|Description||Magna ChIP™ G Tissue Kit|
|Overview||Chromatin Immunoprecipitation (ChIP) is an important technique allowing the researcher to analyze in vivo interactions of proteins with genomic DNA. Any chromatin-associated or DNA binding protein can be analyzed with this technique, provided a good antibody to the protein exists. One can measure different proteins localized to a specific region of the genome, or the genome wide distribution of a specific protein. Another powerful application of this technique is to analyze changes in histone modifications that correlate with processes like transcription, mitosis or DNA repair.
Historically, ChIP protocols have been geared towards homogenous populations of cell culture. In contrast, tissue samples are more complex and the cells are heterogeneous thus making ChIP analysis less amenable. The Magna ChIP™ G Tissue Kit provides the tools necessary to obtain repeatable, reliable, and site specific tissue biopsies. Microdissected functionally related populations of cells within a heterogeneous tissue can thus be analyzed with ease, precision and certainty.
|Materials Required but Not Delivered||Cells, stimulated or treated as desired
Antibody for chromatin immunoprecipitation
Taq DNA polymerase and dNTPs
Master Mix for qPCR
DNase and RNase-free sterile H2O
Quant-iT™ dsDNA HS Assay Kit, (Life Technologies catalog #: Q32851)
O.C.T. – Optimal Cutting Temperature compound
Magna Grip™ Rack 8 well (Cat.#20-400) or similar magnetic rack
Thermomixer or Hybridization Oven
Variable temperature water bath or incubator
Variable volume (5-1000 l) pipettors + tips
Microfuge & PCR tubes
Filter-tip pipette tips
|Application||The Magna ChIP G Tissue Kit provides the tools necessary to obtain repeatable, reliable & site specific tissue biopsies.|
|Safety Information according to GHS|
|Storage and Shipping Information|
|Storage Conditions||Upon receipt, store components at the temperatures indicated on the labels. Kit components are stable for 6 months from date of shipment when used and stored as directed.|
|Material Size||22 ChIP assays from tissue samples.|
|Reference overview||Pub Med ID|
|MeCP2 Deficiency Leads to Loss of Glial Kir4.1.|
Kahanovitch, U; Cuddapah, VA; Pacheco, NL; Holt, LM; Mulkey, DK; Percy, AK; Olsen, ML
eNeuro 5 2018
Rett syndrome (RTT) is an X-linked neurodevelopmental disorder usually caused by mutations in methyl-CpG-binding protein 2 (MeCP2). RTT is typified by apparently normal development until 6-18 mo of age, when motor and communicative skills regress and hand stereotypies, autonomic symptoms, and seizures present. Restoration of MeCP2 function selectively to astrocytes reversed several deficits in a murine model of RTT, but the mechanism of this rescue is unknown. Astrocytes carry out many essential functions required for normal brain functioning, including extracellular K+ buffering. Kir4.1, an inwardly rectifying K+ channel, is largely responsible for the channel-mediated K+ regulation by astrocytes. Loss-of-function mutations in Kir4.1 in human patients result in a severe neurodevelopmental disorder termed EAST or SESAME syndrome. Here, we evaluated astrocytic Kir4.1 expression in a murine model of Rett syndrome. We demonstrate by chromatin immunoprecipitation analysis that Kir4.1 is a direct molecular target of MeCP2. Astrocytes from Mecp2-deficient mice express significantly less Kir4.1 mRNA and protein, which translates into a >50% deficiency in Ba2+-sensitive Kir4.1-mediated currents, and impaired extracellular potassium dynamics. By examining astrocytes in isolation, we demonstrate that loss of Kir4.1 is cell autonomous. Assessment through postnatal development revealed that Kir4.1 expression in Mecp2-deficient animals never reaches adult, wild-type levels, consistent with a neurodevelopmental disorder. These are the first data implicating a direct MeCP2 molecular target in astrocytes and provide novel mechanistic insight explaining a potential mechanism by which astrocytic dysfunction may contribute to RTT.
