with strong polyadenylation signals. Thus, our data indicate that dynamic interplay between polyadenylation and splicing leads to widespread polyadenylation in introns and contributes to the complexity of transcriptome in the cell.[Supplemental material is available online at www.genome.org.]Maturation of mRNA involves multiple steps of processing, including capping, splicing, and polyadenylation (Proudfoot et al. 2002). Splicing and polyadenylation are responsible for removing introns and adding poly(A) tails, respectively. Essential signals for splicing out an intron from a pre-mRNA include cis elements at the 5Ј splice site (5Јss), at the 3Ј splice site (3Јss), and at the branchpoint site in the intron (Burge et al. 1999). Splicing involves two steps: First, the 5Јss is attacked by the 2ЈOH of an adenosine at the branchpoint, resulting in a 5Ј exon with a free 3ЈOH and a lariat consisting of the intron and 3Ј exon; second, the 3ЈOH of the 5Ј exon is joined with the 3Јss of the 3Ј exon via a transesterification reaction and the lariat is released. An array of proteins and RNAs are involved in the splicing reaction, including several small nuclear RNAs (snRNAs) and their associated proteins that form small nuclear ribonucleoproteins (snRNPs

Atherosclerotic vascular disease is a leading cause of myocardial infarction and cerebrovascular accident, and independent associations with periodontal disease (PD) are reported. PD is caused by polymicrobial infections and aggressive immune responses. Genomic DNA of Porphyromonas gingivalis, the best-studied bacterial pathogen associated with severe PD, is detected within atherosclerotic plaque. We examined causal relationships between chronic P. gingivalis oral infection, PD, and atherosclerosis in hyperlipidemic ApoEnull mice. ApoEnull mice (n = 24) were orally infected with P. gingivalis for 12 and 24 weeks. PD was assessed by standard clinical measurements while the aorta was examined for atherosclerotic lesions and inflammatory markers by array. Systemic inflammatory markers serum amyloid A, nitric oxide, and oxidized low-density lipoprotein were analyzed. P. gingivalis infection elicited specific antibodies and alveolar bone loss. Fluorescent in situ hybridization detected viable P. gingivalis within oral epithelium and aorta, and genomic DNA was detected within systemic organs. Aortic plaque area was significantly increased in P. gingivalis-infected mice at 24 weeks (P<0.01). Aortic RNA and protein arrays indicated a strong Th2 response. Chronic oral infection with P. gingivalis results in a specific immune response, significant increases in oral bone resorption, aortic inflammation, viable bacteria in oral epithelium and aorta, and plaque development.

Periodontal disease (PD) and atherosclerosis are both polymicrobial and multifactorial and although observational studies supported the association, the causative relationship between these two diseases is not yet established. Polymicrobial infection-induced periodontal disease is postulated to accelerate atherosclerotic plaque growth by enhancing atherosclerotic risk factors of orally infected Apolipoprotein E deficient (ApoEnull) mice. At 16 weeks of infection, samples of blood, mandible, maxilla, aorta, heart, spleen, and liver were collected, analyzed for bacterial genomic DNA, immune response, inflammation, alveolar bone loss, serum inflammatory marker, atherosclerosis risk factors, and aortic atherosclerosis. PCR analysis of polymicrobial-infected (Porphyromonas gingivalis [P. gingivalis], Treponema denticola [T. denticola], and Tannerella forsythia [T. forsythia]) mice resulted in detection of bacterial genomic DNA in oral plaque samples indicating colonization of the oral cavity by all three species. Fluorescent in situ hybridization detected P. gingivalis and T. denticola within gingival tissues of infected mice and morphometric analysis showed an increase in palatal alveolar bone loss (p<0.0001) and intrabony defects suggesting development of periodontal disease in this model. Polymicrobial-infected mice also showed an increase in aortic plaque area (p<0.05) with macrophage accumulation, enhanced serum amyloid A, and increased serum cholesterol and triglycerides. A systemic infection was indicated by the detection of bacterial genomic DNA in the aorta and liver of infected mice and elevated levels of bacterial specific IgG antibodies (p<0.0001). This study was a unique effort to understand the effects of a polymicrobial infection with P. gingivalis, T. denticola and T. forsythia on periodontal disease and associated atherosclerosis in ApoEnull mice.

