Showing papers by "Cold Spring Harbor Laboratory published in 2006"
Food and Drug Administration1, GE Healthcare2, Thermo Fisher Scientific3, Illumina4, Agilent Technologies5, National Institutes of Health6, Applied Biosystems7, University of Toledo8, Stratagene9, United States Environmental Protection Agency10, University of Massachusetts Boston11, Clinical Data, Inc12, University of California, Los Angeles13, SAS Institute14, Biogen Idec15, Yale University16, Cold Spring Harbor Laboratory17, Discovery Institute18, Stanford University19, Harvard University20, Vanderbilt University21, University of Texas at Dallas22, University of Oslo23, Novartis24, University of Texas MD Anderson Cancer Center25, Luminex Corporation26, Wake Forest University27, University of Illinois at Urbana–Champaign28
TL;DR: This study describes the experimental design and probe mapping efforts behind the MicroArray Quality Control project and shows intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed.
Abstract: Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, has raised concerns about the reliability of this technology. The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and data analysis issues. Expression data on four titration pools from two distinct reference RNA samples were generated at multiple test sites using a variety of microarray-based and alternative technology platforms. Here we describe the experimental design and probe mapping efforts behind the MAQC project. We show intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed. This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings.
1,987 citations
TL;DR: Recent breakthroughs in understanding of the role of the PTPs in the regulation of signal transduction and the aetiology of human disease are described.
Abstract: The protein tyrosine phosphatase (PTP) superfamily of enzymes functions in a coordinated manner with protein tyrosine kinases to control signalling pathways that underlie a broad spectrum of fundamental physiological processes. In this review, I describe recent breakthroughs in our understanding of the role of the PTPs in the regulation of signal transduction and the aetiology of human disease.
1,498 citations
TL;DR: A new class of small RNAs that bind to MILI in mouse male germ cells, where they accumulate at the onset of meiosis are described, and are referred to as ‘Piwi-interacting RNAs’ or piRNAs.
Abstract: Small RNAs bound to Argonaute proteins recognize partially or fully complementary nucleic acid targets in diverse gene-silencing processes. A subgroup of the Argonaute proteins--known as the 'Piwi family'--is required for germ- and stem-cell development in invertebrates, and two Piwi members--MILI and MIWI--are essential for spermatogenesis in mouse. Here we describe a new class of small RNAs that bind to MILI in mouse male germ cells, where they accumulate at the onset of meiosis. The sequences of the over 1,000 identified unique molecules share a strong preference for a 5' uridine, but otherwise cannot be readily classified into sequence families. Genomic mapping of these small RNAs reveals a limited number of clusters, suggesting that these RNAs are processed from long primary transcripts. The small RNAs are 26-31 nucleotides (nt) in length--clearly distinct from the 21-23 nt of microRNAs (miRNAs) or short interfering RNAs (siRNAs)--and we refer to them as 'Piwi-interacting RNAs' or piRNAs. Orthologous human chromosomal regions also give rise to small RNAs with the characteristics of piRNAs, but the cloned sequences are distinct. The identification of this new class of small RNAs provides an important starting point to determine the molecular function of Piwi proteins in mammalian spermatogenesis.
1,404 citations
TL;DR: A tractable model of liver cancer is established, two oncogenes that cooperate by virtue of their coamplification in the same genomic locus are identified, and an efficient strategy for the annotation of human cancer genes is suggested.
1,064 citations
TL;DR: It is shown that Abeta employs signaling pathways of long-term depression to drive endocytosis of synaptic AMPA receptors, indicating the central role played by AMPA receptor trafficking in Abeta-induced modification of synaptic structure and function.
1,014 citations
TL;DR: The principles of 2PE microscopy are reviewed, recent applications are highlighted, its limitations are discussed, and areas for future research and development are pointed to.
969 citations
TL;DR: Enhanced neuronal gamma-band synchronization and shortened neuronal response latencies to an attended stimulus seem to have direct effects on visually triggered behaviour, reflecting an early neuronal correlate of efficient visuo-motor integration.