|Bisphenol A regulates rare minnow testicular vitellogenin expression via reducing its promoter Er recruitment.|
Zhang, Y; Guan, Y; Fan, X; Wu, L; Wang, Z
Ecotoxicol Environ Saf 147 423-429 2018
Vitellogenins (Vtgs) are major precursor of the egg-yolk proteins. They are synthesized in liver of adult female ovipara, but normally silent in males. For their sensitive response to estrogen, Vtgs are usually used as biomarkers for environmental estrogenic compounds. In the present study, three vtg subtypes (vtg1, vtg2 and vtg3) were proved to present in the testis of rare minnow Gobiocypris rarus for the first time. Immunohistochemistry result showed that Vtg proteins mainly deposit in spermatogonium and spermatocytes. Following 225μg/L bisphenol A (BPA) exposure 1, 3 and 9 weeks, testicular vtg mRNAs were mostly significantly decreased. The further chromatin immunoprecipitation showed that BPA could decrease estrogen receptor (Er) recruitment in vtg promoter, which possibly reduced Er's transcription activation effect on vtgs. However, different from the continuously decreased vtg mRNA levels, testicular Vtg protein levels were recovered at week 9. Considering the induced hepatic Vtg expression, testicular Vtgs may be replenished by the induced hepatic Vtgs under BPA exposure.
|Genome-wide mapping of estrogen receptor α binding sites by ChIP-seq to identify genes related to sexual maturity in hens.|
Guo, M; Li, Y; Chen, Y; Guo, X; Yuan, Z; Jiang, Y
Gene 642 32-42 2018
In ovarian follicle development, estrogen acts as a regulatory molecule to mediate proliferation and differentiation of follicular cells. ERα (estrogen receptor α) exerts regulatory function classically by binding directly to the estrogen response element, recruiting co-factors and activating or repressing transcription in response to E2. In this study, we used ChIP-seq to map ERα-binding sites in ovaries of Hy-line Brown commercial hens at 45d, 90d and 160d. In total, 24,886, 21,680 and 23,348 binding sites were identified in the ovaries of hens at 45d, 90d and 160d, which are linked to 86, 83 and 74 genes, respectively. The PPI network contains 47 protein nodes and 164 interaction edges, among which, AKT1 (V-Akt Murine Thymoma Viral Oncogene Homolog 1) and ACTN2 (Actinin Alpha 2) with the highest weight in the network, followed by CREB1 (CAMP Responsive Element Binding Protein 1), and EPHA5 (EPH Receptor A5) were identified. These genes are likely related to sexual maturity in hens. This study also provides insight into the regulation of the ERα target gene networks and a reference for understanding ERα-regulated transcription.
|Adult exposure to bisphenol A in rare minnow Gobiocypris rarus reduces sperm quality with disruption of testicular aquaporins.|
Zhang, Y; Guan, Y; Zhang, T; Yuan, C; Liu, Y; Wang, Z
Chemosphere 193 365-375 2018
Bisphenol A (BPA) is an endocrine disrupter which has adverse effects on male reproduction. Aquaporins (AQPs), well known water-selective channels, play important roles in spermatogenesis and sperm functions. However, whether AQPs participate in the process that BPA induces abnormal sperms has not been investigated to date. In the present study, adult male rare minnows Gobiocypris rarus were exposed to environmentally relevant concentrations BPA (15 and 225 μg/L) for 1, 2 and 3 weeks. Results showed that BPA exposure disrupted sperm motility, increased the percentage of abnormal sperm cells, and decreased sperm tolerance to hypotonic solution and sperm fertilization capacity. Meanwhile, protein levels of AQPs were up-regulated, and their distribution in the testis was abnormal following BPA exposure. The following chromatin immune coprecipitation showed that BPA could regulate aqp3 and 8 expression through the ERE in their 5'-flanking region. The present study demonstrated that BPA could decrease the sperm quality in rare minnow, and AQP3 and 8 might play significant roles in this process.
|miR-126-5p promotes retinal endothelial cell survival through SetD5 regulation in neurons.|
Villain, G; Poissonnier, L; Noueihed, B; Bonfils, G; Rivera, JC; Chemtob, S; Soncin, F; Mattot, V
Development 145 2018
MicroRNAs are key regulators of angiogenesis, as illustrated by the vascular defects observed in miR-126-deficient animals. The miR-126 duplex gives rise to two mature microRNAs (miR-126-3p and -5p). The vascular defects in these mutant animals were attributed to the loss of miR-126-3p but the role of miR-126-5p during normal angiogenesis in vivo remains unknown. Here, we show that miR-126-5p is expressed in endothelial cells but also by retinal ganglion cells (RGCs) of the mouse postnatal retina and participates in protecting endothelial cells from apoptosis during the establishment of the retinal vasculature. miR-126-5p negatively controls class 3 semaphorin protein (Sema3A) in RGCs through the repression of SetD5, an uncharacterized member of the methyltransferase family of proteins. In vitro, SetD5 controls Sema3A expression independently of its SET domain and co-immunoprecipitates with BRD2, a bromodomain protein that recruits transcription regulators onto the chromatin. Both SetD5 and BRD2 bind to the transcription start site and to upstream promoter regions of the Sema3a locus and BRD2 is necessary for the regulation of Sema3A expression by SetD5. Thus, neuronally expressed miR-126-5p regulates angiogenesis by protecting endothelial cells of the developing retinal vasculature from apoptosis.
