Analysis of the Hox epigenetic code

Table 1 Methylation of H3K4, H3K9, H3K27 and H3K36

i	H3K4me(i)	H3K9me(i)	H3K27me(i)	H3K36me(i)
0	Off	On	On	Off
1	On	Off	Off	On
2	On	Off	Off	On
3	On	Off	Off	On

i=0 the me(i) part will be equal to zero which means that the histone is not methylated. Here the “On” state represents the transcriptionally euchromatin; and the “off” state represents the constitutive heterochromatin.

Table 2 Known roles of Ras-superfamily GTPases in Caenorhabditis elegans: Homologs in humans

C.elegansgene name	Human homolog	Developmental role(s)
Ras/Rap/Ral family
let-60	K-Ras	Cell fate determination, oocyte meiotic maturation, sex myoblast migration, axon pathfinding, olfaction, response to microbacterium nematophilum infection
Rho family
rho-1	RhoA	Cytokinesis, hypodermal contraction, P cell migration, axon pathfinding
cdc-42	Cdc42	Cytokinesis, embryonic polarity, axon pathfinding
ced-10	Rac1	Gastrulation, cell migration (P cells, distal tip cells), cell corpse phagocytosis, neuronal migration, axon pathfinding, vulval morphogenesis
rac-2	Rac1	Neuronal migration, axon pathfinding
mig-2	Mtl	Cell migration (P-cells, distal tip cells, Q cells and descendants), neuronal migration, axon pathfinding, vulval morphogenesis
Rab family
rab-1	Rab1	Innate immunity gene expression
rab-3	Rab3	Synaptic vesicle trafficking and release
Arf/Sar family
arl-6	Arf6	Ciliary vesicle trafficking and Bardet-Beidl syndromes
evl-20	Arf2	Microtubule organization, vulval cell division, tissue morphogenesis
Ran family
ran-1	Ran	Nuclear trafficking, nuclear reassembly, Kinetechore association with the mitotic spindle

Table 3 Caenorhabditis elegans orthologs of mammalian autophagy-related genes

C. elegans gene	Mammalian gene	Function
erp-1	Bif-1	Bax interacting factor that associates with Uvrag and Beclin 1
C33A11.4	DRAM	p53-induced damage-regulated
ced-9	Bcl-2	Anti-apoptotic protein, negative regulator of Beclin 1-mediated autophagy

Table 4 Ubiquitin-conjugating enzymes in Caenorhabditis elegans: homologs and loss-of-function phenotypes

C. elegans	Peptide-conjugated	Human	Phenotypes
ubc-1	Ub	UBE2A; UBE2B	WT (RNAi)
ubc-2/let-70	Ub	UBE2D1/UBCH5A; UBE2D2/UBCH5B; UBE2D3/UBCH5C	embryonic arrest at pre-comma stage (RNAi)
ubc-3	Ub	CDC34; FLJ20419	WT (RNAi)
ubc-6	Ub	NCUBE1	WT (RNAi)
ubc-7	Ub	UBE2G1	WT (RNAi)
ubc-8	Ub	UBE2H	WT (RNAi)
ubc-9	SUMO	UBE2I	embryonic arrest post- gastrulation before muscle movement (RNAi)
ubc-12	NED-8 (Nedd8)	UBE2M	embryonic arrest at the comma stage (RNAi)
ubc-13	Ub	UBE2N; BAA93711	WT (RNAi)
ubc-14	Ub	UBE2G2	embryonic arrest post- gastrulation before muscle movement (RNAi)
ubc-15	Ub	NCUBE1	WT (RNAi)
ubc-18	Ub	UBE2L1; UBE2L3/ UBCH7; UBE2L6	reduced growth rate and brood size (mut)
ubc-20	Ub	HIP2	impenetrant L3 and L4 larval arrest (RNAi)
ubc-21	Ub	HIP2	WT (RNAi)
ubc-22	Ub	UBE2L1; UBE2L3/ UBCH7; UBE2L6	WT (RNAi)
ubc-23	Ub	HIP2	WT (RNAi)

Table 5 Hox genes of the Caenorhabditis elegans: Homologs of humans

Gene product		Mammalian relative(s)	Molecular function
EGL-5	EGg- laying defects	Hox9-13 (all human posterior Hox genes)	Hox transcription factor. Upregulated by Ras signaling.
LIN-39	Abnormal cell LINeage	HoxB5	Hox transcription factor. Upregulated by Ras signaling.