The Evolution of Alternative Splicing in the Pax Family: The View from the Basal Chordate Amphioxus

Pax3 Hypomorphs Reveal Hidden Pax7 Functional Genetic Compensation in Utero

Pax3 and Pax7 transcription factors are paralogs within the Pax gene family that that are expressed in early embryos in partially overlapping expression domains and have distinct functions. Significantly, mammalian development is largely unaffected by Pax7 systemic deletion but systemic Pax3 deletion results in defects in neural tube closure, neural crest emigration, cardiac outflow tract septation, muscle hypoplasia and in utero lethality by E14. However, we previously demonstrated that Pax3 hypomorphs expressing only 20% functional Pax3 protein levels exhibit normal neural tube and heart development, but myogenesis is selectively impaired. To determine why only some Pax3-expressing cell lineages are affected and to further titrate Pax3 threshold levels required for neural tube and heart development, we generated hypomorphs containing both a hypomorphic and a null Pax3 allele. This resulted in mutants only expressing 10% functional Pax3 protein with exacerbated neural tube, neural crest and muscle defects, but still a normal heart. To examine why the cardiac neural crest appears resistant to very low Pax3 levels, we examined its paralog Pax7. Significantly, Pax7 expression is both ectopically expressed in Pax3-expressing dorsal neural tube cells and is also upregulated in the Pax3-expressing lineages. To test whether this compensatory Pax7 expression is functional, we deleted Pax7 both systemically and lineage-specifically in hypomorphs expressing only 10% Pax3. Removal of one Pax7 allele resulted in partial outflow tract defects, and complete loss of Pax7 resulted in full penetrance outflow tract defects and in utero lethality. Moreover, combinatorial loss of Pax3 and Pax7 resulted in severe craniofacial defects and a total block of neural crest cell emigration from the neural tube. Pax7^Cre lineage mapping revealed ectopic labeling of Pax3-derived neural crest tissues and within the outflow tract of the heart, experimentally confirming the observation of ectopic activation of Pax7 in 10% Pax3 hypomorphs. Finally, genetic cell ablation of Pax7^Cre-marked cells is sufficient to cause outflow tract defects in hypomorphs expressing only 10% Pax3, confirming that ectopic and induced Pax7 can play an overlapping functional genetic compensational role in both cardiac neural crest lineage and during craniofacial development, which is normally masked by the dominant role of Pax3.

Phylogeny of NF-YA trans-activation splicing isoforms in vertebrate evolution

NF-Y is a trimeric pioneer Transcription Factor (TF) whose target sequence -the CCAAT box- is present in ~25% of mammalian promoters. We reconstruct the phylogenetic history of the regulatory NF-YA subunit in vertebrates. We find that in addition to the remarkable conservation of the subunits-interaction and DNA-binding parts, the Transcriptional Activation Domain (TAD) is also conserved (>90% identity among bony vertebrates). We infer the phylogeny of the alternatively spliced exon-3 and partial splicing events of exon-7 -7N and 7C- revealing independent clade-specific losses of these regions. These isoforms shape the TAD. Absence of exon-3 in basal deuterostomes, cartilaginous fishes and hagfish, but not in lampreys, suggests that the "short" isoform is primordial, with emergence of exon-3 in chordates. Exon 7N was present in the vertebrate common ancestor, while 7C is a molecular innovation of teleost fishes. RNA-seq analysis in several species confirms expression of all these isoforms. We identify 3 blocks of amino acids in the TAD shared across deuterostomes, yet structural predictions and sequence analyses suggest an evolutionary drive for maintenance of an Intrinsically Disordered Region -IDR- within the TAD. Overall, these data help reconstruct the logic for alternative splicing of this essential eukaryotic TF.

