Histone methylation is a dynamic process that plays important roles in gene transcription regulation, and a number of enzymes have been shown to catalyze the removal of methyl marks 1. Shi et al. (2004) identified one of the amino oxidases, lysine-specific demethylase 1 (LSD1), as the first specific demethylase for both mono- (me) and dimethylation (me2) of H3K4 and H3K9 in humans 2. Subsequently, a total of 27 JmjC-domain-containing proteins have been discovered within the human genome, and 15 of them exhibit demethylation activities for specific lysines in the H3 tail 1. DmUTX, DmKDM2, DmLid, and DmKDM4 are JmjC-domain-containing histone demethylases found in Drosophila 3, 4, 5, 6. JmjC-domain-containing histone demethylases have also been reported in Arabidopsis 7. Here, we examined the lysine methylation patterns of histone H3 in Bombyx mori, a biological model for lepidopteran insects, and showed that a putative histone H3 lysine demethylase, BmLid, has a much broader in vitro substrate specificity than its homolog in other species, exhibiting demethylase activity toward both tri- (me3) and dimethylated (me2) K4 and K9, as well as dimethylated K27. Evidence is also presented suggesting that the absence of a PLU domain in BmLid may be partially responsible for this broader in vitro H3 lysine substrate specificity.

We then performed a sequence homology search for putative demethylases in the silkworm genome (http://silkworm.genomics.org.cn/), and found only two putative JmjC-domain-containing proteins, BmLid and BmKDM4 (GU365867). We cloned a JmjC-domain-containing protein with 53% (Figure 1B) similarity to DmLid and named it BmLid (GU365866). BmLid was revealed as a 3 589-bp full-length cDNA. The open reading frame (ORF) of BmLid is 2 439 bp, encoding 813 amino acid residues with a predicted molecular weight (MW) of 93.5 kDa and a calculated pI of 5.65 (Supplementary information, Figure S2). Confirmation has been made by PCR using primers derived from both 5′ and 3′ UTR of BmLid (Supplementary information, Table S1). A BLAST search based on the latest version of silkworm genome also confirmed the ORF integrity of BmLid (data not shown). Phylogenetic analysis indicated that BmLid was most closely related to DmLid (Figure 1C, Supplementary information, Table S2). Sequence similarity between BmLid and other JmjC-domain-containing proteins was as follows: DmLid (53%), HsJARID1A (50%), HsJARID1B (50%), HsJARID1C (48%), and HsJARID1D (49%) (Figure 1B). Therefore, the JmjC domain is highly conserved from insects to mammals. The deduced BmLid protein also contains a JmjN domain, an ARID/BRIGHT domain, a zf-C5HC2 zinc-finger (ZF) domain and a PHD zinc-finger domain. We also found that BmLid is shorter (813 amino acids) than members of the JARID1 subfamily and DmLid (> 1 500 amino acids); and it is missing the sequence after the ZF domain, including a PLU domain (Figure 1B) 8. There are fewer JmjC domain proteins in silkworm than in Drosophila and humans 2. The missing sequence in BmLid suggests a different demethylation mechanism in silkworms than that in Drosophila and humans.

Log in or create a free account to read this content

Gain free access to this article, as well as selected content from this journal and more on nature.com

Access through your institution

or

Sign in or create an account
Continue with Google
Continue with ORCiD