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Tudor domain proteins in development
Abstract and Figures
Tudor domain proteins function as molecular adaptors, binding methylated arginine or lysine residues on their substrates to promote physical interactions and the assembly of macromolecular complexes. Here, we discuss the emerging roles of Tudor domain proteins during development, most notably in the Piwi-interacting RNA pathway, but also in other aspects of RNA metabolism, the DNA damage response and chromatin modification.
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... Arginine methylation could potentially alter protein structures, impact protein-DNA/RNA integrations, and generate docking sites for effector proteins (Figure 2). The Tudor domain-containing proteins are the "primary" readers of methylarginine modifications (Chen et al., 2011;Pek et al., 2012). Tudor domains are~60 amino acids in size and use conserved aromatic residues to build an "aromatic cage" and bind methylated-arginine through cation-π and π-π stacking interactions (Selenko et al., 2001;Sprangers et al., 2003;Friberg et al., 2009;Liu et al., 2010). ...
... Although it is not possible to predict the binding specificity based on their primary amino acid sequences, structure analyses suggest that the methylarginine binding Tudor domains form a relatively narrower aromatic cage than the methyllysine Tudor domains, thus, favoring the docking of the planar methyl-guanidinium group of the arginine . A "common" mechanism of action for the Tudor domain containing proteins is to function as a scaffold that links methylated arginine or lysine marks to downstream effectors with specific catalytic activities, so that the methylation signal can be interpretated or transduced in support of cellular function (Pek et al., 2012). This working model is well exemplified by the Tudor domain containing protein 3 (TDRD3), which harbors a Tudor domain at C-terminus that reads active methylarginine histone marks and an oligonucleotide/oligosaccharide binding (OB) fold at N-terminus that interacts with the DNA topoisomerase 3B (TOP3B) (Yang et al., 2010;Siaw et al., 2016). ...
Arginine methylation is a prevalent post-translational modification found in all eukaryotic systems. It involves the addition of a methyl group to the guanidino nitrogen atoms of arginine residues within proteins, and this process is catalyzed by a family of enzymes called protein arginine methyltransferases (PRMTs). In mammals, there exist nine PRMTs (PRMT1–9) that catalyze three distinct types of arginine methylation: monomethylarginine, asymmetric dimethylarginine, and symmetric dimethylarginine. These modifications play critical roles in numerous fundamental cellular processes, including transcription, RNA metabolism, genome maintenance, and signaling transduction. Aberrations in protein arginine methylation have been implicated in various human diseases, such as neurodevelopmental disorders and cancer. This review offers a general overview of arginine methylation, covering its deposition, its impact on protein function, and the diverse regulatory mechanisms involved. We specifically focus on an in-depth view of the role of arginine methylation in transcription and the epigenetic regulation of gene expression. Readers are directed towards additional reviews that encompass other aspects of arginine methylation biology.
... So far, the Tudor domain is the primary reader identified to bind sDMA motifs in eukaryotes (38)(39)(40), and the roles of Tudor domain containing proteins in germline development and fertility have been well described in metazoan (41)(42)(43). Actually, many evidences support that extended T udor domains (eT udor)-containing proteins ( 44 ,45 ) such as TSN ( T udor S taphyloccocal N uclease) are bona fide AGO / PIWI sDMA readers, as has been shown more recently for plants ( 18 -21 ,46 ). Arabidopsis encodes two TSN proteins, AtTSN1 and AtTSN2, which are highly similar (84% of identity) and functionally redundant ( 47 ). ...
Arginine/R methylation (R-met) of proteins is a widespread post-translational modification (PTM), deposited by a family of protein arginine/R methyl transferase enzymes (PRMT). Regulations by R-met are involved in key biological processes deeply studied in metazoan. Among those, post-transcriptional gene silencing (PTGS) can be regulated by R-met in animals and in plants. It mainly contributes to safeguard processes as protection of genome integrity in germlines through the regulation of piRNA pathway in metazoan, or response to bacterial infection through the control of AGO2 in plants. So far, only PRMT5 has been identified as the AGO/PIWI R-met writer in higher eukaryotes. We uncovered that AGO1, the main PTGS effector regulating plant development, contains unique R-met features among the AGO/PIWI superfamily, and outstanding in eukaryotes. Indeed, AGO1 contains both symmetric (sDMA) and asymmetric (aDMA) R-dimethylations and is dually targeted by PRMT5 and by another type I PRMT in Arabidopsis thaliana. We showed also that loss of sDMA didn’t compromise AtAGO1 subcellular trafficking in planta. Interestingly, we underscored that AtPRMT5 specifically promotes the loading of phasiRNA in AtAGO1. All our observations bring to consider this dual regulation of AtAGO1 in plant development and response to environment, and pinpoint the complexity of AGO1 post-translational regulation.
