We identified lamprey homologs of CTCF, and performed ChIP-seq for the CTCF protein in the Arctic lamprey, Lethenteron camtschaticum. Using the same anti-CTCF antibody, ChIP-seq was also carried out for chicken embryos and human GM12878 cells to compare CTCF binding properties between lamprey, chicken and human. As previous genome analysis of the Arctic lamprey did not provide detailed information on the transcripts, transcriptome analysis was performed by RNA-seq using RNAs from the embryo and adult tissues. RNA-seq reads obtained were used for improving the accuracy of gene prediction by the AUGUSTUS program, and also for refining the gene set produced by AUGUSTUS.