PMID-sentid	Pub_year	Sent_text	comp_official_name	comp_offset	protein_name	organism	prot_offset
19666585-3	2009	The role of H4 lysine 16 deacetylation is well established in Sir3 protein recruitment; however, that of the H3 N-terminal tail has remained unclear.	Lysine	15-21	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	62-66
15454564-1	2004	The N-terminal alanine residues of the silencing protein Sir3 and of Orc1 are acetylated by the NatA Nalpha-acetyltransferase.	Alanine	15-22	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	57-61
19217406-7	2009	Additionally, a byproduct of Sir2-mediated NAD hydrolysis, O-acetyl-ADP-ribose, increases the efficiency with which Sir3 and Sir2-3-4 bind nucleosomes.	NAD	43-46	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	116-120
19217406-7	2009	Additionally, a byproduct of Sir2-mediated NAD hydrolysis, O-acetyl-ADP-ribose, increases the efficiency with which Sir3 and Sir2-3-4 bind nucleosomes.	NAD	43-46	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	125-131
19217406-7	2009	Additionally, a byproduct of Sir2-mediated NAD hydrolysis, O-acetyl-ADP-ribose, increases the efficiency with which Sir3 and Sir2-3-4 bind nucleosomes.	O-Acetyl-ADP-Ribose	59-78	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	116-120
19217406-7	2009	Additionally, a byproduct of Sir2-mediated NAD hydrolysis, O-acetyl-ADP-ribose, increases the efficiency with which Sir3 and Sir2-3-4 bind nucleosomes.	O-Acetyl-ADP-Ribose	59-78	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	125-131
18794362-5	2008	The BAH point mutants, but not the L738P mutant, disrupted the interaction between Sir3 and nucleosomes.	bis(5-amidino-2-benzimidazolyl)methane ketone hydrate	4-7	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	83-87
18619469-2	2008	Next, Sir2/3/4 proteins propagate across these loci as histones are deacetylated by the NAD(+)-dependent histone deacetylase Sir2p, ultimately resulting in the cessation of transcription and in the loss of SET1- and DOT1-dependent methylation of histone H3 within silent chromatin.	NAD	88-94	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	6-12
16581798-10	2006	This superhelix may be relevant to the function of the BAH domain of Sir3 in silencing.	bis(5-amidino-2-benzimidazolyl)methane ketone hydrate	55-58	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	69-73
15920479-4	2005	Strains lacking Sas2 histone acetylase or the histone methylases that modify lysines 4 (Set1) or 79 (Dot1) of H3 display accelerated Sir3 accumulation at HMR or its spreading away from the telomere, suggesting that these histone modifications exert distinct inhibitory effects on heterochromatin formation.	Lysine	77-84	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	133-137
15907466-4	2005	Our analysis reveals that deacetylation of histone H4-lysine 16 (K16), which is critical for silencing in vivo, is also critical for the binding of Sir3 and Sir4 to histone H4 peptides in vitro.	histone h4-lysine	43-60	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	148-152
19273586-2	2009	Previous work has shown that the N-terminal alanine residue of Sir3 (Ala2) and its acetylation play an important role in silencing.	Alanine	44-51	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	63-67
19171939-10	2009	We propose that the functional specialization of Sir3, itself a paralog of Orc1, as a silencing protein was facilitated by the tandem duplication of the OIR domain in the Sir1 family, allowing distinct Sir1-Sir3 and Sir1-Orc1 interactions through OIR-BAH domain interactions.	bis(5-amidino-2-benzimidazolyl)methane ketone hydrate	251-254	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	49-53
18775325-5	2008	We show that a Sir3 chimera-bearing Hos3, an unrelated NAD(+)-independent histone deacetylase, substitutes for Sir2 in silencing.	NAD	55-61	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	15-19
18362167-0	2008	The silent information regulator 3 protein, SIR3p, binds to chromatin fibers and assembles a hypercondensed chromatin architecture in the presence of salt.	Salts	150-154	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	44-49
18391024-9	2008	Our results suggest that the BAH domain of Sir3 binds to histone H3K79 and that acetylation of the BAH domain is required for the binding specificity of Sir3 for nucleosomes unmethylated at H3K79.	bis(5-amidino-2-benzimidazolyl)methane ketone hydrate	29-32	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	43-47
