Mecp2 Enforces Foxp3 Expression to Promote Regulatory T
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Detection of Interacting Transcription Factors in Human Tissues Using
Myšičková and Vingron BMC Genomics 2012, 13(Suppl 1):S2 http://www.biomedcentral.com/1471-2164/13/S1/S2 PROCEEDINGS Open Access Detection of interacting transcription factors in human tissues using predicted DNA binding affinity Alena Myšičková*, Martin Vingron From The Tenth Asia Pacific Bioinformatics Conference (APBC 2012) Melbourne, Australia. 17-19 January 2012 Abstract Background: Tissue-specific gene expression is generally regulated by combinatorial interactions among transcription factors (TFs) which bind to the DNA. Despite this known fact, previous discoveries of the mechanism that controls gene expression usually consider only a single TF. Results: We provide a prediction of interacting TFs in 22 human tissues based on their DNA-binding affinity in promoter regions. We analyze all possible pairs of 130 vertebrate TFs from the JASPAR database. First, all human promoter regions are scanned for single TF-DNA binding affinities with TRAP and for each TF a ranked list of all promoters ordered by the binding affinity is created. We then study the similarity of the ranked lists and detect candidates for TF-TF interaction by applying a partial independence test for multiway contingency tables. Our candidates are validated by both known protein-protein interactions (PPIs) and known gene regulation mechanisms in the selected tissue. We find that the known PPIs are significantly enriched in the groups of our predicted TF-TF interactions (2 and 7 times more common than expected by chance). In addition, the predicted interacting TFs for studied tissues (liver, muscle, hematopoietic stem cell) are supported in literature to be active regulators or to be expressed in the corresponding tissue. -
Developmental Delay and the Methyl Binding Genes H Turner, F Macdonald, S Warburton, F Latif, T Webb
1of3 ELECTRONIC LETTER J Med Genet: first published as 10.1136/jmg.40.2.e13 on 1 February 2003. Downloaded from Developmental delay and the methyl binding genes H Turner, F MacDonald, S Warburton, F Latif, T Webb ............................................................................................................................. J Med Genet 2003;40:e13(http://www.jmedgenet.com/cgi/content/full/40/2/e13) he report by Amir et al1 that Rett syndrome (RS) is associ- children referred with a clinical diagnosis of Angelman ated with mutations in the MECP2 gene permitted labora- syndrome (AS) but without an abnormality in 15q11q13 tory diagnosis of this devastating yet common neurode- showed that 4/46 of the girls in one case8 and 5/40 in the T 9 velopmental disorder. Hitherto the paucity of familial cases of other actually had Rett syndrome. Of these nine probands, the syndrome and the failure to identify the syndrome in only one was later found to have a clinical presentation incon- males despite fairly wide clinical criteria had defined it as an sistent with the laboratory diagnosis. This may not be surpris- X linked dominant disorder with male lethality.2 Soon, ing given that in very small girls the two syndromes may however, reports from the few families in which RS is present with overlapping clinical features and so be difficult to segregating showed that male family members who inherited differentiate on clinical grounds alone. the same mutation in the MECP2 gene as their affected female Familial cases of developmental handicap -
Tolerance to Sustained Activation of the Camp/Creb Pathway Activity in Osteoblastic Cells Is Enabled by Loss of P53 Mannu K
