p.E95K mutation in Indian hedgehog causing brachydactyly type A1 impairs IHH/Gli1 downstream transcriptional regulation

Background Brachydactyly type A1 (BDA1, OMIM 112500) is a rare inherited malformation characterized primarily by shortness or absence of middle bones of fingers and toes. It is the first recorded disorder of the autosomal dominant Mendelian trait. Indian hedgehog (IHH) gene is closely associated with BDA1, which was firstly mapped and identified in Chinese families in 2000. Previous studies have demonstrated that BDA1-related mutant IHH proteins affected interactions with its receptors and impaired IHH signaling. However, how the altered signaling pathway affects downstream transcriptional regulation remains unclear. Results Based on the mouse C3H10T1/2 cell model for IHH signaling activation, two recombinant human IHH-N proteins, including a wild type protein (WT, amino acid residues 28–202) and a mutant protein (MT, p.E95k), were analyzed. We identified 347, 47 and 4 Gli1 binding sites in the corresponding WT, MT and control group by chromatin immunoprecipitation and the overlapping of these three sets was poor. The putative cis regulated genes in WT group were enriched in sensory perception and G-protein coupled receptor-signaling pathway. On the other hand, putative cis regulated genes were enriched in Runx2-related pathways in MT group. Differentially expressed genes in WT and MT groups indicated that the alteration of mutant IHH signaling involved cell-cell signaling and cellular migration. Cellular assay of migration and proliferation validated that the mutant IHH signaling impaired these two cellular functions. Conclusions In this study, we performed integrated genome-wide analyses to characterize differences of IHH/Gli1 downstream regulation between wild type IHH signaling and the E95K mutant signaling. Based on the cell model, our results demonstrated that the E95K mutant signaling altered Gli1-DNA binding pattern, impaired downstream gene expressions, and leaded to weakened cellular proliferation and migration. This study may help to deepen the understanding of pathogenesis of BDA1 and the role of IHH signaling in chondrogenesis. Electronic supplementary material The online version of this article (10.1186/s12863-018-0697-5) contains supplementary material, which is available to authorized users.


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References
Kirchhausen Tomas (2000). Three ways to make a vesicle. Nat Rev Mol Cell Biol, 1, 187-98.   Loss of MECP2 binding ability to 5mC-DNA (R-HSA-9022538) 7.      Factor VII, the protease that initiates the normal blood clotting cascade, circulates in the blood in both its proenzyme (factor VII) and its activated (factor VIIa) forms. No clotting occurs, however, because neither form of the protein has any catalytic activity when free in solution. Blood clotting is normally initiated when tissue factor (TF), an intrinsic plasma membrane protein, is exposed to the blood by injury to the wall of a blood vessel. TF is then able to bind factor VIIa from plasma, and possibly also factor VII, to form complexes capable of catalyzing the conversion of factor X, from plasma, into its activated form, factor Xa. Factor Xa catalyzes the conversion of additional factor VII molecules to their activated form, increasing the amount of tissue factor:factor VIIa complex available at the site of injury, accelerating the generation of factor Xa, and allowing the activation of factor IXa as well. This process is self-limiting because as levels of factor Xa increase, tissue factor:factor VIIa complexes become trapped in the form of catalytically inactive heterotetramers with factor Xa and the protein TFPI (tissue pathway factor inhibitor). At this point the intinsic pathway, as an independent source of activated factor X, is thought to become critical for the continuation of clot formation (Broze 1995;Mann et al. 2003).

References
The nature of the initial tissue factor:factor VII complexes formed is controversial. One model, building on the observation that the complex of factor VII and TF has low but measurable proteolytic activity on factor X, suggests that this complex begins the activation of factor X, and that as factor VIIa accumulates, tissue factor:factor VIIa complexes also form, accelerating the process (Nemerson 1988). A second model, building on the observation that normal plasma contains low levels of activated factor VII constitutively, suggests that complexes with factor VIIa form immediately at the onset of clotting (Rapaport and Rao 1995). The two models are not mutually exclusive, and in any event, the central roles of tissue factor and factor VIIa in generating an initial supply of factors IXa and Xa, and the self-limiting nature of the process due to the action of TFPI, are all wellestablished.
These events are outlined in the drawing: black arrows connect the substrates (inputs) and products (outputs) of individual reactions, and blue lines connect output activated enzymes to the other reactions that they catalyze.