... Interestingly, simr-1 mutants de-silence a piRNA sensor and lose small RNAs specifically mapping to piRNA targets (Manage et al., 2020). This mutant phenotype, along with a conserved role of Tudor domain proteins in both piRNA pathways and in protein-protein interactions (Pek et al., 2012), leads to the hypothesis that SIMR foci act in part to direct piRNA target genes to Mutator foci for downstream siRNA amplification (Manage et al., 2020). Furthermore, RSD-2 acts in the exogenous siRNA pathway to ensure efficient RNAi, suggesting that SIMR foci are a compartment of nuage that more generally mediates the transition between primary and secondary small RNA pathways (Han et al., 2008;Manage et al., 2020;Sakaguchi et al., 2014;Zhang et al., 2012). ...
RNA silencing pathways are complex, highly conserved, and perform critical regulatory roles. In C. elegans germlines, RNA surveillance occurs through a series of perinuclear germ granule compartments—P granules, Z granules, SIMR foci, and Mutator foci—multiple of which form via phase separation. While functions of individual germ granule proteins are well-studied, the relationships between germ granule compartments (collectively, “nuage”) are less understood. We find that key germ granule proteins assemble into separate but adjacent condensates, and that boundaries between germ granule compartments reestablish after perturbation. We discover a toroidal P granule morphology which encircles the other germ granule compartments in a consistent exterior-to-interior spatial organization, providing broad implications for the trajectory of an RNA as it exits the nucleus. Moreover, we quantify the stoichiometric relationships between germ granule compartments and RNA to reveal discrete populations of nuage that assemble in a hierarchical manner and differentially associate with RNAi-targeted transcripts, possibly suggesting functional differences between nuage configurations. Our work creates a more accurate model of C. elegans nuage and informs the conceptualization of RNA silencing through the germ granule compartments.
... d Cumulative fraction of variance explained of eGene expression was calculated using sequential addition of the following covariates: SNP, 3 PCs, 10 PEER factors, copy number variation, cell fractions of six cell types, and the cis-eQTLs(ci) in each cell type. The center lines represent the median value gene encodes a plant Tudor-like protein with possible chromatin-associated functions in A. thaliana (Pek et al. 2012;Xu et al. 2014). Gene ontology (GO) functional enrichment analysis (https:// cn. ...
Key message
This study provided important insights into the genetic architecture of variations in A. thalianaleaf ionome in a cell-type-specific manner.
Abstract
The functional interpretation of traits associated variants by expression quantitative trait loci (eQTL) analysis is usually performed in bulk tissue samples. While the regulation of gene expression is context-dependent, such as cell-type-specific manner. In this study, we estimated cell-type abundances from 728 bulk tissue samples using single-cell RNA-sequencing dataset, and performed cis-eQTL mapping to identify cell-type-interaction eQTL (cis-eQTLs(ci)) in A. thaliana. Also, we performed Genome-wide association studies (GWAS) analyses for 999 accessions to identify the genetic basis of variations in A. thaliana leaf ionome. As a result, a total of 5,664 unique eQTL genes and 15,038 unique cis-eQTLs(ci) were significant. The majority (62.83%) of cis-eQTLs(ci) were cell-type-specific eQTLs. Using colocalization, we uncovered one interested gene AT2G25590 in Phloem cell, encoding a kind of plant Tudor-like protein with possible chromatin-associated functions, which colocalized with the most significant cis-eQTL(ci) of a Mo-related locus (Chr2:10,908,806:A:C; P = 3.27 × 10–27). Furthermore, we prioritized eight target genes associated with AT2G25590, which were previously reported in regulating the concentration of Mo element in A. thaliana. This study revealed the genetic regulation of ionomic variations and provided a foundation for further studies on molecular mechanisms of genetic variants controlling the A. thaliana ionome.
