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2_test

pmc-enju-pas

bionlp-st-ge-2016-coref

{"project":"bionlp-st-ge-2016-coref","denotations":[{"id":"T2231","span":{"begin":3056,"end":3089},"obj":"Anaphor"},{"id":"T2232","span":{"begin":3099,"end":3102},"obj":"Antecedent"},{"id":"T2233","span":{"begin":3109,"end":3114},"obj":"Antecedent"},{"id":"T2234","span":{"begin":3121,"end":3126},"obj":"Antecedent"},{"id":"T2235","span":{"begin":3133,"end":3139},"obj":"Antecedent"},{"id":"T2236","span":{"begin":3146,"end":3155},"obj":"Antecedent"},{"id":"T2237","span":{"begin":3156,"end":3160},"obj":"Antecedent"},{"id":"T2238","span":{"begin":3173,"end":3203},"obj":"Anaphor"},{"id":"T2239","span":{"begin":3204,"end":3208},"obj":"Antecedent"},{"id":"T2240","span":{"begin":3209,"end":3212},"obj":"Antecedent"},{"id":"T2241","span":{"begin":3217,"end":3222},"obj":"Antecedent"},{"id":"T2242","span":{"begin":4243,"end":4248},"obj":"Anaphor"},{"id":"T2243","span":{"begin":4211,"end":4222},"obj":"Antecedent"}],"relations":[{"id":"R2022","pred":"boundBy","subj":"T2231","obj":"T2232"},{"id":"R2023","pred":"boundBy","subj":"T2231","obj":"T2233"},{"id":"R2024","pred":"boundBy","subj":"T2231","obj":"T2234"},{"id":"R2025","pred":"boundBy","subj":"T2231","obj":"T2235"},{"id":"R2026","pred":"boundBy","subj":"T2231","obj":"T2236"},{"id":"R2027","pred":"boundBy","subj":"T2231","obj":"T2237"},{"id":"R2030","pred":"boundBy","subj":"T2238","obj":"T2239"},{"id":"R2031","pred":"boundBy","subj":"T2238","obj":"T2240"},{"id":"R2032","pred":"boundBy","subj":"T2238","obj":"T2241"},{"id":"R2034","pred":"boundBy","subj":"T2242","obj":"T2243"}],"namespaces":[{"prefix":"_base","uri":"http://bionlp.dbcls.jp/ontology/ge.owl#"}],"text":"INTRODUCTION\nNuclear factor (NF)-κB transcription factors regulate the transcription of genes that are involved in the immune and inflammatory response (1). The NF-κB family includes RelA/p65, c-Rel, RelB, p50 and p52 that share a highly conserved 300-amino acid Rel homology domain (RHD) for homo- or hetero-dimerization and DNA-binding. The transcriptional activity of the NF-κB complex depends on dimer composition since C-terminal unrelated transcriptional activation domains are present exclusively in p65, RelB and c-Rel (2).\nInhibitors of NF-κB (IκB) associate with the NF-κB complex and interfere with its binding to DNA (3). In the canonical pathway of NF-κB activation, the activated IκB kinase (IKK) phosphorylates IκB at specific serine residues that target the protein to ubiquitination and proteasomal degradation, which releases the functional NF-κB complex in the nucleus. IκB-α, the most abundant inhibitor of NF-κB (4), is phosphorylated by IKK at Ser32 and Ser36 (5), and subsequently ubiquitylated at Lys21 and Lys22 to be degraded by the 26S proteasome (6). The NF-κB activity is enhanced by phosphorylation of p65 at Ser276 by PKA and MSK1 (7,8), Ser311 by PKCζ (9) and Ser536 by IKKα (10,11). Acetylation of p65 at Lys218 and Lys221 increases the DNA binding and impairs the association with IκB-α, and acetylation at Lys310 enhances the p65 transcriptional activity (12,13). Post-activation turn off of NF-κB is regulated by negative feedback loop through inhibitors under the transcriptional control of NF-κB, such as IκB-α and ubiquitin-editing protein A20 (14–20). Deacetylation of p65 by histone deacetylase-3 or SIRT1, or acetylation of p65 at Lys122 and Lys123 down-regulate the NF-κB activity (12,21,22).