In animals, Hox transcription factors define regional identity in distinct anatomical domains. How Hox genes encode this specificity is a paradox, because different Hox proteins bind with high ...affinity in vitro to similar DNA sequences. Here, we demonstrate that the Hox protein Ultrabithorax (Ubx) in complex with its cofactor Extradenticle (Exd) bound specifically to clusters of very low affinity sites in enhancers of the shavenbaby gene of Drosophila. These low affinity sites conferred specificity for Ubx binding in vivo, but multiple clustered sites were required for robust expression when embryos developed in variable environments. Although most individual Ubx binding sites are not evolutionarily conserved, the overall enhancer architecture—clusters of low affinity binding sites—is maintained and required for enhancer function. Natural selection therefore works at the level of the enhancer, requiring a particular density of low affinity Ubx sites to confer both specific and robust expression.
Display omitted
•shavenbaby enhancers contain multiple low affinity binding sites for Ubx-Exd•Replacing low affinity sites with high-affinity sites reduced specificity•Each Ubx-Exd binding site is required for robust enhancer function•Enhancer architecture is evolutionarily conserved, but most single sites are not
Transcriptional enhancers employ a strategy for balancing the need for specificity with the need for robustness with multiple clusters of low affinity binding sites.
DNA binding specificities of transcription factors (TFs) are a key component of gene regulatory processes. Underlying mechanisms that explain the highly specific binding of TFs to their genomic ...target sites are poorly understood. A better understanding of TF−DNA binding requires the ability to quantitatively model TF binding to accessible DNA as its basic step, before additional in vivo components can be considered. Traditionally, these models were built based on nucleotide sequence. Here, we integrated 3D DNA shape information derived with a high-throughput approach into the modeling of TF binding specificities. Using support vector regression, we trained quantitative models of TF binding specificity based on protein binding microarray (PBM) data for 68 mammalian TFs. The evaluation of our models included cross-validation on specific PBM array designs, testing across different PBM array designs, and using PBM-trained models to predict relative binding affinities derived from in vitro selection combined with deep sequencing (SELEX-seq). Our results showed that shape-augmented models compared favorably to sequence-based models. Although both k -mer and DNA shape features can encode interdependencies between nucleotide positions of the binding site, using DNA shape features reduced the dimensionality of the feature space. In addition, analyzing the feature weights of DNA shape-augmented models uncovered TF family-specific structural readout mechanisms that were not revealed by the DNA sequence. As such, this work combines knowledge from structural biology and genomics, and suggests a new path toward understanding TF binding and genome function.
Significance Genomes provide an abundance of putative binding sites for each transcription factor (TF). However, only small subsets of these potential targets are functional. TFs of the same protein family bind to target sites that are very similar but not identical. This distinction allows closely related TFs to regulate different genes and thus execute distinct functions. Because the nucleotide sequence of the core motif is often not sufficient for identifying a genomic target, we refined the description of TF binding sites by introducing a combination of DNA sequence and shape features, which consistently improved the modeling of in vitro TF−DNA binding specificities. Although additional factors affect TF binding in vivo, shape-augmented models reveal binding specificity mechanisms that are not apparent from sequence alone.
Members of transcription factor families typically have similar DNA binding specificities yet execute unique functions in vivo. Transcription factors often bind DNA as multiprotein complexes, raising ...the possibility that complex formation might modify their DNA binding specificities. To test this hypothesis, we developed an experimental and computational platform, SELEX-seq, that can be used to determine the relative affinities to any DNA sequence for any transcription factor complex. Applying this method to all eight
Drosophila Hox proteins, we show that they obtain novel recognition properties when they bind DNA with the dimeric cofactor Extradenticle-Homothorax (Exd). Exd-Hox specificities group into three main classes that obey Hox gene collinearity rules and DNA structure predictions suggest that anterior and posterior Hox proteins prefer DNA sequences with distinct minor groove topographies. Together, these data suggest that emergent DNA recognition properties revealed by interactions with cofactors contribute to transcription factor specificities in vivo.
Display omitted
► Hox DNA binding specificities change when they bind with the cofactor Exd ► The binding specificities of Exd-Hox heterodimers group into three classes ► Preferred binding sites of anterior and posterior Hox proteins have distinct shapes ► Exd-Ubx binding sites are overrepresented in fragments bound by Ubx in vivo
Association of Exd with individual Hox transcription factors changes their preferred DNA binding sites, allowing the highly related proteins to recognize distinct sequences.
Unlike neurons in the central nervous system (CNS), injured neurons in the peripheral nervous system (PNS) can regenerate their axons and reinnervate their targets. However, functional recovery in ...the PNS often remains suboptimal, especially in cases of severe damage. The lack of regenerative ability of CNS neurons has been linked to down-regulation of the mTOR (mammalian target of rapamycin) pathway. We report here that PNS dorsal root ganglial neurons (DRGs) activate mTOR following damage and that this activity enhances axonal growth capacity. Furthermore, genetic up-regulation of mTOR activity by deletion of tuberous sclerosis complex 2 (TSC2) in DRGs is sufficient to enhance axonal growth capacity in vitro and in vivo. We further show that mTOR activity is linked to the expression of GAP-43, a crucial component of axonal outgrowth. However, although TSC2 deletion in DRGs facilitates axonal regrowth, it leads to defects in target innervation. Thus, whereas manipulation of mTOR activity could provide new strategies to stimulate nerve regeneration in the PNS, fine control of mTOR activity is required for proper target innervation.
