Immunohistochemistry of Xenopus embryos

Comparative analysis of fixation techniques for signal detection in avian embryos

The choice of fixation method significantly impacts tissue morphology and visualization of gene expression and proteins after in situ hybridization chain reaction (HCR) or immunohistochemistry (IHC), respectively. In this study, we compared the effects of paraformaldehyde (PFA) and trichloroacetic acid (TCA) fixation techniques prior to HCR and IHC on chicken embryos. Our findings underscore the importance of optimizing fixation methods for accurate visualization and subsequent interpretation of HCR and IHC results, with implications for probe and antibody validation and tissue-specific protein localization studies. We found that TCA fixation resulted in larger and more circular nuclei and neural tubes compared to PFA fixation. Additionally, TCA fixation altered the subcellular fluorescence signal intensity of various proteins, including transcription factors, cytoskeletal proteins, and cadherins. Notably, TCA fixation revealed protein signals in tissues that may be inaccessible with PFA fixation. In contrast, TCA fixation proved ineffective for mRNA visualization. These results highlight the need for optimization of fixation protocols depending on the target and model system, emphasizing the importance of methodological considerations in biological analyses.

Effectiveness of fixation methods for wholemount immunohistochemistry across cellular compartments in chick embryos

The choice of fixation method significantly impacts tissue morphology and protein visualization after immunohistochemistry (IHC). In this study, we compared the effects of paraformaldehyde (PFA) and trichloroacetic acid (TCA) fixation prior to IHC on chicken embryos. Our findings underscore the importance of validating fixation methods for accurate interpretation of IHC results, with implications for antibody validation and tissue-specific protein localization studies. We found that TCA fixation resulted in larger and more circular nuclei compared to PFA fixation. Additionally, TCA fixation altered the appearance of subcellular localization and fluorescence intensity of various proteins, including transcription factors and cytoskeletal proteins. Notably, TCA fixation revealed protein localization domains that may be inaccessible with PFA fixation. These results highlight the need for optimization of fixation protocols depending on the target epitope and model system, emphasizing the importance of methodological considerations in biological analyses.

The histone H4K20 methyltransferase SUV4-20H1/KMT5B is required for multiciliated cell differentiation in Xenopus

H4 lysine 20 dimethylation (H4K20me2) is the most abundant histone modification in vertebrate chromatin. It arises from sequential methylation of unmodified histone H4 proteins by the mono-methylating enzyme PR-SET7/KMT5A, followed by conversion to the dimethylated state by SUV4-20H (KMT5B/C) enzymes. We have blocked the deposition of this mark by depleting Xenopus embryos of SUV4-20H1/H2 methyltransferases. In the larval epidermis, this results in a severe loss of cilia in multiciliated cells (MCC), a key component of mucociliary epithelia. MCC precursor cells are correctly specified, amplify centrioles, but ultimately fail in ciliogenesis because of the perturbation of cytoplasmic processes. Genome-wide transcriptome profiling reveals that SUV4-20H1/H2-depleted ectodermal explants preferentially down-regulate the expression of several hundred ciliogenic genes. Further analysis demonstrated that knockdown of SUV4-20H1 alone is sufficient to generate the MCC phenotype and that its catalytic activity is needed for axoneme formation. Overexpression of the H4K20me1-specific histone demethylase PHF8/KDM7B also rescues the ciliogenic defect in a significant manner. Taken together, this indicates that the conversion of H4K20me1 to H4K20me2 by SUV4-20H1 is critical for the formation of cilia tufts.

Confirming Antibody Specificity in Xenopus

Verifying that a new antibody recognizes its target can be difficult. In this protocol, expression of a target protein in Xenopus embryos is either knocked down using CRISPR-Cas9 technology (for zygotic proteins) or enhanced by microinjection of a synthetic mRNA (for maternal proteins). Western blotting analysis is then performed. If the antibody recognizes the target protein, the western blot will show a relatively weak band for CRISPR-injected embryos and a relatively strong band for RNA-injected embryos. This represents a straightforward, powerful strategy for confirming antibody specificity in Xenopus.

