for datums about location of Nbs1-phos without unphos control go to:
~/evidence/DSB-Evidence/Nbs1.to.DDF.irt.IR.279rej.txt

sensitive to methods - fixation (methanol vs formaldehyde)
                       preextraction (0.2% triton before formaldehyde)
pretreatment with BudR 

==================
Relocation to CHR
==================

not Atm--

  *** Nbs1[Ab] locatedin(DSBs)[IHC] is detectable
    *** cells: mEFs<Atm~null> in BMS "treated with MicroLaser for 8 min"
    *** source: 12792649-Fig-3b

not Brca1--

  *** Nbs1[Ab] locatedin(subnuclear-bodies)[IHC] is increased irt IR (6 hr)
    *** cells: hFibros in BMS
    *** does not req: Brca1 [RNAi]
    *** source: 19001859-Fig-5

H2ax--

  --------------- not required ----------------------------------------
  *** Nbs1[Ab] locatedin(DSBs)[IHC] is increased irt MicroLaser (8 min)
    *** cells: mEFs in BMS
    *** does not req: H2ax [KO]
    *** source: 12792649-Fig-1a
  *** Nbs1[Ab] locatedin(DSBs)[IHC] is increased irt MicroLaser (8 min)
    *** cells: mEFs in BMS
    *** does not req: H2ax [KO]
    *** source: 12792649-Fig-1b
  *** Nbs1[Ab] locatedin(DSBs)[IHC] is increased irt MicroLaser (8 min)
    *** cells: mEFs<H2ax~null><xH2ax> in BMS
    *** does not req: xH2ax [omission]
    *** unaffected by: xH2ax(S137A/S140A) [substitution]
    *** unaffected by: xH2ax(S137E/S140E) [substitution]
    *** source: 12792649-Fig-3
  *** Nbs1[Ab] locatedin(subnuclear-bodies)[IHC] is detectable
    *** cells: mEFs<H2ax~null><xH2ax> in BMS "treated with IR for 30 min"
    *** reqs: xH2ax [omission]
    *** inhibited by: xH2ax(Y143A) [substitution]
    *** source: 16377563-Fig-5b
  --------------- partially required ----------------------------------------
  *** xNbs1[XFP] locatedin(DSBs)[IHC] is increased irt MicroLaser (times)
    *** cells: U2OS<xNbs1> in BMS
    *** times: 0 1+ 2++ 4+++ 8++++ 10++++ min
    *** partially reqs: H2ax [RNAi]
    *** comment: intensity is less in cells without H2ax
    *** source: 15201865-Fig-6e
  *** Nbs1[Ab] locatedin(DSBs)[IHC] is increased irt MicroLaser (1 hr)
    *** cells: U2OS in BMS
    *** does not req: H2ax [RNAi]
    *** comment: intensity is less in cells without H2ax
    *** source: 16618811-Fig-5b
  ----------------- required ---------------------------------------------
  *** Nbs1[Ab] locatedin(subnuclear-bodies)[IHC] is increased irt IR (16 hr)
    *** cells: mEFs<H2ax~null><xH2ax> in BMS
    *** reqs: xH2ax [omission]
    *** inhibited by: xH2ax(S137A/S140A) [substitution]
    *** inhibited by: xH2ax(S137E/S140E) [substitution]
    *** source: 12792649-Fig-3


Mdc1--

  *** xNbs1[XFP] locatedin(DSBs)[IHC] is increased irt MicroLaser (times)
    *** cells: U2OS<xNbs1> in BMS
    *** times: 0 30+ 60++ 120++ 240+++ 720+++ sec
    *** reqs: Mdc1 [RNAi]
    *** source: 15201865-Fig-3a
  *** xNbs1[XFP] locatedin(DSBs)[IHC] is increased irt MicroLaser (10 min)
    *** cells: U2OS<xNbs1> in BMS
    *** partially reqs: Mdc1 [RNAi]
    *** source: 15201865-Fig-7c
  *** Nbs1[Ab] locatedin(DSBs)[IHC] is detectable
    *** cells: U2OS<Mdc1~kd><xMdc1> in BMS "treated with MicroLaser for 30 min"
    *** partially inhibited by: xMdc1(del(196-506)) [substitution] 
    *** source: 18583988-Fig-4e
  *** Nbs1[Ab] locatedin(DSBs)[IHC] is detectable
    *** cells: mEFs in BMS "treated with MicroLaser for 5 min"
    *** does not req: Mdc1 [RNAi]
    *** source: 16427009-Fig-6a
  *** Nbs1[Ab] locatedin(subnuclear-bodies)[IHC] is detectable
    *** cells: HELA in BMS "treated with IR for 15 min"
    *** reqs: Mdc1 [RNAi]
    *** source: 12607003-Fig-4a