Abstract: Our capacity to process and respond behaviourally to multiple incoming stimuli is very limited. To optimize the use of this limited capacity, attentional mechanisms give priority to behaviourally relevant stimuli at the expense of irrelevant distractors. In visual areas, attended stimuli induce enhanced responses and an improved synchronization of rhythmic neuronal activity in the gamma frequency band (40–70 Hz)1,2,3,4,5,6,7,8,9,10,11. Both effects probably improve the neuronal signalling of attended stimuli within and among brain areas1,12,13,14,15,16. Attention also results in improved behavioural performance and shortened reaction times. However, it is not known how reaction times are related to either response strength or gamma-band synchronization in visual areas. Here we show that behavioural response times to a stimulus change can be predicted specifically by the degree of gamma-band synchronization among those neurons in monkey visual area V4 that are activated by the behaviourally relevant stimulus. When there are two visual stimuli and monkeys have to detect a change in one stimulus while ignoring the other, their reactions are fastest when the relevant stimulus induces strong gamma-band synchronization before and after the change in stimulus. This enhanced gamma-band synchronization is also followed by shorter neuronal response latencies on the fast trials. Conversely, the monkeys' reactions are slowest when gamma-band synchronization is high in response to the irrelevant distractor. Thus, enhanced neuronal gamma-band synchronization and shortened neuronal response latencies to an attended stimulus seem to have direct effects on visually triggered behaviour, reflecting an early neuronal correlate of efficient visuo-motor integration.
763 citations
TL;DR: This work solves for the optimal layout of 279 nonpharyngeal neurons using a newly compiled version of the Caenorhabditis elegans wiring diagram, and proposes that biological factors relating to axonal guidance and command neuron functions contribute to these deviations.
Abstract: We pursue the hypothesis that neuronal placement in animals minimizes wiring costs for given functional constraints, as specified by synaptic connectivity. Using a newly compiled version of the Caenorhabditis elegans wiring diagram, we solve for the optimal layout of 279 nonpharyngeal neurons. In the optimal layout, most neurons are located close to their actual positions, suggesting that wiring minimization is an important factor. Yet some neurons exhibit strong deviations from "optimal" position. We propose that biological factors relating to axonal guidance and command neuron functions contribute to these deviations. We capture these factors by proposing a modified wiring cost function.
629 citations
TL;DR: It is suggested that the fluoxetine-induced increase in new neurons arises as a result of the expansion of an early progenitor cell class in the adult brain and defines a cellular target for antidepressant drug therapies.
Abstract: Chronic treatment with antidepressants increases neurogenesis in the adult hippocampus. This increase in the production of new neurons may be required for the behavioral effects of antidepressants. However, it is not known which class of cells within the neuronal differentiation cascade is targeted by the drugs. We have generated a reporter mouse line, which allows identification and classification of early neuronal progenitors. It also allows accurate quantitation of changes induced by neurogenic agents in these distinct subclasses of neuronal precursors. We use this line to demonstrate that the selective serotonin reuptake inhibitor antidepressant fluoxetine does not affect division of stem-like cells in the dentate gyrus but increases symmetric divisions of an early progenitor cell class. We further demonstrate that these cells are the sole class of neuronal progenitors targeted by fluoxetine in the adult brain and suggest that the fluoxetine-induced increase in new neurons arises as a result of the expansion of this cell class. This finding defines a cellular target for antidepressant drug therapies.
618 citations
TL;DR: This work shows that the High-Mobility Group A (HMGA) proteins accumulate on the chromatin of senescent fibroblasts and are essential structural components of SAHFs, and implies that HMGA proteins also act in tumor suppressor networks.
562 citations
TL;DR: Microarray analysis of 12 populations of neurons in the adult mouse forebrain resulted in a taxonomic tree that reflected the expected major relationships between these populations, such as the distinction between cortical interneurons and projection neurons.
Abstract: Identifying the neuronal cell types that comprise the mammalian forebrain is a central unsolved problem in neuroscience. Global gene expression profiles offer a potentially unbiased way to assess functional relationships between neurons. Here, we carried out microarray analysis of 12 populations of neurons in the adult mouse forebrain. Five of these populations were chosen from cingulate cortex and included several subtypes of GABAergic interneurons and pyramidal neurons. The remaining seven were derived from the somatosensory cortex, hippocampus, amygdala and thalamus. Using these expression profiles, we were able to construct a taxonomic tree that reflected the expected major relationships between these populations, such as the distinction between cortical interneurons and projection neurons. The taxonomic tree indicated highly heterogeneous gene expression even within a single region. This dataset should be useful for the classification of unknown neuronal subtypes, the investigation of specifically expressed genes and the genetic manipulation of specific neuronal circuit elements.
