Effects of intron length on differential processing of mouse mu heavy-chain mRNA

Repositioning of an alternative exon sequence of mouse IgM pre-mRNA activates splicing of the preceding intron

Using a transient expression system of mouse IgM mini-gene constructs in mouse B-cell lines and in fibroblast L cell, we investigated splicing of the IgM transcript. We observed that the efficiency of splicing between exons C4 and M1 (C4-to-M1 splicing), the splicing reaction leading to the production of membrane-bound form (microns) mRNA, was drastically affected by mutations in a specific portion of the downstream exon (M2). The results show that the specific exon M2 sequence activates the C4-to-M1 splicing. This activation was not observed when splicing between exons M1 and M2 was abolished by base substitutions at the splice sites. These results indicate that positioning of the downstream exon is crucial for efficient splicing of the preceding intron.

Immunoglobulin heavy chain gene regulation through polyadenylation and splicing competition

The immunoglobulin heavy chain (IgH) genes, which encode one of the two chains of antibody molecules, were the first cellular genes shown to undergo developmentally regulated alternative RNA processing. These genes produce two different mRNAs from a single primary transcript. One mRNA is cleaved and polyadenylated at an upstream poly(A) signal while the other mRNA removes this poly(A) signal by RNA splicing and is cleaved and polyadenylated at a downstream poly(A) site. A broad range of studies have been performed to understand the mechanism of IgH RNA processing regulation during B lymphocyte development. The model that has emerged is much more complex than envisioned by the earliest view of regulation through poly(A) signal choice. Regulation requires that the IgH gene contain competing splice and cleavage-polyadenylation reactions with balanced efficiencies. Because non-IgH genes with these structural features also can be regulated, IgH gene-specific sequence elements are not required for regulation. Changes in cleavage-polyadenylation and RNA splicing, as well as pol II elongation, all contribute to IgH developmental RNA processing regulation. Multiple factors are likely involved in the regulation during B lymphocyte maturation. Additional biologically relevant factors that contribute to IgH regulation remain to be identified and incorporated into a mechanistic model for regulation. Much of the work to date confirms the complex nature of IgH mRNA regulation and suggests that a thorough understanding of this control will remain a challenge. However, it is also likely that such understanding will help elucidate novel mechanisms of RNA processing regulation.

Molecular Basis of the Size Polymorphism of the First Intron of theAdh-1 Gene of the Mediterranean Fruit Fly, Ceratitis capitata

The first intron of the gene encoding one of the alcohol dehydrogenase isoenzymes (ADH-1) in Ceratitis capitata is highly polymorphic in size. Five size variants of this intron were isolated from different strains and populations and characterized. Restriction map and sequence analysis showed that the intron size polymorphism is due to the presence or absence of (a) a copy of a defective mariner-like element, postdoc; (b) an approximately 550-bp 3' indel which exhibits no similarity to any known sequence; and (c) a central duplication of 704 bp consisting of part of the 3' end of the postdoc element, the region between postdoc and the 3' indel, and the first 20 bp of the 3' indel. The homologous Adh-1 intron was amplified from the congeneric species, Ceratitis rosa, in order to obtain an outgroup for comparative and phylogenetic analyses. The C. rosa introns were polymorphic in size, ranging from about 1100 to 2000 bp, the major difference between them being the presence or absence of a mariner-like element Crmar2, unrelated to the postdoc element. Phylogenetic analysis suggests that the shorter intron variants in C. capitata may represent the ancestral form of the intron, the longest variants apparently being the most recent.