|Effects of adolescent social stress and antidepressant treatment on cognitive inflexibility and Bdnf epigenetic modifications in the mPFC of adult mice.|
Xu, H; Wang, J; Zhang, K; Zhao, M; Ellenbroek, B; Shao, F; Wang, W
Psychoneuroendocrinology 88 92-101 2018
Adolescent social stress (ASS) can increase susceptibility to depression in adulthood. However, the underlying psychological and neural mechanisms remain unclear. Cortically mediated cognitive dysfunctions are increasingly recognized as an independent and important risk factor of depression. Using social defeat stress, a classical animal model of depression, our previous studies found that mice subjected to this form of stress during early adolescence displayed cognitive inflexibility (CI) in adulthood. This change was accompanied by a down-regulation of Bdnf gene expression in the medial prefrontal cortex (mPFC); this gene encodes a key molecule involved in depression and antidepressant action. In the present paper, we identified epigenetic modification of Bdnf as a possible mechanism underlying the behavioral and molecular changes. ASS induced a set of depressive phenotypes, including increased social avoidance and CI, as well as reduced levels of total Bdnf and isoform IV but not isoform I or VI transcripts in the mPFC. In parallel with changes in Bdnf gene expression, previously stressed adult mice showed increased levels of dimethylation of histone H3 at lysine K9 (H3K9me2) immediately downstream of the Bdnf IV promoter. On the other hand, no differences were found in trimethylation of histone H3 at lysine K4 (H3K4me3) or in acetylation of histone H3 at lysine K9 (H3K9ac) or at K4 (H3K4ac) in the Bdnf IV promoter. Likewise, no alterations were found in DNA methylation of the Bdnf IV promoter. Additionally, treatment with the chronic antidepressant tranylcypromine reversed Bdnf epigenetic changes and related gene transcription while also reversing CI, but not social avoidance, in previously stressed adult mice. These results suggest that epigenetic changes to the Bdnf gene in the mPFC after adolescent social adversity may be involved in the regulation of cognitive dysfunction in depression and antidepressant action in adulthood.
|NADPH oxidase 4 and endothelial nitric oxide synthase contribute to endothelial dysfunction mediated by histone methylations in metabolic memory.|
Liao, Y; Gou, L; Chen, L; Zhong, X; Zhang, D; Zhu, H; Lu, X; Zeng, T; Deng, X; Li, Y
Free Radic Biol Med 115 383-394 2018
"Metabolic memory" is identified as a phenomenon that transient hyperglycemia can be remembered by vasculature for quite a long term even after reestablishment of normoglycemia. NADPH oxidases (Noxs) and endothelial nitric oxide synthase (eNOS) are important enzymatic sources of reactive oxygen species (ROS) in diabetic vasculature. The aim of this study is to explore the roles of epigenetics and ROS derived from Noxs and eNOS in the metabolic memory. In this study, we demonstrated that vascular ROS was continuously activated in endothelium induced by transient high glucose, as well as sustained vascular endothelial dysfunction. The Nox4 and uncoupled eNOS are the major sources of ROS, while inhibition of Nox4 and eNOS significantly attenuated oxidative stress and almost recovered the endothelial function in metabolic memory. Furthermore, the aberrant histone methylation (H3K4me1, H3K9me2, and H3K9me3) at promoters of Nox4 and eNOS are the main causes for the persistent up-regulation of these two genes. Modifying the histone methylation could reduce the expression levels of Nox4 and eNOS, thus obviously attenuating endothelial dysfunction. These results indicate that histone methylation of Nox4 and eNOS play a key role in metabolic memory and may be the potential intervention targets for metabolic memory.