29 Oct 2006
TL;DR: The Reactome data model allows us to represent many diverse processes in the human system, including the pathways of intermediary metabolism, regulatory pathways, and signal transduction, and high-level processes, such as the cell cycle.
Abstract: Reactome (www.reactome.org) is a curated database describing very diverse biological processes in a computationally accessible format The data is provided by experts in the field and subject to a peer review process The core unit of the Reactome data model is the reaction The entities participating in reactions form a network of biological interactions Reactions are grouped into pathways Reactome data are cross-referenced to a wide selection of publically available databases (such as UniProt, Ensembl, GO, PubMed), facilitating overall integration of biological data In addition to the manually curated, mainly human reactions, electronically inferred reactions to a wide range of other species, are presented on the website All Reactome reactions are displayed as arrows on a Reactionmap The Skypainter tool allows visualisation of user-supplied data by colouring the Reactionmap Reactome data are freely available and can be downloaded in a number of formats.
TL;DR: An emerging idea is that SMC proteins use a diverse array of intramolecular and intermolecular protein–protein interactions to actively fold, tether and manipulate DNA strands.
Abstract: Structural maintenance of chromosomes (SMC) proteins are ubiquitous in organisms from bacteria to humans, and function as core components of the condensin and cohesin complexes in eukaryotes. SMC proteins adopt a V-shaped structure with two long arms, each of which has an ATP-binding head domain at the distal end. It is important to understand how these uniquely designed protein machines interact with DNA strands and how such interactions are modulated by the ATP-binding and -hydrolysis cycle. An emerging idea is that SMC proteins use a diverse array of intramolecular and intermolecular protein-protein interactions to actively fold, tether and manipulate DNA strands.
TL;DR: This structure demonstrates that only one strand of DNA passes through the hexamer channel and that the DNA-binding hairpins of each subunit form a spiral ‘staircase’ that sequentially tracks the oligonucleotide backbone.
Abstract: The E1 protein of papillomavirus is a hexameric ring helicase belonging to the AAA + family. The mechanism that couples the ATP cycle to DNA translocation has been unclear. Here we present the crystal structure of the E1 hexamer with single-stranded DNA discretely bound within the hexamer channel and nucleotides at the subunit interfaces. This structure demonstrates that only one strand of DNA passes through the hexamer channel and that the DNA-binding hairpins of each subunit form a spiral 'staircase' that sequentially tracks the oligonucleotide backbone. Consecutively grouped ATP, ADP and apo configurations correlate with the height of the hairpin, suggesting a straightforward DNA translocation mechanism. Each subunit sequentially progresses through ATP, ADP and apo states while the associated DNA-binding hairpin travels from the top staircase position to the bottom, escorting one nucleotide of single-stranded DNA through the channel. These events permute sequentially around the ring from one subunit to the next.
TL;DR: The results indicate that RNase R treatment can be used to construct an intronic cDNA library, in which majority of the intron lariats are represented, and implies its ability to screen for rare intragenic trans-splice in any target gene with a large background of cis-splicing.
Abstract: Besides linear RNAs, pre-mRNA splicing generates three forms of RNAs: lariat introns, Y-structure introns from trans-splicing, and circular exons through exon skipping. To study the persistence of excised introns in total cellular RNA, we used three Escherichia coli 3 0 to 5 0 exoribonucleases. Ribonuclease R (RNase R) thoroughly degrades the abundant linear RNAs and the Y-structure RNA, while preserving the loop portion of a lariat RNA. Ribonuclease II (RNase II) and polynucleotide phosphorylase (PNPase) also preserve the lariat loop, but are less efficient in degrading linear RNAs. RNase R digestion of the total RNA from human skeletal muscle generates an RNA pool consisting of lariat and circular RNAs. RT–PCR across the branch sites confirmed lariat RNAs and circular RNAs in the pool generated by constitutive and alternative splicing of the dystrophin pre-mRNA. Our results indicate that RNase R treatment can be used to construct an intronic cDNA library, in which majority of the intron lariats are represented. The highly specific activity of RNase R implies its ability to screen for rare intragenic transsplicing in any target gene with a large background of cis-splicing. Further analysis of the intronic RNA pool from a specific tissue or cell will provide insights into the global profile of alternative splicing.