18391024-9	2008	Our results suggest that the BAH domain of Sir3 binds to histone H3K79 and that acetylation of the BAH domain is required for the binding specificity of Sir3 for nucleosomes unmethylated at H3K79.	bis(5-amidino-2-benzimidazolyl)methane ketone hydrate	99-102	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	153-157
18158899-2	2007	The formation of these domains involves the recruitment of the SIR complex, composed of Sir2, Sir3, and Sir4, followed by iterative cycles of NAD-dependent histone deacetylation and spreading of SIR complexes over adjacent chromatin domains.	NAD	142-145	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	94-98
17176117-4	2006	Sir3p self-associates extensively in moderate salt and at micromolar protein concentrations producing a broad range of oligomers that sediment from 8 to in excess of 85 S. These results provide new insight into Sir3p domain organization and quaternary structure and support a nucleosome bridging model for Sir3p-dependent regulation of chromatin architecture.	Salts	46-50	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	0-5
15280381-0	2004	Methylation of H3 lysine 4 at euchromatin promotes Sir3p association with heterochromatin.	Lysine	18-24	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	51-56
12379856-1	2002	The Sir3 protein helps form telomeric heterochromatin by interacting with hypoacetylated histone H4 lysine 16 (H4-Lys16).	Lysine	100-106	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	4-8
12379856-5	2002	We also found that disruption of Sir3p binding in a deacetylase-deficient Sir 2Delta strain can be suppressed by sas2Delta.	sas2delta	113-122	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	33-38
11714726-4	2002	Binding of H4 peptide (residues 1-34) acetylated at lysines Lys-5, Lys-8, Lys-12, and Lys-16 to an immobilized SIR3 protein fragment (residues 510-970) was investigated using surface plasmon resonance.	Lysine	52-59	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	111-115
12080090-6	2002	This defect in telomeric silencing might reflect an interaction between Sir proteins and Lys 79, because dot1 and Lys 79 mutations weaken the interaction of Sir2 and Sir3 with the telomeric region in vivo.	Lysine	89-92	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	166-170
12080090-6	2002	This defect in telomeric silencing might reflect an interaction between Sir proteins and Lys 79, because dot1 and Lys 79 mutations weaken the interaction of Sir2 and Sir3 with the telomeric region in vivo.	Lysine	114-117	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	166-170
11714726-5	2002	We find that acetylation of H4 lysines reduces binding (K(a)) of H4 to SIR3 in a cumulative manner so that the fully acetylated peptide binding is decreased approximately 50-fold relative to unacetylated peptide.	Lysine	31-38	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	71-75
8628316-3	1996	To test this, we tethered Sir3p adjacent to the telomere via LexA binding sites in the rap1-17 mutant that truncates the Rap1p C-terminal 165 amino acids thought to contain sites for Sir3p association.	lexa	61-65	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	26-31
10693811-4	2000	Deacetylation of lysine 16 of H4 is necessary for binding the silencing protein, Sir3.	Lysine	17-23	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	81-85
8628316-7	1996	In addition, LexA-Sir3p(N2O5) hyperrepresses telomeric silencing when tethered to a subtelomeric site 3.6 kb from the telomeric tract.	lexa	13-17	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	18-23
8628316-7	1996	In addition, LexA-Sir3p(N2O5) hyperrepresses telomeric silencing when tethered to a subtelomeric site 3.6 kb from the telomeric tract.	nitrogen pentoxide	24-28	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	18-23
35073254-3	2022	Using a fusion protein between the heterochromatin protein Sir3 and the non-site-specific bacterial adenine methyltransferase M.EcoGII, we mapped sites of Sir3-chromatin interactions genome-wide using long-read Nanopore sequencing to detect adenines methylated by the fusion protein and by ChIP-seq to map the distribution of Sir3-M.EcoGII.	Adenine	241-249	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	59-63
