Alternative Promoter Usage Research Articles

DNA Methylation Profile of Runx1 Regulatory Regions Is Correlated with Transition From Primitive to Definitive Hematopoietic Potential In Vitro and In Vivo

Abstract 389 Introduction:The Runt-related transcription factor Runx1 (AML1) is a central regulator of mammalian hematopoiesis and is required for the generation of hematopoietic stem cells (HSC) from hemogenic endothelium in the embryo. It has been shown that Runx1 is alternatively expressed from two promoters in a temporal fashion, and that their differential activities are influenced by a conserved intronic enhancer (+23) element. Intriguingly, promoter usage follows a pattern whereby the proximal (P2) initiates early in primitive hematopoiesis, while the distal (P1) becomes active later at the time of HSC emergence and is the predominant isoform expressed in fetal liver and adult HSC. While some transcription factor binding sites and cis-regulatory elements have been identified, an explanation for the alternative promoter usage remains elusive. We hypothesized that this regulation may be at the level of chromatin accessibility, and therefore investigated the DNA methylation status of Runx1 cis-elements. Methods/Results:We analyzed bisulfite-treated genomic DNA from E14.5 fibroblast (MEF), E8.5 yolk sac CD41+ (YS), E14.5 fetal liver Lin-Sca-1+CD48-CD150+ (FL), and adult marrow Lin-cKit+Sca-1+ (KLS); representing non-hematopoietic, primitive hematopoietic, and two stages of definitive HSC respectively. In addition, we also examined methylation in hematopoietic populations derived in vitro from murine embryonic stem cells (mESC). Initial exploratory analysis focused on classically defined CpG islands upstream of each promoter, however no significant differential methylation was observed within these regions. Subsequent analysis focused on CpGs near the transcription start site (TSS) and within the +23 enhancer. The P2 promoter was uninformative as it was unmethylated in all populations analyzed, whereas methylation within the +23 enhancer differentiated between hematopoietic and non-hematopoietic cell populations. At the P1 promoter, methylation status was remarkably correlated with primitive vs. definitive status. P1 was highly methylated in MEFs (77%), mESC embryoid body (EB) derived cKit+CD41+ (66%), and E8.5 YS CD41+ (58%); but significantly less methylated in vivo in FL HSC (8.1%) and adult KLS cells (18%). We are currently using this correlation of demethylation and definitive HSC potential to identify conditions that may drive definitive HSC generation from mESC-derived blood progenitors. Since overexpression of HoxB4 coupled with OP9 co-culture is the only confirmed method capable of producing definitive HSC from mESC, and HoxB4 has been shown to bind within the P1 promoter region of Runx1, we cultured HoxB4 or control EB-derived hematopoietic progenitors on OP9 stroma. We observed progressive demethylation in the HoxB4 arm: after 6 days of co-culture 47% vs. 71% in controls, and after 11 days 27% in the HoxB4 arm while the control population failed to proliferate past day 6. Isoform specific RT-PCR confirmed that HoxB4 overexpression resulted in Runx1 expression from the P1 promoter whereas the control vector did not. Within P1, we identify a single CpG that is most highly correlated with definitive HSC potential in vivo, and most significantly demethylated upon HoxB4 overexpression in vitro. Conclusions:These data indicate that differential methylation occurs at Runx1 regulatory regions during hematopoietic development in vitro and in vivo. The +23 enhancer is demethylated in cells with hematopoietic potential, whereas demethylation of the Runx1 P1 promoter is highly correlated with definitive HSPC populations and is promoted in vitro by HoxB4. These data are the first to identify a role for DNA methylation in the regulation of alternative promoter usage at the Runx1 locus, and may serve as a novel biomarker of HSC potential during embryonic development. Disclosures:No relevant conflicts of interest to declare.