TL;DR: A refined functional SELEX screen for motifs that can act as ESEs in response to the human SR protein SF2/ASF is carried out and an increased specificity score matrix is derived that accurately predicts the exon-skipping phenotypes of deleterious point mutations.
Abstract: Numerous disease-associated point mutations exert their effects by disrupting the activity of exonic splicing enhancers (ESEs). We previously derived position weight matrices to predict putative ESEs specific for four human SR proteins. The score matrices are part of ESEfinder, an online resource to identify ESEs in query sequences. We have now carried out a refined functional SELEX screen for motifs that can act as ESEs in response to the human SR protein SF2/ASF. The test BRCA1 exon under selection was internal, rather than the 3'-terminal IGHM exon used in our earlier studies. A naturally occurring heptameric ESE in BRCA1 exon 18 was replaced with two libraries of random sequences, one seven nucleotides in length, the other 14. Following three rounds of selection for in vitro splicing via internal exon inclusion, new consensus motifs and score matrices were derived. Many winner sequences were demonstrated to be functional ESEs in S100-extract-complementation assays with recombinant SF2/ASF. Motif-score threshold values were derived from both experimental and statistical analyses. Motif scores were shown to correlate with levels of exon inclusion, both in vitro and in vivo. Our results confirm and extend our earlier data, as many of the same motifs are recognized as ESEs by both the original and our new score matrix, despite the different context used for selection. Finally, we have derived an increased specificity score matrix that incorporates information from both of our SF2/ASF-specific matrices and that accurately predicts the exon-skipping phenotypes of deleterious point mutations.
TL;DR: How single-cell models on five levels of complexity, from black-box approaches to detailed compartmental simulations, address key questions about neural dynamics and signal processing are examined.
Abstract: The fundamental building block of every nervous system is the single neuron. Understanding how these exquisitely structured elements operate is an integral part of the quest to solve the mysteries of the brain. Quantitative mathematical models have proved to be an indispensable tool in pursuing this goal. We review recent advances and examine how single-cell models on five levels of complexity, from black-box approaches to detailed compartmental simulations, address key questions about neural dynamics and signal processing.
TL;DR: It is shown that chemically induced long-term potentiation (chemLTP) drives robust exocytosis of AMPA receptors and produces similar modification of small and large spines during chemLTP induction, indicating that distinct mechanisms underlie changes in morphology and receptor content.
Abstract: The changes in synaptic morphology and receptor content that underlie neural plasticity are poorly understood. Here, we use a pH-sensitive green fluorescent protein to tag recombinant glutamate receptors and monitor their dynamics onto dendritic spine surfaces. We show that chemically induced long-term potentiation (chemLTP) drives robust exocytosis of AMPA receptors. In contrast, the same stimulus produces a small reduction of NMDA receptors from the spine surface. chemLTP produces similar modification of small and large spines. Interestingly, during chemLTP induction, spines increase in volume before accumulation of AMPA receptors on their surface, indicating that distinct mechanisms underlie changes in morphology and receptor content.
TL;DR: This study provides mechanistic insights into recognition of methylated histone tails by tudor domains and reveals the structural intricacy of methyl-lysine recognition by two closely spaced effector domains.
Abstract: Biological responses to histone methylation critically depend on the faithful readout and transduction of the methyl-lysine signal by "effector" proteins, yet our understanding of methyl-lysine recognition has so far been limited to the study of histone binding by chromodomain and WD40-repeat proteins. The double tudor domain of JMJD2A, a Jmjc domain-containing histone demethylase, binds methylated histone H3-K4 and H4-K20. We found that the double tudor domain has an interdigitated structure, and the unusual fold is required for its ability to bind methylated histone tails. The cocrystal structure of the JMJD2A double tudor domain with a trimethylated H3-K4 peptide reveals that the trimethyl-K4 is bound in a cage of three aromatic residues, two of which are from the tudor-2 motif, whereas the binding specificity is determined by side-chain interactions involving amino acids from the tudor-1 motif. Our study provides mechanistic insights into recognition of methylated histone tails by tudor domains and reveals the structural intricacy of methyl-lysine recognition by two closely spaced effector domains.