Overview of PAX gene family: analysis of human tissue-specific variant expression and involvement in human disease

Paired-box (PAX) genes encode a family of highly conserved transcription factors found in vertebrates and invertebrates. PAX proteins are defined by the presence of a paired domain that is evolutionarily conserved across phylogenies. Inclusion of a homeodomain and/or an octapeptide linker subdivides PAX proteins into four groups. Often termed "master regulators", PAX proteins orchestrate tissue and organ development throughout cell differentiation and lineage determination, and are essential for tissue structure and function through maintenance of cell identity. Mutations in PAX genes are associated with myriad human diseases (e.g., microphthalmia, anophthalmia, coloboma, hypothyroidism, acute lymphoblastic leukemia). Transcriptional regulation by PAX proteins is, in part, modulated by expression of alternatively spliced transcripts. Herein, we provide a genomics update on the nine human PAX family members and PAX homologs in 16 additional species. We also present a comprehensive summary of human tissue-specific PAX transcript variant expression and describe potential functional significance of PAX isoforms. While the functional roles of PAX proteins in developmental diseases and cancer are well characterized, much remains to be understood regarding the functional roles of PAX isoforms in human health. We anticipate the analysis of tissue-specific PAX transcript variant expression presented herein can serve as a starting point for such research endeavors.

The application value of PAX1 and ZNF582 gene methylation in high grade intraepithelial lesion and cervical cancer

PURPOSE

To investigate the possibility of using the methylation level of PAX1/ZNF582 gene as molecular marker to differentiate the progression of cervical cancer.

METHODS

From January 2016 to March 2018, 150 patients, who were admitted to Cervical Disease Diagnosis and Treatment Center of Xuzhu Maternity and Child Care Hospital, were enrolled in this study. Patients were classified into chronic cervicitis (for 19 cases), low-grade squamous intraepithelial lesion (LSIL) (18 cases), high-grade squamous intraepithelial lesion (HSIL) (37 cases) and squamous cell carcinoma (SCC) (31 cases). All patients underwent several tests including Thin-prep cytology test (TCT), HPV DNA detection and detection of methylation level of PAX1/ZNF582 genes.

RESULTS

For diagnosis of HSIL, the area under curve (AUC) was 0.878 (95% CI 0.806 ~ 0.950); the threshold for PAX1 was 12.285, the sensitivity and specificity were 91.9% and 72.8%, respectively. The AUC of ZNF582 gene detection was 0.900 (95% CI 0.842 ~ 0.959), the threshold was 11.56, while the sensitivity and specificity were 97.3% and 76.7%, respectively. Among various tests we conducted, PAX gene detection methods showed the highest specificity (97.30%). PAX1/ZNF582 gene detection method demonstrated the highest accuracy.

CONCLUSIONS

For patients with high-grade cervical lesion and cervical cancer, the methylation level of PAX1/ZNF582 gene could be applied as a noteworthy biomarker for diagnosis and for cervical cancer classification.

The Pax gene family: Highlights from cephalopods

Pax genes play important roles in Metazoan development. Their evolution has been extensively studied but Lophotrochozoa are usually omitted. We addressed the question of Pax paralog diversity in Lophotrochozoa by a thorough review of available databases. The existence of six Pax families (Pax1/9, Pax2/5/8, Pax3/7, Pax4/6, Paxβ, PoxNeuro) was confirmed and the lophotrochozoan Paxβ subfamily was further characterized. Contrary to the pattern reported in chordates, the Pax2/5/8 family is devoid of homeodomain in Lophotrochozoa. Expression patterns of the three main pax classes (pax2/5/8, pax3/7, pax4/6) during Sepia officinalis development showed that Pax roles taken as ancestral and common in metazoans are modified in S. officinalis, most likely due to either the morphological specificities of cephalopods or to their direct development. Some expected expression patterns were missing (e.g. pax6 in the developing retina), and some expressions in unexpected tissues have been found (e.g. pax2/5/8 in dermal tissue and in gills). This study underlines the diversity and functional plasticity of Pax genes and illustrates the difficulty of using probable gene homology as strict indicator of homology between biological structures.

