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bionlp-st-ge-2016-spacy-parsed

2_test

{"project":"2_test","denotations":[{"id":"23472114-1354603-87899177","span":{"begin":659,"end":661},"obj":"1354603"},{"id":"23472114-8916932-87899178","span":{"begin":759,"end":761},"obj":"8916932"},{"id":"23472114-8262378-87899179","span":{"begin":776,"end":778},"obj":"8262378"},{"id":"T40363","span":{"begin":659,"end":661},"obj":"1354603"},{"id":"T4480","span":{"begin":759,"end":761},"obj":"8916932"},{"id":"T43659","span":{"begin":776,"end":778},"obj":"8262378"}],"text":"The SerpinB2 Proximal Promoter Confers LPS Responsiveness\nTo investigate cis-acting regulatory elements responsive to LPS in the 5′ flanking region of the murine SerpinB2 gene, nucleotides −4480 to +92 and a series of generated deletion mutants of the 5′ flanking region were cloned upstream of a promoter-less firefly luciferase reporter gene (pGL3 Basic) (Fig. 2A). The reporter constructs were then transiently transfected into sub-confluent RAW264.7 macrophages and assayed for luciferase activity in the presence and absence of LPS or PMA, for comparison. PMA-induced SerpinB2 gene regulation has been extensively studied in human macrophage cell lines [45]–[47], and has been shown to occur through several proximal and distal AP-1 responsive elements [30]; [37]; [47]–[51]. As shown in Fig. 2B, the SerpinB2 5′ flanking region from −4480 to +92 directs both PMA- and LPS-inducible transcription, approximately 2-fold and 7-fold, respectively. Deletion of the murine SerpinB2 promoter from −1686 to −1341 increased LPS-inducibility to approximately 16-fold, indicating the presence of a silencer element in this region. Further deletion beyond −539 abolished the LPS-response of the promoter, indicating the presence of an essential LPS response element in the region between −539 and −189; however, the response of the murine SerpinB2 promoter to PMA is less affected by this deletion. While deletion of the SerpinB2 promoter from −189 to −87 eliminated the LPS response and marginally reduced the PMA response, the −87 murine SerpinB2 promoter construct was still partially responsive to PMA, indicating that cis-acting elements mediating the response of the murine SerpinB2 promoter to PMA also lie downstream of nucleotide −87.\n10.1371/journal.pone.0057855.g002 Figure 2 Deletion reporter gene analysis of LPS and PMA-responsive regions in the murine SerpinB2 promoter.\n(A) Schematic representation of the murine SerpinB2 promoter and 5′ deletion luciferase reporter constructs. The murine 5′ flanking region from −4480 to +92 was inserted upstream of the luciferase reporter gene and 5′ deletions were generated using restriction enzyme sites or with specific oligonucleotide PCR primers. Construct names indicate the most 5′ nucleotide of murine SerpinB2 5′ flanking sequence. (B) RAW 264.7 macrophages were transiently transfected with the indicated murine SerpinB2 promoter-luciferase reporter constructs and control plasmids. Cells were either left untreated or treated with 100 ng/ml LPS or 40 ng/ml PMA for 16 hrs. Shown is the relative luciferase reporter gene activity following treatment. The results represent the mean and SEM of four independent experiments. (C) DNA sequence conservation between the human and murine SerpinB2 5′ flanking regions. Schematic representation of the human and murine SerpinB2 5′ flanking regions with regions of nucleotide sequence identity indicated by the same colored boxes. Homologous regions are interrupted by repetitive sequence elements in both 5′ flanking regions. Alu = Alu repeat, ID4 = ID4 short interspersed nuclear repeat (SINE), L1 = L1 long interspersed nuclear element (LINE), L2 = L2 LINE, MIR = MIR SINE, MLT1L = MLT1L long terminal repeat (LTR), (TATG)n = TATG tetranucleotide repeat, tis = transcription initiation site."}

