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Respect for the literature

Posted by jchoward on 08 Mar 2012 at 07:05 GMT

Firstly, IRF8 was known for a long time as ICSBP and much excellent work was published on it including descriptions of its binding site, largely but by no means exclusively by Keiichi Ozato at the NIH. It was essential to use the ICSBP synonym right at the beginning, in order to introduce the literature on its binding sites. None of this was done.
Secondly, we published a complete list of the ISREs associated with the promoters of all the IFNg-inducible IRG proteins (p47 GTPases) in 2005 (Bekpen et al, Genome Biology, PMID: 16277747). Since the paper seems to be heavily concentrated towards the p47 IRG proteins it is an astonishing omission not to refer to this paper.
Thirdly, it has been known for a long time that ISREs associated with the promoters of some genes, of which MHC genes and their supporting components (TAP, LMPs etc) are established examples, are closely associated with NFkB sites, and it is known that NFkB physically interacts with IRF1 at the promoter. eg
NF kappa B and interferon regulatory factor 1 physically interact and synergistically induce major histocompatibility class I gene expression.
Drew PD, Franzoso G, Becker KG, Bours V, Carlson LM, Siebenlist U, Ozato K.
J Interferon Cytokine Res. 1995 Dec;15(12):1037-45.
PMID: 8746784
The EMBO Journal (1999) 18, 5028 - 5041 doi:10.1093/emboj/18.18.5028
Crystal structure of an IRF–DNA complex reveals novel DNA recognition and cooperative binding to a tandem repeat of core sequences
Yoshifumi Fujii1, Toshiyuki Shimizu1, Masahiro Kusumoto1, Yoshimasa Kyogoku2, Tadatsugu Taniguchi3 and Toshio Hakoshima1
and many more. It would have been important to have established whether or not the putative IRF8 binding sites identified in this study are associated with NFkB sites.

The authors have not behaved respectfully towards the relatively huge literature that their work in a sense depends on. The steady disappearance of historical continuity in scientific publications is deeply depressing.
Jonathan Howard

Competing interests declared: I am a co-author of the paper by Bekpen et al, 2005, that I refer to in my comment