\nPersistent activation of NF-κB occurs in human immunodeficiency virus-1 (HIV-1)-infected monocytes, macrophages and microglia, and enhances the expression of NF-κB-responsive genes, including pro-inflammatory cytokines, cell adhesion molecules and chemokines (23–25). Chronic inflammation is a major cause of immune and neuron dysfunction in AIDS (26,27). Consistently, non-human primate hosts for simian immunodeficiency virus, such as African green monkeys and sooty mangabey, lack aberrant immune activation and do not develop AIDS despite high virus replication (28,29). Thus, understanding the mechanisms of NF-κB deregulation by HIV-1 may provide further insights into AIDS pathogenesis.\nIn HIV-1 entry, the binding of the gp120 viral envelope to CD4 induces the NF-κB activity by activation of IKK (30) and procaspase 8 (31). Following viral integration, the early encoded HIV-1 Tat protein interacts with the HIV-1 RNA and host cell factors to sustain the viral replication. Tat binds to RNA stem-loop structures generated by the 5′ end of target transcripts, including the HIV-1 transactivation-responsive element (TAR) (32), tumor necrosis factor β (TNFβ) (33) and interleukin-6 (IL-6) (34) to activate gene transcription. Indeed, Tat promotes the transcriptional initiation and elongation by interacting with transacting factors and cofactors, such as Sp1 (35), TFIID (36), E2F-4 (37), C/EBPβ (38), cyclin T1/CDK9 (39,40) and the histone acetyltransferases p300/CBP and P/CAF (41–43). When released from HIV-1-infected cells, Tat deregulates the cell signaling by binding to cell receptors, such as integrins (44), Flk1/KDR receptor (45) and chemokine receptors (46).\nWe first reported that NF-κB was constitutively active in Jurkat cells that stably expressed the Tat gene (47). Following gene transfection or protein transduction, Tat induced the IKK activity and proteasomal degradation of IκB-α (48), and increased the p65 transcriptional activity by inhibiting the SIRT-1-mediated deacetylation of p65 Lys310 (49). These findings suggested that Tat modulates crucial enzymes involved in NF-κB signaling; however, it was unclear how Tat could subvert the negative feedback of NF-κB, which is mainly dependent on de novo synthesis of IκB-α (15,17). We previously found that IκB-α binds to Tat and promotes the nuclear export of the viral transactivator (50,51). In this study, we report that Tat counteracts the post-activation turn off of NF-κB through direct interaction with IκB-α and p65, which enhances the DNA binding and transcriptional activity of the NF-κB complex. The new mechanism of NF-κB deregulation here described may provide further insights into the chronic immune activation of HIV-1 infection."}