pmc-enju-pas

bionlp-st-ge-2016-coref

{"project":"bionlp-st-ge-2016-coref","denotations":[{"id":"T9525","span":{"begin":1134,"end":1142},"obj":"Antecedent"},{"id":"T9524","span":{"begin":1378,"end":1391},"obj":"Anaphor"}],"relations":[{"id":"R6961","pred":"boundBy","subj":"T9524","obj":"T9525"}],"namespaces":[{"prefix":"_base","uri":"http://bionlp.dbcls.jp/ontology/ge.owl#"}],"text":"The SerpinB2 Proximal Promoter Confers LPS Responsiveness\nTo investigate cis-acting regulatory elements responsive to LPS in the 5′ flanking region of the murine SerpinB2 gene, nucleotides −4480 to +92 and a series of generated deletion mutants of the 5′ flanking region were cloned upstream of a promoter-less firefly luciferase reporter gene (pGL3 Basic) (Fig. 2A). The reporter constructs were then transiently transfected into sub-confluent RAW264.7 macrophages and assayed for luciferase activity in the presence and absence of LPS or PMA, for comparison. PMA-induced SerpinB2 gene regulation has been extensively studied in human macrophage cell lines [45]–[47], and has been shown to occur through several proximal and distal AP-1 responsive elements [30]; [37]; [47]–[51]. As shown in Fig. 2B, the SerpinB2 5′ flanking region from −4480 to +92 directs both PMA- and LPS-inducible transcription, approximately 2-fold and 7-fold, respectively. Deletion of the murine SerpinB2 promoter from −1686 to −1341 increased LPS-inducibility to approximately 16-fold, indicating the presence of a silencer element in this region. Further deletion beyond −539 abolished the LPS-response of the promoter, indicating the presence of an essential LPS response element in the region between −539 and −189; however, the response of the murine SerpinB2 promoter to PMA is less affected by this deletion. While deletion of the SerpinB2 promoter from −189 to −87 eliminated the LPS response and marginally reduced the PMA response, the −87 murine SerpinB2 promoter construct was still partially responsive to PMA, indicating that cis-acting elements mediating the response of the murine SerpinB2 promoter to PMA also lie downstream of nucleotide −87.\n10.1371/journal.pone.0057855.g002 Figure 2 Deletion reporter gene analysis of LPS and PMA-responsive regions in the murine SerpinB2 promoter.\n(A) Schematic representation of the murine SerpinB2 promoter and 5′ deletion luciferase reporter constructs. The murine 5′ flanking region from −4480 to +92 was inserted upstream of the luciferase reporter gene and 5′ deletions were generated using restriction enzyme sites or with specific oligonucleotide PCR primers. Construct names indicate the most 5′ nucleotide of murine SerpinB2 5′ flanking sequence. (B) RAW 264.7 macrophages were transiently transfected with the indicated murine SerpinB2 promoter-luciferase reporter constructs and control plasmids. Cells were either left untreated or treated with 100 ng/ml LPS or 40 ng/ml PMA for 16 hrs. Shown is the relative luciferase reporter gene activity following treatment. The results represent the mean and SEM of four independent experiments. (C) DNA sequence conservation between the human and murine SerpinB2 5′ flanking regions. Schematic representation of the human and murine SerpinB2 5′ flanking regions with regions of nucleotide sequence identity indicated by the same colored boxes. Homologous regions are interrupted by repetitive sequence elements in both 5′ flanking regions. Alu = Alu repeat, ID4 = ID4 short interspersed nuclear repeat (SINE), L1 = L1 long interspersed nuclear element (LINE), L2 = L2 LINE, MIR = MIR SINE, MLT1L = MLT1L long terminal repeat (LTR), (TATG)n = TATG tetranucleotide repeat, tis = transcription initiation site."}

