Table 1.

Epigenetic modifications associated with the supernumerary L chromosomes at different stages of development. L chromosomes have epigenetic profile characteristic of constitutive heterochromatin. Apart from the first somatic mitosis, the L chromosomes are de-acetylated. Where investigated, L chromosomes also share the repressive epigenetic modifications and non-histone heterochromatin protein 1 (HP1) chromosomal proteins. Analyses of phosphorylation show that during the somatic eliminations the arms of the L chromosomes retain phosphorylation with H3S10P. During meiosis L chromosomes show a complex pattern of phosphorylation (see text for details). Data for acetylation is taken from [9]. The distribution of repressive epigenetic modifications and HP1 proteins was taken from Figures 6 and 7 of [13] in “pre-meiotic” and “young germ nuclei” that are likely to be in or around larval mitosis I. For description of phosphorylation during the meiotic divisions, the data was taken from [15]. For phosphorylation of L chromosomes in the embryonic soma the data was taken from [16].

Stage	Epigenetic Modifications
First somatic division	L chromosomes are positive for H4K8Ac [9]
Syncytial embryo before elimination	L chromosomes are positive for H3S10P at pro-metaphase [16]. Proceeding to metaphase they become positive for H3S28P [16]. The centromeres are specifically stained with H3T3P antibodies at metaphase [16].
Syncytial embryo during elimination	L chromosome arms are stained with H3S10P at metaphase/anaphase [16]. By contrast, the regulars have lost their H3S10P staining at anaphase.
Resting stage germ cells before elimination of Xp	L chromosomes are negative for H4K8Ac, H4K12Ac and PanH3Ac [9].
Resting stage germ cells after elimination of Xp	L chromosomes are negative for H4K8Ac, H4K12Ac and PanH3Ac [9].
Germ cells undergoing larval mitosis I (9th day after oviposition)	L chromosomes are negative for H4K8Ac [9]. They are positive for H3K9me2, H3K9me3, H4K20me3, 5MeC and the two HP1-like proteins ScoHET1 and ScoHET2 [13].
Germ cells at end of mitosis III in third instar larvae (12th day after oviposition)	L chromosomes are negative for H4K8Ac [9].
Prophase of Meiosis I	L chromosomes are negative for H3S10P, H3S28P and H3T3P but positive for H3T11P [15]
Meiosis I	L chromosomes are negative for H3S10P, H3S28P and H3T3P but positive for H3T11P [15]. They are also negative for H4K8Ac [9].
Meiosis II	L chromosomes are positive for H3S10P, H3S28P and H3T3P and H3T11P [15]. They are also positive for ScoHET1 [13].