7744964-6	1995	Third, overproduction of the Sir4 COOH terminus alters the solubility properties of both Sir3 and full-length Sir4.	Carbonic Acid	34-38	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	89-93
35073254-3	2022	Using a fusion protein between the heterochromatin protein Sir3 and the non-site-specific bacterial adenine methyltransferase M.EcoGII, we mapped sites of Sir3-chromatin interactions genome-wide using long-read Nanopore sequencing to detect adenines methylated by the fusion protein and by ChIP-seq to map the distribution of Sir3-M.EcoGII.	Adenine	241-249	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	155-159
31295433-0	2019	Stabilization of Sir3 interactions by an epigenetic metabolic small molecule, O-acetyl-ADP-ribose, on yeast SIR-nucleosome silent heterochromatin.	O-Acetyl-ADP-Ribose	78-97	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	17-21
31366171-0	2019	The Capability of O-Acetyl-ADP-Ribose, an Epigenetic Metabolic Small Molecule, on Promoting the Further Spreading of Sir3 along the Telomeric Chromatin.	O-Acetyl-ADP-Ribose	18-37	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	117-121
23934150-2	2013	The crystal structure of the N-terminally acetylated BAH domain of Saccharomyces cerevisiae Sir3 bound to the nucleosome core particle reveals that the N-terminal acetylation stabilizes the interaction of Sir3 with the nucleosome.	bis(5-amidino-2-benzimidazolyl)methane ketone hydrate	53-56	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	92-96
25453095-4	2014	Previously, we found that the SWI/SNF chromatin remodeling enzyme can catalyze the ATP-dependent eviction of Sir3p from recombinant nucleosomal arrays, and this activity enhances early steps of recombinational repair in vitro.	Adenosine Triphosphate	83-86	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	109-114
25163529-8	2014	We also find that Sir3 fibres are less compact than canonical magnesium-induced 30 nm fibres.	Magnesium	62-71	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	18-22
23934152-0	2013	Nalpha-acetylated Sir3 stabilizes the conformation of a nucleosome-binding loop in the BAH domain.	bis(5-amidino-2-benzimidazolyl)methane ketone hydrate	87-90	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	18-22
27074556-3	2016	Ethanol-induced reactive oxygen species (ROS) and superoxide signals promoted growth rate during passages that was accompanied by increased expression of sirtuin proteins, Sir1, Sir2 and Sir3, and DNA-binding transcription regulator Rap1.	Ethanol	0-7	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	187-191
27074556-3	2016	Ethanol-induced reactive oxygen species (ROS) and superoxide signals promoted growth rate during passages that was accompanied by increased expression of sirtuin proteins, Sir1, Sir2 and Sir3, and DNA-binding transcription regulator Rap1.	Superoxides	50-60	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	187-191
23934150-2	2013	The crystal structure of the N-terminally acetylated BAH domain of Saccharomyces cerevisiae Sir3 bound to the nucleosome core particle reveals that the N-terminal acetylation stabilizes the interaction of Sir3 with the nucleosome.	bis(5-amidino-2-benzimidazolyl)methane ketone hydrate	53-56	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	205-209
21336256-5	2011	Sir3 also bound to a surprising number of euchromatic sites, largely at genes expressed at high levels, and was dynamically recruited to GAL genes upon galactose induction.	Galactose	152-161	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	0-4
22345352-3	2012	This structure is established by the action of silent information regulator proteins (Sir2, Sir3, and Sir4) that bind to nucleosomes and initiate the deacetylation of multiple lysine residues in histones H3 and H4.	Lysine	176-182	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	92-96
19766565-4	2009	We find that addition of Sir3p to a nucleosomal substrate is sufficient to eliminate yRad51p-catalyzed formation of joints, and that this repression is enhanced by Sir2p/Sir4p.	yrad51p	85-92	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	25-30
19782027-2	2009	Sir3 binds to nucleosomes containing deacetylated histone H4 lysine 16 (H4K16) and, with Sir4, promotes spreading of Sir2 and deacetylation along the chromatin fiber.	Lysine	61-67	chromatin-silencing protein SIR3	Saccharomyces cerevisiae S288C	0-4