Structure, biological activity of the upstream regulatory sequence, and conserved domains of a middle molecular mass neurofilament gene of Xenopus laevis

Comparative gene expression profiling between optic nerve and spinal cord injury in Xenopus laevis reveals a core set of genes inherent in successful regeneration of vertebrate central nervous system axons

BACKGROUND

The South African claw-toed frog, Xenopus laevis, is uniquely suited for studying differences between regenerative and non-regenerative responses to CNS injury within the same organism, because some CNS neurons (e.g., retinal ganglion cells after optic nerve crush (ONC)) regenerate axons throughout life, whereas others (e.g., hindbrain neurons after spinal cord injury (SCI)) lose this capacity as tadpoles metamorphose into frogs. Tissues from these CNS regions (frog ONC eye, tadpole SCI hindbrain, frog SCI hindbrain) were used in a three-way RNA-seq study of axotomized CNS axons to identify potential core gene expression programs for successful CNS axon regeneration.

RESULTS

Despite tissue-specific changes in expression dominating the injury responses of each tissue, injury-induced changes in gene expression were nonetheless shared between the two axon-regenerative CNS regions that were not shared with the non-regenerative region. These included similar temporal patterns of gene expression and over 300 injury-responsive genes. Many of these genes and their associated cellular functions had previously been associated with injury responses of multiple tissues, both neural and non-neural, from different species, thereby demonstrating deep phylogenetically conserved commonalities between successful CNS axon regeneration and tissue regeneration in general. Further analyses implicated the KEGG adipocytokine signaling pathway, which links leptin with metabolic and gene regulatory pathways, and a novel gene regulatory network with genes regulating chromatin accessibility at its core, as important hubs in the larger network of injury response genes involved in successful CNS axon regeneration.

CONCLUSIONS

This study identifies deep, phylogenetically conserved commonalities between CNS axon regeneration and other examples of successful tissue regeneration and provides new targets for studying the molecular underpinnings of successful CNS axon regeneration, as well as a guide for distinguishing pro-regenerative injury-induced changes in gene expression from detrimental ones in mammals.

Post-transcriptional regulation mediated by specific neurofilament introns in vivo

Neurons regulate genes post-transcriptionally to coordinate the supply of cytoskeletal proteins, such as the medium neurofilament (NEFM), with demand for structural materials in response to extracellular cues encountered by developing axons. By using a method for evaluating functionality of cis-regulatory gene elements in vivo through plasmid injection into Xenopus embryos, we discovered that splicing of a specific nefm intron was required for robust transgene expression, regardless of promoter or cell type. Transgenes utilizing the nefm 3'-UTR but substituting other nefm introns expressed little or no protein owing to defects in handling of the messenger (m)RNA as opposed to transcription or splicing. Post-transcriptional events at multiple steps, but mainly during nucleocytoplasmic export, contributed to these varied levels of protein expression. An intron of the β-globin gene was also able to promote expression in a manner identical to that of the nefm intron, implying a more general preference for certain introns in controlling nefm expression. These results expand our knowledge of intron-mediated gene expression to encompass neurofilaments, indicating an additional layer of complexity in the control of a cytoskeletal gene needed for developing and maintaining healthy axons.

A method for using direct injection of plasmid DNA to study cis-regulatory element activity in F0 Xenopus embryos and tadpoles

The ability to express exogenous reporter genes in intact, externally developing embryos, such as Xenopus, is a powerful tool for characterizing the activity of cis-regulatory gene elements during development. Although methods exist for generating transgenic Xenopus lines, more simplified methods for use with F0 animals would significantly speed the characterization of these elements. We discovered that injecting 2-cell stage embryos with a plasmid bearing a ϕC31 integrase-targeted attB element and two dual β-globin HS4 insulators flanking a reporter transgene in opposite orientations relative to each other yielded persistent expression with sufficiently high penetrance for characterizing the activity of the promoter without having to coinject integrase RNA. Expression began appropriately during development and persisted into swimming tadpole stages without perturbing the expression of the cognate endogenous gene. Coinjected plasmids having the same elements but expressing different reporter proteins were reliably coexpressed within the same cells, providing a useful control for variations in injections between animals. To overcome the high propensity of these plasmids to undergo recombination, we developed a method for generating them using conventional cloning methods and DH5α cells for propagation. We conclude that this method offers a convenient and reliable way to evaluate the activity of cis-regulatory gene elements in the intact F0 embryo.