Widespread generation of alternative UTRs contributes to sex-specific RNA binding by UNR

Upstream of N-ras (UNR) is a conserved RNA-binding protein that regulates mRNA translation and stability by binding to sites generally located in untranslated regions (UTRs). In Drosophila, sex-specific binding of UNR to msl2 mRNA and the noncoding RNA roX is believed to play key roles in the control of X-chromosome dosage compensation in both sexes. To investigate broader sex-specific functions of UNR, we have identified its RNA targets in adult male and female flies by high-throughput RNA binding and transcriptome analysis. Here we show that UNR binds to a large set of protein-coding transcripts and to a smaller set of noncoding RNAs in a sex-specific fashion. The analyses also reveal a strong correlation between sex-specific binding of UNR and sex-specific differential expression of UTRs in target genes. Validation experiments indicate that UNR indeed recognizes sex-specifically processed transcripts. These results suggest that UNR exploits the transcript diversity generated by alternative processing and alternative promoter usage to bind and regulate target genes in a sex-specific manner.

Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis

BackgroundApproximately half of all human genes use alternative transcription start sites (TSSs) to control mRNA levels and broaden the transcriptional output in healthy tissues. Aberrant expression patterns promoting carcinogenesis, however, may arise from alternative promoter usage.ResultsBy profiling 108 colorectal samples using exon arrays, we identified nine genes (TCF12, OSBPL1A, TRAK1, ANK3, CHEK1, UGP2, LMO7, ACSL5, and SCIN) showing tumor-specific alternative TSS usage in both adenoma and cancer samples relative to normal mucosa. Analysis of independent exon array data sets corroborated these findings. Additionally, we confirmed the observed patterns for selected mRNAs using quantitative real-time reverse-transcription PCR. Interestingly, for some of the genes, the tumor-specific TSS usage was not restricted to colorectal cancer. A comprehensive survey of the nine genes in lung, bladder, liver, prostate, gastric, and brain cancer revealed significantly altered mRNA isoform ratios for CHEK1, OSBPL1A, and TCF12 in a subset of these cancer types.To identify the mechanism responsible for the shift in alternative TSS usage, we antagonized the Wnt-signaling pathway in DLD1 and Ls174T colorectal cancer cell lines, which remarkably led to a shift in the preferred TSS for both OSBPL1A and TRAK1. This indicated a regulatory role of the Wnt pathway in selecting TSS, possibly also involving TP53 and SOX9, as their transcription binding sites were enriched in the promoters of the tumor preferred isoforms together with their mRNA levels being increased in tumor samples.Finally, to evaluate the prognostic impact of the altered TSS usage, immunohistochemistry was used to show deregulation of the total protein levels of both TCF12 and OSBPL1A, corresponding to the mRNA levels observed. Furthermore, the level of nuclear TCF12 had a significant correlation to progression free survival in a cohort of 248 stage II colorectal cancer samples.ConclusionsAlternative TSS usage in colorectal adenoma and cancer samples has been shown for nine genes, and OSBPL1A and TRAK1 were found to be regulated in vitro by Wnt signaling. TCF12 protein expression was upregulated in cancer samples and correlated with progression free survival.

Twinfilin-2a Is Dispensable for Mouse Development

Twinfilins are evolutionarily conserved regulators of cytoskeletal dynamics. They inhibit actin polymerization by binding both actin monomers and filament barbed ends. Inactivation of the single twinfilin gene from budding yeast and fruit fly results in defects in endocytosis, cell migration, and organization of the cortical actin filament structures. Mammals express three twinfilin isoforms, of which twinfilin-1 and twinfilin-2a display largely overlapping expression patterns in non-muscle tissues of developing and adult mice. The expression of twinfilin-2b, which is generated through alternative promoter usage of the twinfilin-2 gene, is restricted to heart and skeletal muscles. However, the physiological functions of mammalian twinfilins have not been reported. As a first step towards understanding the function of twinfilin in vertebrates, we generated twinfilin-2a deficient mice by deleting exon 1 of the twinfilin-2 gene. Twinfilin-2a knockout mice developed normally to adulthood, were fertile, and did not display obvious morphological or behavioural abnormalities. Tissue anatomy and morphology in twinfilin-2a deficient mice was similar to that of wild-type littermates. These data suggest that twinfilin-2a plays a redundant role in cytoskeletal dynamics with the biochemically similar twinfilin-1, which is typically co-expressed in same tissues with twinfilin-2a.