... A lack of the characteristic aromatic cage and acidic amino acids suggests that they will not bind symmetrically dimethylated arginines and can use these domains to bind PID-2 non-simultaneously. Tudor domains are known to function as 'adaptors' [36], and therefore the role of PID-4/5 may be to act as mediators of the downstream effectors PMRT-5 and APP-1, respectively, for the modification of RNAe proteins. ...
A novel protein, PID-5, has been shown to be a requirement for germline immortality and has recently been implicated in RNA-induced epigenetic silencing in the Caenorhabditis elegans embryo. Importantly, it has been shown to contain both an eTudor and aminopeptidase P-related domain. However, the silencing mechanism has not yet been fully characterised. In this study, bioinformatic tools were used to compare pre-existing aminopeptidase P molecular structures to the AlphaFold2-predicted aminopeptidase P-related domain of PID-5 (PID-5 APP-RD). Structural homology, metal composition, inhibitor-bonding interactions, and the potential for dimerisation were critically assessed through computational techniques, including structural superimposition and protein-ligand docking. Results from this research suggest that the metallopeptidase-like domain shares high structural homology with known aminopeptidase P enzymes and possesses the canonical ‘pita-bread fold’. However, the absence of conserved metal-coordinating residues indicates that only a single Zn2+ may be bound at the active site. The PID-5 APP-RD may form transient interactions with a known aminopeptidase P inhibitor and may therefore recognise substrates in a comparable way to the known structures. However, loss of key catalytic residues suggests the domain will be inactive. Further evidence suggests that heterodimerisation with C. elegans aminopeptidase P is feasible and therefore PID-5 is predicted to regulate proteolytic cleavage in the silencing pathway. PID-5 may interact with PID-2 to bring aminopeptidase P activity to the Z-granule, where it could influence WAGO-4 activity to ensure the balanced production of 22G-RNA signals for transgenerational silencing. Targeted experiments into APPs implicated in malaria and cancer are required in order to build upon the biological and therapeutic significance of this research.
... We show here that the DNMT domains among the different DNMT5s are conserved but show a divergence compared to other DNMTs, thus supporting a common evolutionary origin for all DNMT5 enzymes. DNMT5b enzymes could be multifunctional enzymes as suggested by the presence of N-terminal HAND domains found in chromatin remodelers 49 , by TUDOR domains found in histone modifying enzymes, histone post-translational modification readers 50 as well as small RNA interacting proteins 51,52 . They also contain an SNF2 ATPase domain 11 which plays a chaperone-like enzyme-remodeling role important for DNA methylation and its targeting to specific sites 15,53 . ...
Cytosine methylation is an important epigenetic mark involved in the transcriptional control of transposable elements in mammals, plants and fungi. The Stramenopiles-Alveolate-Rhizaria (SAR) lineages are a major group of ecologically important marine microeukaryotes, including the phytoplankton groups diatoms and dinoflagellates. However, little is known about their DNA methyltransferase diversity. Here, we performed an in-silico analysis of DNA methyltransferases found in marine microeukaryotes and showed that they encode divergent DNMT3, DNMT4, DNMT5 and DNMT6 enzymes. Furthermore, we found three classes of enzymes within the DNMT5 family. Using a CRISPR/Cas9 strategy we demonstrated that the loss of the DNMT5a gene correlates with a global depletion of DNA methylation and overexpression of young transposable elements in the model diatom Phaeodactylum tricornutum. The study provides a view of the structure and function of a DNMT family in the SAR supergroup using an attractive model species.
... The protein consists of five staphylococcal nucleaselike (SN) domain repeats and a C-terminal Tudor-domain that belongs to a family of methyl-arginine and -lysine binding proteins implicated in regulation of RNA metabolism. 1 The SN domains show similarity to Staphylococcus aureus Ca 2+ -dependent extracellular nucleases and contain a conserved oligonucleotide-binding scaffold. ...