Dynamic endogenous association of neurofilament mRNAs with K-homology domain ribonucleoproteins in developing cerebral cortex

The low, middle, and high molecular mass neurofilament subunit proteins (NF-L, NF-M, and NF-H) co-polymerize to form neurofilaments (NFs). During development, NF subunit expression is highly regulated, and in neurodegenerative disease, aberrant regulation of this expression can lead to the formation of harmful aggregates. NF expression in both development and disease is under significant post-transcriptional control, but the specific ribonucleoproteins (RNPs) involved are only poorly understood. Previously, mass spectrometry on affinity purified proteins from rat brain identified three K-homology (KH) domain RNPs - hnRNP K, hnRNP E1, hnRNP E2 - as being capable of binding NF-M RNA. In the current study, to determine whether these RNPs associate with NF mRNAs endogenously, we performed a co-immunoprecipitation assay on homogenates of postnatal and developing rat cerebral cortex. We found that all three NF mRNAs indeed associated endogenously with these RNPs and that the degree of this association changed during postnatal development, a period when NF expression is under significant post-transcriptional control. The degree of these associations changed independently of the abundance of either the RNPs or the NF messages, indicating that the RNA-protein interactions themselves are directly regulated. This study is consistent with a model whereby these RNPs and NF mRNAs are components of a dynamic post-transcriptional regulatory module that influences the cytoskeletal compositions of neurons.

Post-transcriptional control of neurofilaments in development and disease

Tight coordination of the expression of neurofilament subunits is integral to the normal development and function of the nervous system. Imbalances in their expression are increasingly implicated in the induction of neurodegeneration in which formation of neurofilamentous aggregates is central to the pathology. Neurofilament expression can be controlled not only at the transcriptional level but also through post-transcriptional regulation of mRNA localization, stability, and translational efficiency. The critical role that post-transcriptional mechanisms play in maintaining neurofilament homeostasis is highlighted, for example, by the human disease amyotrophic lateral sclerosis, in which selective destabilization of NF-L mRNA (or failure to stabilize it) is associated with the formation of neurofilamentous aggregates - a hallmark of the disease process. This review discusses the post-transcriptional regulatory mechanisms and associated ribonucleoproteins that have been implicated to date in controlling neurofilament expression during normal development and in disrupting neurofilament homeostasis during neurodegenerative disease.

Phylogenetically conserved binding of specific K homology domain proteins to the 3'-untranslated region of the vertebrate middle neurofilament mRNA

As axons mature, neurofilament-M (NF-M) expression rises, contributing to maturation of the axonal cytoskeleton and an expansion in axon caliber. This increase is partly due to a rise in NF-M mRNA stability. Such post-transcriptional regulation is often mediated through the binding of specific proteins to the 3'-untranslated region (3'-UTR) of mRNAs. Vertebrate NF-M 3'-UTRs are remarkably well conserved, prompting us to test whether similar proteins bind the 3'-UTRs of different vertebrate NF-Ms. Identification of such proteins could lead to insights into the regulation of NF-M expression during development and in response to trauma or disease. Ultraviolet cross-linking analysis of proteins isolated from adult frog (Xenopus laevis), mouse, and rat brains revealed three ribonucleoprotein complexes (97, 70, and 47 kDa) that were present in all species and bound specifically to NF-M 3'-UTRs. Affinity purification of NF-M 3'-UTR-binding proteins from rat brain followed by mass spectrometry and immunoprecipitation assays identified heterogeneous nuclear ribonucleoprotein (hnRNP) K and hnRNP E1 as the proteins forming the 70- and 47-kDa complexes, respectively. These RNA-binding proteins of the KH domain family recognize CU-rich motifs identical to ones present in NF-M 3'-UTRs. Ultraviolet cross-linking assays performed on Xenopus embryos at different stages of neural development demonstrated that whereas hnRNP K binding occurred at all stages, hnRNP E binding occurred only at the most mature stages of axon development. Since hnRNP E is known to stabilize mRNAs, these results raise the hypothesis that these proteins may contribute to the increases in cytoplasmic levels of NF-M mRNA that accompany axonal maturation.

Proinsulin C-peptide replacement in type 1 diabetic BB/Wor-rats prevents deficits in nerve fiber regeneration

We recently reported that early gene responses and expression of cytoskeletal proteins are perturbed in regenerating nerve in type 1 insulinopenic diabetes but not in type 2 hyperinsulinemic diabetes. We hypothesized that these differences were due to impaired insulin action in the former type of diabetes. To test this hypothesis, type 1 diabetic BB/Wor-rats were replaced with proinsulin C-peptide, which enhances insulin signaling without lowering blood glucose. Following sciatic nerve crush injury, early gene responses such as insulin-like growth factor, c-fos, and nerve growth factor were examined longitudinally in sciatic nerve. Neurotrophic factors, their receptors, and beta-tubulin and neurofilament expression were examined in dorsal root ganglia. C-peptide replacement significantly normalized early gene responses in injured sciatic nerve and partially corrected the expression of endogenous neurotrophic factors and their receptors, as well as neuroskeletal protein in dorsal root ganglia. These effects translated into normalization of axonal radial growth and significantly improved axonal elongation of regenerating fibers in C-peptide-replaced BB/Wor-rats. The findings in C-peptide replaced type 1 diabetic rats were similar to those previously reported in hyperinsulinemic and iso-hyperglycemic type 2 BB/Z-rats. We conclude that impaired insulin action may be more important than hyperglycemia in suppressing nerve fiber regeneration in type 1 diabetic neuropathy.