Transcriptional divergence between cDC1s and cDC2s: an AP1–IRF composite element-dependent program

Author(s):  
Shan Zhu ◽  
Chao Niu ◽  
Jingtao Chen
Keyword(s):  
2006 ◽  
Vol 20 (4) ◽  
pp. 795-808 ◽  
Author(s):  
Chung S. Song ◽  
Ibtissam Echchgadda ◽  
Young-Kyo Seo ◽  
Taesung Oh ◽  
Soyoung Kim ◽  
...  

Abstract The vitamin D receptor (VDR) regulates steroid and drug metabolism by inducing the genes encoding phase I and phase II enzymes. SULT2A1 is a liver- and intestine-expressed sulfo-conjugating enzyme that converts the alcohol-OH of neutral steroids, bile acids, and drugs to water-soluble sulfated metabolites. 1α,25-Dihydroxyvitamin D3 [1,25-(OH)2D3] induces SULT2A1 gene transcription after the recruitment of VDR to the vitamin D-responsive chromatin region of SULT2A1. A composite element in human SULT2A1 directs the 1,25-(OH)2D3-mediated induction of natural and heterologous promoters. This element combines a VDR/retinoid X receptor-α-binding site [vitamin D response element (VDRE)], which is an imperfect inverted repeat 2 of AGCTCA, and a CAAT/enhancer binding protein (C/EBP)-binding site located 9 bp downstream to VDRE. The binding sites were identified by EMSA, antibody supershift, and deoxyribonuclease I footprinting. C/EBP-α at the composite element plays an essential role in the VDR regulation of SULT2A1, because 1) induction was lost for promoters with inactivating mutations at the VDRE or C/EBP element; 2) SULT2A1 induction by 1,25-(OH)2D3 in C/EBP-α-deficient cells required the expression of cotransfected C/EBP-α; and 3) C/EBP-β did not substitute for C/EBP-α in this regulation. VDR and C/EBP-α were recruited concurrently to the composite element along with the coactivators p300, steroid receptor coactivator 1 (SRC-1), and SRC-2, but not SRC-3. VDR and C/EBP-α associated endogenously as a DNA-dependent, coimmunoprecipitable complex, which was detected at a markedly higher level in 1,25-(OH)2D3-treated cells. These results provide the first example of the essential role of the interaction in cis between C/EBP-α and VDR in directing 1,25-(OH)2D3-induced expression of a VDR target gene.


2013 ◽  
Vol 2013 ◽  
pp. 1-10
Author(s):  
Ling Huang ◽  
Zhongrong Lv ◽  
Weihuan Chen ◽  
Jike Liu

An approach based on homotopy iteration algorithm is proposed to identify the crack parameters in beam structures. In the forward problem, a fully open crack model with the composite element method is employed for the vibration analysis. The dynamic responses of the cracked beam in time domain are obtained from the Newmark direct integration method. In the inverse analysis, an identification approach based on homotopy iteration algorithm is studied to identify the location and the depth of a cracked beam. The identification equation is derived by minimizing the error between the calculated acceleration response and the simulated measured one. Newton iterative method with the homotopy equation is employed to track the correct path and improve the convergence of the crack parameters. Two numerical examples are conducted to illustrate the correctness and efficiency of the proposed method. And the effects of the influencing parameters, such as measurement time duration, measurement points, division of the homotopy parameter and measurement noise, are studied.


2008 ◽  
Vol 28 (8) ◽  
pp. 1596-1600
Author(s):  
贾宏燕 Jia Hongyan ◽  
高劲松 Gao Jinsong ◽  
冯晓国 Feng Xiaoguo ◽  
孙连春 Sun Lianchun

2011 ◽  
Vol 55 (4) ◽  
pp. 1453-1459 ◽  
Author(s):  
Marina Mingoia ◽  
Emily Tili ◽  
Esther Manso ◽  
Pietro E. Varaldo ◽  
Maria Pia Montanari

ABSTRACTSeveral drug resistances inStreptococcus pneumoniaeare associated with mobile genetic elements, which are loosely subdivided into a group of smaller (18- to 27-kb) and a group of larger (>50-kb) elements. While the elements of the former group, which typically carry the tetracycline resistance determinanttet(M) and whose prototype is Tn916(18 kb), have been studied extensively, the larger elements, whose prototype is Tn5253(∼65.5 kb), are not as well explored. Tn5253is a composite structure consisting of two independent conjugative transposons, Tn5251(which is virtually identical to Tn916) and Tn5252(∼47.5 kb), with the former inserted into the latter. Tn5252, which so far has only partially been sequenced, carries an integrase gene, driving its site-specific insertion into the host cell genome, and the chloramphenicol resistancecatpC194determinant. This study investigated 20 clinical isolates ofS. pneumoniae, which were selected on the basis ofcatpC194-mediated chloramphenicol resistance. All 20 isolates harbored a Tn5253-like element. The composite elements (some of which have been completely sequenced) demonstrated considerable heterogeneity that stemmed from a dual variability: in the Tn5252-like element, due primarily to differences in the integrase gene but also to differences in cargo genes and in the overall genetic organization, and in the Tn916-like element, with the possible involvement, besides Tn916, of a number of Tn916family pneumococcal elements carrying different erythromycin resistance genes. In mating experiments, only one composite element, containing a less typical Tn916family element, appeared to be nonmobile. Being part of a Tn5253-like composite element may confer on some Tn916-like transposons, which are apparently nontransferable as independent genetic elements, the ability to be mobilized.


Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 1226-1226
Author(s):  
Kirby D Johnson ◽  
Xin Gao ◽  
Rajendran Sanalkumar ◽  
Amy P Hsu ◽  
Myung-Jeom Ryu ◽  
...  

Abstract Abstract 1226 How transcriptional and post-transcriptional mechanisms control the levels/activities of master developmental regulators has fundamental importance for understanding complex developmental processes such as hematopoiesis and associated pathological disorders. GATA-2 is an essential regulator of hematopoiesis, and GATA-2 mutations characterize heritable disease associated with myelodysplastic syndrome and acute myeloid leukemia, including MonoMAC (syndrome of monocytopendia, B and NK cell lymphopenia, and mycobacterial, fungal and viral infection). However, many questions remain unanswered regarding mechanisms underlying GATA-2 regulation and function. We demonstrated that a MonoMAC patient harbors a 28 bp deletion within GATA2 intron 5 that eliminates a conserved E-box and 5 base pairs of an 8 base pair spacer between the E-box and a conserved GATA motif, which constitutes an E-box-GATA composite element. This composite element resides within the +9.5 kb “GATA switch site” that binds GATA-2 and GATA-1 in the transcriptionally active and repressed states, respectively, and confers hematopoietic and vascular endothelial enhancer activities in transgenic mouse embryos. Importantly, this patient lacked mutations in the GATA2 coding sequence characteristic of other MonoMAC patients, but exhibited prototypical MonoMAC. To elucidate the mechanism underlying the function of the +9.5 composite element, we generated a targeted deletion of the murine element, which yielded embryonic lethality at E13 to E14. Prior to death, +9.5−/− mice exhibit reduced liver size, hemorrhaging, and edema. Nucleated primitive red cells are abundant in the +9.5−/− embryos, in contrast to Gata2 knockout mice, which die at approximately E10.5 from anemia due to failure of primitive and definitive hematopoiesis. Furthermore, primitive erythroid (EryP) colony assays conducted with yolk sacs revealed that the mutation does not affect primitive erythroid precursor functionality. However, the +9.5 deletion strongly reduced Gata2 expression at sites of definitive hematopoiesis, including the fetal liver (8.1 fold, P < 0.004) and cultured explants of the hematopoietic stem cell-generating Aortic Gonadal Mesonephric (AGM) region (4.0 fold, P < 0.001). The homozygous mutant animals exhibited a nearly complete loss of hematopoietic stem cells as determined by flow cytometry (20-fold reduction of Lin-Mac1+CD41-CD48-CD150+Sca+Kit+ cells, P < 0.005) and competitive repopulation (complete loss, P < 0.02) assays, as well as progenitors as determined by colony assays (BFU-E, 60-fold reduction, P < 0.002; CFU-GM, 8.8-fold reduction, P < 0.0001; CFU-GEMM, 19-fold reduction, P < 0.001). To investigate the underlying mechanisms, we developed an allele-specific Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) assay with heterozygous fetal liver cells to test whether the deletion influences Gata2 chromatin accessibility at the +9.5 region. The deletion significantly reduced (8.4 fold reduction, P < 0.001) chromatin accessibility at this region within the mutant allele, while the wild type allele was unaffected. Thus, any potential remaining cis-elements are insufficient to confer chromatin accessibility, supporting a model in which the transcription factors that normally occupy this GATA switch site lose the capacity to access their respective cis-elements in the context of the mutant allele. Our human and murine studies have therefore revealed a cis-element indispensable for the regulation of Gata2 expression in multiple developmental contexts and necessary for the generation of the definitive hematopoietic stem/progenitor cell compartment. As additional elements are likely to confer Gata2 expression in distinct contexts, including primitive erythropoiesis, we have implemented a multi-faceted effort to identify such elements and to compare their mechanisms with that of the +9.5 site, which will provide fundamental insights into genetic mechanisms controlling normal and malignant hematopoiesis. Disclosures: No relevant conflicts of interest to declare.


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