A New Family of ‘‘H3L-Like’’ Histone Genes P. Mancini, 1 G. Pulcrano, 1 M. Piscopo, 1 F. Aniello, 1 M. Branno, 2 L. Fucci 1 1 Department of Genetics, General and Molecular Biology, University of Naples Federico II, Via Mezzocannone 8, 80134 Naples, Italy 2 Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy Received: 22 October 2003 / Accepted: 18 March 2004 Abstract. The H3L histone variant gene in Para- centrotus lividus (sea urchin) shows almost all typical features of the replication-dependent histone genes, but it codes for the H3.3 histone protein with the S.//. A.IG amino acid motif, which is typical of the vari- ants synthesized in a replication-independent manner. ‘‘H3L-like’’ histone genes have been found in several unrelated organisms. These genes are intronless and encode for the typical H3.3 histone proteins. The newly described family of H3L-like variants, nearly ubiquitous within the animal kingdom, could repre- sent the common ancestor of H3 and H3.3 histone genes. Key words: Histones — Genes — cDNAs — Re- plication-dependent genes — Replacement variants — H3.3 histones — H3L histones In eukaryotic cells, different levels of chromatin condensation might act as key regulators in the as- sessment of peculiar profiles of gene regulation (Gregory and Ho¨rz 1998; Kingston and Narlikar 1999). Such structural flexibility of chromatin de- pends on several factors such as histone type and their modifications (Davie 1998; Suto et al. 2000). Histone genes are usually classified into ‘‘replica- tion-dependent’’ and ‘‘replication-independent’’ var- iants based on their expression profile (Osley 1991). Replication-dependent histone genes are actively ex- pressed only at the G1/S boundary during the cell cycle. Unlike other eukaryotic genes, they are intronless and are transcribed into short mRNAs with very short 3¢ untranslated regions (3¢ UTRs). Moreover, transcripts of replication-dependent hi- stone genes are not polyadenylated and terminate with a well-conserved, stem-loop palindromic se- quence (Osley 1991; Schu¨mperli 1986). These genes are often present in the genome in multiple copies with different organization (Maxson et al. 1983). By contrast, replication-independent histone genes, also called ‘‘replacement’’ or ‘‘basal’’ variants, are tran- scribed constitutively at the basal level during the entire cell cycle. They are also expressed in terminally differentiated or quiescent cells. With the exception of lower eukaryotes, whose histone genes are always intronless (Thatcher et al. 1994), most of the re- placement histone genes are generally splitted by in- trons. Mature transcripts of these genes are quite large, show long 3¢ UTRs, and are usually poly- adenylated (Osley 1991; Schu¨mperli 1986). H3.3 histone proteins, which have been studied in several organisms (Thatcher et al. 1994), are encoded by the replacement variant genes. Such proteins show only four differences compared with the consensus amino-acid sequence of the ‘‘major’’ H3 histone family. In particular, S residue substitutes A in po- sition 31, and residues A, I, and G, respectively, re- place S, V, and M in positions 87, 89, and 90 (S.//.A. IG motif). Recently, Frank et al. (2003) showed that human H3.3 genes are essentially expressed in adult tissue, whereas H3 is transcribed in fetal tissue. A large number of H3.3 pseudogenes were identified in humans by Wells et al. in 1987. Correspondence to: L. Fucci; email: fucci@cds.unina.it J Mol Evol (2004) 59:458–463 DOI: 10.1007/s00239-004-2637-4