No abstract

Biological responses to histone methylation critically depend on the faithful readout and transduction of the methyl-lysine signal by "effector" proteins, yet our understanding of methyl-lysine recognition has so far been limited to the study of histone binding by chromodomain and WD40-repeat proteins. The double tudor domain of JMJD2A, a Jmjc domain-containing histone demethylase, binds methylated histone H3-K4 and H4-K20. We found that the double tudor domain has an interdigitated structure, and the unusual fold is required for its ability to bind methylated histone tails. The cocrystal structure of the JMJD2A double tudor domain with a trimethylated H3-K4 peptide reveals that the trimethyl-K4 is bound in a cage of three aromatic residues, two of which are from the tudor-2 motif, whereas the binding specificity is determined by side-chain interactions involving amino acids from the tudor-1 motif. Our study provides mechanistic insights into recognition of methylated histone tails by tudor domains and reveals the structural intricacy of methyl-lysine recognition by two closely spaced effector domains.

Highlights d RNA-BisSeq revealed a dynamic RNA m 5 C landscape during zebrafish embryogenesis d Ybx1 preferentially recognizes m 5 C-modified mRNAs d Ybx1 deficiency leads to early gastrulation defects in zebrafish embryos d Ybx1 and Pabpc1a coordinately regulate m 5 C-modified maternal mRNA stability

SUMMARYIron excess is closely associated with tumorigenesis in multiple types of human cancers, with underlying mechanisms yet unclear. Recently, iron deprivation has emerged as a major strategy for chemotherapy, but it exerts tumor suppression only on select human malignancies. Here, we report that the tumor suppressor protein p53 is downregulated during iron excess. Strikingly, the iron polyporphyrin heme binds to p53 protein, interferes with p53-DNA interactions, and triggers both nuclear export and cytosolic degradation of p53. Moreover, in a tumorigenicity assay, iron deprivation suppressed wild-type p53-dependent tumor growth, suggesting that upregulation of wild-type p53 signaling underlies the selective efficacy of iron deprivation. Our findings thus identify a direct link between iron/heme homeostasis and the regulation of p53 signaling, which not only provides mechanistic insights into iron-excess-associated tumorigenesis but may also help predict and improve outcomes in iron-deprivation-based chemotherapy.

Piwi proteins are modified by symmetric dimethylation of arginine (sDMA), and the methylarginine-dependent interaction with Tudor domain proteins is critical for their functions in germline development. Cocrystal structures of an extended Tudor domain (eTud) of Drosophila Tudor with methylated peptides of Aubergine, a Piwi family protein, reveal that sDMA is recognized by an asparagine-gated aromatic cage. Furthermore, the unexpected Tudor-SN/p100 fold of eTud is important for sensing the position of sDMA. The structural information provides mechanistic insights into sDMA-dependent Piwi-Tudor interaction, and the recognition of sDMA by Tudor domains in general.Supplemental material is available at http://www.genesdev.org.Received June 3, 2010; revised version accepted July 13, 2010.Piwi proteins are a conserved subfamily of Argonaute proteins that, together with small RNAs with which they associate (piRNA ½Piwi-interacting RNA), safeguard germline development by silencing transposons (Aravin and Hannon 2008;Lin and Yin 2008). Certain arginine residues at the N termini of Piwi proteins are symmetrically dimethylated by PRMT5, and the post-translational modification is required for interaction with Tudor domain proteins Kirino et al. 2009;Nishida et al. 2009;Reuter et al. 2009;Vagin et al. 2009;Vasileva et al. 2009;Wang et al. 2009;Siomi et al. 2010). In Drosophila, the Piwi family protein Aub is symmetrically dimethylated at Arg11, Arg13, and Arg15, and loss of methylation at these sites disrupts the interaction with the maternal effect protein Tud and reduces association with piRNA (Kirino et al. 2009(Kirino et al. , 2010Nishida et al. 2009). However, a mechanistic understanding of methylarginine-dependent Tud-Aub interaction is lacking. At present, no structure of any protein in complex with a symmetric dimethylation of arginine (sDMA)-modified protein/peptide has been reported. The best characterized sDMA-Tudor interaction to date is the binding of sDMA-modified spliceosomal Sm proteins by the Tudor domain of Survival Motor Neuron (SMN) (Brahms et al. 2001;Friesen et al. 2001;Sprangers et al. 2003), although an understanding of their binding mode in atomic resolution details is still lacking. Interestingly, several Tudor domains have been shown to bind histone tails with methylated lysine residues, and an understanding of the structural basis for methyllysine recognition by Tudor domains has been developed (Botuyan et al. 2006;Huang et al. 2006;Kim et al. 2006). Thus, a pressing matter for understanding the biological functions of Tudor domain proteins is to elucidate the structural determinants responsible for Tudor domain's binding preference for an sDMA or methyllysine, which necessitates the determination of a Tudor domain structure in complex with an sDMA ligand. Results and DiscussionTudor domains 7-11 are sufficient for germ cell formation and Aubergine binding Tud is a large protein (2515 amino acids) comprised of 11 copies of a defined sequence motif, which can be found in many eukaryotic proteins and...