References
Broze GJ Jr (1995 Gamma-carboxylation of protein precursors (R-HSA-159740) 12. Gamma-carboxylation of a cluster of glutamate residues near the amino termini of thrombin, factor VII, factor IX, factor X, protein C, protein S, protein Z, and Gas 6 is required for these proteins to bind Ca++ and function efficiently in blood clotting. A single enzyme, vitamin K-dependent gammacarboxylase, catalyzes the gamma-carboxylation of all eight proteins involved in clotting (Morris et al. 1995;Brenner et al. 1998;Spronk et al. 2000). In the carboxylation reaction, the enzyme binds its substrate protein via a sequence motif on the amino terminal side of the glutamate residues to be carboxylated (Furie et al. 1999 Regulation of gene expression by Hypoxia-inducible Factor (R-HSA-1234158) 13. importin 4/7 (Chachami et al. 2009) and importin alpha/beta (Depping et al. 2008). Once in the nucleus HIF-alpha heterodimerizes with HIF-beta (ARNT) (Wang et al. 1995, Jiang et al. 1996, Tian et al. 1997, Gu et al. 1998, Erbel et al. 2003 and recruits CBP and p300 to promoters of target genes (Ebert and Bunn 1998, Kallio et al. 1998, Ema et al. 1999, Gu et al. 2001, Dames et al. 2002, Freedman et al. 2002. DDX58/IFIH1-mediated induction of interferon-alpha/beta (R-HSA-168928) 14.     The kinase activity of PTK6 is negatively regulated by both PTPN1 phosphatase (Fan et al. 2013), which dephosphorylates tyrosine Y342 of PTK6, and SRMS kinase (Fan et al. 2015), which phosphorylates PTK6 on tyrosine residue Y447.

Date Action Author
Loss of phosphorylation of MECP2 at T308 (R-HSA-9022535) 17. Missense mutations of methyl-CpG-binding protein 2 (MECP2) in the vicinity of its threonine T308 phosphorylation site can negatively affect the ability of MECP2 to be phosphorylated at T308 in response to neuronal membrane depolarization (neuronal activity) ).

Loss of phosphorylation of MECP2 at T308
Diseases: Rett syndrome.
Loss of function mutations in methyl-CpG-binding protein 2 (MECP2), an epigenetic regulator of transcription, are the major cause of Rett syndrome, a neurodevelopmental disorder that affects 1 in 10,000-15,000 female births. The symptoms of Rett syndrome appear after 6-18 months of apparently normal postnatal development and include regression of acquired language and motor skills, stereotypic hand movements, intellectual disability, epileptic seizures and respiratory disturbances. Besides Rett syndrome, aberrant MECP2 expression is implicated as an underlying cause of other neuropsychiatric disorders (reviewed by Banerjee et al. 2012, Lyst and Bird 2015. Only functionally characterized MECP2 mutations are annotated. For a comprehensive list of MECP2 mutations reported in Rett syndrome, please refer to the RettBASE (http://mecp2.chw.edu.au), a database dedicated to curation of disease variants of MECP2, CDKL5 and FOXG1 in Rett syndrome (Krishnaraj et al. 2017

Loss of function of MECP2 in Rett syndrome
Diseases: pervasive developmental disorder.
Pervasive developmental disorders (PDDs) largely overlap with the autism spectrum disorders

Metabolism of vitamin K
A number of proteins, including eight required for normal blood clot formation and its regulation (Prothrombin (factor II), factor VII, factor IX, factor X, protein C, protein S, protein Z, and Gas6) share a sequence motif rich in glutamate residues near their amino termini. Carboxylation of the glutamate residues within this motif followed by removal of an aminoterminal propeptide is required for each of these proteins to function. These modifications occur as the proteins move through the endoplasmic reticulum and Golgi apparatus.  After proteins are imported into the peroxisome a subset of proteins are cleaved by the protease TYSND1 (Okumoto et al. 2011). Based onmutagenesis of human TYSND1 (Okumoto et al. 2011) and the homolog in Arabidopsis (Schuhmann et al. 2008), TYSND1 appears to be a trypsin-like serine protease containing a conserved histidine aspartate serine triad essential for catalysis. Mice lacking Tysnd1 have reduced peroxisomal localization of some peroxisomal enzymes and exhibit reduced beta-oxidation of fatty acids and metabolism of phytanic acid (Mizuno et al. 2013 Besides binding to the NCoR/SMRT co-repressor complex (Lyst et al. 2013, MECP2

