for datums about location of Atm-phos without unphos control go to:
~/evidence/DSB-Evidence/Atm.to.DDF.irt.IR.322rej.txt

==================
Relocation to DSBs - short times (less than 1 hr)
==================

MRN-- these are treated together because KD of one tends to KD the others

  *** xAtm[XFP] locatedin(DSBs)[IHC] is increased irt MicroLaser (3 min)
    *** cells: HT1080<xAtm> in BMS
    *** reqs: Mre11 [RNAi]
    *** reqs: Nbs1 [RNAi]
    *** reqs: Rad50 [RNAi]
    *** source: 20026654-Fig-S1e
  *** xAtm[XFP] locatedin(DSBs)[IHC] is increased irt MicroLaser (times)
    *** cells: HT1080<xAtm> in BMS
    *** times: 0 1+ 2++ 3+++ min
    *** reqs: Mre11 [RNAi]
    *** reqs: Nbs1 [RNAi]
    *** reqs: Rad50 [RNAi]
    *** source: 20026654-Fig-1c

  *** xAtm[XFP] locatedin(DSBs)[IHC] is detectable
    *** cells: GM07166<Nbs1~fmut><xNbs1><xAtm> in BMS "treated with MicroLaser for 10 min"
    *** unaffected by: xNbs1(mnr)"delFHA" [substitution]
    *** source: 20026654-Fig-6b

not Rnf8--

  *** xAtm[XFP] locatedin(DSBs)[IHC] is detectable
    *** cells: AT5BIVA<Atm~fmut><xAtm> in BMS "treated with MicroLaser for 10 min"
    *** does not req: Rnf8 [RNAi]
    *** source: 20026654-Fig-6c


Atm features - does not req phos(S1981)

  *** xAtm[XFP] locatedin(DSBs)[IHC] is detectable
    *** cells: AT5BIVA<Atm~fmut><xAtm> in BMS "treated with MicroLaser for 10 min"
    *** unaffected by: xAtm(S1981A) [substitution]
    *** source: 20026654-Fig-6c
  *** xAtm[XFP] locatedin(DSBs)[IHC] is detectable
    *** cells: AT5BIVA<Atm~fmut><xAtm> in BMS "treated with MicroLaser for 10 min"
    *** unaffected by: xAtm(S1981A) [substitution]
    *** source: 20026654-Fig-5b
  *** xAtm[XFP] locatedin(DSBs)[IHC] is detectable
    *** cells: GM07166<Nbs1~fmut><xNbs1><xAtm> in BMS "treated with MicroLaser for 10 min"
    *** unaffected by: xAtm(S1981A) [substitution]
    *** source: 20026654-Fig-6b
  *** xAtm[XFP] locatedin(DSBs)[IHC] is increased irt MicroLaser (10 min)
    *** cells: AT5BIVA<Atm~fmut><xAtm> in BMS
    *** unaffected by: xAtm(S1981A) [substitution]
    *** source: 20026654-Fig-2a
  *** xAtm[XFP] locatedin(DSBs)[IHC] is increased irt MicroLaser (times)
    *** cells: AT5BIVA<Atm~fmut><xAtm> in BMS
    *** times: 0 1+ 3++ 5+++ 10++ min
    *** unaffected by: xAtm(S1981A) [substitution]
    *** source: 20026654-Fig-2b
  *** xAtm[XFP] locatedin(subnuclear-bodies)[IHC] is detectable
    *** cells: AT5BIVA<Atm~fmut><xAtm> in BMS "treated with IR for 10 min"
    *** unaffected by: xAtm(S1981A) [substitution]
    *** source: 20026654-Fig-2e

no extras

  *** xAtm[XFP] locatedin(DSBs)[IHC] is increased irt MicroLaser (10 min)
    *** cells: AT5BIVA<Atm~fmut><xAtm> in BMS
    *** comment: xAtm at DSBs is phosed on S1981
    *** source: 20026654-Fig-1b
  *** xAtm[XFP] locatedin(DSBs)[IHC] is increased irt MicroLaser (10 min)
    *** cells: HT1080<xAtm> in BMS
    *** comment: xAtm at DSBs is phosed on S1981
    *** source: 20026654-Fig-1b
  *** xAtm[XFP] locatedin(DSBs)[IHC] is increased irt MicroLaser (10 min)
    *** cells: U2OS<xAtm> in BMS
    *** comment: xAtm at DSBs is phosed on S1981
    *** source: 20026654-Fig-S1b
  *** xAtm[XFP] locatedin(DSBs)[IHC] is increased irt MicroLaser (times)
    *** cells: AT5BIVA<Atm~fmut><xAtm> in BMS
    *** times: 0 1+ 3++ min
    *** source: 20026654-Fig-1a
  *** xAtm[XFP] locatedin(DSBs)[IHC] is increased irt MicroLaser (times)
    *** cells: HT1080<xAtm> in BMS
    *** times: 0 1+ 3++ min
    *** source: 20026654-Fig-1a
  *** xAtm[XFP] locatedin(DSBs)[IHC] is increased irt MicroLaser (times)
    *** cells: U2OS<xAtm> in BMS
    *** times: 0 1+ 3++ min
    *** source: 20026654-Fig-S1a

