scholarly journals Activation of stably silenced genes by recruitment of a synthetic de-methylating module

2021 ◽  
Author(s):  
Wing Fuk Chan ◽  
Christine R. Keenan ◽  
Timothy M. Johanson ◽  
Rhys S. Allan

AbstractStably silenced genes that display a high level of CpG dinucleotide methylation are refractory to the current generation of dCas9-based activation systems. To counter this, we created an improved activation system by coupling the catalytic domain of DNA demethylating enzyme TET1 with transcriptional activators (TETact). TETact induces transcription of heavily suppressed non-coding RNA and surface protein, and the reactivation of embryonic haemoglobin genes in non-erythroid cells.

1982 ◽  
Vol 208 (1) ◽  
pp. 239-242 ◽  
Author(s):  
D C Wraith ◽  
C J Chesterton

Current evidence suggests that the major cell-surface modification occurring during mammalian erythropoiesis could be generated by two separate mechanisms: either selective loss of membrane proteins during enucleation or endocytosis at the subsequent reticulocyte and erythrocyte stages. The former idea was tested by collecting developing rabbit erythroid cells before and after the enucleation step and comparing their cell-surface protein composition via radiolabelling and electrophoresis. Few changes were observed. Our data thus lend support to the endocytosis mechanism.


Blood ◽  
1984 ◽  
Vol 64 (4) ◽  
pp. 930-936 ◽  
Author(s):  
I Max-Audit ◽  
U Testa ◽  
D Kechemir ◽  
M Titeux ◽  
W Vainchenker ◽  
...  

To further investigate the erythroid nature of the two human erythroleukemia cell lines, K562 and HEL-60, and to define the ontogeny of pyruvate kinase (PK) isozymes (R, M2) in developing human erythroid cells, we have studied the isozymic alterations, if any, during differentiation of these cell lines in vitro and normoblasts isolated from fetal liver in vivo. PK activity of erythroleukemic cell lines was intermediate between that observed in leukocytes and in fetal liver erythroblasts. These cell lines contained a high level of M2-PK, but R- PK was always present, albeit at low concentrations, in all the clones or subclones we studied. Erythroblasts from fetal liver were separated according to density on a Stractan gradient. R-PK levels were nearly constant in the different fractions, whereas M2-PK levels markedly decreased as the erythroblasts became mature and almost completely disappeared in late erythroid cells. Thus, these results clearly demonstrate the erythroid origin of these cell lines.


1992 ◽  
Vol 20 (5) ◽  
pp. 997-1003 ◽  
Author(s):  
M. Needham ◽  
C. Gooding ◽  
K. Hudson ◽  
M. Antoniou ◽  
F. Grosveld ◽  
...  

mBio ◽  
2018 ◽  
Vol 9 (3) ◽  
Author(s):  
Sandra Wydau-Dematteis ◽  
Imane El Meouche ◽  
Pascal Courtin ◽  
Audrey Hamiot ◽  
René Lai-Kuen ◽  
...  

ABSTRACTClostridium difficileis the major etiologic agent of antibiotic-associated intestinal disease. Pathogenesis ofC. difficileis mainly attributed to the production and secretion of toxins A and B. Unlike most clostridial toxins, toxins A and B have no signal peptide, and they are therefore secreted by unusual mechanisms involving the holin-like TcdE protein and/or autolysis. In this study, we characterized the cell surface protein Cwp19, a newly identified peptidoglycan-degrading enzyme containing a novel catalytic domain. We purified a recombinant His6-tagged Cwp19 protein and showed that it has lytic transglycosylase activity. Moreover, we observed that Cwp19 is involved in cell autolysis and that aC. difficilecwp19mutant exhibited delayed autolysis in stationary phase compared to the wild type when bacteria were grown in brain heart infusion (BHI) medium. Wild-type cell autolysis is correlated to strong alterations of cell wall thickness and integrity and to release of cytoplasmic material. Furthermore, we demonstrated that toxins were released into the extracellular medium as a result of Cwp19-induced autolysis when cells were grown in BHI medium. In contrast, Cwp19 did not induce autolysis or toxin release when cells were grown in tryptone-yeast extract (TY) medium. These data provide evidence for the first time that TcdE and bacteriolysis are coexisting mechanisms for toxin release, with their relative contributionsin vitrodepending on growth conditions. Thus, Cwp19 is an important surface protein involved in autolysis of vegetative cells ofC. difficilethat mediates the release of the toxins from the cell cytosol in response to specific environment conditions.IMPORTANCEClostridium difficile-associated disease is mainly known as a health care-associated infection. It represents the most problematic hospital-acquired infection in North America and Europe and exerts significant economic pressure on health care systems. Virulent strains ofC. difficilegenerally produce two toxins that have been identified as the major virulence factors. The mechanism for release of these toxins from bacterial cells is not yet fully understood but is thought to be partly mediated by bacteriolysis. Here we identify a novel peptidoglycan hydrolase inC. difficile, Cwp19, exhibiting lytic transglycosylase activity. We show that Cwp19 contributes toC. difficilecell autolysis in the stationary phase and, consequently, to toxin release, most probably as a response to environmental conditions such as nutritional signals. These data highlight that Cwp19 constitutes a promising target for the development of new preventive and curative strategies.


