Article No.5
Mol Cell Biol. 2009 Jan;29(1):83-92. Epub 2008 Nov 3.
Coactivation of estrogen receptor beta by gonadotropin-induced cofactor GIOT-4.
Kouzu-Fujita M, Mezaki Y, Sawatsubashi S, Matsumoto T, Yamaoka I, Yano T, Taketani Y, Kitagawa H, Kato S.
Source
Institute of Molecular and Cellular Biosciences, University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
Alleged misconduct #24-#25 on the article No.5
About this paper, the material & method section is terrible.
ReplyDelete1) murine ZFP709 does not seems to be the genuine orthologue of human ZNF14.
They called human zinc finger protein (ZNF14 NM_021030) as GIOT-4. Furthermore, they call murine zinc finger protein 709 (Zfp709, NM_145624) as mouse GIOT-4, which is understood that they assume Zfp709 as murine orthologue of human ZNF14. In fact, when you search the human homologues of murine Zfp709 with BLASTP, you can find tremendous amount of homologues of such a gene. Among them, human zinc finger protein 709 (ZNF709, NM_152601) hits with the most significant similarity, as the name suggests, which is supposed to be the orthologue of murine Zfp709 without persuasive reason. In turn, when you BLASTP the Mus musculus genome with human ZNF14, ZFP709 hits with less significance than other genes. (In my opinion, human ZNF14, human ZNF709 and murine Zfp709 seem to evolve independently, as the synteny suggests, that is, neighbouring genes are distinct.) If Zfp709 is not the orthologue of ZNF14, it seems difficult to understand why they could obtain such results in the paper.
2) PCR primers are incorrect.
human GIOT-4 gene
mouse chr9:109988045-109988814 770bp CTGTGTGGGTGTCGAGAGCAAATG TGCCACTGTCATGGCTCAGCAATG
mouse GIOT-4 gene (located in chr.8)
chr9:59790956-59791160 205bp GGGCAGCACATCTTAGAAGC TTGCCAAAGCTGTTTCTCCT
With these 2 primer-pairs, I wonder if they could amplify anything other than Mus musculus nuclear receptor subfamily 2, group E, member 3 (Nr2e3 NM_013708.4) and Mus musculus DEAH (Asp-Glu-Ala-His) box polypeptide 30 (Dhx30 NM_133347.1), respectively. Of course, they are not human GIOT-4 or mouse GIOT-4. It seems so easy to corrects errors with a corrigendum. But, I suppose they purchased primers from somewhere else, there should be records that demonstrate they ordered 'correct' primers about GIOT-4 in those days.
3) GAPDH primers will pick up many pseudogenes
It is widely known that there are many pseudogenes of GAPDH, which resulted from reverse-transcripts of GAPDH mRNA. I wonder if they ruled out possible contamination of genomic DNA. Else, it is possible that they amplified many pseudogenes, which you can confirm with the help of 'UCSC In-Silico PCR'.
>chr12:6646087+6646784 698bp CGAGATCCCTCCAAAATCAA GTCTTCTGGGTGGCAGTGAT
>chr4:88128474+88128796 323bp CGAGATCCCTCCAAAATCAA GTCTTCTGGGTGGCAGTGAT
>chr5:173940541+173940860 320bp CGAGATCCCTCCAAAATCAA GTCTTCTGGGTGGCAGTGAT
>chr15:64821310-64821631 322bp CGAGATCCCTCCAAAATCAA GTCTTCTGGGTGGCAGTGAT
>chr16:28251457-28251777 321bp CGAGATCCCTCCAAAATCAA GTCTTCTGGGTGGCAGTGAT
>chr5:159377949-159378269 321bp CGAGATCCCTCCAAAATCAA GTCTTCTGGGTGGCAGTGAT
>chr6:80663169-80663491 323bp CGAGATCCCTCCAAAATCAA GTCTTCTGGGTGGCAGTGAT
>chrX:39646831-39647153 323bp CGAGATCCCTCCAAAATCAA GTCTTCTGGGTGGCAGTGAT