Introduction 2007 2007 2005 2003 Drosophila Caenorhabditis elegans Drosophila melanogaster 2003 Drosophila Drosophila 2003 2007 1996 Bombyx mori 2004 C. elegans 2003 Oikopleura dioica 2004 2002 2003 2005 2003 2007 2007 2003 1994 2005 2006 Apis 2006 2006 Anopheles 2002 2007 Tribolium castaneum Drosophila Tribolium 2002 Tribolium 1987 Tribolium 1993 1989 2000 2000 2006 1991 1993 2005 Tribolium Materials and methods Sequence and transposable element analysis Tribolium http://www.hgsc.bcm.tmc.edu/blast/blast.cgi?organism= Tcastaneum http://www.ncbi.nlm.nih.gov/genome/seq/BlastGen/BlastGen.cgi?taxid= 7070 http://www.genboree.org/java-bin/login.jsp http://www.ncbi.nlm.nih.gov/mapview/ 2006 Array design and probe synthesis Tribolium dme-miR-iab-4 http://www.affymetrix.com/support/developer/tools/download_igb.affx Tribolium 2002 2006 Fluorescent in situ hybridization 2004 Tribolium AGATAAGATATAATGAGGTGTAGAGTTG TGATTAACATGGACGGCTTCATTAG CATCCTATGCACATGCGTTC CGTTTTAATGGGTGCATCGT Genetics 1989 mxp Dch-3 Ey Cx 6 A Es ptl KT76 Cx 61 A Es ptl D60 Ey Dfd 1 A Es Eyeless Ey 1996 Abdominal Extra sclerite A Es 1989 2000 RNAi ptl Tc-Antp ptl D60 ptl D60 1993 1997 1993 Tribolium mxp Dch-3 Tribolium mxp Dch-3 Ey A Es Ey 1990 mxp Dch-3 Hin mxp Tc-pb 1988 mxp Dch-3 mxp Dch-3 Ey Eco Hin Rsa Tribolium ptl KT76 ptl KT76 2007 Results Tribolium Tribolium 2002 Tribolium Tribolium Ultrabithorax Ubx 1999 abdominal-A abd-A 1998 Abdominal-B Abd-B Drosophila 1987 2002 Tribolium Tribolium 2008 Tc-Deformed Tc-Dfd Tc-zen1 prothoraxless Tc-Antennapedia ptl Tc-Antp Tc-fushi tarazu Tc-ftz Tribolium Tribolium Drosophila fushi tarazu zerknüllt zen Tribolium 2008 1 zen Tribolium zen Drosophila 2002 Apis 2006 2007 Drosophila Anopheles 2007 Tribolium 1 miR-10 miR-iab-4 Tribolium 2005 1 Fig. 1 Tribolium Tribolium below PPI upper left and right corners of the panel cyan gray arrow Red arrows  Drosophila melanogaster Tribolium Tribolium 2008 Tribolium Tribolium D. melanogaster Tribolium Tribolium Tribolium 2003 2007 Drosophila 2004 Tribolium 1 Drosophila Apis 2006 Tribolium 2005 Tribolium Tribolium Tc-chaoptic Tc-labial Tc-lab 2001 Tc_00927 D. melanogaster Tc-Abd-B Tc_00887 Tc_00664 Tc_00665 Tc_00666 D. melanogaster Tc_00886 D. melanogaster Anopheles gambiae Apis mellifera lab Abd-B D. melanogaster Tribolium Tribolium Tribolium maxillopedia Tc-proboscipedia mxp Tc-pb Tc-Abd-B 1 tca-miR-10 tca-miR-iab-4 tca-miR-10 tca-miR-iab-4 2 Fig. 2 Tribolium 1 a ptl Tc-Antp b Tribolium tca-miR-iab-4  ptl Tc-Antp Ultrathorax Tc-Ultrabithorax Utx Tc-Ubx ptl Tc-Antp Utx Tc-Ubx 1 2 Tribolium tca-miR-10 rRNA ptl Tc-Antp Utx Tc-Ubx Utx Tc-Ubx mxp Dch-3 mxp Tc-pb Cx Tc-Scr mxp Dch-3 mxp Tc-pb 