bionlp-st-ge-2016-test-proteins

{"project":"bionlp-st-ge-2016-test-proteins","denotations":[{"id":"T22718","span":{"begin":2820,"end":2828},"obj":"Protein"},{"id":"T22717","span":{"begin":2741,"end":2749},"obj":"Protein"},{"id":"T22716","span":{"begin":2555,"end":2565},"obj":"Protein"},{"id":"T22715","span":{"begin":2371,"end":2408},"obj":"Protein"},{"id":"T22714","span":{"begin":2259,"end":2267},"obj":"Protein"},{"id":"T22713","span":{"begin":2067,"end":2077},"obj":"Protein"},{"id":"T22712","span":{"begin":1924,"end":1977},"obj":"Protein"},{"id":"T22711","span":{"begin":1862,"end":1870},"obj":"Protein"},{"id":"T9536","span":{"begin":1674,"end":1682},"obj":"Protein"},{"id":"T9535","span":{"begin":1534,"end":1542},"obj":"Protein"},{"id":"T9534","span":{"begin":1415,"end":1423},"obj":"Protein"},{"id":"T9533","span":{"begin":1333,"end":1341},"obj":"Protein"},{"id":"T9532","span":{"begin":973,"end":981},"obj":"Protein"},{"id":"T9531","span":{"begin":806,"end":814},"obj":"Protein"},{"id":"T9530","span":{"begin":573,"end":581},"obj":"Protein"},{"id":"T9529","span":{"begin":482,"end":492},"obj":"Protein"},{"id":"T9528","span":{"begin":319,"end":329},"obj":"Protein"},{"id":"T9527","span":{"begin":162,"end":170},"obj":"Protein"},{"id":"T9526","span":{"begin":4,"end":12},"obj":"Protein"}],"namespaces":[{"prefix":"_base","uri":"http://bionlp.dbcls.jp/ontology/ge.owl#"}],"text":"The SerpinB2 Proximal Promoter Confers LPS Responsiveness\nTo investigate cis-acting regulatory elements responsive to LPS in the 5′ flanking region of the murine SerpinB2 gene, nucleotides −4480 to +92 and a series of generated deletion mutants of the 5′ flanking region were cloned upstream of a promoter-less firefly luciferase reporter gene (pGL3 Basic) (Fig. 2A). The reporter constructs were then transiently transfected into sub-confluent RAW264.7 macrophages and assayed for luciferase activity in the presence and absence of LPS or PMA, for comparison. PMA-induced SerpinB2 gene regulation has been extensively studied in human macrophage cell lines [45]–[47], and has been shown to occur through several proximal and distal AP-1 responsive elements [30]; [37]; [47]–[51]. As shown in Fig. 2B, the SerpinB2 5′ flanking region from −4480 to +92 directs both PMA- and LPS-inducible transcription, approximately 2-fold and 7-fold, respectively. Deletion of the murine SerpinB2 promoter from −1686 to −1341 increased LPS-inducibility to approximately 16-fold, indicating the presence of a silencer element in this region. Further deletion beyond −539 abolished the LPS-response of the promoter, indicating the presence of an essential LPS response element in the region between −539 and −189; however, the response of the murine SerpinB2 promoter to PMA is less affected by this deletion. While deletion of the SerpinB2 promoter from −189 to −87 eliminated the LPS response and marginally reduced the PMA response, the −87 murine SerpinB2 promoter construct was still partially responsive to PMA, indicating that cis-acting elements mediating the response of the murine SerpinB2 promoter to PMA also lie downstream of nucleotide −87.\n10.1371/journal.pone.0057855.g002 Figure 2 Deletion reporter gene analysis of LPS and PMA-responsive regions in the murine SerpinB2 promoter.\n(A) Schematic representation of the murine SerpinB2 promoter and 5′ deletion luciferase reporter constructs. The murine 5′ flanking region from −4480 to +92 was inserted upstream of the luciferase reporter gene and 5′ deletions were generated using restriction enzyme sites or with specific oligonucleotide PCR primers. Construct names indicate the most 5′ nucleotide of murine SerpinB2 5′ flanking sequence. (B) RAW 264.7 macrophages were transiently transfected with the indicated murine SerpinB2 promoter-luciferase reporter constructs and control plasmids. Cells were either left untreated or treated with 100 ng/ml LPS or 40 ng/ml PMA for 16 hrs. Shown is the relative luciferase reporter gene activity following treatment. The results represent the mean and SEM of four independent experiments. (C) DNA sequence conservation between the human and murine SerpinB2 5′ flanking regions. Schematic representation of the human and murine SerpinB2 5′ flanking regions with regions of nucleotide sequence identity indicated by the same colored boxes. Homologous regions are interrupted by repetitive sequence elements in both 5′ flanking regions. Alu = Alu repeat, ID4 = ID4 short interspersed nuclear repeat (SINE), L1 = L1 long interspersed nuclear element (LINE), L2 = L2 LINE, MIR = MIR SINE, MLT1L = MLT1L long terminal repeat (LTR), (TATG)n = TATG tetranucleotide repeat, tis = transcription initiation site."}