Snd1 is an evolutionarily conserved RNA‐binding protein implicated in several regulatory processes in gene expression including activation of transcription, mRNA splicing and microRNA decay. Here we have investigated the outcome of Snd1 gene deletion in the mouse. The knockout mice are viable showing no gross abnormalities apart from decreased fertility, organ and body size, and decreased number of myeloid cells concomitant with decreased expression of granule protein genes. Deletion of Snd1 affected the expression of relatively small number of genes in spleen and liver. However, mRNA expression changes in the knockout mouse liver showed high similarity to expression profile in adaptation to hypoxia. MicroRNA expression in liver showed upregulation of the hypoxia‐induced microRNAs miR‐96 and ‐182. Similar to Snd1 deletion, mimics of miR‐96/182 enhanced hypoxia‐responsive reporter activity. To further elucidate the function of SND1, BioID biotin proximity ligation assay was performed in HEK‐293T cells to identify interacting proteins. Over 50% of the identified interactors were RNA‐binding proteins, including stress granule proteins. Taken together, our results show that in normal growth conditions Snd1 is not a critical factor for mRNA transcription in the mouse and describe a function for Snd1 in hypoxia adaptation through negatively regulating hypoxia‐related miRNAs and hypoxia‐induced transcription consistent with a role as stress response regulator.
During development, progenitor cell survival is essential for proper tissue functions, but the underlying mechanisms are not fully understood. Here we show that ERCC6L2, a member of the Snf2 family of helicase‐like proteins, plays an essential role in the survival of developing chick neural cells. ERCC6L2 expression is induced by the Sonic Hedgehog (Shh) signalling molecule by a mechanism similar to that of the known Shh target genes Ptch1 and Gli1 . ERCC6L2 rescues programmed cell death induced by Shh inhibition and this inhibition is independent of neural tube patterning. Inhibition of ERCC6L2 expression by siRNA resulted in the aberrant appearance of apoptotic cells. Furthermore, ERCC6L2 cooperates with Shh signal and plays an essential role in the induction of the anti‐apoptotic factor Bcl‐2 . Taken together, ERCC6L2 acts as a key factor in ensuring the survival of neural progenitor cells.
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The pancreatic β cell synthesizes, packages, and secretes insulin in response to glucose-stimulation to maintain blood glucose homeostasis. Under diabetic conditions, a subset of β cells fail and lose expression of key transcription factors (TFs) required for insulin secretion. Among these TFs is Pancreatic and duodenal homeobox 1 (PDX1), which recruits a unique subset of transcriptional coregulators to modulate its activity. Here we describe a novel interacting partner of PDX1, the Staphylococcal Nuclease and Tudor domain-containing protein (SND1), which has been shown to facilitate protein-protein interactions and transcriptional control through diverse mechanisms in a variety of tissues. PDX1:SND1 interactions were confirmed in rodent β cell lines, mouse islets, and human islets. Utilizing CRISPR-Cas9 gene editing technology, we deleted Snd1 from the mouse β cell lines, which revealed numerous differentially expressed genes linked to insulin secretion and cell proliferation, including limited expression of Glp1r. We observed Snd1 deficient β cell lines had reduced cell expansion rates, GLP1R protein levels, and limited cAMP accumulation under stimulatory conditions, and further show that acute ablation of Snd1 impaired insulin secretion in rodent and human β cell lines. Lastly, we discovered that PDX1:SND1 interactions were profoundly reduced in human β cells from donors with type 2 diabetes (T2D). These observations suggest the PDX1:SND1 complex formation is critical for controlling a subset of genes important for β cell function and is targeted in diabetes pathogenesis.
RNA silencing pathways are complex, highly conserved, and perform widespread, critical regulatory roles. In C. elegans germlines, RNA surveillance occurs through a series of perinuclear germ granule compartments—P granules, Z granules, SIMR foci, and Mutator foci—multiple of which form via phase separation and exhibit liquid-like properties. The functions of individual proteins within germ granules are well-studied, but the spatial organization, physical interaction, and coordination of biomolecule exchange between compartments within germ granule “nuage” is less understood. Here we find that key proteins are sufficient for compartment separation, and that the boundary between compartments can be reestablished after perturbation. Using super-resolution microscopy, we discover a toroidal P granule morphology which encircles the other germ granule compartments in a consistent exterior-to-interior spatial organization. Combined with findings that nuclear pores primarily interact with P granules, this nuage compa rtment organization has broad implications for the trajectory of an RNA as it exits the nucleus and enters small RNA pathway compartments. Furthermore, we quantify the stoichiometric relationships between germ granule compartments and RNA to reveal discrete populations of nuage that differentially associate with RNAi-targeted transcripts, possibly suggesting functional differences between nuage configurations. Together, our work creates a more spatially and compositionally accurate model of C. elegans nuage which informs the conceptualization of RNA silencing through different germ granule compartments.