bionlp-st-ge-2016-spacy-parsed

GO-BP

GO-MF

GO-CC

{"project":"GO-CC","denotations":[{"id":"T3205","span":{"begin":375,"end":388},"obj":"http://purl.obolibrary.org/obo/GO_0071159"},{"id":"T3206","span":{"begin":577,"end":590},"obj":"http://purl.obolibrary.org/obo/GO_0071159"},{"id":"T3207","span":{"begin":859,"end":872},"obj":"http://purl.obolibrary.org/obo/GO_0071159"},{"id":"T3208","span":{"begin":4310,"end":4323},"obj":"http://purl.obolibrary.org/obo/GO_0071159"},{"id":"T3209","span":{"begin":880,"end":887},"obj":"http://purl.obolibrary.org/obo/GO_0005634"},{"id":"T3210","span":{"begin":1063,"end":1073},"obj":"http://purl.obolibrary.org/obo/GO_0000502"},{"id":"T3211","span":{"begin":1149,"end":1152},"obj":"http://purl.obolibrary.org/obo/GO_0005952"},{"id":"T3212","span":{"begin":1956,"end":1960},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T3213","span":{"begin":2672,"end":2676},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T3214","span":{"begin":3293,"end":3297},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T3215","span":{"begin":3322,"end":3326},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T3216","span":{"begin":3480,"end":3485},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T3217","span":{"begin":2124,"end":2129},"obj":"http://purl.obolibrary.org/obo/GO_0018995"},{"id":"T3218","span":{"begin":2667,"end":2671},"obj":"http://purl.obolibrary.org/obo/GO_0018995"},{"id":"T3219","span":{"begin":2471,"end":2485},"obj":"http://purl.obolibrary.org/obo/GO_0019031"},{"id":"T3220","span":{"begin":2477,"end":2485},"obj":"http://purl.obolibrary.org/obo/GO_0009274"},{"id":"T3221","span":{"begin":2667,"end":2676},"obj":"http://purl.obolibrary.org/obo/GO_0043657"}],"text":"INTRODUCTION\nNuclear factor (NF)-κB transcription factors regulate the transcription of genes that are involved in the immune and inflammatory response (1). The NF-κB family includes RelA/p65, c-Rel, RelB, p50 and p52 that share a highly conserved 300-amino acid Rel homology domain (RHD) for homo- or hetero-dimerization and DNA-binding. The transcriptional activity of the NF-κB complex depends on dimer composition since C-terminal unrelated transcriptional activation domains are present exclusively in p65, RelB and c-Rel (2).\nInhibitors of NF-κB (IκB) associate with the NF-κB complex and interfere with its binding to DNA (3). In the canonical pathway of NF-κB activation, the activated IκB kinase (IKK) phosphorylates IκB at specific serine residues that target the protein to ubiquitination and proteasomal degradation, which releases the functional NF-κB complex in the nucleus. IκB-α, the most abundant inhibitor of NF-κB (4), is phosphorylated by IKK at Ser32 and Ser36 (5), and subsequently ubiquitylated at Lys21 and Lys22 to be degraded by the 26S proteasome (6). The NF-κB activity is enhanced by phosphorylation of p65 at Ser276 by PKA and MSK1 (7,8), Ser311 by PKCζ (9) and Ser536 by IKKα (10,11). Acetylation of p65 at Lys218 and Lys221 increases the DNA binding and impairs the association with IκB-α, and acetylation at Lys310 enhances the p65 transcriptional activity (12,13). Post-activation turn off of NF-κB is regulated by negative feedback loop through inhibitors under the transcriptional control of NF-κB, such as IκB-α and ubiquitin-editing protein A20 (14–20). Deacetylation of p65 by histone deacetylase-3 or SIRT1, or acetylation of p65 at Lys122 and Lys123 down-regulate the NF-κB activity (12,21,22).\nPersistent activation of NF-κB occurs in human immunodeficiency virus-1 (HIV-1)-infected monocytes, macrophages and microglia, and enhances the expression of NF-κB-responsive genes, including pro-inflammatory cytokines, cell adhesion molecules and chemokines (23–25). Chronic inflammation is a major cause of immune and neuron dysfunction in AIDS (26,27). Consistently, non-human primate hosts for simian immunodeficiency virus, such as African green monkeys and sooty mangabey, lack aberrant immune activation and do not develop AIDS despite high virus replication (28,29). Thus, understanding the mechanisms of NF-κB deregulation by HIV-1 may provide further insights into AIDS pathogenesis.\nIn HIV-1 entry, the binding of the gp120 viral envelope to CD4 induces the NF-κB activity by activation of IKK (30) and procaspase 8 (31). Following viral integration, the early encoded HIV-1 Tat protein interacts with the HIV-1 RNA and host cell factors to sustain the viral replication. Tat binds to RNA stem-loop structures generated by the 5′ end of target transcripts, including the HIV-1 transactivation-responsive element (TAR) (32), tumor necrosis factor β (TNFβ) (33) and interleukin-6 (IL-6) (34) to activate gene transcription. Indeed, Tat promotes the transcriptional initiation and elongation by interacting with transacting factors and cofactors, such as Sp1 (35), TFIID (36), E2F-4 (37), C/EBPβ (38), cyclin T1/CDK9 (39,40) and the histone acetyltransferases p300/CBP and P/CAF (41–43). When released from HIV-1-infected cells, Tat deregulates the cell signaling by binding to cell receptors, such as integrins (44), Flk1/KDR receptor (45) and chemokine receptors (46).\nWe first reported that NF-κB was constitutively active in Jurkat cells that stably expressed the Tat gene (47). Following gene transfection or protein transduction, Tat induced the IKK activity and proteasomal degradation of IκB-α (48), and increased the p65 transcriptional activity by inhibiting the SIRT-1-mediated deacetylation of p65 Lys310 (49). These findings suggested that Tat modulates crucial enzymes involved in NF-κB signaling; however, it was unclear how Tat could subvert the negative feedback of NF-κB, which is mainly dependent on de novo synthesis of IκB-α (15,17). We previously found that IκB-α binds to Tat and promotes the nuclear export of the viral transactivator (50,51). In this study, we report that Tat counteracts the post-activation turn off of NF-κB through direct interaction with IκB-α and p65, which enhances the DNA binding and transcriptional activity of the NF-κB complex. The new mechanism of NF-κB deregulation here described may provide further insights into the chronic immune activation of HIV-1 infection."}