Constitutive Notch pathway activation in murine ZMYM2-FGFR1–induced T-cell lymphomas associated with atypical myeloproliferative disease

AbstractThe ZMYM2-FGFR1 (formerly known as ZNF198-FGFR1) fusion kinase induces stem cell leukemia–lymphoma syndrome (SCLL), a hematologic malignancy characterized by rapid transformation to acute myeloid leukemia and T-lymphoblastic lymphoma. In the present study, we demonstrate frequent, constitutive activation of Notch1 and its downstream target genes in T-cell lymphomas that arose in a murine model of ZMYM2-FGFR1 SCLL. Notch up-regulation was also demonstrated in human SCLL- and FGFR1OP2-FGFR1-expressing KG-1 cells. To study the role of Notch in T-cell lymphomagenesis, we developed a highly tumorigenic cell line from ZMYM2-FGFR1–expressing cells. Pharmacologic inhibition of Notch signaling in these cells using γ-secretase inhibitors significantly delayed leukemogenesis in vivo. shRNA targeting of Notch1, as well as c-promoter–binding factor 1 (CBF1) and mastermind-like 1 (MAML1), 2 essential cofactors involved in transcriptional activation of Notch target genes, also significantly delayed or inhibited tumorigenesis in vivo. Mutation analysis demonstrated that 5′ promoter deletions and alternative promoter usage were responsible for constitutive activation of Notch1 in all T-cell lymphomas. These data demonstrate the importance of Notch signaling in the etiology of SCLL, and suggest that targeting this pathway could provide a novel strategy for molecular therapies to treat SCLL patients.

Identification and characterization of the major alternative promoter regulating Bcrp1/Abcg2 expression in the mouse intestine

Mouse models are often used to predict drug absorption in humans. Mouse Bcrp1 protein exhibits sequence and functional homology with human BCRP protein. Additionally, BCRP/Bcrp1 expression is regulated by alternative promoter usage in humans and mice; however, the precise intestine-specific alternative promoter utilized in either species is yet to be determined. Therefore we sought to identify and characterize the mouse intestinal Bcrp1 promoter. Using real-time quantitative RT-PCR and 5′ RACE PCR we first established the predominance of a single Bcrp1 first exon (E1b) in the Bcrp1 mRNA isolated throughout the mouse intestine. Simultaneously using 5′ RACE PCR we identified E1C as the predominant BCRP 5′ UTR expressed in the human intestine. Next we established functional activity for the murine promoter upstream of E1b using reporter assays. Subsequently using deletion-construct analysis we found the core promoter region to span − 231 to − 42 bps from the transcriptional start site of E1b. We then predicted a cAMP response element (CRE) as a transcription factor binding site unique only to the E1b promoter region, using in silico methods. We finally established functional interaction of phospho-CREB (p-CREB) protein with the CRE on the E1b promoter using both functional assays and chromatin immunoprecipitation assays. In conclusion, mouse intestinal Bcrp1 expression is regulated by a single alternative promoter upstream of E1b, the predominant Bcrp1 mRNA isoform expressed in the mouse intestine. Furthermore, Bcrp1 E1b mRNA expression is regulated by binding of p-CREB to its cis site on the mouse E1b promoter region.

Alternative promoter usage and differential expression of multiple transcripts of mouse Prkar1a gene