Walia et al. Cell Death and Disease (2018) 9:844 DOI 10.1038/s41419-018-0944-8 Cell Death & Disease ARTICLE Open Access Tolerance to sustained activation of the cAMP/Creb pathway activity in osteoblastic cells is enabled by loss of p53 Mannu K. Walia1, Scott Taylor1,PatriciaW.M.Ho1,T.JohnMartin1,2 and Carl R. Walkley 1,2,3 Abstract The loss of p53 function is a central event in the genesis of osteosarcoma (OS). How mutation of p53 enables OS development from osteoblastic lineage cells is poorly understood. We and others have reported a key role for elevated and persistent activation of the cAMP/PKA/Creb1 pathway in maintenance of OS. In view of the osteoblast lineage being the cell of origin of OS, we sought to determine how these pathways interact within the context of the normal osteoblast. Normal osteoblasts (p53 WT) rapidly underwent apoptosis in response to acute elevation of cAMP levels or activity, whereas p53-deficient osteoblasts tolerated this aberrant cAMP/Creb level and activity. Using the p53 activating small-molecule Nutlin-3a and cAMP/Creb1 activator forskolin, we addressed the question of how p53 responds to the activation of cAMP. We observed that p53 acts dominantly to protect cells from excessive cAMP accumulation. We identify a Creb1-Cbp complex that functions together with and interacts with p53. Finally, translating these results we find that a selective small-molecule inhibitor of the Creb1-Cbp interaction demonstrates selective toxicity to OS cells where this pathway is constitutively active. This highlights the cAMP/Creb axis as a potentially actionable therapeutic vulnerability in p53-deficient tumors such as OS. -
Methyl-Cpg2-Binding Protein 2 Mediates Overlapping Mechanisms Across Brain Disorders
bioRxiv preprint doi: https://doi.org/10.1101/819573; this version posted October 28, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Methyl-CpG2-binding protein 2 mediates overlapping mechanisms across brain disorders. Snow Bach1,2, Niamh M. Ryan2, Paolo Guasoni1,3, Aiden Corvin2, Daniela Tropea2,4* 1 School of Mathematical Sciences, Dublin City University, Glasnevin, Dublin 9, D09 W6Y4, Ireland 2 Neuropsychiatric Genetics, Department of Psychiatry, Trinity College Dublin, School of Medicine, Trinity Translational Medicine Institute, St James Hospital, Dublin, Ireland 3 Department of Mathematics and Statistics, Boston University, 111 Cummington Street, Boston, MA 02215, USA 4 Trinity College Institute of Neuroscience, Trinity College Dublin, Lloyd Building, Dublin 2, Dublin, Ireland *Correspondence should be addressed to D.T. (email: [email protected]) bioRxiv preprint doi: https://doi.org/10.1101/819573; this version posted October 28, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Methyl-CpG binding protein 2 (MeCP2) is a chromatin-binding protein and a modulator of gene expression. Initially identified as an oncogene, MECP2 is now mostly associated to Rett Syndrome, a neurodevelopmental condition, though there is evidence of its influence in other brain disorders. We design a procedure that considers several binding properties of MeCP2 and we screen for potential targets across neurological and neuropsychiatric conditions. We find MeCP2 target genes associated to a range of disorders, including - among others- Alzheimer Disease, Autism, Attention Deficit Hyperactivity Disorder and Multiple Sclerosis. -
Soothing Sensory Sensitivity May Ease Social Problems in Mice
Spectrum | Autism Research News https://www.spectrumnews.org NEWS Soothing sensory sensitivity may ease social problems in mice BY NICHOLETTE ZELIADT 12 NOVEMBER 2017 Dampening the signals that relay touch from the limbs to the brain can ease anxiety and social problems in two mouse models of autism, a new study suggests. Peripheral neurons typically relay these signals. The findings suggest that some features of autism arise from malfunctioning neurons outside the brain and spinal cord, says Lauren Orefice, a research fellow in David Ginty’s lab at Harvard University. They also hint that treatments targeting these peripheral neurons could help to ease some features of the condition. Orefice presented the unpublished findings yesterday at the 2017 Society for Neuroscience annual meeting in Washington, D.C. Last year, Orefice and her colleagues showed that mice with mutations in various genes tied to autism — including MECP2, GABRB3 and SHANK3 — in only their touch neurons are hypersensitive to small puffs of air on their backs early in life. The animals later show signs of anxiety and social difficulties. In the new work, the researchers explored how loss of any of these genes affects the function of touch neurons. They found that touch neurons lacking a copy of either MECP2 or GABRB3 have decreased levels of GABRB3 protein. This protein helps to dampen signals relayed by touch neurons to the spinal cord. Touch neurons in the mutant mice also fire unusually easily when stimulated with electricity. “The flow of information from those neurons to the spinal cord and brain is enhanced,” Orefice says. -