Cloning and molecular characterization of the rat CB2 cannabinoid receptor

The rat peripheral cannabinoid receptor (rCB2) was cloned from a Sprague-Dawley rat spleen cDNA library and when translated, encodes a protein of 410 amino acids. Alignment of rCB2 with mouse (mCB2) and human (hCB2) peripheral cannabinoid receptors reveals a high degree of homology except in the carboxy terminus where rCB2 is 50 and 63 residues longer than hCB2 and mCB2, respectively. PCR screening and sequencing of rat genomic DNA showed that rCB2 is encoded by three exons interrupted by two introns, one of which is polymorphic and contains a 209 base pair B2 (SINE) element. By Northern hybridization and ribonuclease protection assay (RPA), rCB2 mRNA was detected in rat spleen, testis, thymus and lung but not in rat brain, heart, kidney or liver. Like hCB2 and mCB2 receptors, rCB2 activates mitogen-activated protein kinase when it is stably expressed in Chinese Hamster Ovary (CHO) cells. The importance of the carboxy terminus in regulating CB2 receptor desensitization and internalization is well-established. Thus, the profound differences identified in this region of the CB2 receptor between species mandates caution when extrapolating experimental results from non-human models to the effects of chronic CB2 receptor stimulation in humans.

The correlation between intron length and recombination in drosophila. Dynamic equilibrium between mutational and selective forces

Intron length is negatively correlated with recombination in both Drosophila melanogaster and humans. This correlation is not likely to be the result of mutational processes alone: evolutionary analysis of intron length polymorphism in D. melanogaster reveals equivalent ratios of deletion to insertion in regions of high and low recombination. The polymorphism data do reveal, however, an excess of deletions relative to insertions (i.e., a deletion bias), with an overall deletion-to-insertion events ratio of 1.35. We propose two types of selection favoring longer intron lengths. First, the natural mutational bias toward deletion must be opposed by strong selection in very short introns to maintain the minimum intron length needed for the intron splicing reaction. Second, selection will favor insertions in introns that increase recombination between mutations under the influence of selection in adjacent exons. Mutations that increase recombination, even slightly, will be selectively favored because they reduce interference among selected mutations. Interference selection acting on intron length mutations must be very weak, as indicated by frequency spectrum analysis of Drosophila intron length polymorphism, making the equilibrium for intron length sensitive to changes in the recombinational environment and population size. One consequence of this sensitivity is that the advantage of longer introns is expected to decrease inversely with the rate of recombination, thus leading to a negative correlation between intron length and recombination rate. Also in accord with this model, intron length differs between closely related Drosophila species, with the longest variant present more often in D. melanogaster than in D. simulans. We suggest that the study of the proposed dynamic model, taking into account interference among selected sites, might shed light on many aspects of the comparative biology of genome sizes including the C value paradox.

Correct immunoglobulin alpha mRNA processing depends on specific sequence in the C alpha 3-alpha M intron

The maturation of IgM-expressing B cells to IgM-secreting plasma cells is associated with both an increase in mu mRNA and the ratio of secreted to membrane forms of mu mRNA which differ at the 3' termini. In contrast, both in vitro and in vivo the secreted form of alpha mRNA is predominant at all stages in the development of a secretory IgA response. Previous studies demonstrated that preferential usage of the alpha s poly(A) site does not result from transcription termination and is independent of either the poly(A) sites or the 3' splice site associated with the exon encoding the membrane exon of IgA (alpha M). The present study demonstrates that a 349-bp region located 774 bp 3' to the alpha s poly(A) site is required for the preferential usage of the alpha s terminus. This region, which is the first isotype-specific cis-acting regulatory sequence not immediately adjacent to a secretory poly(A) site to be identified, contains regulatory elements that increase the efficiency of polyadenylation/cleavage. A ubiquitous, approximately 58-kDa RNA-binding protein interacts specifically with this regulatory region. These studies support the premise that cis-acting elements unique to each CH gene can impinge upon a common mechanism regulating Ig mRNA processing.

Developmental regulation of immunoglobulin mRNA processing and the IgA response: establishing a paradigm

IgA, which is protective at mucosal sites, is derived from memory B cells that develop in the organized lymphoid tissue of the gastrointestinal tract and subsequently mature to plasma cells in the lamina propria. Similarly to B cells expressing other isotypes, the maturation of IgA-expressing B cells is associated with both an increase in the steady-state level of immunoglobulin mRNA and the ratio of secreted to membrane forms of mRNA, which differ in 3' terminus. In contrast to B cells expressing other isotypes, at all stages in the development of an IgA response, the secreted form of alpha mRNA predominates. In this article, studies on the general features of IgA B cell development, mechanisms regulating 3' terminus usage of Ig mRNAs, and isotype-specific regulation of 3' terminus usage particularly in regard to alpha mRNA are discussed.