|Histone deacetylase inhibitors reverse age-related increases in side effects of haloperidol in mice.|
Montalvo-Ortiz, JL; Fisher, DW; Rodríguez, G; Fang, D; Csernansky, JG; Dong, H
Psychopharmacology (Berl) 234 2385-2398 2017
Older patients can be especially susceptible to antipsychotic-induced side effects, and the pharmacodynamic mechanism underlying this phenomenon remains unclear. We hypothesized that age-related epigenetic alterations lead to decreased expression and functionality of the dopamine D2 receptor (D2R), contributing to this susceptibility.In this study, we treated young (2-3 months old) and aged (22-24 months old) C57BL/6 mice with the D2R antagonist haloperidol (HAL) once a day for 14 days to evaluate HAL-induced motor side effects. In addition, we pretreated separate groups of young and aged mice with histone deacetylase (HDAC) inhibitors valproic acid (VPA) or entinostat (MS-275) and then administered HAL.Our results show that the motor side effects of HAL are exaggerated in aged mice as compared to young mice and that HDAC inhibitors are able to reverse the severity of these deficits. HAL-induced motor deficits in aged mice are associated with an age- and drug-dependent decrease in striatal D2R protein levels and functionality. Further, histone acetylation was reduced while histone tri-methylation was increased at specific lysine residues of H3 and H4 within the Drd2 promoter in the striatum of aged mice. HDAC inhibitors, particularly VPA, restored striatal D2R protein levels and functionality and reversed age- and drug-related histone modifications at the Drd2 promoter.These results suggest that epigenetic changes at the striatal Drd2 promoter drive age-related increases in antipsychotic side effect susceptibility, and HDAC inhibitors may be an effective adjunct treatment strategy to reduce side effects in aged populations.
|A Wnt/Notch/Pax7 signaling network supports tissue integrity in tongue development.|
Zhu, XJ; Yuan, X; Wang, M; Fang, Y; Liu, Y; Zhang, X; Yang, X; Li, Y; Li, J; Li, F; Dai, ZM; Qiu, M; Zhang, Z; Zhang, Z
J Biol Chem 292 9409-9419 2017
The tongue is one of the major structures involved in human food intake and speech. Tongue malformations such as aglossia, microglossia, and ankyloglossia are congenital birth defects, greatly affecting individuals' quality of life. However, the molecular basis of the tissue-tissue interactions that ensure tissue morphogenesis to form a functional tongue remains largely unknown. Here we show that ShhCre -mediated epithelial deletion of Wntless (Wls), the key regulator for intracellular Wnt trafficking, leads to lingual hypoplasia in mice. Disruption of epithelial Wnt production by Wls deletion in epithelial cells led to a failure in lingual epidermal stratification and loss of the lamina propria and the underlying superior longitudinal muscle in developing mouse tongues. These defective phenotypes resulted from a reduction in epithelial basal cells positive for the basal epidermal marker protein p63 and from impaired proliferation and differentiation in connective tissue and paired box 3 (Pax3)- and Pax7-positive muscle progenitor cells. We also found that epithelial Wnt production is required for activation of the Notch signaling pathway, which promotes proliferation of myogenic progenitor cells. Notch signaling in turn negatively regulated Wnt signaling during tongue morphogenesis. We further show that Pax7 is a direct Notch target gene in the embryonic tongue. In summary, our findings demonstrate a key role for the lingual epithelial signals in supporting the integrity of the lamina propria and muscular tissue during tongue development and that a Wnt/Notch/Pax7 genetic hierarchy is involved in this development.
|Myc suppresses tumor invasion and cell migration by inhibiting JNK signaling.|
Ma, X; Huang, J; Tian, Y; Chen, Y; Yang, Y; Zhang, X; Zhang, F; Xue, L
Oncogene 36 3159-3167 2017
Tumor metastasis, but not primary overgrowth, is the leading cause of mortality for cancer patients. During the past decade, Drosophila melanogaster has been well-accepted as an excellent model to address the intrinsic mechanism of different aspects of cancer progression, ranging from tumor initiation to metastasis. In a genetic screen performed in Drosophila, aiming to find novel modulators of tumor invasion, we identified the oncoprotein Myc as a negative regulator. While expression of Myc dramatically blocks tumor invasion and cell migration, loss of Myc promotes cell migration in vivo. The activity of Myc is further enhanced by the co-expression of its transcription partner Max. Mechanistically, we found Myc/Max directly upregulates the transcription of puc, which encodes an inhibitor of JNK signaling crucial for tumor invasion and cell migration. Furthermore, we demonstrated that human cMyc potently suppresses JNK-dependent cell invasion and migration in both Drosophila and lung adenocarcinoma cell lines. These findings provide novel molecular insights into Myc-mediated cancer progression and raise the noteworthy problem in therapeutic strategies as inhibiting Myc might conversely accelerate tumor metastasis.
|Magna ChIP¿ G Tissue Kit|