JE. Click JAHAs: conformationally restricted ferrocene-based histone deacetylase inhibitors

The ferrocene analogue 4b had an IC₅₀ = 4 nM (HDAC1), 180 nM (HDAC8) and was effective in a Xenopus model of tubulin deacetylation. Analogue 4a displayed mainly μM IC₅₀ values against HDACs apart from HDAC6 (IC₅₀ = 69 nM).

Whole-mount fluorescence immunocytochemistry on Xenopus embryos

INTRODUCTIONImmunocytochemistry (ICC) is widely exploited in studying mammalian systems, but is underutilized among Xenopus developmental biologists. This stems, in part, from the relatively small number of Xenopus antibodies available for use in research. Common misconceptions about ICC in Xenopus embryos also prevail, discouraging researchers from trying the procedure. However, ICC with Xenopus is simple and effective. This article describes methods for whole-mount ICC in Xenopus embryos. Also included are simple procedures to quench autofluorescence of Xenopus and to remove surface pigment from embryos which may interfere with fluorescence imaging. The methods described here are useful for detecting tissue-specific probes (e.g., 12/101 to detect somites). They are also effective for imaging the cytoskeleton (e.g., α-tubulin to detect microtubules) or localizing specific proteins at the subcellular level (e.g., ZO-1 to detect tight junctions). In addition, combining ICC with in situ hybridization is simple and highly effective.

Genetic screens for mutations affecting development of Xenopus tropicalis

We present here the results of forward and reverse genetic screens for chemically-induced mutations in Xenopus tropicalis. In our forward genetic screen, we have uncovered 77 candidate phenotypes in diverse organogenesis and differentiation processes. Using a gynogenetic screen design, which minimizes time and husbandry space expenditures, we find that if a phenotype is detected in the gynogenetic F2 of a given F1 female twice, it is highly likely to be a heritable abnormality (29/29 cases). We have also demonstrated the feasibility of reverse genetic approaches for obtaining carriers of mutations in specific genes, and have directly determined an induced mutation rate by sequencing specific exons from a mutagenized population. The Xenopus system, with its well-understood embryology, fate map, and gain-of-function approaches, can now be coupled with efficient loss-of-function genetic strategies for vertebrate functional genomics and developmental genetics.

Intact RNA-binding domains are necessary for structure-specific DNA binding and transcription control by CBTF122 during Xenopus development

CBTF122 is a subunit of the Xenopus CCAAT box transcription factor complex and a member of a family of double-stranded RNA-binding proteins that function in both transcriptional and post-transcriptional control. Here we identify a region of CBTF122 containing the double-stranded RNA-binding domains that is capable of binding either RNA or DNA. We show that these domains bind A-form DNA in preference to B-form DNA and that the -59 to -31 region of the GATA-2 promoter (an in vivo target of CCAAT box transcription factor) adopts a partial A-form structure. Mutations in the RNA-binding domains that inhibit RNA binding also affect DNA binding in vitro. In addition, these mutations alter the ability of CBTF122 fusions with engrailed transcription repressor and VP16 transcription activator domains to regulate transcription of the GATA-2 gene in vivo. These data support the hypothesis that the double-stranded RNA-binding domains of this family of proteins are important for their DNA binding both in vitro and in vivo.

RNA-dependent cytoplasmic anchoring of a transcription factor subunit during Xenopus development

The CCAAT box transcription factor (CBTF) is a multimeric transcription factor that activates expression of the haematopoietic regulatory factor, GATA-2. The 122 kDa subunit of this complex, CBTF(122), is cytoplasmic in fertilized Xenopus eggs and subsequently translocates to the nucleus prior to activation of zygotic GATA-2 transcription at gastrulation. Here we present data suggesting both a role for CBTF(122) prior to its nuclear translocation and the mechanism that retains it in the cytoplasm before the midblastula transition (MBT). CBTF(122) and its variant CBTF(98) are associated with translationally quiescent mRNP complexes. We show that CBTF(122) RNA binding activity is both necessary and sufficient for its cytoplasmic retention during early development. The introduction of an additional nuclear localization signal to CBTF(122) is insufficient to overcome this retention, suggesting that RNA binding acts as a cytoplasmic anchor for CBTF(122). Destruction of endogenous RNA by microinjection of RNase promotes premature nuclear translocation of CBTF(122). Thus, the nuclear translocation of CBTF(122) at the MBT is likely to be coupled to the degradation of maternal mRNA that occurs at that stage.