2000 mxp Dch-3 mxp Tc-pb mxp Tc-pb Cephalothorax Tc-Sex combs reduced Cx Tc-Scr mxp Tc-pb mxp Dch-3 mxp Tc-pb 2000 mxp Dch-3 Cx Tc-Scr Cx Tc-Scr Tc-Dfd ptl Tc-Antp mxp Dch-3 mxp Dch-3 Tc-zen1 Tc-zen2, Tc-Dfd Cx Tc-Scr Tc-ftz 3 mxp Dch-3 1996 mxp Dch-3 2000 TFIIA-L 1993 groucho Drosophila 1997 1994 Tc-ftz ptl Tc-Antp mxp Dch-3 Cx Tc-Scr mxp Tc-pb Cx Tc-Scr mxp Tc-pb mxp Dch-3 Fig. 3 underlined purple a mxp Dch-3 b ptl D60 ptl Tc-Antp  Cx Tc-Scr ptl Tc-Antp 1993 Cx Tc-Scr ptl Tc-Antp ptl D60 ptl Tc-Antp ptl D60 ptl Tc-Antp 1993 ptl D60 ptl D2 ptl Tc-Antp 2005 ptl Tc-Antp Cx Tc-Scr ptl D60 ptl Tc-Antp 4 ptl D60 4 ptl D60 ptl Tc-Antp ptl D60 ptl Tc-Antp ptl D60 Tribolium 2006 2000 1991 1997 ptl D60 ptl Tc-Antp Cx Tc-Scr Fig. 4 ptl Tc-Antp ant lab T1–T3 a e a ptl Tc-Antp b ptl D60 ptl D60 c ptl KT76 ptl KT76 d ptl KT76 ptl D60 e ptl KT76 f purple g ptl KT76 h i  ptl D60 ptl Tc-Antp Cx Tc-Scr ptl D60 ptl Tc-Antp 3 ptl Tc-Antp ptl D60 Reindeer 1996 ptl Tc-Antp ptl Tc-Antp Cx Tc-Scr Cx Tc-Scr Discussion Cx Tc-Scr ptl Tc-Antp ptl 5 4 4 Cx Tc-Scr 2001 4 Cx Tc-Scr Cx Tc-Scr 4 ptl D60 ptl D60 ptl D60 4 Cx 61 Cx Tc-Scr 2006 ptl Tc-Antp ptl KT76 mxp Dch-3 ptl D60 Cx Tc-Scr ptl KT76 Cx Tc-Scr ptl Tc-Antp Fig. 5 Cx Tc-Scr ptl Tc-Antp ptl Tc-Antp shaded gray Cx Tc-Scr ptl Tc-Antp below the diagram  Discussion Drosophila of Apis Anopheles Tribolium Tribolium Tribolium Temporal colinearity 2006 Tribolium Tribolium ptl D60 ptl Tc-Antp Cx Tc-Scr mxp Dch-3 Tc-zen Tc-Dfd Cx Tc-Scr Tc-ftz Tc-Dfd mxp Dch-3 Tc-Dfd mxp Tc-pb Drosophila 1986 1988 Tribolium Tribolium Regulatory elements Drosophila 2005 2007 abd-A Abd-B Drosophila 2007 Drosophila Drosophila Drosophila abd-A and Abd-B 2007 Tribolium 2003 2001 2007 Tribolium ptl Tc-Antp Tribolium Cx Tc-Scr pt Tc-Antp 5 Cx Tc-Scr mxp Dch-3 ptl D60 mxp Dch-3 ptl D60 mxp Tc-pb Cx Tc-Scr mxp Dch-3 mxp Tc-pb Tc-ftz ptl Tc-Antp Cx Tc-Scr ptl Tc-Antp ptl D60 Cx Tc-Scr ptl Tc-Antp piggyBac ptl Tc-Antp ptl K76 Cx Tc-Scr Drosophila Scr ftz Antp 1995 Scr Antp Scr Drosophila Drosophila Tribolium Noncoding transcripts 1990 1987 1989 miR-196 miR-iab-4 2005 2005 2002 2007 2006 Drosophila 2006 2006 2007 Tribolium ptl Tc-Antp Utx Tc-Ubx Antp Ubx 2006 2006 The data available thus far indicate that noncoding transcripts are prevalent in both intact and broken Hox clusters. However, it is not clear whether these transcripts perform the same functions in all organisms. Perhaps, noncoding RNAs play a different or more critical role in organisms with intact clusters. Future studies in this area are likely to provide important insights into Hox gene function and possibly into Hox cluster conservation. Conclusions 2003 Tribolium