PIF1-Interacting Transcription Factors and Their Binding Sequence Elements Determine the in Vivo Targeting Sites of PIF1.
The bHLH transcription factor PHYTOCHROME INTERACTING FACTOR1 (PIF1) binds G-box elements in vitro and inhibits light-dependent germination in Arabidopsis thaliana A previous genome-wide analysis of PIF1 targeting indicated that PIF1 binds 748 sites in imbibed seeds, only 59% of which possess G-box elements. This suggests the G-box is not the sole determinant of PIF1 targeting. The targeting of PIF1 to specific sites could be stabilized by PIF1-interacting transcription factors (PTFs) that bind other nearby sequence elements. Here, we report PIF1 targeting sites are enriched with not only G-boxes but also with other hexameric sequence elements we named G-box coupling elements (GCEs). One of these GCEs possesses an ACGT core and serves as a binding site for group A bZIP transcription factors, including ABSCISIC ACID INSENSITIVE5 (ABI5), which inhibits seed germination in abscisic acid signaling. PIF1 interacts with ABI5 and other group A bZIP transcription factors and together they target a subset of PIF1 binding sites in vivo. In vitro single-molecule fluorescence imaging confirms that ABI5 facilitates PIF1 binding to DNA fragments possessing multiple G-boxes or the GCE alone. Thus, we show in vivo PIF1 targeting to specific binding sites is determined by its interaction with PTFs and their binding to GCEs.
Department of Biological Sciences, KAIST, Daejeon 34141, Korea.
Junghyun
0000-0001-8112-4897
J
Kim
Department of Convergence Technology Research, KISTI, Daejeon 34141, Korea.
Hyojin
H
Kang
Department of Biological Sciences, KAIST, Daejeon 34141, Korea.
Jeongmoo
0000-0003-2555-5929
J
Park
Department of Biological Sciences, KAIST, Daejeon 34141, Korea.
Woohyun
W
Kim
Department of Physics, KAIST, Daejeon 34141, Korea.
Janghyun
0000-0002-2330-4053
J
Yoo
Department of Biological Sciences, KAIST, Daejeon 34141, Korea.
Nayoung
N
Lee
Department of Biological Sciences, KAIST, Daejeon 34141, Korea.
Jaewook
J
Kim
Department of Physics, KAIST, Daejeon 34141, Korea.
Tae-Young
TY
Yoon
Department of Biological Sciences, KAIST, Daejeon 34141, Korea gchoi@kaist.edu.
Giltsu
G
Choi
D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics / Q000378:metabolism*; D050976:Basic-Leucine Zipper Transcription Factors / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites / Q000235:genetics / Q000502:physiology; D018506:Gene Expression Regulation, Plant / Q000235:genetics / Q000502:physiology; D011485:Protein Binding / Q000235:genetics / Q000502:physiology; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
D029681:Arabidopsis Proteins; D051792:Basic Helix-Loop-Helix Proteins; D050976:Basic-Leucine Zipper Transcription Factors; D014157:Transcription Factors; C409743:ABI5 protein, Arabidopsis; C508068:At2g20180 protein, Arabidopsis