Olfactory receptor coding sequences cause silencing of episomal constructs in multiple cell lines

2021 ◽  
pp. 103681
Author(s):  
Ghazia Abbas ◽  
Spencer Tang ◽  
Joyce Noble ◽  
Robert P. Lane
Keyword(s):  
Cell Lines ◽  
Olfactory Receptor ◽  
Coding Sequences ◽  
Multiple Cell

scholarly journals Combinatorial CRISPR screen identifies fitness effects of gene paralogues

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nicola A. Thompson ◽  
Marco Ranzani ◽  
Louise van der Weyden ◽  
Vivek Iyer ◽  
Victoria Offord ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Cell Lines ◽  
Unknown Function ◽  
Single Copy ◽  
Genetic Redundancy ◽  
Synthetic Lethal ◽  
Fitness Effects ◽  
Synthetic Lethal Interactions ◽  
Crispr Screen ◽  
Multiple Cell

AbstractGenetic redundancy has evolved as a way for human cells to survive the loss of genes that are single copy and essential in other organisms, but also allows tumours to survive despite having highly rearranged genomes. In this study we CRISPR screen 1191 gene pairs, including paralogues and known and predicted synthetic lethal interactions to identify 105 gene combinations whose co-disruption results in a loss of cellular fitness. 27 pairs influence fitness across multiple cell lines including the paralogues FAM50A/FAM50B, two genes of unknown function. Silencing of FAM50B occurs across a range of tumour types and in this context disruption of FAM50A reduces cellular fitness whilst promoting micronucleus formation and extensive perturbation of transcriptional programmes. Our studies reveal the fitness effects of FAM50A/FAM50B in cancer cells.

scholarly journals Labeling of multiple cell lines using a new iron oxide agent for cell tracking by MRI

2011 ◽  
Vol 6 (6) ◽  
pp. 514-522 ◽  
Author(s):  
C. McFadden ◽  
C. L. Mallett ◽  
P. J. Foster
Keyword(s):  
Iron Oxide ◽  
Cell Lines ◽  
Cell Tracking ◽  
Multiple Cell

scholarly journals Characterization of the BCR promoter in Philadelphia chromosome-positive and -negative cell lines.

1991 ◽  
Vol 11 (4) ◽  
pp. 1854-1860 ◽  
Author(s):  
N P Shah ◽  
O N Witte ◽  
C T Denny
Keyword(s):  
Transcription Factor ◽  
Cell Lines ◽  
Transcription Initiation ◽  
Transcriptional Control ◽  
Philadelphia Chromosome ◽  
Gc Content ◽  
Cellular Transformation ◽  
Nucleotide Sequence Analysis ◽  
Coding Sequences ◽  
Gene Assay

The t(9;22) Philadelphia chromosome translocation fuses 5' regulatory and coding sequences of the BCR gene to the c-ABL proto-oncogene. This results in the formation of hybrid BCR-ABL mRNAs and proteins. The shift in ABL transcriptional control to the BCR promoter may play a role in cellular transformation mediated by this rearrangement. We have functionally localized the BCR promoter to a region 1 kb 5' of BCR exon 1 coding sequences by using a chloramphenicol acetyltransferase reporter gene assay. Nucleotide sequence analysis of this region revealed many consensus binding sequences for transcription factor SP1 as well as two potential CCAAT box binding factor sites and one putative helix-loop-helix transcription factor binding site. No TATA-like or "initiator" element sequences were found. Because of low steady-state levels of BCR mRNA and the high GC content (78%) of the promoter region, definitive mapping of transcription start sites required artificial amplification of BCR promoter-directed transcripts. Overexpression from the BCR promoter in a COS cell system was effective in demonstrating multiple transcription initiation sites. In order to assess the effects of chromosomal translocation on the transcriptional control of the BCR gene, we determined S1 nuclease protection patterns of poly(A)+ RNA from tumor cell lines. No differences were observed in the locations and levels of BCR transcription initiation sites between those lines that harbored the t(9;22) translocation and those that did not. This demonstrates that BCR promoter function remains intact in spite of genomic rearrangement. The BCR promoter is structurally similar to the ABL promoters. Together, this suggests that the structural fusion of BCR-ABL and not its transcriptional deregulation is primarily responsible for the transforming effect of the t(9;22) translocation.

Substantial variation in the cardiac differentiation of human embryonic stem cell lines derived and propagated under the same conditions—a comparison of multiple cell lines

2009 ◽  
Vol 41 (5) ◽  
pp. 360-370 ◽  
Author(s):  
Mari Pekkanen-Mattila ◽  
Erja Kerkelä ◽  
Jarno M. A. Tanskanen ◽  
Mika Pietilä ◽  
Markku Pelto-Huikko ◽  
...  
Keyword(s):  
Stem Cell ◽  
Embryonic Stem Cell ◽  
Cell Lines ◽  
Human Embryonic Stem Cell ◽  
Embryonic Stem ◽  
Cardiac Differentiation ◽  
Substantial Variation ◽  
Multiple Cell ◽  
Stem Cell Lines

scholarly journals Invasion performance-similarity found among multiple cell systems

