Long intergenic non-coding RNAs (lincRNAs) are defined as RNA transcripts that are longer than 200 nucleotides. By definition, these RNAs must not have open reading frames that encode proteins. Many of these transcripts are encoded by RNA polymerase II, are spliced, and are poly-adenylated. This final fact indicates that there is a trove of information about lincRNAs in databases such as the Gene Expression Omnibus (GEO), which is a repository for RNAseq and microarray data. Recent experiments indicate that there are upwards of 15,000 lincRNAs encoded by the human genome. The term "intergenic" refers to the identification of these transcripts from regions of the genome that do not contain protein-encoding genes. These regions coincide with what was once labeled as the "junk DNA" portions of our genomes, which, upon careful examination by whole genome RNA sequencing experiments, clearly encode RNA transcripts. LincRNAs also contain promoter- or enhancer-associated RNAs that are gene proximal and can be either in the sense or antisense orientation, relative to the protein-coding gene with which they are associated. In this review, we describe the functions of lincRNAs playing roles in biological processes such as gene expression control, scaffold formation, and epigenetic control.
e Insults to cellular health cause p53 protein accumulation, and loss of p53 function leads to tumorigenesis. Thus, p53 has to be tightly controlled. Here we report that the BTB/POZ domain transcription factor PATZ1 (MAZR), previously known for its transcriptional suppressor functions in T lymphocytes, is a crucial regulator of p53. The novel role of PATZ1 as an inhibitor of the p53 protein marks its gene as a proto-oncogene. PATZ1-deficient cells have reduced proliferative capacity, which we assessed by transcriptome sequencing (RNA-Seq) and real-time cell growth rate analysis. PATZ1 modifies the expression of p53 target genes associated with cell proliferation gene ontology terms. Moreover, PATZ1 regulates several genes involved in cellular adhesion and morphogenesis. Significantly, treatment with the DNA damage-inducing drug doxorubicin results in the loss of the PATZ1 transcription factor as p53 accumulates. We find that PATZ1 binds to p53 and inhibits p53-dependent transcription activation. We examine the mechanism of this functional inhibitory interaction and demonstrate that PATZ1 excludes p53 from DNA binding. This study documents PATZ1 as a novel player in the p53 pathway. Wild-type (WT) p53 is a stress-responsive, sequence-specific transcription factor that inhibits the cell cycle, promotes senescence, and, if the insult to cellular health is not resolved, induces apoptotic death (1). p53 mutations that allow cells to escape this death are the most common genetic event in human cancer (2). Alternative mechanisms of escape rely on the overexpression of MDM2 and MDMX, major negative regulators of p53 that keep p53 levels low under unstressed conditions through ubiquitination-mediated degradation (3). Moreover, many DNA tumor viruses encode proteins that can inactivate p53 (2). However, the list of p53 regulators is far from complete. Various stress conditions result in the upregulation of p53, controlled by feedback loops, posttranslational modifications, and epigenetic changes. In the present study, we aimed to find new players that modify p53 function.p53 is composed of an N-terminal transactivation domain (through which it interacts with MDM2), a proline-rich domain, central DNA binding and tetramerization domains, and a C-terminal regulatory domain. p53 binds response elements (REs) in nuclear DNA, which results in stress-induced changes (either upor downregulation) in gene expression. Tetrameric p53 binds REs that are composed of two half-sites, each with a consensus of RR RCWWGYYY, separated by 0 to 21 bases (where R is a purine, Y is a pyrimidine, and W is either an A or T) (4). p53 REs can be subcategorized as those that respond to low levels of wild-type p53, those that respond to stabilized p53 after stress, and those that respond to p53 with mutations in its DNA binding domain. A recent study found 160 p53 REs controlling 129 genes in the human genome (5). Another study using chromatin immunoprecipitation (ChIP) with paired-end ditag (PET) sequencing identified 542 functional p53 binding sites...
Background: Expression of the IL-7R␣ gene is up-/down-regulated during T/B-lymphocyte development. Results: IL-7R␣ gene transcription is repressed by the transcription factor Gfi1, specifically in CD8 ϩ T-lymphocytes. Conclusion:Treatment by dexamethasone down-regulates Gfi1, which contributes to glucocorticoid receptor mediated upregulation of IL-7R expression. Significance: The mechanism by which the IL-7R gene gets turned on and off during development is a critical issue in biology. Interleukin-7 receptor ␣ (IL-7R␣) is essential for T cell survival and differentiation. Glucocorticoids are potent enhancers of IL-7R␣ expression with diverse roles in T cell biology.Here we identify the transcriptional repressor, growth factor independent-1 (Gfi1), as a novel intermediary in glucocorticoid-induced IL-7R␣ up-regulation. We found Gfi1 to be a major inhibitory target of dexamethasone by microarray expression profiling of 3B4.15 T-hybridoma cells. Concordantly, retroviral transduction of Gfi1 significantly blunted IL-7R␣ up-regulation by dexamethasone. To further assess the role of Gfi1 in vivo, we generated bacterial artificial chromosome (BAC) transgenic mice, in which a modified Il7r locus expresses GFP to report Il7r gene transcription. By introducing this BAC reporter transgene into either Gfi1-deficient or Gfi1-transgenic mice, we document in vivo that IL-7R␣ transcription is up-regulated in the absence of Gfi1 and down-regulated when Gfi1 is overexpressed. Strikingly, the in vivo regulatory role of Gfi1 was specific for CD8 ؉ , and not CD4 ؉ T cells or immature thymocytes. These results identify Gfi1 as a specific transcriptional repressor of the Il7r gene in CD8 T lymphocytes in vivo.
CD81 (TAPA-1) is a ubiquitously expressed tetraspanin protein identified as a component of the B lymphocyte receptor (BCR) and as a receptor for the Hepatitis C Virus. In an effort to identify trans-membrane proteins that interact with the T-cell antigen receptor (TCR), we performed a membrane yeast two hybrid screen and identified CD81 as an interactor of the CD3delta subunit of the TCR. We found that in the absence of CD81, in thymocytes from knockout mice, TCR engagement resulted in stronger signals. These results were recapitulated in T cell lines that express low levels of CD81 through shRNA mediated silencing. Increased signaling did not result from alterations in the levels of TCR on the surface of T lymphocytes. Although CD81 is not essential for normal T lymphocyte development, it plays an important role in regulating TCR and possibly pre-TCR signal transduction by controlling the strength of signaling. CD81 dependent alterations in thymocyte signaling are evident in increased CD5 expression on CD81 deficient double positive (DP) thymocytes. We conclude that CD81 interacts with the T cell receptor to suppress signaling.
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