not Kdm6b-- Kdm4a-- Kdm4d--

  *** Nbs1[Ab] locatedin(subnuclear-bodies)[IHC] is detectable
    *** cells: HEK293T<xTip60> in BMS "treated with IR for tnr"
    *** unaffected by: xKdm6b [addition]
    *** unaffected by: xKdm4a [addition]
    *** unaffected by: xKdm4d [addition]
    *** source: 19783983-Fig-4c

Mdc1--

  ----------- required ---------------------------------------------
  *** Nbs1[Ab] locatedin(subnuclear-bodies)[IHC] is increased irt IR (6 hr)
    *** cells: hFibros in BMS
    *** reqs: Mdc1 [RNAi]
    *** source: 19001859-Fig-5
  *** Nbs1[Ab] locatedin(subnuclear-bodies)[IHC] is increased irt IR (4 hr)
    *** cells: U2OS in BMS
    *** reqs: Mdc1 [RNAi]
    *** source: 18583988-Fig-4c
  *** Nbs1[Ab] locatedin(subnuclear-bodies)[IHC] is increased irt IR (4 hr)
    *** cells: U2OS<Mdc1~kd><xMdc1> in BMS
    *** reqs: xMdc1 [omission]
    *** inhibited by: xMdc1(del(196-506)) [substitution] 
    *** source: 18583988-Fig-4c
  *** Nbs1[Ab] locatedin(subnuclear-bodies)[IHC] is detectable
    *** cells: HELA in BMS "treated with IR for 60 min"
    *** reqs: Mdc1 [RNAi]
    *** source: 12607003-Fig-4a
  *** Nbs1[Ab] locatedin(subnuclear-bodies)[IHC] is detectable
    *** cells: U2OS in BMS "treated with IR for 6 hr"
    *** reqs: Mdc1 [RNAi]
    *** source: 12607005-Fig-2c
  *** Nbs1[Ab] locatedin(subnuclear-bodies)[IHC] is detectable
    *** cells: mEFs in BMS "treated with IR for tnr"
    *** reqs: Mdc1 [KO]
    *** source: 18678890-Fig-4a
  *** xNbs1[tAb] locatedin(DSBs)[IHC] is detectable
    *** cells: U2OS in BMS "treated with MicroLaser for 1 hr"
    *** reqs: Mdc1 [RNAi]
    *** source: 18411307-Fig-S3
  *** Nbs1[Ab] locatedin(DSBs)[IHC] is detectable
    *** cells: mEFs in BMS "treated with MicroLaser for 4 hr"
    *** reqs: Mdc1 [RNAi]
    *** source: 16427009-Fig-6a
  -------------- not required --------------------------------------
  *** Nbs1[Ab] locatedin(DSBs)[IHC] is detectable
    *** cells: U2OS<Mdc1~kd> in BMS "treated with MicroLaser of 1 hr"
    *** source: 16618811-Fig-5c
  -------------------- Mdc1 features --------------------------
  *** Nbs1[Ab] locatedin(subnuclear-bodies)[IHC] is detectable
    *** cells: mEFs<Mdc1~null><xMdc1> in BMS "treated with IR for tnr"
    *** inhibited by: xMdc1(del(200-420))"dSDTD" [substitution]
    *** unaffected by: xMdc1(del(698-768))"dTQXF" [substitution]
    *** source: 18678890-Fig-4b
  *** xNbs1[tAb] locatedin(subnuclear-bodies)[IHC] is detectable
    *** cells: HELA<xMdc1><xNbs1> in BMS "treated with IR for tnr"
    *** unaffected by: xMdc1(del(33-154))"D1" [substitution]
    *** unaffected by: xMdc1(del(125-170))"D2" [substitution]
    *** inhibited by: xMdc1(del(200-420))"D3" [substitution]
    *** unaffected by: xMdc1(del(421-624))"D4" [substitution]
    *** unaffected by: xMdc1(del(625-1129))"D5" [substitution]
    *** unaffected by: xMdc1(del(1130-1661))"D6" [substitution]
    *** unaffected by: xMdc1(del(1662-1892))"D7" [substitution]
    *** inhibited by: xMdc1(del(1893-2092))"D8" [substitution]
    *** source: 18678890-Fig-2a
  *** Nbs1[Ab] locatedin(subnuclear-bodies)[IHC] is detectable
    *** cells: HELA in BMS "treated with IR for 30 min"
    *** inhibited by: xMdc1(2-220)"FHA" [addition]
    *** source: 12607003-Fig-4d
  *** xNbs1[tAb] locatedin(DSBs)[IHC] is detectable
    *** cells: U2OS<Mdc1~kd><xMdc1> in BMS "treated with MicroLaser for 1 hr"
    *** inhibited by: xMdc1(S299A/T301A/S453A/T455A) [substitution]
    *** inhibited by: xMdc1(S299A/T301A/S329A/T331A/S402A/T404A/S453A/T455A) [substitution]
    *** source: 18411307-Fig-7b
  *** Nbs1[Ab] locatedin(DSBs)[IHC] is detectable
    *** cells: U2OS<Mdc1~kd><xMdc1> in BMS "treated with MicroLaser for tnr"
    *** unaffected by: xMdc1(T699A/T719A/T752A) [substitution]
    *** source: 18001824-Fig-S3c

