Synthetic genome readers target clustered binding sites across diverse chromatin states.
Targeting the genome with sequence-specific DNA-binding molecules is a major goal at the interface of chemistry, biology, and precision medicine. Polyamides, composed of N-methylpyrrole and N-methylimidazole monomers, are a class of synthetic molecules that can be rationally designed to "read" specific DNA sequences. However, the impact of different chromatin states on polyamide binding in live cells remains an unresolved question that impedes their deployment in vivo. Here, we use cross-linking of small molecules to isolate chromatin coupled to sequencing to map the binding of two bioactive and structurally distinct polyamides to genomes directly within live H1 human embryonic stem cells. This genome-wide view from live cells reveals that polyamide-based synthetic genome readers bind cognate sites that span a range of binding affinities. Polyamides can access cognate sites within repressive heterochromatin. The occupancy patterns suggest that polyamides could be harnessed to target loci within regions of the genome that are inaccessible to other DNA-targeting molecules.
Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706.
Graham S
GS
Erwin
Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706.
Matthew P
MP
Grieshop
Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706.|Department of Electrical and Computer Engineering, University of Wisconsin-Madison, Madison, WI 53706.
Devesh
D
Bhimsaria
Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706.
Truman J
0000-0002-4285-1773
TJ
Do
Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706.
José A
JA
Rodríguez-Martínez
Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706.
Charu
C
Mehta
Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706.
Kanika
K
Khanna
Morgridge Institute for Research, Madison, WI 53715.
Scott A
SA
Swanson
Morgridge Institute for Research, Madison, WI 53715.
Ron
R
Stewart
Morgridge Institute for Research, Madison, WI 53715.|The Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706.
James A
JA
Thomson
Department of Electrical and Computer Engineering, University of Wisconsin-Madison, Madison, WI 53706.
Parameswaran
P
Ramanathan
Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, azansari@wisc.edu.|The Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706.
Aseem Z
0000-0003-1432-4498
AZ
Ansari
D001665:Binding Sites; D002460:Cell Line; D002843:Chromatin / Q000737:chemistry / Q000235:genetics*; D003432:Cross-Linking Reagents; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D015894:Genome, Human; D000066449:Human Embryonic Stem Cells / Q000166:cytology; D006801:Humans; D009757:Nylons / Q000378:metabolism*; D017422:Sequence Analysis, DNA / Q000379:methods*; D054852:Small Molecule Libraries / Q000737:chemistry
D002843:Chromatin; D003432:Cross-Linking Reagents; D009757:Nylons; D054852:Small Molecule Libraries; D004247:DNA
COSMIC; chemical genomics; genome targeting; molecular recognition; polyamide