bionlp-st-ge-2016-uniprot

UBERON-AE

{"project":"UBERON-AE","denotations":[{"id":"T9468","span":{"begin":607,"end":618},"obj":"http://purl.obolibrary.org/obo/UBERON_2000106"}],"text":"The SerpinB2 Proximal Promoter Confers LPS Responsiveness\nTo investigate cis-acting regulatory elements responsive to LPS in the 5′ flanking region of the murine SerpinB2 gene, nucleotides −4480 to +92 and a series of generated deletion mutants of the 5′ flanking region were cloned upstream of a promoter-less firefly luciferase reporter gene (pGL3 Basic) (Fig. 2A). The reporter constructs were then transiently transfected into sub-confluent RAW264.7 macrophages and assayed for luciferase activity in the presence and absence of LPS or PMA, for comparison. PMA-induced SerpinB2 gene regulation has been extensively studied in human macrophage cell lines [45]–[47], and has been shown to occur through several proximal and distal AP-1 responsive elements [30]; [37]; [47]–[51]. As shown in Fig. 2B, the SerpinB2 5′ flanking region from −4480 to +92 directs both PMA- and LPS-inducible transcription, approximately 2-fold and 7-fold, respectively. Deletion of the murine SerpinB2 promoter from −1686 to −1341 increased LPS-inducibility to approximately 16-fold, indicating the presence of a silencer element in this region. Further deletion beyond −539 abolished the LPS-response of the promoter, indicating the presence of an essential LPS response element in the region between −539 and −189; however, the response of the murine SerpinB2 promoter to PMA is less affected by this deletion. While deletion of the SerpinB2 promoter from −189 to −87 eliminated the LPS response and marginally reduced the PMA response, the −87 murine SerpinB2 promoter construct was still partially responsive to PMA, indicating that cis-acting elements mediating the response of the murine SerpinB2 promoter to PMA also lie downstream of nucleotide −87.\n10.1371/journal.pone.0057855.g002 Figure 2 Deletion reporter gene analysis of LPS and PMA-responsive regions in the murine SerpinB2 promoter.\n(A) Schematic representation of the murine SerpinB2 promoter and 5′ deletion luciferase reporter constructs. The murine 5′ flanking region from −4480 to +92 was inserted upstream of the luciferase reporter gene and 5′ deletions were generated using restriction enzyme sites or with specific oligonucleotide PCR primers. Construct names indicate the most 5′ nucleotide of murine SerpinB2 5′ flanking sequence. (B) RAW 264.7 macrophages were transiently transfected with the indicated murine SerpinB2 promoter-luciferase reporter constructs and control plasmids. Cells were either left untreated or treated with 100 ng/ml LPS or 40 ng/ml PMA for 16 hrs. Shown is the relative luciferase reporter gene activity following treatment. The results represent the mean and SEM of four independent experiments. (C) DNA sequence conservation between the human and murine SerpinB2 5′ flanking regions. Schematic representation of the human and murine SerpinB2 5′ flanking regions with regions of nucleotide sequence identity indicated by the same colored boxes. Homologous regions are interrupted by repetitive sequence elements in both 5′ flanking regions. Alu = Alu repeat, ID4 = ID4 short interspersed nuclear repeat (SINE), L1 = L1 long interspersed nuclear element (LINE), L2 = L2 LINE, MIR = MIR SINE, MLT1L = MLT1L long terminal repeat (LTR), (TATG)n = TATG tetranucleotide repeat, tis = transcription initiation site."}

GO-BP

{"project":"GO-BP","denotations":[{"id":"T22719","span":{"begin":3267,"end":3280},"obj":"http://purl.obolibrary.org/obo/GO_0006351"},{"id":"T9547","span":{"begin":1505,"end":1517},"obj":"http://purl.obolibrary.org/obo/GO_1904627"},{"id":"T9546","span":{"begin":1465,"end":1477},"obj":"http://purl.obolibrary.org/obo/GO_0032496"},{"id":"T9545","span":{"begin":1239,"end":1251},"obj":"http://purl.obolibrary.org/obo/GO_0032496"},{"id":"T9544","span":{"begin":1169,"end":1181},"obj":"http://purl.obolibrary.org/obo/GO_0032496"},{"id":"T9543","span":{"begin":888,"end":901},"obj":"http://purl.obolibrary.org/obo/GO_0006351"},{"id":"T9542","span":{"begin":587,"end":597},"obj":"http://purl.obolibrary.org/obo/GO_0065007"},{"id":"T9541","span":{"begin":482,"end":501},"obj":"http://purl.obolibrary.org/obo/GO_0050397"},{"id":"T9540","span":{"begin":482,"end":501},"obj":"http://purl.obolibrary.org/obo/GO_0050248"},{"id":"T9539","span":{"begin":482,"end":501},"obj":"http://purl.obolibrary.org/obo/GO_0047712"},{"id":"T9538","span":{"begin":482,"end":501},"obj":"http://purl.obolibrary.org/obo/GO_0047077"},{"id":"T9537","span":{"begin":482,"end":501},"obj":"http://purl.obolibrary.org/obo/GO_0045289"}],"text":"The SerpinB2 Proximal Promoter Confers LPS Responsiveness\nTo investigate cis-acting regulatory elements responsive to LPS in the 5′ flanking region of the murine SerpinB2 gene, nucleotides −4480 to +92 and a series of generated deletion mutants of the 5′ flanking region were cloned upstream of a promoter-less firefly luciferase reporter gene (pGL3 Basic) (Fig. 2A). The reporter constructs were then transiently transfected into sub-confluent RAW264.7 macrophages and assayed for luciferase activity in the presence and absence of LPS or PMA, for comparison. PMA-induced SerpinB2 gene regulation has been extensively studied in human macrophage cell lines [45]–[47], and has been shown to occur through several proximal and distal AP-1 responsive elements [30]; [37]; [47]–[51]. As shown in Fig. 2B, the SerpinB2 5′ flanking region from −4480 to +92 directs both PMA- and LPS-inducible transcription, approximately 2-fold and 7-fold, respectively. Deletion of the murine SerpinB2 promoter from −1686 to −1341 increased LPS-inducibility to approximately 16-fold, indicating the presence of a silencer element in this region. Further deletion beyond −539 abolished the LPS-response of the promoter, indicating the presence of an essential LPS response element in the region between −539 and −189; however, the response of the murine SerpinB2 promoter to PMA is less affected by this deletion. While deletion of the SerpinB2 promoter from −189 to −87 eliminated the LPS response and marginally reduced the PMA response, the −87 murine SerpinB2 promoter construct was still partially responsive to PMA, indicating that cis-acting elements mediating the response of the murine SerpinB2 promoter to PMA also lie downstream of nucleotide −87.\n10.1371/journal.pone.0057855.g002 Figure 2 Deletion reporter gene analysis of LPS and PMA-responsive regions in the murine SerpinB2 promoter.\n(A) Schematic representation of the murine SerpinB2 promoter and 5′ deletion luciferase reporter constructs. The murine 5′ flanking region from −4480 to +92 was inserted upstream of the luciferase reporter gene and 5′ deletions were generated using restriction enzyme sites or with specific oligonucleotide PCR primers. Construct names indicate the most 5′ nucleotide of murine SerpinB2 5′ flanking sequence. (B) RAW 264.7 macrophages were transiently transfected with the indicated murine SerpinB2 promoter-luciferase reporter constructs and control plasmids. Cells were either left untreated or treated with 100 ng/ml LPS or 40 ng/ml PMA for 16 hrs. Shown is the relative luciferase reporter gene activity following treatment. The results represent the mean and SEM of four independent experiments. (C) DNA sequence conservation between the human and murine SerpinB2 5′ flanking regions. Schematic representation of the human and murine SerpinB2 5′ flanking regions with regions of nucleotide sequence identity indicated by the same colored boxes. Homologous regions are interrupted by repetitive sequence elements in both 5′ flanking regions. Alu = Alu repeat, ID4 = ID4 short interspersed nuclear repeat (SINE), L1 = L1 long interspersed nuclear element (LINE), L2 = L2 LINE, MIR = MIR SINE, MLT1L = MLT1L long terminal repeat (LTR), (TATG)n = TATG tetranucleotide repeat, tis = transcription initiation site."}