TL;DR: It is suggested that Her2(YVMA) activates cellular substrates more potently than HER2(WT); and cancer cells expressing this mutation remain sensitive to HER2-targeted therapies but insensitive to EGFR TKIs.
TL;DR: The results demonstrate that Arc/Arg3.1 reduces the number of GluR2/3 receptors leading to a decrease in AMPAR-mediated synaptic currents, consistent with a role in the homeostatic regulation of synaptic strength.
TL;DR: The HpaII tiny fragment Enrichment by Ligation-mediated PCR assay is robust, quantitative, and accurate and is providing new insights into the distribution and dynamic nature of cytosine methylation in the genome.
Abstract: The distribution of cytosine methylation in 6.2 Mb of the mouse genome was tested using cohybridization of genomic representations from a methylation-sensitive restriction enzyme and its methylation-insensitive isoschizomer. This assay, termed HELP (HpaII tiny fragment Enrichment by Ligation-mediated PCR), allows both intragenomic profiling and intergenomic comparisons of cytosine methylation. The intragenomic profile shows most of the genome to be contiguous methylated sequence with occasional clusters of hypomethylated loci, usually but not exclusively at promoters and CpG islands. Intergenomic comparison found marked differences in cytosine methylation between spermatogenic and brain cells, identifying 223 new candidate tissue-specific differentially methylated regions (T-DMRs). Bisulfite pyrosequencing confirmed the four candidates tested to be T-DMRs, while quantitative RT-PCR for two genes with T-DMRs located at their promoters showed the HELP data to be correlated with gene activity at these loci. The HELP assay is robust, quantitative, and accurate and is providing new insights into the distribution and dynamic nature of cytosine methylation in the genome.
TL;DR: In vitro reconstitution experiments demonstrate that Wapl forms a stoichiometric, ternary complex with two regulatory subunits of cohesin, implicating its noncatalytic function in inactivating cohesIn's ability to interact with chromatin.
TL;DR: The results implicate p63 as a key regulator of cellular adhesion and survival in basal cells of the mammary gland and other stratified epithelial tissues.
Abstract: p63 is critical for epithelial development yet little is known about the transcriptional programmes it regulates. By characterising transcriptional changes and cellular effects following modulation of p63 expression, we have defined a vital role for p63 in cellular adhesion. Knockdown of p63 expression caused downregulation of cell adhesion-associated genes, cell detachment and anoikis in mammary epithelial cells and keratinocytes. Conversely, overexpression of the TAp63gamma or deltaNp63alpha isoforms of p63 upregulated cell adhesion molecules, increased cellular adhesion and conferred resistance to anoikis. Apoptosis induced by loss of p63 was rescued by signalling downstream of beta4 integrin. Our results implicate p63 as a key regulator of cellular adhesion and survival in basal cells of the mammary gland and other stratified epithelial tissues.
TL;DR: It is proposed that RA3 regulates inflorescence branching by modification of a sugar signal that moves into axillary meristems, and the fact thatRA3 acts upstream of RA1 supports a hypothesis that RA2 itself may have a transcriptional regulatory function.
Abstract: Inflorescence branching is a major yield trait in crop plants controlled by the developmental fate of axillary shoot meristems. Variations in branching patterns lead to diversity in flower-bearing architectures (inflorescences) and affect crop yield by influencing seed number or harvesting ability. Several growth regulators such as auxins, cytokinins and carotenoid derivatives regulate branching architectures. Inflorescence branching in maize is regulated by three RAMOSA genes. Here we show that one of these genes, RAMOSA3 (RA3), encodes a trehalose-6-phosphate phosphatase expressed in discrete domains subtending axillary inflorescence meristems. Genetic and molecular data indicate that RA3 functions through the predicted transcriptional regulator RAMOSA1 (RA1). We propose that RA3 regulates inflorescence branching by modification of a sugar signal that moves into axillary meristems. Alternatively, the fact that RA3 acts upstream of RA1 supports a hypothesis that RA3 itself may have a transcriptional regulatory function.
TL;DR: The results support the existence of an obligatory stressed intermediate, with approximately one turn of additional DNA unwinding, in escape and are consistent with the proposal that stress in this intermediate provides the driving force to break RNAP-promoter andRNAP-initiation-factor interactions in escape.