Expression of Two Classes of Pax6 Transcripts in Reprogramming Retinal Pigment Epithelium Cells of the Adult Newt

The adult newt has the remarkable ability to regenerate a functional retina from retinal pigment epithelium (RPE) cells, even when the neural retina (NR) is completely lost from the eye. In this system, RPE cells are reprogrammed into a unique state of multipotent cells, named RPESCs, in an early phase of retinal regeneration. However, the signals that trigger reprogramming remain unknown. Here, to approach this issue we focused on Pax6, a transcription factor known to be expressed in RPESCs. We first identified four classes (v1, v2, v3 and v4) of Pax6 variants in the eye of adult newt, Cynops pyrrhogaster. These variants were expressed in most tissues of the intact eye in different combinations but not in the RPE, choroid or sclera. On the basis of this information, we investigated the expression of Pax6 in RPE cells after the NR was removed from the eye by surgery (retinectomy), and found that two classes (v1 and v2) of Pax6 variants were newly expressed in RPE cells 10 days after retinectomy, both in vivo and in vitro (RLEC system). In the RLEC system, we found that Pax6 expression is mediated through a pathway separate from the MEK-ERK pathway, which is required for cell cycle re-entry of RPE cells. These results predict the existence of a pathway that may be of fundamental importance to a better understanding of the reprogramming of RPE cells in vivo.

Pax2/5/8 and Pax6 alternative splicing events in basal chordates and vertebrates: a focus on paired box domain

Paired box transcription factors play important role in development and tissue morphogenesis. The number of Pax homologs varies among species studied so far, due to genome and gene duplications that have affected PAX family to a great extent. Based on sequence similarity and functional domains, four Pax classes have been identified in chordates, namely Pax1/9, Pax2/5/8, Pax3/7, and Pax4/6. Numerous splicing events have been reported mainly for Pax2/5/8 and Pax6 genes. Of significant interest are those events that lead to Pax proteins with presumed novel properties, such as altered DNA-binding or transcriptional activity. In the current study, a thorough analysis of Pax2/5/8 splicing events from cephalochordates and vertebrates was performed. We focused more on Pax2/5/8 and Pax6 splicing events in which the paired domain is involved. Three new splicing events were identified in Oryzias latipes, one of which seems to be conserved in Acanthomorphata. Using representatives from deuterostome and protostome phyla, a comparative analysis of the Pax6 exon-intron structure of the paired domain was performed, during an attempt to estimate the time of appearance of the Pax6(5a) mRNA isoform. As shown in our analysis, this splicing event is characteristic of Gnathostomata and is absent in the other chordate subphyla. Moreover, expression pattern of alternative spliced variants was compared between cephalochordates and fish species. In summary, our data indicate expansion of alternative mRNA variants in paired box region of Pax2/5/8 and Pax6 genes during the course of vertebrate evolution.

Alternative splicing of the trout Pax5 gene and identification of novel B cell populations using Pax5 signatures

Pax5 is an alternatively spliced transcription factor that regulates B cell development and activation. The function of specific Pax5 isoforms is unknown. Here we report the existence of seven alternatively spliced isoforms of Pax5 in the rainbow trout. We hypothesized that B cells differentially express specific Pax5 isoforms as a means of modulating Pax5 activity during cell maturation. Flow cytometric analyses using Pax5-specific antibodies recognizing the paired domain, a central (exon 6-encoding) domain, or the C-terminus, revealed the existence of distinct Pax5-expressing cell populations in trout immune tissues. Additionally, using the transcription factor EBF, we show that Pax5 isoforms lacking a paired domain are already expressed at the earliest stages of trout (B) lymphopoiesis, and unexpectedly, that minor populations of such cells reside in blood and spleen. These data support use of differentially expressed Pax5 isoforms to identify novel B cell subsets in the form of Pax5 tissue signatures, and as such, provides new biomarkers for malignancy, infectious disease, and disease resistance in trout and humans.

Characterization of pax1, pax9, and uncx sclerotomal genes during Xenopus laevis embryogenesis

BACKGROUND

The axial skeleton develops from the sclerotome, a mesenchymal cell population derived from somites. Sclerotomal cells migrate from somites to the perinotochordal and perineural space where they differentiate into chondrocytes to form cartilage and bone. In anurans, little is known about the way how the sclerotome changes as development proceeds and how these events are regulated at the molecular level. Pax1, Pax9, and Uncx4.1 genes play a central role in the morphogenesis of the axial skeleton in vertebrates, regulating cell proliferation and chondrogenic specification of the sclerotome.