Effect of upstream RNA processing on selection of mu S versus mu M poly(A) sites

All of the regulatory factors responsible for augmenting microseconds mRNA levels preceding the dramatic increase in secretory IgM production upon B cell activation has not been totally elucidated. Whereas previous experiments have centered on the region of the gene specifying the choice between splicing to mu M exons versus selection of the mu S poly(A) site, we have found that upstream sequences within the Cmu gene, specifically the Cmu 4 acceptor splice site together with intronic sequences between the Cmu 3++ and Cmu 4 exons, play an important role in dictating the precision or the extent of splicing to the mu M exons even under conditions in which functional polyadenylation factors should be in excess. Therefore, splicing of upstream exons can affect remotely located downstream exons. These findings suggest that regulation of differential mu S/mu M mRNA expression may involve general processing enzymes that recognize specific cis -regulatory sequences residing within the body of the mu gene and account for the unique ability of activated B cells to secrete copious amounts of IgM.

Sequence and spatial requirements for regulated muscle-specific processing of the sarco/endoplasmic reticulum Ca(2+)-ATPase 2 gene transcript

Expression of the muscle-specific 2a isoform of the sarco/endoplasmic reticulum Ca2+ ATPase (SERCA2) requires activation of an otherwise inefficient splicing process at the 3'-end of the primary gene transcript. The sequence and topology requirements for this regulated splicing event were studied in the BC3H1 myogenic cell line using a minigene containing the 3'-end of the SERCA2 gene. In undifferentiated BC3H1 cells, the splice process is made inefficient by the presence of a weak muscle-type 5'-donor site (5'D1) and a long terminal intron. Both optimizing the 5'D1 and decreasing the length of the muscle-specific intron, induced muscle-type splicing in undifferentiated myogenic cells. Moreover, the induction of muscle-type transcripts was only observed when two competing processing sites, the polyadenylation site (pAu) used in non-muscle cells and the second neuronal 5'-donor site (5'D2), were weak. Indeed, making 5'D2 consensus induced neuronal-type splicing in undifferentiated myocytes and prevented the appearance of muscle-type transcripts. Similarly, replacing the polyadenylation site (pAu) with a strong site almost completely inhibited muscle-type splicing after myogenic differentiation. We conclude that weak processing sites and a long terminal intron are required for tissue-dependent mRNA processing of the SERCA2 transcript.

Analysis of a mouse gene encoding three steps of purine synthesis reveals use of an intronic polyadenylation signal without alternative exon usage

A single mouse genomic locus encodes proteins catalyzing three steps of purine synthesis, glycinamide ribonucleotide synthetase (GARS), aminoimidazole ribonucleotide synthetase (AIRS), and glycinamide ribonucleotide formyltransferase (GART). This gene has 22 exons and spans 28 kilobases. The existence of a second genetic locus and closely related pseudogenes was ruled out by Southern analysis. Mouse tissues express two related classes of messages encoded by this single locus: a trifunctional GARS-AIRS-GART mRNA and a monofunctional GARS mRNA. These transcripts used the same set of multiple transcriptional start sites, and both used the same first 10 exons. CCAAT and TATA elements were not found for this locus. Exon 11, which represented the last coding sequence of the GARS domain, was differentially utilized for the two messages. The trifunctional mRNA was generated by splicing exon 11 to exon 12, the first coding sequence for the AIRS domain with subsequent use of a polyadenylation signal at the end of exon 22. Genomic sequence corresponding to the 3'-UTR of the monofunctional GARS mRNA was contiguous with exon 11, so that the smaller message arose from the recognition of one of the multiple polyadenylation signals present within the intron between exons 11 and 12. Hence, polyadenylation of the primary transcript at a position corresponding to an intron of the genomic locus was responsible for the generation of the monofunctional GARS class of mRNAs. This utilization of an intronic polyadenylation site without alternative exon usage is comparable to the mechanism whereby both secreted and membrane-bound forms of the immunoglobulin mu heavy chain are made from a single genetic locus.