Prkar1a gene encodes regulatory type 1 alpha subunit (RIα) of cAMP-dependent protein kinase (PKA) in mouse. The role of this gene has been implicated in Carney complex and many cancer types that suggest its involvement in physiological processes like cell cycle regulation, growth and/or proliferation. We have identified and sequenced partial cDNA clones encoding four alternatively spliced transcripts of mouse Prkar1a gene. These transcripts have alternate 5' UTR structure which results from splicing of three exons (designated as E1a, E1b, and E1c) to canonical exon 2. The designated transcripts T1, T2, T3, and T4 contain 5' UTR exons as E1c, E1a + E1b, E1a, and E1b, respectively. The transcript T1 corresponded to earlier reported transcript in GenBank. In silico study of genomic DNA sequence revealed three distinct promoter regions namely, P1, P2, and P3 upstream of the exons E1a, E1b, and E1c, respectively. P1 is non-CpG-related promoter but P2 and P3 are CpG-related promoters; however, all three are TATA less. RT-PCR analysis demonstrated the expression of all four transcripts in late postnatal stages; however, these were differentially regulated in early postnatal stages of 0.5 day, 3 day, and 15 day mice in different tissue types. Variations in expression of Prkar1a gene transcripts suggest their regulation from multiple promoters that respond to a variety of signals arising in or out of the cell in tissue and developmental stage-specific manner.

Host Response to Polyomavirus Infection Is Modulated by RNA Adenosine Deaminase ADAR1 but Not by ADAR2

Adenosine deaminases acting on RNA (ADARs) catalyze the C-6 deamination of adenosine (A) to produce inosine (I), which behaves as guanine (G), thereby altering base pairing in RNAs with double-stranded character. Two genes, adar1 and adar2, are known to encode enzymatically active ADARs in mammalian cells. Furthermore, two size forms of ADAR1 are expressed by alternative promoter usage, a short (p110) nuclear form that is constitutively made and a long (p150) form that is interferon inducible and present in both the cytoplasm and nucleus. ADAR2 is also a constitutively expressed nuclear protein. Extensive A-to-G substitution has been described in mouse polyomavirus (PyV) RNA isolated late times after infection, suggesting modification by ADAR. To test the role of ADAR in PyV infection, we used genetically null mouse embryo fibroblast cells deficient in either ADAR1 or ADAR2. The single-cycle yields and growth kinetics of PyV were comparable between adar1(-/-) and adar2(-/-) genetic null fibroblast cells. While large T antigen was expressed to higher levels in adar1(-/-) cells than adar2(-/-) cells, less difference was seen in VP1 protein expression levels between the two knockout MEFs. However, virus-induced cell killing was greatly enhanced in PyV-infected adar1(-/-) cells compared to that of adar2(-/-) cells. Complementation with p110 protected cells from PyV-induced cytotoxicity. UV-irradiated PyV did not display any enhanced cytopathic effect in adar1(-/-) cells. Reovirus and vesicular stomatitis virus single-cycle yields were comparable between adar1(-/-) and adar2(-/-) cells, and neither reovirus nor VSV showed enhanced cytotoxicity in adar1(-/-)-infected cells. These results suggest that ADAR1 plays a virus-selective role in the host response to infection.

Endospanins Regulate a Postinternalization Step of the Leptin Receptor Endocytic Pathway

Endospanin-1 is a negative regulator of the cell surface expression of leptin receptor (OB-R), and endospanin-2 is a homologue of unknown function. We investigated the mechanism for endospanin-1 action in regulating OB-R cell surface expression. Here we show that endospanin-1 and -2 are small integral membrane proteins that localize in endosomes and the trans-Golgi network. Antibody uptake experiments showed that both endospanins are transported to the plasma membrane and then internalized into early endosomes but do not recycle back to the trans-Golgi network. Overexpression of endospanin-1 or endospanin-2 led to a decrease of OB-R cell surface expression, whereas shRNA-mediated depletion of each protein increased OB-R cell surface expression. This increased cell surface expression was not observed with OB-Ra mutants defective in endocytosis or with transferrin and EGF receptors. Endospanin-1 or endospanin-2 depletion did not change the internalization rate of OB-Ra but slowed down its lysosomal degradation. Thus, both endospanins are regulators of postinternalization membrane traffic of the endocytic pathway of OB-R.