Abstract: Using single-molecule DNA nanomanipulation, we show that abortive initiation involves DNA "scrunching"-in which RNA polymerase (RNAP) remains stationary and unwinds and pulls downstream DNA into itself-and that scrunching requires RNA synthesis and depends on RNA length. We show further that promoter escape involves scrunching, and that scrunching occurs in most or all instances of promoter escape. Our results support the existence of an obligatory stressed intermediate, with approximately one turn of additional DNA unwinding, in escape and are consistent with the proposal that stress in this intermediate provides the driving force to break RNAP-promoter and RNAP-initiation-factor interactions in escape.
TL;DR: The enrichment of Regulatory sequences in the relatively small unmethylated compartment suggests that cytosine methylation constrains the effective size of the genome through the selective exposure of regulatory sequences.
Abstract: The mammalian genome depends on patterns of methylated cytosines for normal function, but the relationship between genomic methylation patterns and the underlying sequence is unclear. We have characterized the methylation landscape of the human genome by global analysis of patterns of CpG depletion and by direct sequencing of 3073 unmethylated domains and 2565 methylated domains from human brain DNA. The genome was found to consist of short (<4 kb) unmethylated domains embedded in a matrix of long methylated domains. Unmethylated domains were enriched in promoters, CpG islands, and first exons, while methylated domains comprised interspersed and tandem-repeated sequences, exons other than first exons, and non-annotated single-copy sequences that are depleted in the CpG dinucleotide. The enrichment of regulatory sequences in the relatively small unmethylated compartment suggests that cytosine methylation constrains the effective size of the genome through the selective exposure of regulatory sequences. This buffers regulatory networks against changes in total genome size and provides an explanation for the C value paradox, which concerns the wide variations in genome size that scale independently of gene number. This suggestion is compatible with the finding that cytosine methylation is universal among large-genome eukaryotes, while many eukaryotes with genome sizes <5 x 10(8) bp do not methylate their DNA.
TL;DR: This review summarizes current understanding of early events in olfactory processing, and focuses on how odors are encoded by the activity of primary Olfactory receptor neurons, how odor codes may be transformed in the olfaction bulb, and what relevance these codes may have for downstream neurons in higher brain centers.
Abstract: Olfactory space has a higher dimensionality than does any other class of sensory stimuli, and the olfactory system receives input from an unusually large number of unique information channels. This suggests that aspects of olfactory processing may differ fundamentally from processing in other sensory modalities. This review summarizes current understanding of early events in olfactory processing. We focus on how odors are encoded by the activity of primary olfactory receptor neurons, how odor codes may be transformed in the olfactory bulb, and what relevance these codes may have for downstream neurons in higher brain centers. Recent findings in synaptic physiology, neural coding, and psychophysics are discussed, with reference to both vertebrate and insect model systems.
TL;DR: It is shown that phosphorylation of GluR1 by PKC at a highly conserved serine 818 residue is increased during LTP and critical for LTP expression, and this event is a critical event in the plasticity-driven synaptic incorporation of AMPA receptors.
TL;DR: This study proves that the identification of broad patterns in naturally-occurring splice sites, through the analysis of genomic datasets, provides mechanistic and evolutionary insights into pre-mRNA splicing.
Abstract: We have collected over half a million splice sites from five species-Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans and Arabidopsis thaliana-and classified them into four subtypes: U2-type GT-AG and GC-AG and U12-type GT-AG and AT-AC. We have also found new examples of rare splice-site categories, such as U12-type introns without canonical borders, and U2-dependent AT-AC introns. The splice-site sequences and several tools to explore them are available on a public website (SpliceRack). For the U12-type introns, we find several features conserved across species, as well as a clustering of these introns on genes. Using the information content of the splice-site motifs, and the phylogenetic distance between them, we identify: (i) a higher degree of conservation in the exonic portion of the U2-type splice sites in more complex organisms; (ii) conservation of exonic nucleotides for U12-type splice sites; (iii) divergent evolution of C.elegans 3' splice sites (3'ss) and (iv) distinct evolutionary histories of 5' and 3'ss. Our study proves that the identification of broad patterns in naturally-occurring splice sites, through the analysis of genomic datasets, provides mechanistic and evolutionary insights into pre-mRNA splicing.