GO-MF

{"project":"GO-MF","denotations":[{"id":"T9552","span":{"begin":482,"end":501},"obj":"http://purl.obolibrary.org/obo/GO_0050397"},{"id":"T9551","span":{"begin":482,"end":501},"obj":"http://purl.obolibrary.org/obo/GO_0050248"},{"id":"T9550","span":{"begin":482,"end":501},"obj":"http://purl.obolibrary.org/obo/GO_0047712"},{"id":"T9549","span":{"begin":482,"end":501},"obj":"http://purl.obolibrary.org/obo/GO_0047077"},{"id":"T9548","span":{"begin":482,"end":501},"obj":"http://purl.obolibrary.org/obo/GO_0045289"}],"text":"The SerpinB2 Proximal Promoter Confers LPS Responsiveness\nTo investigate cis-acting regulatory elements responsive to LPS in the 5′ flanking region of the murine SerpinB2 gene, nucleotides −4480 to +92 and a series of generated deletion mutants of the 5′ flanking region were cloned upstream of a promoter-less firefly luciferase reporter gene (pGL3 Basic) (Fig. 2A). The reporter constructs were then transiently transfected into sub-confluent RAW264.7 macrophages and assayed for luciferase activity in the presence and absence of LPS or PMA, for comparison. PMA-induced SerpinB2 gene regulation has been extensively studied in human macrophage cell lines [45]–[47], and has been shown to occur through several proximal and distal AP-1 responsive elements [30]; [37]; [47]–[51]. As shown in Fig. 2B, the SerpinB2 5′ flanking region from −4480 to +92 directs both PMA- and LPS-inducible transcription, approximately 2-fold and 7-fold, respectively. Deletion of the murine SerpinB2 promoter from −1686 to −1341 increased LPS-inducibility to approximately 16-fold, indicating the presence of a silencer element in this region. Further deletion beyond −539 abolished the LPS-response of the promoter, indicating the presence of an essential LPS response element in the region between −539 and −189; however, the response of the murine SerpinB2 promoter to PMA is less affected by this deletion. While deletion of the SerpinB2 promoter from −189 to −87 eliminated the LPS response and marginally reduced the PMA response, the −87 murine SerpinB2 promoter construct was still partially responsive to PMA, indicating that cis-acting elements mediating the response of the murine SerpinB2 promoter to PMA also lie downstream of nucleotide −87.\n10.1371/journal.pone.0057855.g002 Figure 2 Deletion reporter gene analysis of LPS and PMA-responsive regions in the murine SerpinB2 promoter.\n(A) Schematic representation of the murine SerpinB2 promoter and 5′ deletion luciferase reporter constructs. The murine 5′ flanking region from −4480 to +92 was inserted upstream of the luciferase reporter gene and 5′ deletions were generated using restriction enzyme sites or with specific oligonucleotide PCR primers. Construct names indicate the most 5′ nucleotide of murine SerpinB2 5′ flanking sequence. (B) RAW 264.7 macrophages were transiently transfected with the indicated murine SerpinB2 promoter-luciferase reporter constructs and control plasmids. Cells were either left untreated or treated with 100 ng/ml LPS or 40 ng/ml PMA for 16 hrs. Shown is the relative luciferase reporter gene activity following treatment. The results represent the mean and SEM of four independent experiments. (C) DNA sequence conservation between the human and murine SerpinB2 5′ flanking regions. Schematic representation of the human and murine SerpinB2 5′ flanking regions with regions of nucleotide sequence identity indicated by the same colored boxes. Homologous regions are interrupted by repetitive sequence elements in both 5′ flanking regions. Alu = Alu repeat, ID4 = ID4 short interspersed nuclear repeat (SINE), L1 = L1 long interspersed nuclear element (LINE), L2 = L2 LINE, MIR = MIR SINE, MLT1L = MLT1L long terminal repeat (LTR), (TATG)n = TATG tetranucleotide repeat, tis = transcription initiation site."}