Membrane mu poly(A) signal and 3' flanking sequences function as a transcription terminator for immunoglobulin-encoding genes

Developmentally regulated mechanisms involving alternative RNA splicing and/or polyadenylation, as well as transcription termination, are implicated in controlling the levels of secreted mu (mu s), membrane mu (mu m) and delta immunoglobulin (Ig) heavy chain mRNAs during B cell differentiation (mu gene encodes the mu heavy chain). Using expression vectors constructed with genomic DNA segments composed of the mu m polyadenylation signal region, we analyzed poly(A) site utilization and termination of transcription in stably transfected myeloma cells and in murine fibroblast L cells. We found that the gene segment containing the mu m poly(A) signals, along with 536 bp of downstream flanking sequence, acted as a transcription terminator in both myeloma cells and L cell fibroblasts. Neither a 141-bp DNA fragment (which directed efficient polyadenylation at the mu m site), nor the 536-bp flanking nucleotide sequence alone, were sufficient to obtain a similar regulation. This shows that the mu m poly(A) region plays a central role in controlling developmentally regulated transcription termination by blocking downstream delta gene expression. Because this gene segment exhibited the same RNA processing and termination activities in fibroblasts, it appears that these processes are not tissue-specific.

Balanced efficiencies of splicing and cleavage-polyadenylation are required for mu-s and mu-m mRNA regulation

The relative abundance of the RNAs encoding the membrane (mu-m) and secreted (mu-s) forms of immunoglobulin mu heavy chain is regulated during B cell maturation by a change in the mode of RNA processing. This regulation depends on a competition between two mutually exclusive RNA processing reactions, cleavage-polyadenylation at the microseconds poly(A) site and splicing of the Cmu4 and M1 exons. Previously, the efficiencies of these two reactions were altered independently. When an efficient processing signal replaced the normal suboptimal signals of the mu gene, a single RNA product was produced exclusively. In this report, two efficient signals are combined in a single mu transcript and shown to restore a processing balance such that two mRNAs can once again be alternatively processed from a single RNA precursor. The ratio of the two RNAs generated from these mu genes containing balanced competing strong splice and cleavage-polyadenylation reactions display the expected developmental shift when expressed in B cells and plasma cells. Therefore, the balance between cleavage-polyadenylation and splicing efficiencies is critical to the developmentally regulated expression of mu-s and mu-m mRNA. Also shown here is that the entire mu-m region, including the M1 and M2 exons and the mu-m poly(A) site, can be replaced with SV40 splice and poly(A) sequences. Regulation is maintained in these mu genes, indicating that no specific sequences within the mu-m region are required.

Regulation of the production of secretory and membrane immunoglobulin during lymphocyte development

An area of great controversy in molecular immunology is the mechanism by which the differential expression of secretory and membrane immunoglobulin heavy chain is regulated during B cell development. Since the changes in expression of the two proteins are determined largely by the steady state levels of the mRNAs that encode them, recent work has focused on the regulation of the expression of the two messages. This problem is central to understanding humoral immunity, with the specific antigen driven switch from antibody as receptor to antibody as secreted product and may be of direct relevance to some forms of the common variable immunodeficiency syndrome. In addition, numerous other genes have been shown to be regulated by alternative RNA processing. Since its beginnings, research in immunology has brought about profound changes in our view of biology. Jenner's landmark experiment, inducing a minor illness to prevent a major one, showed that the body's future susceptibility to a particular disease could be manipulated. More recently the demonstration that immunoglobulin V, D, and J gene segments, originally spread over many kilobases (kbs) in the genome, must be assembled to form a functional heavy chain gene has shattered both the concept of a genome fixed at fertilization and the "one gene, one protein" rule. The alternative processing of heavy chain transcripts to produce secretory and membrane forms of immunoglobulin has demonstrated how the same gene can give rise to proteins with alternative structures. Since the discovery of the role of alternative RNA processing in heavy chain mRNA synthesis, numerous other cellular genes have been shown to be regulated by modulation of RNA processing pathways.