Genetics of Gene Expression in Primary Immune Cells Identifies Cell
ARTICLES Genetics of gene expression in primary immune cells identifies cell type–specific master regulators and roles of HLA alleles Benjamin P Fairfax1, Seiko Makino1, Jayachandran Radhakrishnan1, Katharine Plant1, Stephen Leslie2, Alexander Dilthey3, Peter Ellis4, Cordelia Langford4, Fredrik O Vannberg1,5 & Julian C Knight1 Trans-acting genetic variants have a substantial, albeit poorly characterized, role in the heritable determination of gene expression. Using paired purified primary monocytes and B cells, we identify new predominantly cell type–specific cis and trans expression quantitative trait loci (eQTLs), including multi-locus trans associations to LYZ and KLF4 in monocytes and B cells, respectively. Additionally, we observe a B cell–specific trans association of rs11171739 at 12q13.2, a known autoimmune disease locus, with IP6K2 (P = 5.8 × 10−15), PRIC285 (P = 3.0 × 10−10) and an upstream region of CDKN1A (P = 2 × 10−52), suggesting roles for cell cycle regulation and peroxisome proliferator-activated receptor γ (PPARγ) signaling in autoimmune pathogenesis. We also find that specific human leukocyte antigen (HLA) alleles form trans associations with the expression of AOAH and ARHGAP24 in monocytes but not in B cells. In summary, we show that mapping gene expression in defined primary cell populations identifies new cell type–specific trans-regulated networks and provides insights into the genetic basis of disease susceptibility. Defining the genetic determinants of gene expression is crucial to especially pertinent in the elucidation of trans-acting eQTLs, where understanding the biological and medical significance of genetic var- context specificity may be of greater relevance12. iation. This is particularly relevant in the drive to identify functional Here we sought to determine cell type–specific eQTLs relevant to variants underlying observed disease associations from genome- immunity and inflammation in paired samples of primary monocytes wide association studies (GWAS)1. -
Molecular Pathogenesis and Regulation of the Mir-29-3P-Family: Involvement of ITGA6 and ITGB1 in Intra-Hepatic Cholangiocarcinoma
cancers Article Molecular Pathogenesis and Regulation of the miR-29-3p-Family: Involvement of ITGA6 and ITGB1 in Intra-Hepatic Cholangiocarcinoma Yuto Hozaka 1 , Naohiko Seki 2,* , Takako Tanaka 1, Shunichi Asai 2, Shogo Moriya 3, Tetsuya Idichi 1, Masumi Wada 1, Kiyonori Tanoue 1, Yota Kawasaki 1, Yuko Mataki 1 , Hiroshi Kurahara 1 and Takao Ohtsuka 1 1 Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; [email protected] (Y.H.); [email protected] (T.T.); [email protected] (T.I.); [email protected] (M.W.); [email protected] (K.T.); [email protected] (Y.K.); [email protected] (Y.M.); [email protected] (H.K.); [email protected] (T.O.) 2 Department of Functional Genomics, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; [email protected] 3 Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; [email protected] * Correspondence: [email protected]; Tel.: +81-43-226-2971 Simple Summary: Even today, there are no effective targeted therapies for intrahepatic cholan- giocarcinoma (ICC) patients. Clarifying the molecular pathogenesis of ICC will contribute to the Citation: Hozaka, Y.; Seki, N.; development of treatment strategies for this disease. In this study, we searched for the role of the Tanaka, T.; Asai, S.; Moriya, S.; Idichi, miR-29-3p-family and its association with oncogenic pathway. Interestingly, aberrant expression of T.; Wada, M.; Tanoue, K.; Kawasaki, ITGA6 and ITGB1 was directly regulated by the miR-29-3p-family which are involved in multiple Y.; Mataki, Y.; et al. -
Genequery™ Human Stem Cell Transcription Factors Qpcr Array
