Alternative pre-mRNA splicing is a central mode of genetic regulation in higher eukaryotes. Variability in splicing patterns is a major source of protein diversity from the genome. In this review, I describe what is currently known of the molecular mechanisms that control changes in splice site choice. I start with the best-characterized systems from the Drosophila sex determination pathway, and then describe the regulators of other systems about whose mechanisms there is some data. How these regulators are combined into complex systems of tissue-specific splicing is discussed. In conclusion, very recent studies are presented that point to new directions for understanding alternative splicing and its mechanisms.

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Mechanisms of Alternative Pre-Messenger RNA Splicing

It is generally accepted that the differentiated state of a given type of cell is associated with the activity of a particular set of genes, together with the total inactivity of those sets associated with the differentiation of other cell types. It is also clear that the differentiated state of dividing or nondividing cells is often extremely stable. In this article we suggest mechanisms that may account for this stability and that also attempt to explain the ordered switching on or off of genes during development. The phenotype of the organism depends on the genotype, and the genetic contribution from both parents is in almost all cases equal. Since the ultimate control of development resides in the genetic material, the actual program must be written in base sequences in the DNA. It is also clear that cytoplasmic components can have a powerful or overriding influence on genomic activity in particular cells, yet these cytoplasmic components are, of course, usually derived from the activity of genes at some earlier stage in development. A continual interaction between cytoplasmic enzymes and DNA sequences is an essential part of the model to be presented. Modification Enzymes In bacteria, enzymes exist which modify DNA by methylating adenine in the 6-position ( 1 ). These enzymes are extremely specific in their action; they modify bases at particular positions in short defined sequences of DNA, which, at least in some instances, form a palindrome. (A palindrome in DNA is an inverted duplication, with twofold rotational symmetry. The 3′ →...

https://science.sciencemag.org/content/sci/187/4173/226.full.pdf

DNA modification mechanisms and gene activity during development.

https://www.normalesup.org/~vorgogoz/articles/D.pachea-references/alternative-splicing/Stamm2005-alternative-splicing-review.pdf

Function of alternative splicing.

https://www.cell.com/cell/pdf/S0092-8674(00)80582-6.pdf

A spatial map of olfactory receptor expression in the Drosophila antenna.

been clear whether all of these activities occur during the removal of each intron+ Recent studies now suggest that all of the proposed SR protein functions are carried out during each round of splicing, and at least some of these functions are performed by independent SR protein molecules+ This review discusses recent advances in understanding the diverse functions of SR proteins in metazoan pre-mRNA splicing and presents a model that takes these new findings into account+ Although the reader should keep in mind that the activity of SR proteins in vivo can be influenced by modulating their subcellular localization, this review focuses on biochemical experiments that specifically address the mechanisms by which SR proteins directly function in the splicing reaction+ (The reader may also refer to related reviews recently published elsewhere (Tacke & Manley, 1999; Blencowe, 2000)+)

Sorting out the complexity of SR protein functions.

Nature has evolved an astonishing variety of genetic and epigenetic sex-determining systems which all achieve the same result, the generation of two sexes. Genetic and molecular analyses, mainly performed during the last 20 years, have gradually revealed the mechanisms that govern sexual differentiation in a few model organisms. In this review, we will introduce the sex-determining system of Drosophila and compare the fruitfly to the housefly Musca domestica and other Dipteran insects. Despite the ostensible variety, all these insects use the same basic strategy: a primary genetic signal that is different in males and females, a key gene that responds to the primary signal, and a double-switch gene that eventually selects between two alternative sexual programmes. These parallels, however, do not extend to the molecular level. Except for the double-switch gene doublesex at the end of the cascade, no functional homologies were found between more distantly related insects. In particular, Sex-lethal, the key gene that controls sexual differentiation in Drosophila, does not have a sex-determining function in any other genus studied so far. These results show that sex-determining cascades, in comparison to other regulatory pathways, evolve much more rapidly.

Structure, function and evolution of sex-determining systems in Dipteran insects.

The sex-determining gene tra-2 of Drosophila encodes a putative RNA binding protein.

https://www.zora.uzh.ch/id/eprint/517/1/89-StZwSchmid_N%C3%B6CellV.pdf

Cell-autonomous and inductive signals can determine the sex of the germ line of drosophila by regulating the gene Sxl

Sex-lethal (Sxl) is the master switch gene for somatic sex determination in Drosophila melanogaster. In XX animals, Sxl becomes activated and imposes female development; in X(Y) animals, Sxl remains inactive and male development ensues. A switch gene for sex determination, called F, has also been identified in the housefly, Musca domestica. An active F dictates female development, while male development ensues when F is inactive. To test if the switch functions of Sxl and F are founded on a common molecular basis, we isolated the homologous Sxl gene in the housefly. Though highly conserved in sequence, Musca-Sxl is not sex-specifically regulated: the same transcripts and protein isoforms are expressed in both male and female animals throughout development. Musca-Sxl is apparently not controlled by the primary sex-determining signal and, thus, is unlikely to correspond to the F gene. Ectopic expression of Musca-SXL protein in Drosophila does not exert any noticeable effects on the known target genes of endogenous Sxl. Instead, forced overexpression of the transgene eventually results in lethality of both XY and XX animals and in developmental abnormalities in some escaper XY animals. Similar results were obtained with the Sxl homologue of Ceratitis capitata (Saccone, G., Peluso, I., Artiaco, D. , Giodano, E., Bopp, D. and Polito, L. C. (1998) Development 125, 1495-1500) suggesting that, in these non-drosophilid species, Sxl performs a function different from that in sex determination.

/pdf/sex-lethal-the-master-sex-determining-gene-in-drosophila-is-zfb2r1o4hy.pdf

Sex-lethal, the master sex-determining gene in Drosophila, is not sex-specifically regulated in Musca domestica

The life of holometabolous insects, such as Drosophila, is characterized by two separate and completely different phases of development. Out of the egg hatches a larva which then becomes transformed during metamorphosis into the adult insect, the imago. The future adult is “hidden” within the larva in the form of the so-called imaginal cells. After fertilization a series of syncytial divisions produces a homogeneous population of nuclei (energids) which later move into the cortical periplasm at the egg’s periphery where they form the cellular blastoderm (review by Anderson, 1972). This is probably the stage at which the presumptive imaginal cells are segregated from the larval cells (seep. 8). These two distinct populations of cells perform their specific vital functions at entirely different periods of development. During metamorphosis, the larval organization breaks down, and the adult insect is formed anew from the imaginal cells. (There are a few exceptional organ systems, e.g. the Malpighian tubules, that persist through metamorphosis.)

Rolf Nöthiger

Papers

Structure, function and evolution of sex-determining systems in Dipteran insects.

The sex-determining gene tra-2 of Drosophila encodes a putative RNA binding protein.

Cell-autonomous and inductive signals can determine the sex of the germ line of drosophila by regulating the gene Sxl

Sex-lethal, the master sex-determining gene in Drosophila, is not sex-specifically regulated in Musca domestica

The Larval Development of Imaginal Disks