PMID- 28155083
OWN - NLM
STAT- MEDLINE
DCOM- 20180305
LR  - 20181113
IS  - 1573-6849 (Electronic)
IS  - 0967-3849 (Print)
IS  - 0967-3849 (Linking)
VI  - 25
IP  - 2
DP  - 2017 Jun
TI  - The long zinc finger domain of PRDM9 forms a highly stable and long-lived complex 
      with its DNA recognition sequence.
PG  - 155-172
LID - 10.1007/s10577-017-9552-1 [doi]
AB  - PR domain containing protein 9 (PRDM9) is a meiosis-specific, multi-domain 
      protein that regulates the location of recombination hotspots by targeting its 
      DNA recognition sequence for double-strand breaks (DSBs). PRDM9 specifically 
      recognizes DNA via its tandem array of zinc fingers (ZnFs), epigenetically marks 
      the local chromatin by its histone methyltransferase activity, and is an 
      important tether that brings the DNA into contact with the recombination 
      initiation machinery. A strong correlation between PRDM9-ZnF variants and 
      specific DNA motifs at recombination hotspots has been reported; however, the 
      binding specificity and kinetics of the ZnF domain are still obscure. Using two 
      in vitro methods, gel mobility shift assays and switchSENSE, a quantitative 
      biophysical approach that measures binding rates in real time, we determined that 
      the PRDM9-ZnF domain forms a highly stable and long-lived complex with its 
      recognition sequence, with a dissociation halftime of many hours. The ZnF domain 
      exhibits an equilibrium dissociation constant (K (D)) in the nanomolar (nM) 
      range, with polymorphisms in the recognition sequence directly affecting the 
      binding affinity. We also determined that alternative sequences (15-16 
      nucleotides in length) can be specifically bound by different subsets of the ZnF 
      domain, explaining the binding plasticity of PRDM9 for different sequences. 
      Finally, longer binding targets are preferred than predicted from the numbers of 
      ZnFs contacting the DNA. Functionally, a long-lived complex translates into an 
      enzymatically active PRDM9 at specific DNA-binding sites throughout meiotic 
      prophase I that might be relevant in stabilizing the components of the 
      recombination machinery to a specific DNA target until DSBs are initiated by 
      Spo11.
FAU - Striedner, Yasmin
AU  - Striedner Y
AD  - Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, 
      Linz, Austria.
FAU - Schwarz, Theresa
AU  - Schwarz T
AD  - Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, 
      Linz, Austria.
FAU - Welte, Thomas
AU  - Welte T
AD  - Dynamic Biosensors GmbH, 82152, Planegg, Germany.
FAU - Futschik, Andreas
AU  - Futschik A
AD  - Department of Applied Statistics, Johannes Kepler University, 4040, Linz, 
      Austria.
FAU - Rant, Ulrich
AU  - Rant U
AD  - Dynamic Biosensors GmbH, 82152, Planegg, Germany.
FAU - Tiemann-Boege, Irene
AU  - Tiemann-Boege I
AUID- ORCID: 0000-0002-3621-7020
AD  - Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, 
      Linz, Austria. irene.tiemann@jku.at.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20170202
PL  - Netherlands
TA  - Chromosome Res
JT  - Chromosome research : an international journal on the molecular, supramolecular 
      and evolutionary aspects of chromosome biology
JID - 9313452
RN  - EC 2.1.1.43 (Histone-Lysine N-Methyltransferase)
RN  - EC 2.1.1.43 (PRDM9 protein, human)
SB  - IM
MH  - Animals
MH  - Binding Sites
MH  - DNA Breaks, Double-Stranded
MH  - Histone-Lysine N-Methyltransferase/*metabolism
MH  - Meiosis
MH  - Mice
MH  - *Nucleotide Motifs
MH  - Protein Binding
MH  - Protein Stability
MH  - Recombination, Genetic
MH  - *Zinc Fingers
PMC - PMC5440498
OTO - NOTNLM
OT  - PRDM9
OT  - binding affinity
OT  - enzyme kinetics
OT  - equilibrium dissociation constant
OT  - gel mobility shift
OT  - meiotic recombination
OT  - protein-DNA interaction
OT  - switchSENSE
OT  - zinc finger
COIS- The authors declare that they have no conflicts of interest.
EDAT- 2017/02/06 06:00
MHDA- 2018/03/06 06:00
PMCR- 2017/02/02
CRDT- 2017/02/04 06:00
PHST- 2016/09/23 00:00 [received]
PHST- 2017/01/18 00:00 [accepted]
PHST- 2017/01/09 00:00 [revised]
PHST- 2017/02/06 06:00 [pubmed]
PHST- 2018/03/06 06:00 [medline]
PHST- 2017/02/04 06:00 [entrez]
PHST- 2017/02/02 00:00 [pmc-release]
AID - 10.1007/s10577-017-9552-1 [pii]
AID - 9552 [pii]
AID - 10.1007/s10577-017-9552-1 [doi]
PST - ppublish
SO  - Chromosome Res. 2017 Jun;25(2):155-172. doi: 10.1007/s10577-017-9552-1. Epub 2017 
      Feb 2.