GO-CC

{"project":"GO-CC","denotations":[{"id":"T9553","span":{"begin":647,"end":651},"obj":"http://purl.obolibrary.org/obo/GO_0005623"}],"text":"The SerpinB2 Proximal Promoter Confers LPS Responsiveness\nTo investigate cis-acting regulatory elements responsive to LPS in the 5′ flanking region of the murine SerpinB2 gene, nucleotides −4480 to +92 and a series of generated deletion mutants of the 5′ flanking region were cloned upstream of a promoter-less firefly luciferase reporter gene (pGL3 Basic) (Fig. 2A). The reporter constructs were then transiently transfected into sub-confluent RAW264.7 macrophages and assayed for luciferase activity in the presence and absence of LPS or PMA, for comparison. PMA-induced SerpinB2 gene regulation has been extensively studied in human macrophage cell lines [45]–[47], and has been shown to occur through several proximal and distal AP-1 responsive elements [30]; [37]; [47]–[51]. As shown in Fig. 2B, the SerpinB2 5′ flanking region from −4480 to +92 directs both PMA- and LPS-inducible transcription, approximately 2-fold and 7-fold, respectively. Deletion of the murine SerpinB2 promoter from −1686 to −1341 increased LPS-inducibility to approximately 16-fold, indicating the presence of a silencer element in this region. Further deletion beyond −539 abolished the LPS-response of the promoter, indicating the presence of an essential LPS response element in the region between −539 and −189; however, the response of the murine SerpinB2 promoter to PMA is less affected by this deletion. While deletion of the SerpinB2 promoter from −189 to −87 eliminated the LPS response and marginally reduced the PMA response, the −87 murine SerpinB2 promoter construct was still partially responsive to PMA, indicating that cis-acting elements mediating the response of the murine SerpinB2 promoter to PMA also lie downstream of nucleotide −87.\n10.1371/journal.pone.0057855.g002 Figure 2 Deletion reporter gene analysis of LPS and PMA-responsive regions in the murine SerpinB2 promoter.\n(A) Schematic representation of the murine SerpinB2 promoter and 5′ deletion luciferase reporter constructs. The murine 5′ flanking region from −4480 to +92 was inserted upstream of the luciferase reporter gene and 5′ deletions were generated using restriction enzyme sites or with specific oligonucleotide PCR primers. Construct names indicate the most 5′ nucleotide of murine SerpinB2 5′ flanking sequence. (B) RAW 264.7 macrophages were transiently transfected with the indicated murine SerpinB2 promoter-luciferase reporter constructs and control plasmids. Cells were either left untreated or treated with 100 ng/ml LPS or 40 ng/ml PMA for 16 hrs. Shown is the relative luciferase reporter gene activity following treatment. The results represent the mean and SEM of four independent experiments. (C) DNA sequence conservation between the human and murine SerpinB2 5′ flanking regions. Schematic representation of the human and murine SerpinB2 5′ flanking regions with regions of nucleotide sequence identity indicated by the same colored boxes. Homologous regions are interrupted by repetitive sequence elements in both 5′ flanking regions. Alu = Alu repeat, ID4 = ID4 short interspersed nuclear repeat (SINE), L1 = L1 long interspersed nuclear element (LINE), L2 = L2 LINE, MIR = MIR SINE, MLT1L = MLT1L long terminal repeat (LTR), (TATG)n = TATG tetranucleotide repeat, tis = transcription initiation site."}