sentences

ICD10

{"project":"ICD10","denotations":[{"id":"T3222","span":{"begin":1783,"end":1799},"obj":"http://purl.bioontology.org/ontology/ICD10/D84.9"},{"id":"T3223","span":{"begin":2141,"end":2157},"obj":"http://purl.bioontology.org/ontology/ICD10/D84.9"}],"text":"INTRODUCTION\nNuclear factor (NF)-κB transcription factors regulate the transcription of genes that are involved in the immune and inflammatory response (1). The NF-κB family includes RelA/p65, c-Rel, RelB, p50 and p52 that share a highly conserved 300-amino acid Rel homology domain (RHD) for homo- or hetero-dimerization and DNA-binding. The transcriptional activity of the NF-κB complex depends on dimer composition since C-terminal unrelated transcriptional activation domains are present exclusively in p65, RelB and c-Rel (2).\nInhibitors of NF-κB (IκB) associate with the NF-κB complex and interfere with its binding to DNA (3). In the canonical pathway of NF-κB activation, the activated IκB kinase (IKK) phosphorylates IκB at specific serine residues that target the protein to ubiquitination and proteasomal degradation, which releases the functional NF-κB complex in the nucleus. IκB-α, the most abundant inhibitor of NF-κB (4), is phosphorylated by IKK at Ser32 and Ser36 (5), and subsequently ubiquitylated at Lys21 and Lys22 to be degraded by the 26S proteasome (6). The NF-κB activity is enhanced by phosphorylation of p65 at Ser276 by PKA and MSK1 (7,8), Ser311 by PKCζ (9) and Ser536 by IKKα (10,11). Acetylation of p65 at Lys218 and Lys221 increases the DNA binding and impairs the association with IκB-α, and acetylation at Lys310 enhances the p65 transcriptional activity (12,13). Post-activation turn off of NF-κB is regulated by negative feedback loop through inhibitors under the transcriptional control of NF-κB, such as IκB-α and ubiquitin-editing protein A20 (14–20). Deacetylation of p65 by histone deacetylase-3 or SIRT1, or acetylation of p65 at Lys122 and Lys123 down-regulate the NF-κB activity (12,21,22).\nPersistent activation of NF-κB occurs in human immunodeficiency virus-1 (HIV-1)-infected monocytes, macrophages and microglia, and enhances the expression of NF-κB-responsive genes, including pro-inflammatory cytokines, cell adhesion molecules and chemokines (23–25). Chronic inflammation is a major cause of immune and neuron dysfunction in AIDS (26,27). Consistently, non-human primate hosts for simian immunodeficiency virus, such as African green monkeys and sooty mangabey, lack aberrant immune activation and do not develop AIDS despite high virus replication (28,29). Thus, understanding the mechanisms of NF-κB deregulation by HIV-1 may provide further insights into AIDS pathogenesis.\nIn HIV-1 entry, the binding of the gp120 viral envelope to CD4 induces the NF-κB activity by activation of IKK (30) and procaspase 8 (31). Following viral integration, the early encoded HIV-1 Tat protein interacts with the HIV-1 RNA and host cell factors to sustain the viral replication. Tat binds to RNA stem-loop structures generated by the 5′ end of target transcripts, including the HIV-1 transactivation-responsive element (TAR) (32), tumor necrosis factor β (TNFβ) (33) and interleukin-6 (IL-6) (34) to activate gene transcription. Indeed, Tat promotes the transcriptional initiation and elongation by interacting with transacting factors and cofactors, such as Sp1 (35), TFIID (36), E2F-4 (37), C/EBPβ (38), cyclin T1/CDK9 (39,40) and the histone acetyltransferases p300/CBP and P/CAF (41–43). When released from HIV-1-infected cells, Tat deregulates the cell signaling by binding to cell receptors, such as integrins (44), Flk1/KDR receptor (45) and chemokine receptors (46).\nWe first reported that NF-κB was constitutively active in Jurkat cells that stably expressed the Tat gene (47). Following gene transfection or protein transduction, Tat induced the IKK activity and proteasomal degradation of IκB-α (48), and increased the p65 transcriptional activity by inhibiting the SIRT-1-mediated deacetylation of p65 Lys310 (49). These findings suggested that Tat modulates crucial enzymes involved in NF-κB signaling; however, it was unclear how Tat could subvert the negative feedback of NF-κB, which is mainly dependent on de novo synthesis of IκB-α (15,17). We previously found that IκB-α binds to Tat and promotes the nuclear export of the viral transactivator (50,51). In this study, we report that Tat counteracts the post-activation turn off of NF-κB through direct interaction with IκB-α and p65, which enhances the DNA binding and transcriptional activity of the NF-κB complex. The new mechanism of NF-κB deregulation here described may provide further insights into the chronic immune activation of HIV-1 infection."}

events-check-again

bionlp-st-ge-2016-reference-tees

test2

bionlp-st-ge-2016-reference

bionlp-st-ge-2016-uniprot

PMC:3333881 / 1360-5823 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:3333881 / 1360-5823 JSON TXT