Post-translational modification of chromatin has profound effects on many biological processes including transcriptional regulation, heterochromatin organization, and X-chromosome inactivation. Recent studies indicate that methylation on specific histone lysine (K) residues participates in many of these processes. Lysine methylation occurs in three distinct states, having either one (me1), two (me2) or three (me3) methyl groups attached to the amine group of the lysine side chain. These differences in modification state have an important role in defining how methylated chromatin is recognized and interpreted. Until recently, histone lysine methylation was considered a stable modification, but the identification of histone demethylase enzymes has demonstrated the reversibility of this epigenetic mark. So far, all characterized histone demethylases show enzymatic activity towards lysine residues modified in the me1 or me2 state, leaving open the possibility that me3 constitutes an irreversible modification. Here we demonstrate that JHDM3A (jumonji C (JmjC)-domain-containing histone demethylase 3A; also known as JMJD2A) is capable of removing the me3 group from modified H3 lysine 9 (H3K9) and H3 lysine 36 (H3K36). Overexpression of JHDM3A abrogates recruitment of HP1 (heterochromatin protein 1) to heterochromatin, indicating a role for JHDM3A in antagonizing methylated H3K9 nucleated events. siRNA-mediated knockdown of JHDM3A leads to increased levels of H3K9 methylation and upregulation of a JHDM3A target gene, ASCL2, indicating that JHDM3A may function in euchromatin to remove histone methylation marks that are associated with active transcription.
1G5V
Spinal muscular atrophy (SMA) is a common motor neuron disease that results
from mutations in the Survival of Motor Neuron (SMN) gene. The SMN
protein plays a crucial role in the assembly of spliceosomal uridine-rich
small nuclear ribonucleoprotein (U snRNP) complexes via binding to
the spliceosomal Sm core proteins. SMN contains a central Tudor domain that
facilitates the SMN–Sm protein interaction. A SMA-causing point mutation
(E134K) within the SMN Tudor domain prevents Sm binding. Here, we have determined
the three-dimensional structure of the Tudor domain of human SMN. The structure
exhibits a conserved negatively charged surface that is shown to interact
with the C-terminal Arg and Gly-rich tails of Sm proteins. The E134K mutation
does not disrupt the Tudor structure but affects the charge distribution within
this binding site. An intriguing structural similarity between the Tudor domain
and the Sm proteins suggests the presence of an additional binding interface
that resembles that in hetero-oligomeric complexes of Sm proteins. Our data
provide a structural basis for a molecular defect underlying SMA.
Reports. Submitted on March 5, 2008 Accepted on March 31, 2008. .
The accumulation of the human tumor suppressor 53BP1 at DNA damage sites requires the ubiquitin ligases RNF8 and RNF168. As 53BP1 recognizes dimethylated Lys20 in histone H4 (H4K20me2), the requirement for RNF8- and RNF168-mediated ubiquitylation has been unclear. Here we show that RNF8-mediated ubiquitylation facilitates the recruitment of the AAA-ATPase valosin-containing protein (VCP, also known as p97) and its cofactor NPL4 to sites of double-strand breaks. RIDDLE cells, which lack functional RNF168, also show impaired recruitment of VCP to DNA damage. The ATPase activity of VCP promotes the release of the Polycomb protein L3MBTL1 from chromatin, which also binds the H4K20me2 histone mark, thereby facilitating 53BP1 recruitment. Consistent with this, nematodes lacking the VCP orthologs CDC-48.1 or CDC-48.2, or cofactors UFD-1 or NPL-4, are highly sensitive to ionizing radiation. Our data suggest that human RNF8 and RNF168 promote VCP-mediated displacement of L3MBTL1 to unmask 53BP1 chromatin binding sites.