sentences

simple1

{"project":"simple1","denotations":[{"id":"T22727","span":{"begin":2820,"end":2828},"obj":"Protein"},{"id":"T22726","span":{"begin":2741,"end":2749},"obj":"Protein"},{"id":"T22725","span":{"begin":2555,"end":2565},"obj":"Protein"},{"id":"T22724","span":{"begin":2371,"end":2408},"obj":"Protein"},{"id":"T22723","span":{"begin":2259,"end":2267},"obj":"Protein"},{"id":"T22722","span":{"begin":2067,"end":2077},"obj":"Protein"},{"id":"T22721","span":{"begin":1924,"end":1977},"obj":"Protein"},{"id":"T22720","span":{"begin":1862,"end":1870},"obj":"Protein"},{"id":"T9564","span":{"begin":1674,"end":1682},"obj":"Protein"},{"id":"T9563","span":{"begin":1534,"end":1542},"obj":"Protein"},{"id":"T9562","span":{"begin":1415,"end":1423},"obj":"Protein"},{"id":"T9561","span":{"begin":1333,"end":1341},"obj":"Protein"},{"id":"T9560","span":{"begin":973,"end":981},"obj":"Protein"},{"id":"T9559","span":{"begin":806,"end":814},"obj":"Protein"},{"id":"T9558","span":{"begin":573,"end":581},"obj":"Protein"},{"id":"T9557","span":{"begin":482,"end":492},"obj":"Protein"},{"id":"T9556","span":{"begin":319,"end":329},"obj":"Protein"},{"id":"T9555","span":{"begin":162,"end":170},"obj":"Protein"},{"id":"T9554","span":{"begin":4,"end":12},"obj":"Protein"}],"text":"The SerpinB2 Proximal Promoter Confers LPS Responsiveness\nTo investigate cis-acting regulatory elements responsive to LPS in the 5′ flanking region of the murine SerpinB2 gene, nucleotides −4480 to +92 and a series of generated deletion mutants of the 5′ flanking region were cloned upstream of a promoter-less firefly luciferase reporter gene (pGL3 Basic) (Fig. 2A). The reporter constructs were then transiently transfected into sub-confluent RAW264.7 macrophages and assayed for luciferase activity in the presence and absence of LPS or PMA, for comparison. PMA-induced SerpinB2 gene regulation has been extensively studied in human macrophage cell lines [45]–[47], and has been shown to occur through several proximal and distal AP-1 responsive elements [30]; [37]; [47]–[51]. As shown in Fig. 2B, the SerpinB2 5′ flanking region from −4480 to +92 directs both PMA- and LPS-inducible transcription, approximately 2-fold and 7-fold, respectively. Deletion of the murine SerpinB2 promoter from −1686 to −1341 increased LPS-inducibility to approximately 16-fold, indicating the presence of a silencer element in this region. Further deletion beyond −539 abolished the LPS-response of the promoter, indicating the presence of an essential LPS response element in the region between −539 and −189; however, the response of the murine SerpinB2 promoter to PMA is less affected by this deletion. While deletion of the SerpinB2 promoter from −189 to −87 eliminated the LPS response and marginally reduced the PMA response, the −87 murine SerpinB2 promoter construct was still partially responsive to PMA, indicating that cis-acting elements mediating the response of the murine SerpinB2 promoter to PMA also lie downstream of nucleotide −87.\n10.1371/journal.pone.0057855.g002 Figure 2 Deletion reporter gene analysis of LPS and PMA-responsive regions in the murine SerpinB2 promoter.\n(A) Schematic representation of the murine SerpinB2 promoter and 5′ deletion luciferase reporter constructs. The murine 5′ flanking region from −4480 to +92 was inserted upstream of the luciferase reporter gene and 5′ deletions were generated using restriction enzyme sites or with specific oligonucleotide PCR primers. Construct names indicate the most 5′ nucleotide of murine SerpinB2 5′ flanking sequence. (B) RAW 264.7 macrophages were transiently transfected with the indicated murine SerpinB2 promoter-luciferase reporter constructs and control plasmids. Cells were either left untreated or treated with 100 ng/ml LPS or 40 ng/ml PMA for 16 hrs. Shown is the relative luciferase reporter gene activity following treatment. The results represent the mean and SEM of four independent experiments. (C) DNA sequence conservation between the human and murine SerpinB2 5′ flanking regions. Schematic representation of the human and murine SerpinB2 5′ flanking regions with regions of nucleotide sequence identity indicated by the same colored boxes. Homologous regions are interrupted by repetitive sequence elements in both 5′ flanking regions. Alu = Alu repeat, ID4 = ID4 short interspersed nuclear repeat (SINE), L1 = L1 long interspersed nuclear element (LINE), L2 = L2 LINE, MIR = MIR SINE, MLT1L = MLT1L long terminal repeat (LTR), (TATG)n = TATG tetranucleotide repeat, tis = transcription initiation site."}