Abstract 3080: Novel splicing activity for RNA binding protein CUGBP2 in radiation-induced mitotic catastrophe

Abstract RNA binding protein CUGBP2 encodes various functions at the posttranscriptional level including alternative splicing (e.g. tau, troponin T), RNA editing (apolipoprotein B) and mRNA translation (cyclooxygenase-2, Mcl1). CUGBP2 contains two RNA recognition motifs (RRMs) near the N terminus, a divergent domain loaded with alanine and glutamine residues, and a third RRM near the C terminus. Based on deletion analyses, the divergent domain is believed to encode activation modules necessary for splicing activity. Recently, we have demonstrated that there are three promoters that drive the expression of the CUGBP2 gene, transcription from which results in three variant forms of the protein. Translation of the transcripts driven from the upstream promoters adds additional amino acids to the N-terminus of CUGBP2. In mouse intestine, the predominant form of the protein is variant 2. However, after exposure to 6 Gy γ-irradiation (IR), the levels of CUGBP2 mRNA shift to being predominantly variant 1. In colon cancer cells, IR induced the cells to undergo mitotic catastrophe, a poorly understood form of cell death where cells escape the G2/M checkpoint, enter mitosis prematurely and concurrently induce an apoptotic pathway. Interestingly, there was an increase in the CUGBP2 variant that is expressed from the proximal promoter (var 1). Furthermore, downregulation of CUGBP2 through specific siRNA significantly reduced the IR-induced mitotic catastrophe. While var 1 predominantly localizes to the nucleus, the other isoforms primarily reside in the cytoplasm. We next sought to determine the mechanism by which CUGBP2 induces mitotic catastrophe. We have observed that it occurs in part through inhibiting the translation of transcripts encoding anti-apoptotic proteins Bcl-2 and Mcl1. CUGBP2 also affected the splicing of two transcripts that encode microtubule-binding proteins. MARK2 (microtubule affinity regulating kinase 2) is involved in the breakdown of the microtubule network, which is important for cell division and CKAP5 (cytoskeleton associated protein 5) is a protein present in the microtubule-microfilament complex. Exons 15 and 36 are alternatively spliced in MARK2 and CKAP5, respectively. Using RT-PCR analyses, we observed that following CUGBP2 var 1 overexpression, these two exons, 15 and 36 were spliced out from the MARK2 and CKAP5 mRNA, respectively. This was associated with the cells undergoing radiation-induced mitotic catastrophe. In summary, CUGBP2 has been shown to undergo alternative promoter usage and alternative use of the first exon following exposure of cells to IR. With the increase in var 1, we observe inhibition of Bcl2 and Mcl1 translation, and increased alternative splicing of MARK2 and CKAP5. These data, taken together, suggest that CUGBP2 regulates cell viability by two different posttranscriptional mechanisms of alternative splicing and translation. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3080. doi:10.1158/1538-7445.AM2011-3080

Novel transcript variants arise from alternate promoter usage and alternative splicing in 5′ regions of cAMP‐dependent Protein kinase A subunit genes in mouse

Protein kinase A (PKA) is composed of four membered structure with two regulatory (R) and two catalytic (C) subunits. There are four different R subunits (Iα and Iβ, IIα and IIβ) and two different C subunits (Cα and Cβ) in mouse, each encoded by separate gene. Earlier, few alternative spliced variants have been identified with tissue specific function. The objective of this study was to analyze splicing events in 5′ region of R and C subunit genes of PKA in mouse.Analysis was done with the help of combinatorial approach of bioinformatics tools and molecular biology techniques like gene and exon prediction programmes, ORF finders, EST searches, alignment tools, 5′ RACE, RT‐PCR, sub‐cloning, sequencing etc. We were able to sequence two types of cDNA clones from mouse tissues, one type having alternative 5′ untranslated exon (s) and other type having alternative 5′ first coding exon. In former the variants arise either from alternate promoter usage or splicing of 5′ untranslated exons and in later new exon replaces the canonical first coding exon to exhibit different N‐terminal to translated protein. However, alternate promoter usage is mostly linked to regulatory subunit genes.The numbers of new transcript variants sequenced were four in Cα, two in Cβ, three in R Iα and four in R Iβ. Their expression profiles showed variation across the tissues together at different development stages. The research was funded by DBT, India.

P53 Isoforms: An Intracellular Microprocessor?