RESULTS

In this work, we cloned and examined through whole-mount in situ hybridization and reverse transcriptase-polymerase chain reaction the expression patterns of pax1, pax9, and uncx transcription factors in the anuran Xenopus laevis.

CONCLUSIONS

We found that these genes are similarly expressed in the sclerotome and in the pharyngeal pouch. A detailed analysis of the location of these transcripts showed that they are expressed in different subdomains of the sclerotomal compartment and differ from that observed in other vertebrates.

Evolution of new characters after whole genome duplications: insights from amphioxus

Additional copies of genes resulting from two whole genome duplications at the base of the vertebrates have been suggested as enabling the evolution of vertebrate-specific structures such as neural crest, a midbrain/hindbrain organizer and neurogenic placodes. These structures, however, did not evolve entirely de novo, but arose from tissues already present in an ancestral chordate. This review discusses the evolutionary history of co-option of old genes for new roles in vertebrate development as well as the relative contributions of changes in cis-regulation and in protein structure. Particular examples are the FoxD, FGF8/17/18 and Pax2/5/8 genes. Comparisons with invertebrate chordates (amphioxus and tunicates) paint a complex picture with co-option of genes into new structures occurring both after and before the whole genome duplications. In addition, while cis-regulatory changes are likely of primary importance in evolution of vertebrate-specific structures, changes in protein structure including alternative splicing are non-trivial.

The function and developmental expression of alternatively spliced isoforms of amphioxus and Xenopus laevis Pax2/5/8 genes: revealing divergence at the invertebrate to vertebrate transition

Pax genes encode highly conserved transcription factors vital for metazoan development. Pax transcripts, particularly those in Group II (Pax2/5/8), are extensively alternatively spliced. This study compares the transcriptional activation capacity and developmental stage-specific expression of major isoforms of Group II Pax proteins in amphioxus (Branchiostoma floridae) and in Xenopus laevis. The comparison reveals considerable divergence of splice forms between the lineages, with the X. laevis Group II Pax genes (Pax2, Pax5, and Pax8) possessing a greater repertoire of regulated and functionally distinct splice forms than the single amphioxus gene (Pax2/5/8). Surprisingly, some apparently conserved splice forms are expressed at quite different levels during development in the two organisms and present different capacities to activate transcription. However, despite this divergence, the combinatorial transcriptional activation capacity of the isoforms present in early X. laevis and amphioxus development are broadly similar. This suggests that the some of the conserved functional roles, implied by the expression of Group II Pax genes in homologous tissues of amphioxus and X. laevis embryos, may depend upon the combination of isoforms expressed in a particular tissue at a particular time in development. Thus, during early development, the evolutionary constraint on the net effect of several isoforms co-expressed in a given tissue may be more strict than that on specific isoforms. This flexibility may facilitate the appearance of new exons and splicing patterns in the vertebrate duplicates, leading to isoforms with subtly distinct functions critical to the subsequent development of vertebrate-specific cell types and structures.

Alternative splicing: a potential source of functional innovation in the eukaryotic genome

Alternative splicing (AS) is a common posttranscriptional process in eukaryotic organisms, by which multiple distinct functional transcripts are produced from a single gene. The release of the human genome draft revealed a much smaller number of genes than anticipated. Because of its potential role in expanding protein diversity, interest in alternative splicing has been increasing over the last decade. Although recent studies have shown that 94% human multiexon genes undergo AS, evolution of AS and thus its potential role in functional innovation in eukaryotic genomes remain largely unexplored. Here we review available evidence regarding the evolution of AS prevalence and functional role. In addition we stress the need to correct for the strong effect of transcript coverage in AS detection and set out a strategy to ultimately elucidate the extent of the role of AS in functional innovation on a genomic scale.