RNA silencing is a conserved regulatory mechanism in fungi, plants and animals that regulates gene expression and defence against viruses and transgenes1. Small silencing RNAs of ~20–30 nucleotides and their associated effector proteins, the Argonaute family proteins, are the central components in RNA silencing2. A subset of small RNAs, such as microRNAs and small interfering RNAs (siRNAs) in plants, Piwi-interacting RNAs in animals and siRNAs in Drosophila, requires an additional crucial step for their maturation; that is, 2′-O-methylation on the 3′ terminal nucleotide3–6. A conserved S-adenosyl-l-methionine-dependent RNA methyltransferase, HUA ENHANCER 1 (HEN1), and its homologues are responsible for this specific modification3–5,7,8. Here we report the 3.1 Å crystal structure of full-length HEN1 from Arabidopsis in complex with a 22-nucleotide small RNA duplex and cofactor product S-adenosyl-l-homocysteine. Highly cooperative recognition of the small RNA substrate by multiple RNA binding domains and the methyltransferase domain in HEN1 measures the length of the RNA duplex and determines the substrate specificity. Metal ion coordination by both 2′ and 3′ hydroxyls on the 3′-terminal nucleotide and four invariant residues in the active site of the methyltransferase domain suggests a novel Mg2+-dependent 2′-O-methylation mechanism.

Alterations in cellular ubiquitin (Ub) homeostasis, known as Ub stress, feature and affect cellular responses in multiple conditions, yet the underlying mechanisms are incompletely understood. Here we report that autophagy receptor p62/sequestosome-1 interacts with E2 Ub conjugating enzymes, UBE2D2 and UBE2D3. Endogenous p62 undergoes E2-dependent ubiquitylation during upregulation of Ub homeostasis, a condition termed as Ub stress, that is intrinsic to Ub overexpression, heat shock or prolonged proteasomal inhibition by bortezomib, a chemotherapeutic drug. Ubiquitylation of p62 disrupts dimerization of the UBA domain of p62, liberating its ability to recognize polyubiquitylated cargoes for selective autophagy. We further demonstrate that this mechanism might be critical for autophagy activation upon Ub stress conditions. Delineation of the mechanism and regulatory roles of p62 in sensing Ub stress and controlling selective autophagy could help to understand and modulate cellular responses to a variety of endogenous and environmental challenges, potentially opening a new avenue for the development of therapeutic strategies against autophagy-related maladies.

Small RNAs have important functions. However, small RNAs in primate oocytes remain unexplored. Herein, we develop CAS-seq, a single-cell small RNA sequencing method, and profile the small RNAs in human oocytes and embryos. We discover a class of ~20-nt small RNAs that are predominantly expressed in human and monkey oocytes, but not in mouse oocytes. They are specifically associated with HIWI3 (PIWIL3), whereas significantly shorter than the commonly known PIWI-interacting RNAs (piRNAs), designated as oocyte short piRNAs (os-piRNAs). Notably, the os-piRNAs in human oocytes lack 2’-O-methylation at the 3’ end, a hallmark of the classic piRNAs. In addition, the os-piRNAs have a strong 1U/10 A bias and are enriched on the antisense strands of recently evolved transposable elements (TEs), indicating the potential function of silencing TEs by cleavage. Therefore, our study has identified an oocyte-specific piRNA family with distinct features and provides valuable resources for studying small RNAs in primate oocytes.