Upon mating, females of many animal species undergo dramatic changes in their behavior. In Drosophila melanogaster, postmating behaviors are triggered by sex peptide (SP), which is produced in the male seminal fluid and transferred to female during copulation. SP modulates female behaviors via sex peptide receptor (SPR) located in a small subset of internal sensory neurons that innervate the female uterus and project to the CNS. Although required for postmating responses only in these female sensory neurons, SPR is expressed broadly in the CNS of both sexes. Moreover, SPR is also encoded in the genomes of insects that lack obvious SP orthologs. These observations suggest that SPR may have additional ligands and functions. Here, we identify myoinhibitory peptides (MIPs) as a second family of SPR ligands that is conserved across a wide range of invertebrate species. MIPs are potent agonists for Drosophila, Aedes, and Aplysia SPRs in vitro, yet are unable to trigger postmating responses in vivo. In contrast to SP, MIPs are not produced in male reproductive organs, and are not required for postmating behaviors in Drosophila females. We conclude that MIPs are evolutionarily conserved ligands for SPR, which are likely to mediate functions other than the regulation of female reproductive behaviors.Drosophila | female post-mating behavior | G protein-coupled receptor | neuropeptide | neuromodulation P eptide signaling through G protein-coupled receptors is a widely used mechanism for reversibly modulating the behavioral output of innate neural circuits (for review see ref. 1). A prominent example of peptidergic modulation of behavior is the regulation of female reproductive behavior in Drosophila melanogaster by the male's sex peptide (SP). SP is a small peptide present in the male seminal fluid. Upon mating, SP is transferred to the female, where it triggers dramatic changes in reproductive and other behaviors (2, 3). These behavioral modifications typically last for about a week, the period for which the female is able to store and use sperm from the initial mating (for review see ref. 4). Within females, SP is thought to activate a specific G protein-coupled receptor (SPR) (5) in a small set of internal sensory neurons of the female reproductive tract (6, 7). Signaling by SP and SPR is essential for the modulation of female behavior as these changes do not occur if the male lacks SP (8, 9) or the female lacks SPR (5).The modulation of female reproductive behavior in response to SP (and its closely related homolog DUP99B) (10, 11) is currently the only known role of SPR. Nonetheless, several lines of evidence have hinted that SPR may have other ligands and possibly also other functions. First, SPR is broadly expressed throughout the central nervous system (5), yet it is required only in reproductive tract sensory neurons for the postmating behavioral switch (6, 7). Second, SPR is also expressed in the central nervous system of males (5), where it is not likely to be exposed to SP. Third, orthologs of SPR are clearly d...

Background: Alternative polyadenylation is one of the mechanisms in human cells that give rise to a variety of transcripts from a single gene. More than half of the human genes have multiple polyadenylation sites (poly(A) sites), leading to variable mRNA and protein products. Previous studies of individual genes have indicated that alternative polyadenylation could occur in a tissuespecific manner.

BackgroundDramatic changes in gene expression occur in response to extracellular stimuli and during differentiation. Although transcriptional effects are important, alterations in mRNA decay also play a major role in achieving rapid and massive changes in mRNA abundance. Moreover, just as transcription factor activity varies between different cell types, the factors influencing mRNA decay are also cell-type specific.Principal FindingsWe have established the rates of decay for over 7000 transcripts expressed in mouse C2C12 myoblasts. We found that GU-rich (GRE) and AU-rich (ARE) elements are over-represented in the 3′UTRs of short-lived mRNAs and that these mRNAs tend to encode factors involved in cell cycle and transcription regulation. Stabilizing elements were also identified. By comparing mRNA decay rates in C2C12 cells with those previously measured for pluripotent and differentiating embryonic stem (ES) cells, we identified several groups of transcripts that exhibit cell-type specific decay rates. Further, whereas in C2C12 cells the impact of GREs on mRNA decay appears to be greater than that of AREs, AREs are more significant in ES cells, supporting the idea that cis elements make a cell-specific contribution to mRNA stability. GREs are recognized by CUGBP1, an RNA-binding protein and instability factor whose function is affected in several neuromuscular diseases. We therefore utilized RNA immunoprecipitation followed by microarray (RIP-Chip) to identify CUGBP1-associated transcripts. These mRNAs also showed dramatic enrichment of GREs in their 3′UTRs and encode proteins linked with cell cycle, and intracellular transport. Interestingly several CUGBP1 substrate mRNAs, including those encoding the myogenic transcription factors Myod1 and Myog, are also bound by the stabilizing factor HuR in C2C12 cells. Finally, we show that several CUGBP1-associated mRNAs containing 3′UTR GREs, including Myod1, are stabilized in cells depleted of CUGBP1, consistent with the role of CUGBP1 as a destabilizing factor.ConclusionsTaken together, our results systematically establish cis-acting determinants of mRNA decay rates in C2C12 myoblast cells and demonstrate that CUGBP1 associates with GREs to regulate decay of a wide range of mRNAs including several that are critical for muscle development.

Polyadenylation of nascent transcripts is one of the key mRNA processing events in eukaryotic cells. A large number of human and mouse genes have alternative polyadenylation sites, or poly(A) sites, leading to mRNA variants with different protein products and/or 3′-untranslated regions (3′-UTRs). PolyA_DB 2 contains poly(A) sites identified for genes in several vertebrate species, including human, mouse, rat, chicken and zebrafish, using alignments between cDNA/ESTs and genome sequences. Several new features have been added to the database since its last release, including syntenic genome regions for human poly(A) sites in seven other vertebrates and cis-element information adjacent to poly(A) sites. Trace sequences are used to provide additional evidence for poly(A/T) tails in cDNA/ESTs. The updated database is intended to broaden poly(A) site coverage in vertebrate genomes, and provide means to assess the authenticity of poly(A) sites identified by bioinformatics. The URL for this database is .