GeneQuery™ Human Stem Cell Transcription Factors qPCR Array Kit (GQH-SCT) Catalog #GK125 Product Description ScienCell's GeneQuery™ Human Stem Cell Transcription Factors qPCR Array Kit (GQH-SCT) surveys a panel of 88 transcription factors related to stem cell maintenance and differentiation. Transcription factors are proteins that can regulate target gene transcription level by binding to specific regions of the genome known as enhancers or silencers. Brief examples of how genes may be grouped according to their functions are shown below: • Pluripotency transcription factors: NANOG, POU5F1, SOX2 • Embryonic development: EOMES, FOXC2/D3/O1, HOXA9/A10, KLF2/5, LIN28B, MAX, PITX2, SMAD1, TBX5, ZIC1 • Germ layer formation and differentiation: FOXA2, GATA6, HAND1, ISL1, KLF4, SMAD2, SOX9 • Organ morphogenesis: EZH2, HOXA11/B3/B5/C9, MSX2, MYC, PAX5/8, VDR • Angiogenesis: CDX2, JUN, NR2F2, RUNX1, WT1 • Hematopoiesis and osteogenesis: EGR3, ESR1, GATA1/2/3, GLI2, NFATC1, PAX9, RB1, SOX6, SP1, STAT1 • Neural stem cell maintenance and differentiation: ATF2, CREB1, FOSB, FOXO3, HES1, HOXD10, MCM2/7, MEF2C, NEUROD1/G1, OLIG1/2, PAX3/6, POU4F1, PPARG, SMAD3/4, SNAI1, STAT3 Note : all gene names follow their official symbols by the Human Genome Organization Gene Nomenclature Committee (HGNC). GeneQuery™ qPCR array kits are qPCR ready in a 96-well plate format, with each well containing one primer set that can specifically recognize and efficiently amplify a target gene's cDNA. The carefully designed primers ensure that: (i) the optimal annealing temperature in qPCR analysis is 65°C (with 2 mM Mg 2+ , and no DMSO); (ii) the primer set recognizes all known transcript variants of target gene, unless otherwise indicated; and (iii) only one gene is amplified. -
NF-Y Controls Fidelity of Transcription Initiation at Gene Promoters
ARTICLE https://doi.org/10.1038/s41467-019-10905-7 OPEN NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region Andrew J. Oldfield 1,6, Telmo Henriques1,2,8, Dhirendra Kumar1,8, Adam B. Burkholder3,8, Senthilkumar Cinghu1, Damien Paulet4,5, Brian D. Bennett3, Pengyi Yang 1,7, Benjamin S. Scruggs1, Christopher A. Lavender3, Eric Rivals 4,5, Karen Adelman1,2 & Raja Jothi1 1234567890():,; Faithful transcription initiation is critical for accurate gene expression, yet the mechanisms underlying specific transcription start site (TSS) selection in mammals remain unclear. Here, we show that the histone-fold domain protein NF-Y, a ubiquitously expressed transcription factor, controls the fidelity of transcription initiation at gene promoters in mouse embryonic stem cells. We report that NF-Y maintains the region upstream of TSSs in a nucleosome- depleted state while simultaneously protecting this accessible region against aberrant and/or ectopic transcription initiation. We find that loss of NF-Y binding in mammalian cells disrupts the promoter chromatin landscape, leading to nucleosomal encroachment over the canonical TSS. Importantly, this chromatin rearrangement is accompanied by upstream relocation of the transcription pre-initiation complex and ectopic transcription initiation. Further, this phenomenon generates aberrant extended transcripts that undergo translation, disrupting gene expression profiles. These results suggest NF-Y is a central player in TSS selection in metazoans and highlight the deleterious consequences of inaccurate transcription initiation. 1 Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, NC 27709, USA. 2 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. -
Onl Er Msb 145504 GA 1..19
UC Irvine UC Irvine Previously Published Works Title Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes. Permalink https://escholarship.org/uc/item/1fz5r77k Journal Molecular systems biology, 11(1) ISSN 1744-4292 Authors Li, Xu Wang, Wenqi Wang, Jiadong et al. Publication Date 2015-01-21 DOI 10.15252/msb.20145504 License https://creativecommons.org/licenses/by/4.0/ 4.0 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Article Proteomic analyses reveal distinct chromatin- associated and soluble transcription factor complexes Xu Li1,†, Wenqi Wang1,†, Jiadong Wang1, Anna Malovannaya2, Yuanxin Xi2,3, Wei Li2,3, Rudy Guerra4, David H Hawke5, Jun Qin2 & Junjie Chen1,* Abstract living organisms. Sophisticated signal transduction pathways are required for the development and survival of any organism, a minor The current knowledge on how transcription factors (TFs), the ulti- disruption of which may cause developmental defects and diseases mate targets and executors of cellular signalling pathways, are such as cancer (Fig 1A). The examples of these highly conserved regulated by protein–protein