==================
Retention at DSBs - longer times (1 hr or longer)
==================

Mdc1--

  *** xAtm[XFP] locatedin(DSBs)[IHC] is increased irt MicroLaser (times)
    *** cells: AT5BIVA<Atm~fmut><xAtm> in BMS
    *** times: 0 10+++ 20++ 30++ 60+ 80+ 120+ min
    *** comment: KD of Mdc1 with RNAi caused a faster decrease after 10 min
    *** source: 20026654-Fig-5a

Nbs1--  but not Nbs1-FHA domain

  *** Atm[Ab] boundto(RN28S1-gene)[ChIP] is increased irt DSB-Induction (16 hr)
    *** cells: NBS1LBI<Nbs1~fmut><xNbs1> in BMS
    *** comment: Atm is phosed on S1981
    *** reqs: xNbs1 [omission]
    *** source: 17486112-Fig-S3b
  *** xAtm[XFP] locatedin(DSBs)[IHC] is detectable
    *** cells: GM07166<Nbs1~fmut><xNbs1><xAtm> in BMS "treated with MicroLaser for 60 min"
    *** unaffected by: xNbs1(mnr)"delFHA" [substitution]
    *** source: 20026654-Fig-6b

not Rnf8--

  *** xAtm[XFP] locatedin(DSBs)[IHC] is detectable
    *** cells: AT5BIVA<Atm~fmut><xAtm> in BMS "treated with MicroLaser for 60 min"
    *** does not req: Rnf8 [RNAi]
    *** source: 20026654-Fig-6c
  *** xAtm[XFP] locatedin(DSBs)[IHC] is increased irt MicroLaser (times)
    *** cells: AT5BIVA<Atm~fmut><xAtm> in BMS
    *** times: 0 10+++ 20++ 30+ 60+ 80+ 120+ min
    *** does not req: Rnf8 [RNAi]
    *** source: 20026654-Fig-6c

Atm features - reqs phos(S1981)

  *** xAtm[tAb] boundto(Dab1-gene)[ChIP] is increased irt DSB-Induction (24 hr)
    *** cells: GM9607<Atm~fmut><xAtm> in BMS
    *** inhibited by: xAtm(D2870A/N2875K)"KD" [substitution]
    *** inhibited by: xAtm(S1981A) [substitution]
    *** source: 17486112-Fig-2c
  *** xAtm[XFP] locatedin(DSBs)[IHC] is detectable
    *** cells: AT5BIVA<Atm~fmut><xAtm> in BMS "treated with MicroLaser for 60 min"
    *** partially inhibited by: xAtm(S1981A) [substitution]
    *** source: 20026654-Fig-5b
  *** xAtm[XFP] locatedin(DSBs)[IHC] is detectable
    *** cells: GM07166<Nbs1~fmut><xNbs1><xAtm> in BMS "treated with MicroLaser for 60 min"
    *** partially inhibited by: xAtm(S1981A) [substitution]
    *** source: 20026654-Fig-6b
  *** xAtm[XFP] locatedin(DSBs)[IHC] is increased irt MicroLaser (times)
    *** cells: AT5BIVA<Atm~fmut><xAtm> in BMS
    *** times: 0 10+++ 20+++ 30+++ 60++ 80+ 120+ min
    *** comment: substitution with xAtm(S1981A) caused a faster decrease after 10 min
    *** source: 20026654-Fig-2c
  *** xAtm[XFP] locatedin(DSBs)[IHC] is increased irt MicroLaser (times)
    *** cells: AT5BIVA<Atm~fmut><xAtm> in BMS
    *** times: 0 10+++ 20++ 30++ 60+ 80+ 120+ min
    *** comment: substitution with xAtm(S1981A) caused a faster decrease after 10 min
    *** source: 20026654-Fig-5a
  *** xAtm[XFP] locatedin(subnuclear-bodies)[IHC] is detectable
    *** cells: AT5BIVA<Atm~fmut><xAtm> in BMS "treated with IR for 2 hr"
    *** inhibited by: xAtm(S1981A) [substitution]
    *** source: 20026654-Fig-2e

no extras

  *** Atm[Ab] locatedin(DSBs)[IHC] is increased irt MicroLaser (1 hr)
    *** cells: U2OS in BMS
    *** comment: colocates with H2ax-phos(S140)
    *** comment: Atm at DSBs is phosed on S1981
    *** source: 16618811-Fig-2a