Haematologica ◽  
2019 ◽  
Vol 104 (12) ◽  
pp. 2361-2371 ◽  
Author(s):  
Xiaofei Yu ◽  
Alexander Azzo ◽  
Stephanie M. Bilinovich ◽  
Xia Li ◽  
Mikhail Dozmorov ◽  
...  

Blood ◽  
1984 ◽  
Vol 64 (4) ◽  
pp. 930-936 ◽  
Author(s):  
I Max-Audit ◽  
U Testa ◽  
D Kechemir ◽  
M Titeux ◽  
W Vainchenker ◽  
...  

Abstract To further investigate the erythroid nature of the two human erythroleukemia cell lines, K562 and HEL-60, and to define the ontogeny of pyruvate kinase (PK) isozymes (R, M2) in developing human erythroid cells, we have studied the isozymic alterations, if any, during differentiation of these cell lines in vitro and normoblasts isolated from fetal liver in vivo. PK activity of erythroleukemic cell lines was intermediate between that observed in leukocytes and in fetal liver erythroblasts. These cell lines contained a high level of M2-PK, but R- PK was always present, albeit at low concentrations, in all the clones or subclones we studied. Erythroblasts from fetal liver were separated according to density on a Stractan gradient. R-PK levels were nearly constant in the different fractions, whereas M2-PK levels markedly decreased as the erythroblasts became mature and almost completely disappeared in late erythroid cells. Thus, these results clearly demonstrate the erythroid origin of these cell lines.


Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 1195-1195
Author(s):  
Heather M. Rogers ◽  
Xiaobing Yu ◽  
Constance Tom Noguchi

Abstract The basic-helix-loop-helix transcription factor SCL/TAL1, is required for erythropoiesis during development, and conditional deletion in adult hematopoiesis results in hematopoietic stem cells with a competitive repopulation disadvantage and defective erythropoiesis in vitro. However, adult mice with a conditional SCL/TAL1 deletion survive with mild anemia, suggesting defective erythroid proliferation and indicating that SCL/TAL1 is important, but not essential in mature red blood cell production. We find that during erythroid differentiation of primary human hematopoietic CD34+ cells, SCL/TAL1 expression peaks at day 8–10 following erythropoietin (EPO) stimulation, concomitant with peak expression of GATA-1 and EKLF. Treatment with SCL/TAL1 antisense oligonucleotides during erythroid differentiation markedly decreases erythroid differentiation as indicated by decreased expression of GATA-1 and both b- and g-globin expression, along with the absence of the characteristic decrease in GATA-2. Microarray analysis of erythroid cells overexpressing SCL/TAL1 indicate increased gene expression for b- and g-globin, and other genes related to erythropoiesis including EPO receptor (EPO-R), and these results are confirmed in stable cell lines with increasing SCL/TAL1 expression. Examination of EPO-R transcription regulation indicates that E-boxes in the 5′ UTR can bind SCL/TAL1 in vitro and, in addition to the GATA-1 binding motif, provide transcription activity in reporter gene assays. These data indicate that in addition to the importance of SCL/TAL1 DNA binding for proliferation of BFU-E and expression of glycophorin A and protein 4.2, SCL/TAL1 is also necessary for high level expression of EPO-R. Reduction in EPO-R expression likely contributes to the anemia associated with the conditional adult deletion of SCL/TAL1 and to the proliferative defect of erythroid cells observed in vitro. Early expression of SCL/TAL1 in hematopoietic cells may activate expression of EPO-R prior to EPO stimulation of erythropoiesis and induction of GATA-1.


2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yu Zhang ◽  
Yahui Long ◽  
Chee Keong Kwoh

Abstract Background Long non-coding RNAs (lncRNAs) play significant roles in varieties of physiological and pathological processes.The premise of the lncRNA functional study is that the lncRNAs are identified correctly. Recently, deep learning method like convolutional neural network (CNN) has been successfully applied to identify the lncRNAs. However, the traditional CNN considers little relationships among samples via an indirect way. Results Inspired by the Siamese Neural Network (SNN), here we propose a novel network named Class Similarity Network in coding RNA and lncRNA classification. Class Similarity Network considers more relationships among input samples in a direct way. It focuses on exploring the potential relationships between input samples and samples from both the same class and the different classes. To achieve this, Class Similarity Network trains the parameters specific to each class to obtain the high-level features and represents the general similarity to each class in a node. The comparison results on the validation dataset under the same conditions illustrate the superiority of our Class Similarity Network to the baseline CNN. Besides, our method performs effectively and achieves state-of-the-art performances on two test datasets. Conclusions We construct Class Similarity Network in coding RNA and lncRNA classification, which is shown to work effectively on two different datasets by achieving accuracy, precision, and F1-score as 98.43%, 0.9247, 0.9374, and 97.54%, 0.9990, 0.9860, respectively.


Sign in / Sign up

Export Citation Format

Share Document