BioNLP16_DUT

BioNLP16_Messiy

DLUT931

bionlp-st-ge-2016-test-ihmc

bionlp-st-ge-2016-test-tees

testone

{"project":"testone","denotations":[{"id":"T22673","span":{"begin":2820,"end":2828},"obj":"Protein"},{"id":"T22672","span":{"begin":2741,"end":2749},"obj":"Protein"},{"id":"T22671","span":{"begin":2555,"end":2565},"obj":"Protein"},{"id":"T22670","span":{"begin":2371,"end":2408},"obj":"Protein"},{"id":"T22669","span":{"begin":2259,"end":2267},"obj":"Protein"},{"id":"T22668","span":{"begin":2067,"end":2077},"obj":"Protein"},{"id":"T22667","span":{"begin":1924,"end":1977},"obj":"Protein"},{"id":"T22666","span":{"begin":1862,"end":1870},"obj":"Protein"},{"id":"T9444","span":{"begin":1011,"end":1020},"obj":"Positive_regulation"},{"id":"T9443","span":{"begin":950,"end":958},"obj":"Negative_regulation"},{"id":"T9442","span":{"begin":1674,"end":1682},"obj":"Protein"},{"id":"T9441","span":{"begin":1534,"end":1542},"obj":"Protein"},{"id":"T9440","span":{"begin":1415,"end":1423},"obj":"Protein"},{"id":"T9439","span":{"begin":1333,"end":1341},"obj":"Protein"},{"id":"T9438","span":{"begin":973,"end":981},"obj":"Protein"},{"id":"T9437","span":{"begin":806,"end":814},"obj":"Protein"},{"id":"T9436","span":{"begin":573,"end":581},"obj":"Protein"},{"id":"T9435","span":{"begin":482,"end":492},"obj":"Protein"},{"id":"T9434","span":{"begin":319,"end":329},"obj":"Protein"},{"id":"T9433","span":{"begin":162,"end":170},"obj":"Protein"},{"id":"T9432","span":{"begin":4,"end":12},"obj":"Protein"}],"text":"The SerpinB2 Proximal Promoter Confers LPS Responsiveness\nTo investigate cis-acting regulatory elements responsive to LPS in the 5′ flanking region of the murine SerpinB2 gene, nucleotides −4480 to +92 and a series of generated deletion mutants of the 5′ flanking region were cloned upstream of a promoter-less firefly luciferase reporter gene (pGL3 Basic) (Fig. 2A). The reporter constructs were then transiently transfected into sub-confluent RAW264.7 macrophages and assayed for luciferase activity in the presence and absence of LPS or PMA, for comparison. PMA-induced SerpinB2 gene regulation has been extensively studied in human macrophage cell lines [45]–[47], and has been shown to occur through several proximal and distal AP-1 responsive elements [30]; [37]; [47]–[51]. As shown in Fig. 2B, the SerpinB2 5′ flanking region from −4480 to +92 directs both PMA- and LPS-inducible transcription, approximately 2-fold and 7-fold, respectively. Deletion of the murine SerpinB2 promoter from −1686 to −1341 increased LPS-inducibility to approximately 16-fold, indicating the presence of a silencer element in this region. Further deletion beyond −539 abolished the LPS-response of the promoter, indicating the presence of an essential LPS response element in the region between −539 and −189; however, the response of the murine SerpinB2 promoter to PMA is less affected by this deletion. While deletion of the SerpinB2 promoter from −189 to −87 eliminated the LPS response and marginally reduced the PMA response, the −87 murine SerpinB2 promoter construct was still partially responsive to PMA, indicating that cis-acting elements mediating the response of the murine SerpinB2 promoter to PMA also lie downstream of nucleotide −87.\n10.1371/journal.pone.0057855.g002 Figure 2 Deletion reporter gene analysis of LPS and PMA-responsive regions in the murine SerpinB2 promoter.\n(A) Schematic representation of the murine SerpinB2 promoter and 5′ deletion luciferase reporter constructs. The murine 5′ flanking region from −4480 to +92 was inserted upstream of the luciferase reporter gene and 5′ deletions were generated using restriction enzyme sites or with specific oligonucleotide PCR primers. Construct names indicate the most 5′ nucleotide of murine SerpinB2 5′ flanking sequence. (B) RAW 264.7 macrophages were transiently transfected with the indicated murine SerpinB2 promoter-luciferase reporter constructs and control plasmids. Cells were either left untreated or treated with 100 ng/ml LPS or 40 ng/ml PMA for 16 hrs. Shown is the relative luciferase reporter gene activity following treatment. The results represent the mean and SEM of four independent experiments. (C) DNA sequence conservation between the human and murine SerpinB2 5′ flanking regions. Schematic representation of the human and murine SerpinB2 5′ flanking regions with regions of nucleotide sequence identity indicated by the same colored boxes. Homologous regions are interrupted by repetitive sequence elements in both 5′ flanking regions. Alu = Alu repeat, ID4 = ID4 short interspersed nuclear repeat (SINE), L1 = L1 long interspersed nuclear element (LINE), L2 = L2 LINE, MIR = MIR SINE, MLT1L = MLT1L long terminal repeat (LTR), (TATG)n = TATG tetranucleotide repeat, tis = transcription initiation site."}

test3

PMC:3589482 / 18622-21919 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:3589482 / 18622-21919 JSON TXT