Normal function of the p53 pathway is ubiquitously lost in cancers either through mutation or inactivating interaction with viral or cellular proteins. However, it is difficult in clinical studies to link p53 mutation status to cancer treatment and clinical outcome, suggesting that the p53 pathway is not fully understood. We have recently reported that the human p53 gene expresses not only 1 but 12 different p53 proteins (isoforms) due to alternative splicing, alternative initiation of translation, and alternative promoter usage. p53 isoform proteins thus contain distinct protein domains. They are expressed in normal human tissues but are abnormally expressed in a wide range of cancer types. We have recently reported that p53 isoform expression is associated with breast cancer prognosis, suggesting that they play a role in carcinogenesis. Indeed, the cellular response to damages can be switched from cell cycle arrest to apoptosis by only manipulating p53 isoform expression. This may provide an explanation to the hitherto inconsistent relationship between p53 mutation, treatment response, and outcome in breast cancer. However, the molecular mechanism is still unknown. Recent reports suggest that it involves modulation of gene expression in a p53-dependent and -independent manner. In this review, we summarize our current knowledge about the biological activities of p53 isoforms and propose a molecular mechanism conciliating our current knowledge on p53 and integrating p63 and p73 isoforms in the p53 pathway.

Paradox of sonic hedgehog (SHH) transcriptional regulation: Alternative transcription initiation overrides the effect of downstream promoter DNA methylation

Recently, DNA methylation has been suggested as a potential mechanism involved in the transcriptional regulation of SHH gene expression in cancer. However, detailed analyses on the underlying transcriptional mechanisms of SHH expression have not been presented so far and were therefore the focus of this study. We found that the genomic region of SHH contains two different transcriptional start sites and four CpG islands spread from the 5' promoter region to the 3' end of the SHH gene. Based on this CpG island topology we analyzed the influence of DNA methylation within the promoter region as well as in exon 2 and exon 3 on SHH mRNA expression in a large set (n = 14) of benign and malignant human cell lines, and further elucidated the functionality of the two identified SHH transcription initiation sites. Methylation-specific PCR (MSP) clearly showed that SHH is expressed independently of DNA methylation within exon 2 and exon 3 of its genomic region, while methylation of the promoter region is able to abrogate SHH expression. Most interesting, we found activation of the upstream SHH promoter in several breast cancer cell lines when the downstream SHH promoter is methylated. These observations lead us to propose a transcriptional model for the SHH gene, in which combined mechanisms of DNA methylation and alternative promoter usage coordinate the transcriptional activity of this important developmental gene.

Complex organization of the 5′-untranslated region of the mouse estrogen receptor α gene: Identification of numerous mRNA transcripts with distinct 5′-ends

The 5′-untranslated region (5′-UTR) of the estrogen receptor α (ERα) gene plays an important role in determining its tissue-specific expression. We examined the 5′-UTRs of the mouse ERα mRNA variants in depth using the Basic Local Alignment Search Tool (BLAST), rapid amplification of 5′-cDNA ends (5′-RACE) and RT-PCR. We demonstrated the presence of multiple variants containing unique 5′-UTRs. We mapped the cDNA sequences onto the mouse genome, and found that both alternative splicing from four different leader exons (A, C, F1, and H) to exon 1, and combinations of 12 internal exons (X1, X2, X3, X4, F2/X5, X6, X7, X8, X9, X10, X11, and B) generate multiple ERα transcripts. Mouse exon B, that has homologies with human exon B and rat exon 0T, was used as an internal exon, not as a leader exon. RT-PCR analysis revealed distinct expression patterns of the variants, suggesting that the alternative promoter usage and alternative splicing are regulated in a tissue-specific manner. Our results indicate that the genomic organization of the mouse ERα gene is complicated as previously shown in the rat ERα gene. In addition, both alternative promoter usage and alternative splicing contribute to the remarkable mRNA diversity of the mouse ERα gene.

