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On T, et al.  (2010) The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses. Proteins 78(9):2075-89

Abstract: Model organisms such as yeast, fly, and worm have played a defining role in the study of many biological systems. A significant challenge remains in translating this information to humans. Of critical importance is the ability to differentiate those components where knowledge of function and interactions may be reliably inferred from those that represent lineage-specific innovations. To address this challenge, we use chromatin modification (CM) as a model system for exploring the evolutionary properties of their components in the context of their known functions and interactions. Collating previously identified components of CM from yeast, worm, fly, and human, we identified a "core" set of 50 CM genes displaying consistent orthologous relationships that likely retain their interactions and functions across taxa. In addition, we catalog many components that demonstrate lineage specific expansions and losses, highlighting much duplication within vertebrates that may reflect an expanded repertoire of regulatory mechanisms. Placed in the context of a high-quality protein-protein interaction network, we find, contrary to existing views of evolutionary modularity, that CM complex components display a mosaic of evolutionary histories: a core set of highly conserved genes, together with sets displaying lineage specific innovations. Although focused on CM, this study provides a template for differentiating those genes which are likely to retain their functions and interactions across species. As such, in addition to informing on the evolution of CM as a system, this study provides a set of comparative genomic approaches that can be generally applied to any biological systems.

Status: Published Type: Journal Article | Research Support, Non-U.S. Gov't PubMed ID: 20455264

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ABF1 ACS1 ACS2 ACT1 ADA2 AHC1 AIM3 ARD1 ARP4 ARP5
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Computational analysis yg ball
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ARP6 ARP7 ARP8 ARP9 ASF1 ASF2 ASH1 BDF1 BDP1 BRE1
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BRE2 BRF1 BRN1 BUD6 CAC2 CDC14 CDC45 CDC6 CDC7 CDC73
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Topics Genes linked to topics (#31 - 40 )
CHD1 CHZ1 CKA1 CPR1 CSM1 CSM3 CTI6 CTR9 CUL3 CYC8
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DBF4 DDC1 DEP1 DLS1 DOT1 DOT6 DPB2 DPB3 DPB4 EAF1
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Topics Genes linked to topics (#51 - 60 )
EAF3 EAF5 EAF6 EAF7 ECM14 ELA1 ELC1 ELP2 ELP3 ELP4
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Topics Genes linked to topics (#61 - 70 )
ELP6 EPL1 ESA1 ESC1 ESC2 ESC8 FCF1 FKH1 FMS1 FOB1
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FPR4 FUN30 GCD11 GCN5 GIS1 GLC7 GTR1 GUA1 HAT1 HAT2
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Topics Genes linked to topics (#81 - 90 )
HCM1 HCS1 HDA1 HDA2 HDA3 HFI1 HHF1 HHF2 HHO1 HHT1
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Topics Genes linked to topics (#91 - 100 )
HHT2 HIF1 HIR1 HIR2 HIR3 HMT1 HOS2 HOS3 HOS4 HPA2
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Topics Genes linked to topics (#101 - 110 )
HPA3 HPC2 HPR1 HSL7 HST1 HST2 HST3 HST4 HTA1 HTA2
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Non-Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#111 - 120 )
HTB1 HTB2 HTL1 HTZ1 IES1 IES2 IES3 IES4 IES5 IES6
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Non-Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#121 - 130 )
IFH1 IKI1 IKI3 IME1 INO80 IOC2 IOC3 IOC4 IPL1 IPP1
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Topics Genes linked to topics (#131 - 140 )
IRS4 ISW1 ISW2 ITC1 JHD1 JHD2 LDB7 LEO1 LGE1 LRS4
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Topics Genes linked to topics (#141 - 150 )
MCM1 MCM10 MCM2 MCM3 MCM4 MCM5 MCM6 MCM7 MEC1 MEC3
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Non-Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#151 - 160 )
MFT1 MIA40 MKS1 MOT1 MPT5 MRC1 MSH2 MSH3 MSH6 MSI1
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Non-Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#161 - 170 )
NAM7 NAP1 NAT1 NAT4 NAT5 NET1 NGG1 NHP10 NHP6A NHP6B
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Non-Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#171 - 180 )
NNT1 NPL6 NPT1 NTO1 NUP2 ORC1 ORC2 ORC3 ORC4 ORC5
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Topics Genes linked to topics (#181 - 190 )
ORC6 PAF1 PHB1 PHO13 PHO23 PNC1 POB3 POL1 POL12 POL2
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Non-Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#191 - 200 )
POL30 PRI1 PRI2 PUF4 RAD16 RAD17 RAD18 RAD53 RAD54 RAD6
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Topics Genes linked to topics (#201 - 210 )
RAD7 RAP1 RCO1 RFM1 RIF1 RKR1 RLF2 RNA1 RPB4 RPD3
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Topics Genes linked to topics (#211 - 220 )
RPH1 RPN10 RPN12 RSC1 RSC2 RSC3 RSC30 RSC4 RSC58 RSC6
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Topics Genes linked to topics (#221 - 230 )
RSC8 RSC9 RTF1 RTG2 RTT102 RTT106 RTT109 RVB1 RVB2 RXT2
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Non-Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#231 - 240 )
RXT3 SAP30 SAS2 SAS3 SAS4 SAS5 SCP160 SCS2 SDC1 SDS3
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Non-Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#241 - 250 )
SET1 SET2 SET3 SFH1 SGF11 SGF29 SGF73 SHG1 SIF2 SIN3
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Non-Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#251 - 260 )
SIR1 SIR2 SIR3 SIR4 SMC2 SMC4 SMT3 SNF11 SNF12 SNF2
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Non-Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#261 - 270 )
SNF5 SNF6 SNT1 SPP1 SPT10 SPT15 SPT16 SPT20 SPT3 SPT4
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Non-Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#271 - 280 )
SPT5 SPT6 SPT7 SPT8 SSA1 SSA2 SSA3 SSA4 STB2 STH1
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Non-Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#281 - 290 )
SUB2 SUM1 SUS1 SWC3 SWC4 SWC5 SWC7 SWD1 SWD2 SWD3
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Non-Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#291 - 300 )
SWI1 SWI3 SWP82 SWR1 TAF1 TAF10 TAF11 TAF12 TAF13 TAF14
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Non-Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#301 - 310 )
TAF2 TAF3 TAF4 TAF5 TAF6 TAF7 TAF8 TAF9 TBF1 TEL1
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Non-Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#311 - 320 )
TFG1 TFG2 THO2 THP2 TOF1 TOM1 TOP1 TOP2 TRA1 TUP1
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Topics Genes linked to topics (#321 - 330 )
UBA2 UBC13 UBC9 UBP10 UBP8 UME1 UME6 UTH1 VPS71 VPS72
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Topics Genes linked to topics (#331 - 340 )
VPS75 YAF9 YCG1 YCS4 YKU70 YKU80 YNG1 YNG2 YPR015C YRB2
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Topics Genes linked to topics (#341 - 342 )
ZDS1 ZDS2
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