Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail

Abstract

The canonical histone proteins are encoded by replication-dependent genes and must rapidly reach high levels of expression during S phase. In metazoans the genes that encode these proteins produce mRNAs that, instead of being polyadenylated, contain a unique 3' end structure. By contrast, the synthesis of the variant, replication-independent histones, which are encoded by polyadenylated mRNAs, persists outside of S phase. Accurate positioning of both histone types in chromatin is essential for proper transcriptional regulation, the demarcation of heterochromatic boundaries and the epigenetic inheritance of gene expression patterns. Recent results suggest that the coordinated synthesis of replication-dependent and variant histone mRNAs is achieved by signals that affect formation of the 3' end of the replication-dependent histone mRNAs.

Figure 1. Structure and formation of canonical histone mRNAs

a The structure of a metazoan canonical histone mRNA. There are no introns in these genes, and the mRNAs have short 5′ and 3′ UTRs. The distance from the stop codon to the start of the conserved 26 nucleotide (nt) sequence at the 3′ end of the mRNA is 25–60 nucleotides and this distance is crucial for regulation of histone mRNA stability. b Processing of mammalian canonical histone pre-mRNA. These pre-mRNAs contain the conserved stem–loop sequence that binds stem–loop binding protein (SLBP) followed by the histone downstream element (HDE), which base-pairs with U7 small nuclear RNA (snRNA). A cleavage complex containing CPSF73 (cleavage and polyadenylation specificity factor subunit 73), CPSF100, symplekin, and possibly FIP1 as well as some unknown factors (not shown) is recruited to cleave the pre-mRNA. Within this complex, CPSF73 is the endonuclease that performs the cleavage (arrow), which occurs five nucleotides downstream of the stem–loop and upstream of the HDE. The U7 snRNA is a component of the U7 small nuclear ribonucleoprotein (snRNP), which contains a heptameric ring of five Sm proteins (blue circles) and two U7 snRNP-specific Sm-like proteins, LSM11 and LSM10 (blue ovals). LSM11 contacts a 100 kDa zinc finger protein (ZFP100), which also interacts with the SLBP–stem–loop complex. c The stem–loop structure of the three histone mRNAs from metazoans that show the greatest divergence (top), and from four protozoans (bottom), showing the limited range of sequence divergence. Nucleotide positions identified as crucial for SLBP binding, in mammals are shown in red. Deviations from the consensus stem–loop are in green. Asterisks indicate lack of Watson–Crick base-pairing.

Figure 2. Global view of histone mRNA metabolism in mammalian cells

Transcription of the canonical histone genes and processing of the resulting pr e -mRNA occur close to a Cajal body. The U7 small nuclear ribonucleoprotein (snRNP), stem–loop binding protein (SLBP), and the cleavage complex are responsible for the cleavage of the pre-mRNA from the DNA template, forming the mature histone mRNA. SLBP remains bound to the histone mRNA as it goes to the cytoplasm, where histone mRNA is circularized through a complex of proteins including at least SLBP, SLBP-interacting protein 1 (SLIP1) and eukaryotic translation initiation factor 4-γ (EIF4G) mediating translation of histone mRNA. At the end of S phase, a short U tail is added to histone mRNA in the cytoplasm. The LSM1–7 ring binds the oligo(U) to cooperate in the recruitment of the decapping complex and the exosome to degrade the mRNA in both the 5′ to 3′ and 3′ to 5′ direction. In addition, cyclin A (CycA)–CDK1 (cyclin-dependent kinase 1) phosphorylates SLBP to trigger its degradation at the end of S phase, preventing further histone mRNA synthesis. CPSF, cleavage and polyadenylation specificity factor; DCP, mRNA decapping enzyme; HDE, histone downstream element; LSM, Sm-like protein; NPAT, nuclear protein, ataxia-telangiectasia locus; Pol, polymerase; TUTase, terminal uridylyltransferase; XRN1, 5′–3′ exoribonuclease 1.