2020 ◽  
Author(s):  
Om Prakash
Keyword(s):  
Cell Lines ◽  
Drug Repositioning ◽  
Biological Research ◽  
Multiple Systems ◽  
Biologically Relevant ◽  
Selective Targeting ◽  
Ann Models ◽  
Multiple Cell ◽  
Artificial Neural Network Ann ◽  
Network Mapping

ABSTRACTUnderstanding of inter-system behavior develops biologically relevant intuition for drug repositioning as well as other biological research. But combining all the possible genes interactions into a system, and furthermore comparisons of multiple systems are a challenge on time ground with feasible experiments. In present study, 64 cell lines from 11 different organs were compared for their invasion performance. RNA expressions of 23 genes were used to create systems artificial neural network (ANN) models. ANN models were prepared for all 64 cell lines and observed for their invasion performance through network mapping. The resulted cell line clusters bear feasible capacity to perform experiments for biologically relevant research motivations as drug repositioning and selective targeting etc.; and can be used for analysis of invasion related aspects.

scholarly journals Unequal signal and coding joint formation in human V(D)J recombination.

1993 ◽  
Vol 13 (7) ◽  
pp. 3900-3906 ◽  
Author(s):  
G H Gauss ◽  
M R Lieber
Keyword(s):  
Cell Lines ◽  
Relative Efficiency ◽  
Chromosomal Rearrangements ◽  
The Other ◽  
Combined Effects ◽  
Recombination Activity ◽  
Coding Sequences ◽  
Joint Formation ◽  
Differential Reaction ◽  
Endogenous Loci

Substrates for studying V(D)J recombination in human cells and two human pre-B-cell lines that have active V(D)J recombination activity are described. Using these substrates, we have been able to analyze the relative efficiency of signal joint and coding joint formation. Coding joint formation was five- to sixfold less efficient than signal joint formation in both cell lines. This imbalance between the two halves of the reaction was demonstrated on deletional substrates, where each joint is assayed individually. In both cell lines, the inversional reaction (which requires formation of both a signal and a coding joint) was more than 20-fold less efficient than signal joint formation alone. The signal and coding sequences are identical in all of these substrates. Hence, the basis for these differential reaction ratios appears to be that coding joint and signal joint formation are both inefficient and their combined effects are such that inversions (two-joint reactions) reflect the product of these inefficiencies. Physiologically, these results have two implications. First, they show how signal and coding joint formation efficiencies can affect the ratio of deletional to inversional products at endogenous loci. Second, the fact that not all signal and coding joints go to completion implies that the recombinase is generating numerous broken ends. Such unresolved ends may participate in pathologic chromosomal rearrangements even when the other half of the same reaction may have proceeded to resolution.

scholarly journals β-catenin-mediated Wnt signal transduction proceeds through an endocytosis-independent mechanism

2020 ◽  
Vol 31 (13) ◽  
pp. 1425-1436 ◽  
Author(s):  
Ellen Youngsoo Rim ◽  
Leigh Katherine Kinney ◽  
Roeland Nusse
Keyword(s):  
Signal Transduction ◽  
Real Time ◽  
Cell Lines ◽  
Wnt Pathway ◽  
Receptor Endocytosis ◽  
Pathway Activation ◽  
Independent Mechanism ◽  
Multiple Cell ◽  
Wnt Signal ◽  
Time Assessment

A novel tool for quantitative, real-time assessment of Wnt pathway activation was combined with genetic disruption of endocytosis to determine whether receptor endocytosis is required for Wnt signal transduction. Our results in multiple cell lines support that clathrin- or caveolin-mediated endocytosis is dispensable for Wnt signal transduction.

scholarly journals Cell Line Classification Using Electric Cell-Substrate Impedance Sensing (ECIS)

2019 ◽  
Vol 16 (1) ◽  
Author(s):  
Megan L. Gelsinger ◽  
Laura L. Tupper ◽  
David S. Matteson
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Mammalian Cells ◽  
Statistical Tests ◽  
Classification Methods ◽  
Impedance Sensing ◽  
Mammalian Cell Lines ◽  
Cell Substrate ◽  
Multiple Cell ◽  
Line Classification

AbstractWe present new methods for cell line classification using multivariate time series bioimpedance data obtained from electric cell-substrate impedance sensing (ECIS) technology. The ECIS technology, which monitors the attachment and spreading of mammalian cells in real time through the collection of electrical impedance data, has historically been used to study one cell line at a time. However, we show that if applied to data from multiple cell lines, ECIS can be used to classify unknown or potentially mislabeled cells, factors which have previously been associated with the reproducibility crisis in the biological literature. We assess a range of approaches to this new problem, testing different classification methods and deriving a dictionary of 29 features to characterize ECIS data. Most notably, our analysis enriches the current field by making use of simultaneous multi-frequency ECIS data, where previous studies have focused on only one frequency; using classification methods to distinguish multiple cell lines, rather than simple statistical tests that compare only two cell lines; and assessing a range of features derived from ECIS data based on their classification performance. In classification tests on fifteen mammalian cell lines, we obtain very high out-of-sample predictive accuracy. These preliminary findings provide a baseline for future large-scale studies in this field.

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