Inferring transcript phylogenies

Alternative splicing, an unknown mechanism 20 years ago, is now recognized as a major mechanism for proteome and transcriptome diversity, particularly in mammals--some researchers conjecture that up to 90% of human genes are alternatively spliced. Despite much research on exon and intron evolution, little is known about the evolution of transcripts.

In this paper, we present a model of transcript evolution and an associated algorithm to reconstruct transcript phylogenies. The evolution of the gene structure--exons and introns--is used as basis for the reconstruction of transcript phylogenies. We apply our model and reconstruction algorithm on two well-studied genes, MAG and PAX6, obtaining results consistent with current knowledge and thereby providing evidence that a phylogenetic analysis of transcripts is feasible and likely to be informative.

EST and transcriptome analysis of cephalochordate amphioxus--past, present and future

The cephalochordates, commonly known as amphioxus or lancelets, are now considered the most basal chordate group, and the studies of these organisms therefore offer important insights into various levels of evolutionary biology. In the past two decades, the investigation of amphioxus developmental biology has provided key knowledge for understanding the basic patterning mechanisms of chordates. Comparative genome studies of vertebrates and amphioxus have uncovered clear evidence supporting the hypothesis of two-round whole-genome duplication thought to have occurred early in vertebrate evolution and have shed light on the evolution of morphological novelties in the complex vertebrate body plan. Complementary to the amphioxus genome-sequencing project, a large collection of expressed sequence tags (ESTs) has been generated for amphioxus in recent years; this valuable collection represents a rich resource for gene discovery, expression profiling and molecular developmental studies in the amphioxus model. Here, we review previous EST analyses and available cDNA resources in amphioxus and discuss their value for use in evolutionary and developmental studies. We also discuss the potential advantages of applying high-throughput, next-generation sequencing (NGS) technologies to the field of amphioxus research.

New insights from hemichordate genomes: prebilaterian origin and parallel modifications in the paired domain of the Pax gene eyegone

The evolutionary origin of the Drosophila Pax transcription factor gene eyegone (eyg) has long been enigmatic owing to the failure in detecting orthologs in other species and the unusual N-terminal truncation of the DNA-binding paired domain (PD). Based on the discovery of eyg orthologs in representatives of hemichordate phyla, we show that the origin of eyg predated metazoan diversification and that the PD experienced similar but independent N-terminal modifications in the lineages to sea urchins and insects. Sequence conservation patterns further raise the possibility of persisting functionality in the N-terminal PD of strongly modified eyg orthologs. Finally, we note that the evolutionary histories of eyg and the vertebrate Pax6 isoform 5a, which have been considered functional homologs, are not correlated. Taken together, these findings identify Drosophila eyg as the baptizing member of an ancient Pax gene subfamily and recommend abandoning its classification as Pax6(5a)-related gene.

The Pax gene eyegone facilitates repression of eye development in Tribolium

BACKGROUND

The Pax transcription factor gene eyegone (eyg) participates in many developmental processes in Drosophila, including the Notch signaling activated postembryonic growth of the eye primordium, global development of the adult head and the development of the antenna. In contrast to other Pax genes, the functional conservation of eyg in species other than Drosophila has not yet been explored.

RESULTS

We investigated the role of eyg during the postembryonic development of the red flour beetle Tribolium castaneum. Our results indicate conserved roles in antennal but not in eye development. Besides segmentation defects in the antenna, Tribolium eyg knockdown animals were characterized by eye enlargement due to the formation of surplus ommatidia at the central anterior edge of the compound eye. This effect resulted from the failure of the developing gena to locally repress retinal differentiation, which underlies the formation of the characteristic anterior notch in the Tribolium eye. Neither varying the induction time point of eyg knockdown nor knocking down components of the Janus kinase/Signal Transducer and Activators of Transcription signaling pathway in combination with eyg reduced eye size like in Drosophila.

CONCLUSIONS

Taken together, expression and knockdown data suggest that Tribolium eyg serves as a competence factor that facilitates the repression of retinal differentiation in response to an unknown signal produced in the developing gena. At the comparative level, our findings reveal diverged roles of eyg associated with the evolution of different modes of postembryonic head development in endopterygote insects as well as diversified head morphologies in darkling beetles.