Figure 3. The Cajal body and the histone locus body (HLB)

a HLB in Drosophila melanogaster embryonic blastoderm nuclei. LSM11 and MPM2 co-localize with the histone locus (detected by fluorescence in situ hybridization). Note that these diploid cells have either one or two HLBs, depending on whether homologous chromosomes are paired. Images reproduced, with permission, from REF. © 2007 The American Society for Cell Biology. b HLB (LSM11) and Cajal bodies (coilin) are distinct in D. melanogaster ovarian nurse cells. Note the multiple HLB in these highly polyploid cells. Image provided by Joe Gall, Carnegie Institute, Baltimore, USA. c NPAT and coilin localize to histone genes in a human HeLa cell. Image provided by Greg Matera, The University of North Carolina at Chapel Hill, USA.

Figure 4. Cell-cycle regulation of canonical hist one mRNA

The levels of canonical histone mRNA, SLBP protein and SLBP mRNA during the mammalian cell cycle are shown. Synchronous Chinese hamster ovary (CHO) cells selected by mitotic shake-off were used for measurement of histone mRNA levels by S1 nuclease protection. Histone mRNA degradation and SLBP degradation were measured in detail in HeLa cells synchronized by double thymidine block,. Essentially identical results have been observed in CHO, HeLa and U2OS cells synchronized by mitotic shake-off, nocodazole block or double thymidine block. During G1 there are low levels of both SLBP and histone mRNA. Accumulation of histone mRNA requires activation of cyclin E (cycE)–CDK2 (cyclin-dependent kinase 2) and phosphorylation of nuclear protein, ataxia-telangiectasia locus (NPAT). Histone mRNAs then increase rapidly as cells enter S phase. Completion of DNA synthesis at the end of S phase, or the inhibition of DNA replication owing to DNA damage, results in a rapid reduction in the levels of histone mRNA. SLBP protein levels also increase rapidly as cells approach S phase, and are reduced by activation of cycA–CDK1 activity at the conclusion of S phase but not by inhibiting DNA replication during S phase. A defect in active U7 small nuclear ribonucleoprotein (snRNP) results in an arrest in G1, suggesting the existence of a ‘histone checkpoint’ in G1. By contrast, replication-independent histone H3.3 mRNA levels are constant and SLBP mRNA levels only vary slightly during the cell cycle.

Figure 5. Two models for histone variant function in core histone mRNA 3′ end formation

The two sets of histone chaperones, for canonical histones (CAF1 for H3.1 and NAB2 for histone H2A.1) and for replacement variant histones (HIRA for H3.3 and CHZ1 for H2Av), are shown. In the cis model of histone variant function in 3′ end formation, the histone variants are enriched in histone gene chromatin. The presence of the histone variants is necessary for the recruitment of the histone pre-mRNA processing machinery and incorporation of U7 small nuclear ribonucleoprotein (snRNP) into the histone locus body. In the trans model of histone variant function, the lack of sufficient histone variant proteins assembled into bulk chromatin results in the generation of an unknown signal that results in failure to maintain a fully formed histone locus body. One possibility is that ASF1, present in multiple chromatin assembly complexes, has a direct role in the signalling process.

Figure 6. Strategies for supplying canonical histones in early embryogenesis

a In Drosophila melanogaster, histone mRNA is synthesized at the end of oogenesis, translated, and histone protein and mRNA is loaded into the oocyte from the nurse cells. In the early embryo, stem–loop binding protein (SLBP) is not active and no histone mRNA is transcribed, and the stored histone protein provides the supply of histone until histone gene transcription is activated. b In Xenopus laevis, histone mRNA is made early in oogenesis and translated to provide a store of histone protein. Histone mRNA made later in oogenesis is stored in association with a distinct SLBP, SLBP2, which represses histone mRNA translation. SLBP2 is destroyed during oocyte maturation and SLBP1 can then bind, activating translation of the stored histone mRNA. The combination of stored histone protein, synthesized early in oogenesis, and newly synthesized histone protein provides the histones until zygotic transcription is activated. c In the sea urchin Strongylocentrus purpuratus, histone mRNA is synthesized and retained in the pronucleus after completion of meiosis, where it is probably complexed with SLBP. The histone messenger ribonucleoprotein (mRNP) is released after the first mitosis, allowing translation of histone mRNA in the next cell cycle. d In the mouse, histone mRNA and SLBP mRNA are synthesized in the oocyte but SLBP protein does not accumulate. During oocyte maturation, SLBP rapidly accumulates owing to translation of the maternal mRNA. This SLBP can then activate the translation of maternal histone mRNA.