Identification of the imprinted KLF14 transcription factor undergoing human-specific accelerated evolution.
Imprinted genes are expressed in a parent-of-origin manner and are located in clusters throughout the genome. Aberrations in the expression of imprinted genes on human Chromosome 7 have been suggested to play a role in the etiologies of Russell-Silver Syndrome and autism. We describe the imprinting of KLF14, an intronless member of the Krüppel-like family of transcription factors located at Chromosome 7q32. We show that it has monoallelic maternal expression in all embryonic and extra-embryonic tissues studied, in both human and mouse. We examine epigenetic modifications in the KLF14 CpG island in both species and find this region to be hypomethylated. In addition, we perform chromatin immunoprecipitation and find that the murine Klf14 CpG island lacks allele-specific histone modifications. Despite the absence of these defining features, our analysis of Klf14 in offspring from DNA methyltransferase 3a conditional knockout mice reveals that the gene's expression is dependent upon a maternally methylated region. Due to the intronless nature of Klf14 and its homology to Klf16, we suggest that the gene is an ancient retrotransposed copy of Klf16. By sequence analysis of numerous species, we place the timing of this event after the divergence of Marsupialia, yet prior to the divergence of the Xenarthra superclade. We identify a large number of sequence variants in KLF14 and, using several measures of diversity, we determine that there is greater variability in the human lineage with a significantly increased number of nonsynonymous changes, suggesting human-specific accelerated evolution. Thus, KLF14 may be the first example of an imprinted transcript undergoing accelerated evolution in the human lineage.
Parker-Katiraee
Layla
L
Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.
Carson
Andrew R
AR
Yamada
Takahiro
T
Arnaud
Philippe
P
Feil
Robert
R
Abu-Amero
Sayeda N
SN
Moore
Gudrun E
GE
Kaneda
Masahiro
M
Perry
George H
GH
Stone
Anne C
AC
Lee
Charles
C
Meguro-Horike
Makiko
M
Sasaki
Hiroyuki
H
Kobayashi
Keiko
K
Nakabayashi
Kazuhiko
K
Scherer
Stephen W
SW
D000015:Abnormalities, Multiple / Q000235:genetics; D000818:Animals; D001321:Autistic Disorder / Q000235:genetics; D018899:CpG Islands / Q000235:genetics; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000378:metabolism; D019175:DNA Methylation; D000090205:DNA Methyltransferase 3A; D019143:Evolution, Molecular; D005321:Extraembryonic Membranes / Q000378:metabolism; D018507:Gene Expression Regulation, Developmental; D014644:Genetic Variation; D018392:Genomic Imprinting; D006657:Histones / Q000378:metabolism; D006801:Humans; D051741:Kruppel-Like Transcription Factors / Q000235:genetics* / Q000378:metabolism; D051379:Mice; D008969:Molecular Sequence Data; D011506:Proteins / Q000235:genetics; D012333:RNA, Messenger; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D051703:Sp Transcription Factors; D013045:Species Specificity; D013577:Syndrome; D026801:Synteny / Q000235:genetics
C000717967:DNMT3A protein, human; C000715535:Dnmt3a protein, mouse; D006657:Histones; C417549:KLF14 protein, human; D051741:Kruppel-Like Transcription Factors; D011506:Proteins; D012333:RNA, Messenger; D051703:Sp Transcription Factors; C498818:Sp6 protein, mouse; C103637:mesoderm specific transcript protein; D004248:DNA (Cytosine-5-)-Methyltransferases; D000090205:DNA Methyltransferase 3A