not Rnf8--

  *** Nbs1[Ab] locatedin(DSBs)[IHC] is detectable
    *** cells: U2OS in BMS "treated with MicroLaser for 1 hr"
    *** does not req: Rnf8 [RNAi]
    *** source: 18001824-Fig-4a
  *** Nbs1[Ab] locatedin(subnuclear-bodies)[IHC] is increased irt IR (1 hr)
    *** cells: HELA in BMS
    *** does not req: Rnf8 [RNAi]
    *** source: 18006705-Fig-S9b
  *** Nbs1[Ab] locatedin(subnuclear-bodies)[IHC] is detectable
    *** cells: HELA in BMS "treated with IR for 6 hr"
    *** does not req: Rnf8 [RNAi]
    *** source: 18001825-Fig-S4c

Tp53bp1-- ???

  *** Nbs1[Ab] locatedin(subnuclear-bodies)[IHC] is increased irt IR (6 hr)
    *** cells: hFibros in BMS
    *** partially reqs: Tp53bp1 [RNAi]
    *** source: 19001859-Fig-5
  *** Nbs1[Ab] locatedin(subnuclear-bodies)[IHC] is detectable
    *** cells: HELA in BMS "treated with IR for 6 hr"
    *** does not req: Tp53bp1 [RNAi]
    *** source: 12607003-Fig-4b

Nbs1 features

  *** xNbs1[tAb] locatedin(subnuclear-bodies)[IHC] is detectable
    *** cells: NBST<Nbs1~fmut><xNbs1> in BMS "treated with IR for tnr"
    *** inhibited by: xNbs1(del(24-108))"D1" [substitution]
    *** inhibited by: xNbs1(del(109-196))"D2" [substitution]
    *** partially inhibited by: xNbs1(del(361-460))"D3" [substitution]
    *** inhibited by: xNbs1(del(261-460))"D4" [substitution]
    *** inhibited by: xNbs1(del(219-460))"D5" [substitution]
    *** source: 18678890-Fig-5a
  *** xNbs1[XFP] locatedin(DSBs)[IHC] is increased irt MicroLaser (10 min)
    *** cells: U2OS<xNbs1> in BMS
    *** inhibited by: xNbs1(R28A)"mutFHA" [substitution]
    *** comment: substitution changes binding to DSB/chromatin to ssDNA
    *** source: 15201865-Fig-7c
  *** xNbs1[XFP] locatedin(DSBs)[IHC] is detectable
    *** cells: GM07166<Nbs1~fmut><xNbs1> in BMS "treated with MicroLaser for 60 min"
    *** inhibited by: xNbs1(mnr)"delFHA" [substitution]
    *** comment: pre-extraction shows residual xNbs1(mnr)"delFHA" staining
    *** source: 20026654-Fig-6a

chemicals

  *** Nbs1[Ab] boundto(RN28S1-gene)[ChIP] is increased irt DSB-Induction (16 hr)
    *** cells: MCF7 in BMS
    *** unaffected by: KU55933 [cotreatment]
    *** source: 17486112-Fig-2b