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binds the SIN3A co-repressor complex. This interaction involves the transcriptional repressor domain of MECP2 and the amino terminal part of the HDAC interaction domain (HID) of SIN3A.
HDAC1 and HDAC2 are part of the SIN3A co-repressor complex that co-immunoprecipitates with MECP2 (Nan et al. 1998). While binding of MECP2 to SIN3A at target genes is associated with transcriptional repression, binding to CREB1 at target genes is associated with transcriptional activation , Chen et al. 2013. Function of MECP2 can be affected by binding to  Under a variety of stress conditions, TP53 (p53), stabilized by stress-induced phosphorylation at least on S15 and S20 serine residues, can induce the transcription of genes involved in cell cycle arrest. Cell cycle arrest provides cells an opportunity to repair the damage before division, thus preventing the transmission of genetic errors to daughter cells. In addition, it allows cells to attempt a recovery from the damage and survive, preventing premature cell death.
TP53 controls transcription of genes involved in both G1 and G2 cell cycle arrest. The most prominent TP53 target involved in G1 arrest is the inhibitor of cyclin-dependent kinases CDKN1A (p21).
CDKN1A is one of the earliest genes induced by TP53 (El-Deiry et al. 1993). CDKN1A binds and inactivates CDK2 in complex with cyclin A (CCNA) or E (CCNE), thus preventing G1/S transition (Harper et al. 1993). Nevertheless, under prolonged stress, the cell destiny may be diverted towards an apoptotic outcome. For instance, in case of an irreversible damage, TP53 can induce transcription of an RNA binding protein PCBP4, which can bind and destabilize CDKN1A mRNA, thus alleviating G1 arrest and directing the affected cell towards G2 arrest and, possibly, apoptosis Chen 2000, Scoumanne et al. 2011). Expression of E2F7 is directly induced by TP53. E2F7 contributes to G1 cell cycle arrest by repressing transcription of E2F1, a transcription factor that promotes expression of many genes needed for G1/S transition (Aksoy et al. 2012, Carvajal et al. 2012 TP53 contributes to the establishment of G2 arrest by inducing transcription of GADD45A and SFN, and by inhibiting transcription of CDC25C. TP53 induces GADD45A transcription in cooperation with chromatin modifying enzymes EP300, PRMT1 and CARM1 (An et al. 2004). GADD45A binds Aurora kinase A (AURKA), inhibiting its catalytic activity and preventing AURKA-mediated G2/M transition (Shao et al. 2006, Sanchez et al. 2010. GADD45A also forms a complex with PCNA. PCNA is involved in both normal and repair DNA synthesis. The effect of GADD45 interaction with PCNA, if any, on S phase progression, G2 arrest and DNA repair is not known (Smith et al. 1994, Hall et al. 1995, Sanchez et al. 2010, Kim et al. 2013. SFN (14-3-3-sigma) is induced by TP53 (Hermeking et al. 1997) and contributes to G2 arrest by binding to the complex of CDK1 and CCNB1 (cyclin B1) and preventing its translocation to the nucleus. Phosphorylation of a number of nuclear proteins by the complex of CDK1 and CCNB1 is needed for G2/M transition (Chan et al. 1999). While promoting G2 arrest, SFN can simultaneously inhibit apoptosis by binding to BAX and preventing its translocation to mitochondria, a step involved in cytochrome C release (Samuel et al. 2001). TP53 binds the promoter of the CDC25C gene in cooperation with the transcriptional repressor E2F4 and represses CDC25C transcription, thus maintaining G2 arrest (St Clair et al. 2004, Benson et al. 2014.