Dear Editor, Urticarial vasculitis (UV) is characterized by long-lasting urticarial rashes and the histopathologic finding of leukocytoclastic vasculitis or lymphocytic vasculitis. UV comprises ...normocomplementemic urticarial vasculitis (NUV), which has normal serum complement levels, hypocomplementemic urticarial vasculitis (HUV), which has low serum complement levels, and hypocomplementemic urticarial vasculitis syndrome (HUVS), which is associated with pulmonary or renal disease, episcleritis, and uveitis. Previous studies found that 6-12.5% of UV cases were related to infection and that 7-7.8% of UV cases were related to malignancy. Herein we present two cases of normocomplementemic urticarial vasculitis with increased perivascular mast cell infiltration which were successfully treated using omalizumab. Case 1 was that of a 49-year-old Japanese male patient who experienced recurrent episodes of wheal-like erythema for four weeks. His symptoms failed to respond to a double dose of second-generation antihistamine at the previous clinic.
Dear Editor, Auricularia auricula-judae, known as Jew's ear, wood ear, jelly ear, etc., is a species of edible Auriculariales fungus found worldwide. It is a popular food item in East Asian countries ...including Japan, Korea, and China. The patient described in the present case experienced a few anaphylactic episodes after ingesting Chinese food containing fried Auricularia. A 37-year-old Japanese woman had a 10-year history of recurrent episodes of stomach ache, diarrhea, vomiting, and urticaria after eating Chinese food at restaurants.
Dear Editor, Fish collagen peptides have recently been used as an ingredient in various foods and supplements for their putative benefits for beauty and health. We present herein a rare case of ...anaphylaxis due to fish collagen in a gummy candy. An otherwise healthy, 25-year-old Japanese female had recurrent episodes of anaphylaxis shock after eating a gummy candy containing artificial fruit flavor and fish collagen. After treatment at the emergency room in a hospital, she visited our hospital to determine the cause of her allergy. Her medical history did not have atopic dermatitis and hand eczema but her past-history, she experienced anaphylaxis after eating grilled fish but not after eating raw fish before. Total IgE was 153IU/ml and specific IgE values were as follows: gelatin (0Ua/mL, class 0), tuna (2.23Ua/mL, class 2), cod (0.55Ua/mL, class 1), turbot (0.40Ua/mL, class 1), anisakis (0Ua/mL, class 0), pork (0Ua/mL, class 0) and beef (0Ua/mL, class 0). A prick-to-prick test was performed as previously reported using 10mg/ml of histamine as a positive control and saline as a negative control.
Dear Editor, Mushrooms are a common food item worldwide and some species are commonly consumed depending on the geographical area. Shiitake (Lentinula edodes), Matsutake (Tricoloma matsutake), ...Maitake (Grifola frondosa), and Shimeji (Lyophyllum decastes, Hypsizygus ulmerius) are popular mushrooms consumed in East Asia, including Japan, Korea, and China, and food allergy caused by these mushrooms have been reported in these regions. We herein present a rare case which is immediate type of allergy due to three kinds of mushroom allergens by IgE immunoblotting. An 18-year-old Japanese female had a 10-year history of recurrent episodes of Quincke edema and urticaria after consuming each intake of Shiitake or Maitake or Shimeji mushrooms. She had never worked at the mushroom plantations and had no other history of asthma and hypersensitivity pneumonitis related by fungal antigen. Before visiting our hospital, she experienced severe anaphylaxis after consuming dumplings and pasta, and was treated at the emergency room of another hospital. After recovering from her anaphylaxis, she visited our hospital in order to determine to know the cause of her allergy.
Palmoplantar pustulosis (PPP) sometimes presents with nail lesions, which affect the patients’ quality of life (QOL). However, little is known about nail lesions in PPP, and there is currently no ...established method for assessing them.
This study aimed to analyze the impact of PPP-related nail lesions with the patients’ QOL. In addition, we considered whether they might constitute a risk factor of pustulotic arthro-osteitis (PAO).’
A total of 178 patients with PPP were enrolled. Among the 178 patients, 66 patients participated in the following quality of life questionnaires; GHQ28, DLQI, and Skindex-16. The severity of the nail lesions was classified according to the Nail Psoriasis Severity Index (NAPSI), and the types of nail lesion were investigated.
The DLQI, Skindex-16 and PPPASI scores were significantly higher in patients with nail lesions than in those without them. Indentions, transverse ridging, and nail thickening were relatively common in PPP. Nail lesions were unrelated to the presence of PAO complications, but leukonychia and discoloration were likely to be related to PAO lesion site.
The study demonstrated that the presence of nail lesions is associated with a decreased QOL regardless of the severity of the skin lesions. The nail lesions were not a risk factor of PAO, but a predictor of skin lesion severity and PAO lesion site. Given this association, indention, transverse ridging, and thickening of the nail, currently not included in the NAPSI, should be added as an assessment item in the evaluation of PPP nail lesions.
•Nail lesions are affected by the severity of skin conditions.•The QOL is related to the presence of nail lesions of palmoplantar pustulosis.•In the absence of nail lesions, the QOL is related to skin lesion severity.•Nail lesions are unlikely to be a risk factor of pustulotic arthro-osteitis.•Nail lesions may impair QOL of palmoplantar pustulosis.
PDF