======================
Fractionation Evidence
======================

  *** Atm[Ab] infraction(chromatin)[WB] is increased irt IR (1 hr)
    *** cells: NBS1LBI<Nbs1~fmut><xNbs1> in BMS
    *** reqs: xNbs1 [omission]
    *** inhibited by: xNbs1(1-734)"delC" [substitution]
    *** source: 15758953-Fig-2e
  *** Atm[Ab] infraction(chromatin)[WB] is increased irt IR (45 min)
    *** cells: RAJI in BMS
    *** unaffected by: Wortmannin [pretreatment]
    *** source: 16461339-Fig-2a
  *** Atm[Ab] infraction(chromatin)[WB] is increased irt IR (30 min)
    *** cells: mEFs in BMS
    *** reqs: Mdc1 [KO]
    *** source: 16427009-Fig-4d
  *** xAtm[tAb] infraction(chromatin)[WB] is increased irt IR (times)
    *** cells: AT5BIVA<Atm~fmut><xAtm> in BMS
    *** times: 0+ 10++ 60++ min
    *** inhibited by: xAtm(S1981A) [substitution]
    *** comment: increase is slight and it is unclear whether chromatin contains DNA
    *** source: 20026654-Fig-2d

================================================================
site-specific DSB-Induction by transfection of inducible I-PpoI 
================================================================

  *** Atm[Ab] boundto(Dab1-gene)[ChIP] is decreased irt DSB-Induction (times)
    *** cells: MCF7 in BMS "arrested in G1 by serum-depletion for 24 hr"
    *** times: 0++ 2+ 4+ 6 8+ 10+ 12+ 16+ 20+ 24+ hr
    *** source: 17486112-Fig-3b
  *** Atm[Ab] boundto(Dab1-gene)[ChIP] is increased irt DSB-Induction (16 hr)
    *** cells: MCF7 in BMS
    *** source: 17486112-Fig-1e
  *** Atm[Ab] boundto(Dab1-gene)[ChIP] is increased irt DSB-Induction (times)
    *** cells: MCF7 in BMS "arrested in G1 by serum-depletion for 24 hr"
    *** times: 0 2+ 4++ 6+++ 8 10+ 12++ 16++ 20+ 24 hr
    *** source: 17486112-Fig-3b
  *** Atm[Ab] boundto(RN28S1-gene)[ChIP] is increased irt DSB-Induction (16 hr)
    *** cells: MCF7 in BMS
    *** inhibited by: KU55933 [cotreatment]
    *** source: 17486112-Fig-2b
  *** Atm[Ab] boundto(RN28S1-gene)[ChIP] is increased irt DSB-Induction (16 hr)
    *** cells: MCF7 in BMS
    *** source: 17486112-Fig-1c
  *** Atm[Ab] boundto(RN28S1-gene)[ChIP] is increased irt DSB-Induction (24 hr)
    *** cells: HEK293T in BMS
    *** source: 17486112-Fig-S1b

=================
ATM dsDNA binding
=================

does not req Nbs1

  *** xAtm{dimer}[tAb]IP boundby[WB] dsDNA[biotin] is detectable
    *** cells: none
    *** IPfrom: HEK293T<xAtm{dimer}> in BMS
    *** comment: reaction also contains rRad50 + rMre11 + rNbs1
    *** comment: binding does not req rNbs1 [omission]
    *** source: 15790808-Fig-2d

reqs Rad50--  but not Rad50(S1202)

  *** xAtm{dimer}[tAb]IP boundby[WB] dsDNA[biotin] is detectable
    *** cells: none
    *** IPfrom: HEK293T<xAtm{dimer}> in BMS
    *** comment: reaction also contains rRad50 + rMre11 + rNbs1
    *** comment: binding reqs rNbs1 and/or rRad50 [omission]
    *** source: 15790808-Fig-2e
  *** xAtm{dimer}[tAb]IP boundby[WB] dsDNA[biotin] is detectable
    *** cells: none
    *** IPfrom: HEK293T<xAtm{dimer}> in BMS
    *** comment: reaction also contains rRad50 + rMre11 + rNbs1
    *** unaffected by: rRad50(S1202R) [substitution]
    *** source: 15790808-Fig-4b

requires Rad50-- and/or rMre11--

  *** xAtm{dimer}[tAb]IP boundby[WB] dsDNA[biotin] is detectable
    *** cells: none
    *** IPfrom: HEK293T<xAtm{dimer}> in BMS
    *** comment: reaction also contains rRad50 + rMre11 + rNbs1
    *** comment: binding reqs rRad50 and/or rMre11 and/or rNbs1 [omission]
    *** source: 15790808-Fig-2c