Changes in aromatase (CYP19) gene promoter usage in non-small cell lung cancer

In humans, aromatase (CYP19) gene expression is regulated via alternative promoters. Activation of each promoter gives rise to a CYP19 mRNA species with a unique 5′-untranslated region. Inhibition of aromatase has been reported to downregulate lung tumor growth. The genetic basis for CYP19 gene expression and aromatase activity in lung cancer remains poorly understood. We analyzed tissues from 15 patients with non-small cell lung cancer (NSCLC) to evaluate CYP19 promoter usage and promoter-specific aromatase mRNA levels in NSCLC tumor tissues and adjacent non-malignant tissues. CYP19 promoter usage was determined by multiplex RT-PCR and aromatase mRNA levels were measured with real-time RT-PCR. In non-malignant tissues, aromatase mRNA was primarily derived from activation of CYP19 promoter I.4. Although promoter I.4 usage was also dominant in tumor tissues, I.4 activation was significantly lower compared with adjacent non-malignant tissues. Activity of promoters I.3, I.1 and I.7 was significantly higher in tumor tissues compared with non-malignant tissues. In 4 of 15 cases of non-small cell lung cancer, switching from CYP19 promoter I.4 to the alternative promoters II, I.1 or I.7 was observed. In 9 cases, there were significantly higher levels of aromatase mRNA in lung tumor tissues compared with adjacent non-malignant tissues. These findings suggest aberrant activation of alternative CYP19 promoters that may lead to upregulation of local aromatase expression in some cases of NSCLC. Further studies are needed to examine the impact of alternative CYP19 promoter usage on local estrogen levels and lung tumor growth.

Whole Transcriptome Sequencing Reveals Gene Expression and Splicing Differences in Brain Regions Affected by Alzheimer's Disease

Recent studies strongly indicate that aberrations in the control of gene expression might contribute to the initiation and progression of Alzheimer's disease (AD). In particular, alternative splicing has been suggested to play a role in spontaneous cases of AD. Previous transcriptome profiling of AD models and patient samples using microarrays delivered conflicting results. This study provides, for the first time, transcriptomic analysis for distinct regions of the AD brain using RNA-Seq next-generation sequencing technology. Illumina RNA-Seq analysis was used to survey transcriptome profiles from total brain, frontal and temporal lobe of healthy and AD post-mortem tissue. We quantified gene expression levels, splicing isoforms and alternative transcript start sites. Gene Ontology term enrichment analysis revealed an overrepresentation of genes associated with a neuron's cytological structure and synapse function in AD brain samples. Analysis of the temporal lobe with the Cufflinks tool revealed that transcriptional isoforms of the apolipoprotein E gene, APOE-001, -002 and -005, are under the control of different promoters in normal and AD brain tissue. We also observed differing expression levels of APOE-001 and -002 splice variants in the AD temporal lobe. Our results indicate that alternative splicing and promoter usage of the APOE gene in AD brain tissue might reflect the progression of neurodegeneration.

A cytoplasm-specific activity encoded by the Trithorax-like ATX1 gene

Eukaryotes produce multiple products from a single gene locus by alternative splicing, translation or promoter usage as mechanisms expanding the complexity of their proteome. Trithorax proteins, including the Arabidopsis Trithorax-like protein ATX1, are histone modifiers regulating gene activity. Here, we report that a novel member of the Trithorax family has a role unrelated to chromatin. It is encoded from an internal promoter in the ATX1 locus as an isoform containing only the SET domain (soloSET). It is located exclusively in the cytoplasm and its substrate is the elongation factor 1A (EF1A). Loss of SET, but not of the histone modifying ATX1-SET activity, affects cytoskeletal actin bundling illustrating that the two isoforms have distinct functions in Arabidopsis cells.

