Correct Identification of Genes from Serial Analysis of Gene Expression Tag Sequences (original) (raw)

Stable transcriptional status in the apoptotic erythroid genome

Biochemical and Biophysical Research Communications, 2007

When a cell is destined for apoptosis, will its genome reprogram its transcriptional machinery to overcome the life-threatening challenge? To address this issue, we performed a genome-wide transcriptome analysis in EPO (erythropoietin) deprivation-induced apoptotic erythroid cells using the SAGE method. The results show that the transcript contents for the majority of the genes remain unchanged in the apoptotic cells, including the apoptotic genes and the heat shock genes. Of the small number of genes with an altered expression, they are mainly associated with cellular structure. Our study reveals that there is no genetic reprogramming for the transcriptional machinery in the apoptotic genome. Apoptosis, as defined by programmed cell death, is not a crisis but a peaceful physiological process.

Screening Poly [dA/dT(-)] cDNA for Gene Identification

Generation of cDNA Libraries, 2003

Apoptosis, guardian of the genome: Review

Zenodo (CERN European Organization for Nuclear Research), 2021

Apoptosis has attracted great attention in the last two decades and the number of publications related to apoptosis has been growing exponentially. The revolution that has occurred in apoptosis research is a direct result of a better understanding of the genetic program and biochemical mechanisms of apoptosis. Apoptosis is not only a common normal event but also essential for the growth and development of organisms. In the adult, apoptosis is mostly abnormal, but in its absence or failure cancer cells obtain immortality by escaping this type of cell death. Apoptosis works synergistically in intrinsic and extrinsic pathways. The first pathway is initiated by the cell itself in response to stress. The second is initiated via death receptors stimulated by cells of the immune system. This review is an attempt to answer questions like: Why is cell death important to study? How cells undergo apoptosis? What controls the decision between life and death? Which cellular events could cause the control of apoptosis to be impaired? The literature cited below shows some sort of unity in the scientific community on the necessity of a sophisticated balance between "prosurvival" and "pro-death" forces to ensure the happiness of cells in multicellular organisms

A Cell’s Fate: An Overview of the Molecular Biology and Genetics of Apoptosis

International Journal of Molecular Sciences

Apoptosis is one of the main types of regulated cell death, a complex process that can be triggered by external or internal stimuli, which activate the extrinsic or the intrinsic pathway, respectively. Among various factors involved in apoptosis, several genes and their interactive networks are crucial regulators of the outcomes of each apoptotic phase. Furthermore, mitochondria are key players in determining the way by which cells will react to internal stress stimuli, thus being the main contributor of the intrinsic pathway, in addition to providing energy for the whole process. Other factors that have been reported as important players of this intricate molecular network are miRNAs, which regulate the genes involved in the apoptotic process. Imbalance in any of these mechanisms can lead to the development of several illnesses, hence, an overall understanding of these processes is essential for the comprehension of such situations. Although apoptosis has been widely studied, the c...

Isolation of genes controlling apoptosis through their effects on cell survival - Research article

Gene Therapy and Molecular Biology, 2006

The identification of the most suitable molecular targets for gene and drug therapy is the crucial first step in the development of new disease treatments. The rational identification of such targets depends on a detailed understanding of the pathological changes occuring at the molecular level. We have applied forward genetics approaches to the identification of the critical genes involved in the control of apoptosis in mammalian cells, since defective control of apoptosis underlies many diseases, including cancer and neurodegenerative diseases. We have identified two groups of genes by their effects on cell survival using retroviral cDNA functional expression cloning and retroviral insertional mutagenesis. The identification of these novel genes opens up new areas for apoptosis research and subsequently for the development of new gene and drug therapies.

Isolation of genes controlling apoptosis through their effects on cell survival

Gene therapy & molecular biology, 2006

Gene networks in glucocorticoid-evoked apoptosis of leukemic cells

The Journal of Steroid Biochemistry and Molecular Biology, 2003

To discover the genes responsible for the apoptosis evoked by glucocorticoids in leukemic lymphoid cells, we have begun gene array analysis on microchips. Three clones of CEM cells were compared: C7-14, C1-15 and C1-6. C7-14 and C1-15 are subclones from the original clones C7 (sensitive to apoptosis by glucocorticoids) and C1 (resistant). C1-6 is a spontaneous revertant to sensitivity from the C1 clone. Previously we presented data on the sets of genes whose expression is altered in these cell clones after 20 h exposure to dexamethasone (Dex). The two sensitive clones, which respond by undergoing apoptosis starting about 24 h after Dex is added, both showed >2.5-fold induction of 39 genes and 2-fold reduction of expressed levels from 21 genes. C1-15, the resistant clone, showed alterations in a separate set of genes.

Comparative study of apoptosis-related gene loci in human, mouse and rat genomes

Acta biochimica et biophysica Sinica, 2005

Many genes are involved in mammalian cell apoptosis pathway. These apoptosis genes often contain characteristic functional domains, and can be classified into at least 15 functional groups, according to previous reports. Using an integrated bioinformatics platform for motif or domain search from three public mammalian proteomes (International Protein Index database for human, mouse, and rat), we systematically cataloged all of the proteins involved in mammalian apoptosis pathway. By localizing those proteins onto the genomes, we obtained a gene locus centric apoptosis gene catalog for human, mouse and rat. Further phylogenetic analysis showed that most of the apoptosis related gene loci are conserved among these three mammals. Interestingly, about one-third of apoptosis gene loci form gene clusters on mammal chromosomes, and exist in the three species, which indicated that mammalian apoptosis gene orders are also conserved. In addition, some tandem duplicated gene loci were revealed...

Correct Identification of Genes from Serial Analysis of Gene Expression Tag Sequences (original) (raw)

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