Alternative splicing in development and function of chordate endocrine systems: a focus on Pax genes

Genome sequencing has facilitated an understanding of gene networks but has also shown that they are only a small part of the answer to the question of how genes translate into a functional organism. Much of the answer lies in epigenetics-heritable traits not directly encoded by the genome. One such phenomenon is alternative splicing, which affects over 75% of protein coding genes and greatly amplifies the number of proteins. Although it was postulated that alternative splicing and gene duplication are inversely proportional and, therefore, have similar effects on the size of the proteome, for ancient duplications such as occurred in the Pax family of transcription factors, that is not necessarily so. The importance of alternative splicing in development and physiology is only just coming to light. However, several techniques for studying isoform functions both in vitro and in vivo have been recently developed. As examples of what is known and what is yet to be discovered, this review focuses on the evolution and roles of the Pax family of transcription factors in development and on alternative splicing of endocrine genes and the factors that regulate them.

Chordate roots of the vertebrate nervous system: expanding the molecular toolkit

The vertebrate brain is highly complex with millions to billions of neurons. During development, the neural plate border region gives rise to the neural crest, cranial placodes and, in anamniotes, to Rohon-Beard sensory neurons, whereas the boundary region of the midbrain and hindbrain develops organizer properties. Comparisons of developmental gene expression and neuroanatomy between vertebrates and the basal chordate amphioxus, which has only thousands of neurons and lacks a neural crest, most placodes and a midbrain-hindbrain organizer, indicate that these vertebrate features were built on a foundation already present in the ancestral chordate. Recent advances in genomics have provided insights into the elaboration of the molecular toolkit at the invertebrate-vertebrate transition that may have facilitated the evolution of these vertebrate characteristics.

Cephalochordates (amphioxus or lancelets): a model for understanding the evolution of chordate characters

Cephalochordates, commonly called amphioxus or lancelets, are marine invertebrate chordates. They were traditionally held as the closest living relatives of vertebrates and have long occupied a key phylogenetic position in our discussions on the origin of vertebrates. However, recent molecular phylogenetic analyses have placed tunicates as the sister taxon of vertebrates and cephalochordates as the most basal chordate group. Therefore, studies on cephalochordates can also provide important insights for understanding the conserved patterning mechanisms for all chordates. Cephalochordates and vertebrates share several key chordate features, namely, the dorsal nerve cord, notochord, segmented somites, and pharyngeal gill slits. However, vertebrates have ~25% more genes than amphioxus and several features not present in cephalochordates, including a more elaborate head and forebrain, migratory neural crest, and neurogenic placodes. During the last two decades, expression patterns of important developmental genes have been used extensively to infer homologies between cephalochordate and vertebrate embryos. These studies have answered some long-standing questions concerning the evolution of vertebrates from their invertebrate ancestors and have also generated interesting hypotheses for further investigations. With the completion of a cephalochordate genome project in 2008, comparison between cephalochordate and vertebrate genomes has allowed us to postulate a picture for the genome of the last common ancestor of all chordates. Such comparisons are also providing important biological insights into the functional biology of cephalochordates and the evolutionary origin of developmental mechanisms that led to the emergence of the vertebrate body plan.

Pigmentation PAX-ways: the role of Pax3 in melanogenesis, melanocyte stem cell maintenance, and disease

Transcription factors initiate programs of gene expression and are catalysts in downstream molecular cascades that modulate a variety of cellular processes. Pax3 is a transcription factor that is important in the melanocyte and influences melanocytic proliferation, resistance to apoptosis, migration, lineage specificity and differentiation. In this review, we focus on Pax3 and the molecular pathways that Pax3 is a part of during melanogenesis and in the melanocyte stem cell. These roles of Pax3 are emphasized during the development of diseases and syndromes resulting from either too much or too little Pax3 function. Due to its key task in melanocyte stem cells and tumors, the Pax3 pathway may provide an ideal target for either stem cell or cancer therapies.