interactions remains limited. Here, signalling pathways include the Wnt (MacDonald et al,2009),TGF-b we performed proteomics analyses of soluble and chromatin- (Massague, 1998) and NF-jB (Hayden & Ghosh, 2004) pathways. associated complexes of 56 TFs, including the targets of many Many of these pathways function by ultimately regulating the signalling pathways involved in development and cancer, and 37 activity of certain transcription factors (TFs), often by changing their members of the Forkhead box (FOX) TF family. Using tandem affin- localizations. Reports on individual proteins suggested that the ity purification followed by mass spectrometry (TAP/MS), we chromatin association of TFs is tightly controlled by upstream signals. -
Electronic Letter 1Of4 J Med Genet: First Published As 10.1136/Jmg.37.12.E41 on 1 December 2000
Electronic letter 1of4 J Med Genet: first published as 10.1136/jmg.37.12.e41 on 1 December 2000. Downloaded from Electronic letter J Med Genet 2000;37 (http://jmedgenet.com/cgi/content/full/37/12/e41) Spectrum of mutations in the MECP2 We screened genomic DNA from 13 sporadic RTT patients and 21 patients with autism and mental gene in patients with infantile autism retardation by DHPLC and by direct DNA sequencing. All and Rett syndrome the subjects were unrelated females and were ethnic Chinese, with no family history of the disease. The clinical findings met the criteria of inclusion and exclusion for the diagnosis of RTT.10 Patients with autism and mental retar- dation were obtained from a previous study.11 The diagno- EDITOR—Rett syndrome (RTT, MIM 312750) is a sis of autism was based on clinical features and evaluated progressive neurological disorder, occurring almost exclu- by diagnostic criteria from DSM-IV.12 Most of them had sively in females during their first two years of life . RTT is onset of autistic features at less than 3 years of age. one of the most common causes of mental retardation in Informed consent was obtained from the patients or the females, with an incidence of 1 in 10 000-15 000 female parents. births. Patients with classical RTT appear to develop nor- Genomic DNA was extracted from peripheral blood mally until 6-18 months of age, then gradually lose speech samples using a QIAamp Blood Kit (Qiagen) according to and purposeful hand use, and, eventually, develop the manufacturer’s instructions. -
MECP2 Disorders: from the Clinic to Mice and Back
MECP2 disorders: from the clinic to mice and back Laura Marie Lombardi, … , Steven Andrew Baker, Huda Yahya Zoghbi J Clin Invest. 2015;125(8):2914-2923. https://doi.org/10.1172/JCI78167. Review Two severe, progressive neurological disorders characterized by intellectual disability, autism, and developmental regression, Rett syndrome and MECP2 duplication syndrome, result from loss and gain of function, respectively, of the same critical gene, methyl-CpG–binding protein 2 (MECP2). Neurons acutely require the appropriate dose of MECP2 to function properly but do not die in its absence or overexpression. Instead, neuronal dysfunction can be reversed in a Rett syndrome mouse model if MeCP2 function is restored. Thus, MECP2 disorders provide a unique window into the delicate balance of neuronal health, the power of mouse models, and the importance of chromatin regulation in mature neurons. In this Review, we will discuss the clinical profiles of MECP2 disorders, the knowledge acquired from mouse models of the syndromes, and how that knowledge is informing current and future clinical studies. Find the latest version: https://jci.me/78167/pdf REVIEW The Journal of Clinical Investigation MECP2 disorders: from the clinic to mice and back Laura Marie Lombardi,1,2,3 Steven Andrew Baker,2,4,5 and Huda Yahya Zoghbi1,2,3,4 1Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA. 2Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, Texas, USA. 3Howard Hughes Medical Institute, 4Program in Developmental Biology, and 5Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas, USA. Two severe, progressive neurological disorders characterized by intellectual disability, autism, and developmental regression, Rett syndrome and MECP2 duplication syndrome, result from loss and gain of function, respectively, of the same critical gene, methyl-CpG–binding protein 2 (MECP2).