no extras

  *** xNbs1[XFP] locatedin(DSBs)[IHC] is increased irt MicroLaser (14 min)
    *** cells: U2OS<xNbs1> in BMS
    *** comment: increase was monitored continuously during MicroLaser
    *** comment: increase was similar to xRnf8 xMdc1 in same system
    *** comment: increase was faster than xBrca1 xTp53bp1 xAtr in same system
    *** source: 18001824-Fig-3b
  *** xNbs1[XFP] locatedin(DSBs)[IHC] is increased irt MicroLaser (times)
    *** cells: U2OS<xNbs1> in BMS
    ***  times: 0 30 60+ 120++ 240+++ 360+++ 480+++ 600+++ sec
    *** source: 15201865-Fig-1a
  *** xNbs1[XFP] locatedin(DSBs)[IHC] is increased irt MicroLaser (times)
    *** cells: U2OS<xNbs1> in BMS
    *** times: 0 1+ 2++ 4++ 6++ 10++ 15++ min
    *** source: 16327781-Fig-5a
  *** xNbs1[Ab] boundto(RN28S1-gene)[ChIP] is increased irt DSB-Induction (16 hr)
    *** cells: NBS1LBI<Nbs1~fmut><xNbs1> in BMS
    *** source: 17486112-Fig-S3b
  *** Nbs1[Ab] boundto(RN28S1-gene)[ChIP] is increased irt DSB-Induction (24 hr)
    *** cells: HEK293T in BMS
    *** source: 17486112-Fig-S1b
  *** xNbs1[XFP] locatedin(DSBs)[IHC] is increased irt MicroLaser (10 min)
    *** cells: GM07166<Nbs1~fmut><xNbs1> in BMS
    *** source: 20026654-Fig-1d
  *** xNbs1[XFP] locatedin(DSBs)[IHC] is increased irt MicroLaser (times)
    *** cells: GM07166<Nbs1~fmut><xNbs1> in BMS
    *** times: 0 1+ 2++ 3++ min
    *** source: 20026654-Fig-1d
  *** Nbs1[Ab] locatedin(DSBs)[IHC] is increased irt MicroLaser (1 hr)
    *** cells: U2OS in BMS
    *** source: 16618811-Fig-5a

chemicals

  *** Nbs1[Ab] locatedin(DSBs)[IHC] is detectable
    *** cells: U2OS in BMS "treated with MG132 for 90 min followed by MicroLaser for 30 min"
    *** source: 18001824-Fig-3c
  *** Nbs1[Ab] locatedin(DSBs)[IHC] is increased irt MicroLaser (1 hr)
    *** cells: U2OS<Mdc1~kd> in BMS
    *** comment: colocates with Rpa2
    *** comment: colocates with BRDU
    *** comment: intensity drops in cells not staining with BRDU
    *** source: 16618811-Fig-5c

==================
Nbs1 dsDNA binding
==================

requires Mre11-- and/or Rad50--

  *** rNbs1[Ab] boundby[WB] dsDNA[biotin] is detectable
    *** cells: none
    *** comment: reaction also contains rMre11 + rRad50
    *** comment: binding reqs rMre11 and/or rRad50 [omission]
    *** unaffected by: xAtm{dimer}[tAb]IP [addition]
    *** source: 15790808-Fig-2c

does not req Rad50 phos site S1202

  *** rNbs1[Ab] boundby[WB] dsDNA[biotin] is detectable
    *** cells: none
    *** comment: reaction also contains rMre11 + rRad50 + xAtm{dimer}[tAb]IP
    *** unaffected by: rRad50(S1202R) [substitution]
    *** source: 15790808-Fig-4b


==================================
what to do about the tnr samples?
==================================

  *** Nbs1[Ab] locatedin(subnuclear-bodies)[IHC] is detectable
    *** cells: mEFs<Mdc1~null><xMdc1> in BMS "treated with IR for tnr"
    *** reqs: xMdc1 [omission]
    *** source: 16427009-Fig-S8
  *** Nbs1[Ab] locatedin(subnuclear-bodies)[IHC] is detectable
    *** cells: U2OS in BMS "treated with IR for tnr"
    *** reqs: Mdc1 [RNAi]
    *** source: 18006705-Fig-S3
  *** Nbs1[Ab] locatedin(subnuclear-bodies)[IHC] is detectable
    *** cells: U2OS<Mdc1~kd><xMdc1> in BMS "treated with IR for tnr"
    *** reqs: xMdc1 [omission]
    *** unaffected by: xMdc1(679-778/T699A/T719A/T752A/T765A) [substitution]
    *** source: 18006705-Fig-S3