Analysis of alternative promoter usage in expression of HSD11B1 including the development of a transcript-specific quantitative real-time PCR method

Overexpression of the microsomal enzyme 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1, human gene HSD11B1 or SDR26C1) associates with the metabolic syndrome as well as some inflammatory diseases. HSD11B1 expression is known to be highly tissue-specific and driven by two distinct promoters, an aspect which to date has been studied very little. Here, we sought to assess differential promoter usage in various glucocorticoid target tissues and cell lines. As transcription from the distal promoter P1 or the proximal promoter P2 results in transcripts differing in the 5′-UTR, we first used 5′-UTR-specific primers for their detection in semi-quantitative PCR after reverse transcription. We also established a quantitative Real-Time PCR method using 5′-UTR-specific fluorescent probes in combination with 5′-UTR-specific primers for absolute quantification of the two human transcripts in a duplex approach. The combined results demonstrate that transcription from P2 predominated in most tissues and cell lines assessed, including human liver, human lung, human subcutaneous adipose tissue, and the cell lines A549, Caco-2, C2C12 and 3T3-L1. Transcription from P1 predominated in the human tumor cell lines A431 and HT-29 and contributed significantly to overall HSD11B1 expression in human lung. Moreover, HSD11B1 transcription was upregulated in C2C12 and 3T3-L1 cells in the course of differentiation to myotubes and adipocytes, respectively, mostly reflecting increased transcription from P2, although also transcription from P1 gradually increased in the differentiation process. Interestingly, HSD11B1 transcript levels in all tested human tumor cell lines, namely A431, A549, Caco-2, HCT-116, HepG2, HT-29 and PANC-1, were either close to detection limit or undetectable. In conclusion, the results provide the first evidence for tissue- and differentiation state-specific promoter usage in expression of human HSD11B1. Finally, HSD11B1 appears to be frequently downregulated in human tumor cell lines.

Feather follicles express two classes of pro-opiomelanocortin (POMC) mRNA using alternative promoters in chickens

Feather coloration in chickens mainly depends on melanin produced by melanocytes located in the feather follicles. The melanocortin 1 receptor (MC1R) on follicular melanocytes regulates melanin synthesis; however, the source of the melanocortins that interact with the receptors remains unclear. In this study, we examine the potential expression of melanocortins and characterize the mRNAs for the precursor pro-opiomelanocortin (POMC) in chicken feather follicles. Reverse transcription-polymerase chain reaction (RT-PCR) revealed the expression of mRNAs for POMC, prohormone convertase 1 (PC1) and PC2, and western blotting detected adrenocorticotropic hormone (ACTH)-related products of POMC processing in feather follicles, suggesting that melanocortins are produced locally in the tissues of chickens. A combination of 5′RACE (rapid amplification of cDNA 5′ end), 3′RACE and RT-PCR analyzes identified two classes of POMC mRNA, class a and class b, which encode the same full-length POMC protein but have different non-coding leader exons. Class a mRNAs were expressed specifically in feather follicles, whereas class b mRNAs were expressed in the pituitary, hypothalamus, and various peripheral tissues that we examined. Within the feather follicles, the class a mRNAs were distributed in epidermal layers from middle to distal locations, whereas the class b mRNAs were mainly expressed in pulp at proximal locations. Our findings suggest that feather pigmentation is regulated by locally produced melanocortins, and indicate that the melanocortins encoded by the different classes of POMC mRNAs may play different intra-follicular roles in chickens. This is the first report that demonstrates alternative promoter usage generating different full-length POMC mRNAs in vertebrates.

First International p53 Isoforms Meeting: ‘p53 isoforms through evolution: from identification to biological function’

After three decades of research, it has been shown that the tumor suppressor TP53 gene expresses diverse p53 protein forms: the mutant p53 proteins (ex: p53R175H); the polymorphic p53 proteins (ex: p53R72P); the post-translationally modified p53 proteins (ex: p53 phosphorylated on Ser15); and finally the p53 protein isoforms. The p53 isoforms, physiologically expressed in normal tissues, are generated by the usage of alternative promoters, splicing sites and translational initiation sites, thus containing different N- and C-terminal domains compared with the canonical p53 protein. p53 isoforms are not newcomers in the field: alternative splicing of mouse and human p53 was first described in the mid-eighties. However, the field took off only after the discovery in 1997–98 of two additional members of the TP53 gene family, TP63 and TP73. Both genes express several p63 or p73 protein isoforms with distinct N- and/or C-termini termini because of presence of internal promoters and alternative splicing sites.