PMID- 31186073
OWN - NLM
STAT- MEDLINE
DCOM- 20190719
LR  - 20231012
IS  - 1474-760X (Electronic)
IS  - 1474-7596 (Print)
IS  - 1474-7596 (Linking)
VI  - 20
IP  - 1
DP  - 2019 Jun 11
TI  - Invasive DNA elements modify the nuclear architecture of their insertion site by 
      KNOT-linked silencing in Arabidopsis thaliana.
PG  - 120
LID - 10.1186/s13059-019-1722-3 [doi]
LID - 120
AB  - BACKGROUND: The three-dimensional (3D) organization of chromosomes is linked to 
      epigenetic regulation and transcriptional activity. However, only few functional 
      features of 3D chromatin architecture have been described to date. The KNOT is a 
      3D chromatin structure in Arabidopsis, comprising 10 interacting genomic regions 
      termed KNOT ENGAGED ELEMENTs (KEEs). KEEs are enriched in transposable elements 
      and associated small RNAs, suggesting a function in transposon biology. RESULTS: 
      Here, we report the KNOT's involvement in regulating invasive DNA elements. 
      Transgenes can specifically interact with the KNOT, leading to perturbations of 
      3D nuclear organization, which correlates with the transgene's expression: high 
      KNOT interaction frequencies are associated with transgene silencing. KNOT-linked 
      silencing (KLS) cannot readily be connected to canonical silencing mechanisms, 
      such as RNA-directed DNA methylation and post-transcriptional gene silencing, as 
      both cytosine methylation and small RNA abundance do not correlate with KLS. 
      Furthermore, KLS exhibits paramutation-like behavior, as silenced transgenes can 
      lead to the silencing of active transgenes in trans. CONCLUSION: Transgene 
      silencing can be connected to a specific feature of Arabidopsis 3D nuclear 
      organization, namely the KNOT. KLS likely acts either independent of or prior to 
      canonical silencing mechanisms, such that its characterization not only 
      contributes to our understanding of chromosome folding but also provides valuable 
      insights into how genomes are defended against invasive DNA elements.
FAU - Grob, Stefan
AU  - Grob S
AUID- ORCID: 0000-0001-6199-7383
AD  - Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, 
      University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland. 
      sgrob@botinst.uzh.ch.
FAU - Grossniklaus, Ueli
AU  - Grossniklaus U
AD  - Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, 
      University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland. 
      grossnik@botinst.uzh.ch.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20190611
PL  - England
TA  - Genome Biol
JT  - Genome biology
JID - 100960660
RN  - 0 (DNA Transposable Elements)
SB  - IM
MH  - Arabidopsis/*genetics
MH  - DNA Transposable Elements
MH  - *Gene Silencing
MH  - *Genome, Plant
MH  - *Nucleic Acid Conformation
MH  - *Transgenes
PMC - PMC6560877
OTO - NOTNLM
OT  - 3D nuclear organization
OT  - Arabidopsis
OT  - Gene silencing
OT  - KNOT
OT  - Paramutation
OT  - Transgene
COIS- The authors declare that they have no competing interests.
EDAT- 2019/06/13 06:00
MHDA- 2019/07/20 06:00
PMCR- 2019/06/11
CRDT- 2019/06/13 06:00
PHST- 2018/11/30 00:00 [received]
PHST- 2019/05/22 00:00 [accepted]
PHST- 2019/06/13 06:00 [entrez]
PHST- 2019/06/13 06:00 [pubmed]
PHST- 2019/07/20 06:00 [medline]
PHST- 2019/06/11 00:00 [pmc-release]
AID - 10.1186/s13059-019-1722-3 [pii]
AID - 1722 [pii]
AID - 10.1186/s13059-019-1722-3 [doi]
PST - epublish
SO  - Genome Biol. 2019 Jun 11;20(1):120. doi: 10.1186/s13059-019-1722-3.