Proteome-wide analysis in Saccharomyces cerevisiae identifies several PHD fingers as novel direct and selective binding modules of histone H3 methylated at either lysine 4 or lysine 36.
The PHD finger motif is a signature chromatin-associated motif that is found throughout eukaryotic proteomes. Here we have determined the histone methyl-lysine binding activity of the PHD fingers present within the Saccharomyces cerevisiae proteome. We provide evidence on the genomic scale that PHD fingers constitute a general class of effector modules for histone H3 trimethylated at lysine 4 (H3K4me3) and histone H3 trimethylated at lysine 36 (H3K36me3). Structural modeling of PHD fingers demonstrates a conserved mechanism for recognizing the trimethyl moiety and provides insight into the molecular basis of affinity for the different methyl-histone ligands. Together, our study suggests that a common function for PHD fingers is to transduce methyl-lysine events and sheds light on how a single histone modification can be linked to multiple biological outcomes.
Shi
Xiaobing
X
Department of Biological Sciences, Stanford University, Stanford, California 94305, USA.
Kachirskaia
Ioulia
I
Walter
Kay L
KL
Kuo
Jen-Hao A
JH
Lake
Aimee
A
Davrazou
Foteini
F
Chan
Steve M
SM
Martin
David G E
DG
Fingerman
Ian M
IM
Briggs
Scott D
SD
Howe
LeAnn
L
Utz
Paul J
PJ
Kutateladze
Tatiana G
TG
Lugovskoy
Alexey A
AA
Bedford
Mark T
MT
Gozani
Or
O
D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D004268:DNA-Binding Proteins; D006657:Histones / Q000378:metabolism*; D018398:Homeodomain Proteins / Q000737:chemistry / Q000378:metabolism; D008239:Lysine; D008745:Methylation; D008969:Molecular Sequence Data; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D020543:Proteome; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000378:metabolism
D004268:DNA-Binding Proteins; D006657:Histones; D018398:Homeodomain Proteins; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins; D008239:Lysine