Abstract:By analyzing 1,780,295 5Ј-end sequences of human full-length cDNAs derived from 164 kinds of oligo-cap cDNA libraries, we identified 269,774 independent positions of transcriptional start sites (TSSs) for 14,628 human RefSeq genes. These TSSs were clustered into 30,964 clusters that were separated from each other by more than 500 bp and thus are very likely to constitute mutually distinct alternative promoters. To our surprise, at least 7674 (52%) human RefSeq genes were subject to regulation by putative alter… Show more
“…There was, however, a statistically significant increase in alternative promoters at class II genes (Figure 6F). Notably, alternative promoter use has been suggested to play a role in generating tissue-specific transcripts (Kimura et al, 2006; Kolle et al, 2011; Pal et al, 2011). 10.7554/eLife.00068.025Figure 10.Classification of additional pluripotency genes as either class I or class II.ChIP analysis monitoring TAF recruitment to the promoters of four pluripotency genes in H9 cells.…”
The general transcription factor TFIID comprises the TATA-box-binding protein (TBP) and approximately 14 TBP-associated factors (TAFs). Here we find, unexpectedly, that undifferentiated human embryonic stem cells (hESCs) contain only six TAFs (TAFs 2, 3, 5, 6, 7 and 11), whereas following differentiation all TAFs are expressed. Directed and global chromatin immunoprecipitation analyses reveal an unprecedented promoter occupancy pattern: most active genes are bound by only TAFs 3 and 5 along with TBP, whereas the remaining active genes are bound by TBP and all six hESC TAFs. Consistent with these results, hESCs contain a previously undescribed complex comprising TAFs 2, 6, 7, 11 and TBP. Altering the composition of hESC TAFs, either by depleting TAFs that are present or ectopically expressing TAFs that are absent, results in misregulated expression of pluripotency genes and induction of differentiation. Thus, the selective expression and use of TAFs underlies the ability of hESCs to self-renew.DOI:
http://dx.doi.org/10.7554/eLife.00068.001
“…There was, however, a statistically significant increase in alternative promoters at class II genes (Figure 6F). Notably, alternative promoter use has been suggested to play a role in generating tissue-specific transcripts (Kimura et al, 2006; Kolle et al, 2011; Pal et al, 2011). 10.7554/eLife.00068.025Figure 10.Classification of additional pluripotency genes as either class I or class II.ChIP analysis monitoring TAF recruitment to the promoters of four pluripotency genes in H9 cells.…”
The general transcription factor TFIID comprises the TATA-box-binding protein (TBP) and approximately 14 TBP-associated factors (TAFs). Here we find, unexpectedly, that undifferentiated human embryonic stem cells (hESCs) contain only six TAFs (TAFs 2, 3, 5, 6, 7 and 11), whereas following differentiation all TAFs are expressed. Directed and global chromatin immunoprecipitation analyses reveal an unprecedented promoter occupancy pattern: most active genes are bound by only TAFs 3 and 5 along with TBP, whereas the remaining active genes are bound by TBP and all six hESC TAFs. Consistent with these results, hESCs contain a previously undescribed complex comprising TAFs 2, 6, 7, 11 and TBP. Altering the composition of hESC TAFs, either by depleting TAFs that are present or ectopically expressing TAFs that are absent, results in misregulated expression of pluripotency genes and induction of differentiation. Thus, the selective expression and use of TAFs underlies the ability of hESCs to self-renew.DOI:
http://dx.doi.org/10.7554/eLife.00068.001
“…Such usage of alternative promoters has been previously described to enable differential transcriptional regulation in different cell types, developmental stages, or upon stimulation (47). Recent evidence suggests that .50% of human protein coding genes have multiple alternative promoters (48). Promoter P2 is therefore likely to be used in cell types other than monocytes and macrophages.…”
ChemR23 is a G protein–coupled receptor that is triggered by two ligands, the peptide chemerin and the eicosapentaenoic acid–derived lipid mediator resolvin E1 (RvE1). Chemerin acts as a chemoattractant for monocytes and macrophages, whereas RvE1 promotes resolution of inflammation-inducing macrophage phagocytosis of apoptotic neutrophils. Although ChemR23-mediated signaling plays a role in mononuclear cell migration to inflamed tissue, as well as in the resolution of inflammation, its regulation in different polarization states of macrophages is largely unknown. We analyzed the expression and function of ChemR23 in monocytes and differently activated human primary macrophages. Using 5′ RACE, we identified three transcription start sites and several splice variants of ChemR23 in both monocytes and macrophages. Although the promoters P1 and P3 are used equally in unpolarized macrophages, stimulation with LPS or IFN-γ leads to increased transcription from P3 in inflammatory M1 macrophages. Such ChemR23-expressing M1 macrophages are chemotactic to chemerin, whereas M2 macrophages not expressing ChemR23 surface receptor are not. Repolarization of ChemR23-expressing M1 macrophages with 10 nM RvE1 increases IL-10 transcription and phagocytosis of microbial particles, leading to a resolution-type macrophage distinct from the M2 phenotype. These results show that ChemR23 is tightly regulated in response to inflammatory and anti-inflammatory stimuli. The restricted expression of ChemR23 in naive and M1 macrophages supports the role of ChemR23 in the attraction of macrophages to inflamed tissue by chemerin and in the initiation of resolution of inflammation through RvE1-mediated repolarization of human M1 macrophages toward resolution-type macrophages.
“…C20orf166-AS1 is a large intergenic noncoding RNA (lincRNA) that shows a high expression in normal prostate tissues, whereas relatively low expression in the prostate cancer tissues. C20orf166-AS1 has also been found to be significantly associated with prostate cancer or prostatitis using other methods (Kimura et al, 2006;Eeles et al, 2013). RP11-267A15.1 is an antisense RNA that also shows a highly specific expression in the prostate cancer cells, but low or no expression in normal prostate tissues.…”
Purpose: To identify prostate cancer lncRNAs using a pipeline proposed in this study, which is applicable for the identification of lncRNAs that are differentially expressed in prostate cancer tissues but have a negligible potential to encode proteins. Materials and Methods: We used two publicly available RNA-Seq datasets from normal prostate tissue and prostate cancer. Putative lncRNAs were predicted using the biological technology, then specific lncRNAs of prostate cancer were found by differential expression analysis and co-expression network was constructed by the weighted gene co-expression network analysis. Results: A total of 1,080 lncRNA transcripts were obtained in the RNA-Seq datasets. Three genes (PCA3, C20orf166-AS1 and RP11-267A15.1) showed a significant differential expression in the prostate cancer tissues, and were thus identified as prostate cancer specific lncRNAs. Brown and black modules had significant negative and positive correlations with prostate cancer, respectively. Conclusions: The pipeline proposed in this study is useful for the prediction of prostate cancer specific lncRNAs. Three genes (PCA3, C20orf166-AS1, and RP11-267A15.1) were identified to have a significant differential expression in prostate cancer tissues. However, there have been no published studies to demonstrate the specificity of RP11-267A15.1 in prostate cancer tissues. Thus, the results of this study can provide a new theoretic insight into the identification of prostate cancer specific genes.
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