Background: The injection of double-stranded RNA (dsRNA) has been shown to induce a potent sequence-specific inhibition of gene function in diverse invertebrate and vertebrate species. The homology-dependent posttranscriptional gene silencing (PTGS) caused by the introduction of transgenes in plants may be mediated by dsRNA. The analysis of Caenorhabditis elegans mutants impaired with dsRNA-mediated silencing and studies in plants implicate a biological role of dsRNA-mediated silencing as a transposon-repression and antiviral mechanism. Results: We investigated the silencing of testis-expressed Stellate genes by paralogous Su(Ste) tandem repeats, which are known to be involved in the maintenance of male fertility in Drosophila melanogaster. We found that both strands of repressor Su(Ste) repeats are transcribed, producing sense and antisense RNA. The Stellate silencing is associated with the presence of short Su(Ste) RNAs. Cotransfection experiments revealed that Su(Ste) dsRNA can target and eliminate Stellate transcripts in Drosophila cell culture. The short fragment of Stellate gene that is homologous to Su(Ste) was shown to be sufficient to confer Su(Ste)-dependent silencing of a reporter construct in testes. We demonstrated that Su(Ste) dsRNA-mediated silencing affects not only Stellate expression but also the level of sense Su(Ste) RNA providing a negative autogenous regulation of Su(Ste) expression. Mutation in the spindle-E gene relieving Stellate silencing also leads to a derepression of the other genomic tandem repeats and retrotransposons in the germline. Conclusions: Homology-dependent gene silencing was shown to be used to inhibit Stellate gene expression in the D. melanogaster germline, ensuring male fertility. dsRNA-mediated silencing may provide a basis for negative autogenous control of gene expression. The related surveillance system is implicated to control expression of retrotransposons in the germline.
The accurate transfer of genetic material in germline cells during the formation of gametes is important for the continuity of the species. However, animal germline cells face challenges from transposons, which seek to spread themselves in the genome. This review focuses on studies in Drosophila melanogaster on how the genome protects itself from such a mutational burden via a class of gonad-specific small interfering RNAs, known as piRNAs (Piwi-interacting RNAs). In addition to silencing transposons, piRNAs also regulate other processes, such as chromosome segregation, mRNA degradation and germline differentiation. Recent studies revealed two modes of piRNA processing - primary processing and secondary processing (also known as ping-pong amplification). The primary processing pathway functions in both germline and somatic cells in the Drosophila ovaries by processing precursor piRNAs into 23-29nt piRNAs. In contrast, the secondary processing pathway functions only in the germline cells where piRNAs are amplified in a feed-forward loop and require the Piwi-family proteins Aubergine and Argonaute3. Aubergine and Argonaute3 localize to a unique structure found in animal germline cells, the nuage, which has been proposed to function as a compartmentalized site for the ping-pong cycle. The nuage and the localized proteins are well-conserved, implying the importance of the piRNA amplification loop in animal germline cells. Nuage components include various types of proteins that are known to interact both physically and genetically, and therefore appear to be assembled in a sequential order to exert their function, resulting in a macromolecular RNA-protein complex dedicated to the silencing of transposons. © 2012 The Authors. Development, Growth & Differentiation
For optimal survival, various environmental and endogenous factors should be monitored to determine the appropriate timing for seed germination. Light is a major environmental factor affecting seed germination, which is perceived by phytochromes. The light-dependent activation of phytochrome B (PHYB) modulates abscisic acid and gibberellic acid signaling and metabolism. Thus far, several negative regulators of seed germination that act when PHYB is inactive have been reported. However, neither positive regulators of seed germination downstream of PHYB nor a direct mechanism for regulation of the hormone levels has been elucidated. Here, we show that the histone arginine demethylases, JMJ20 and JMJ22, act redundantly as positive regulators of seed germination. When PHYB is inactive, JMJ20/JMJ22 are directly repressed by the zinc-finger protein SOMNUS. However, upon PHYB activation, JMJ20/JMJ22 are derepressed, resulting in increased gibberellic acid levels through the removal of repressive histone arginine methylations at GA3ox1/GA3ox2, which in turn promotes seed germination.
Posttranslational modifications (PTMs) of histone proteins, such as acetylation, methylation, phosphorylation, and ubiquitylation,
play essential roles in regulating chromatin dynamics. Combinations of different modifications on the histone proteins, termed
‘histone code’ in many cases, extend the information potential of the genetic code by regulating DNA at the epigenetic level.
Many PTMs occur on non-histone proteins as well as histones, regulating protein–protein interactions, stability, localization,
and/or enzymatic activities of proteins involved in diverse cellular processes. Although protein phosphorylation, ubiquitylation,
and acetylation have been extensively studied, only a few proteins other than histones have been reported that can be modified
by lysine methylation. This review summarizes the current progress on lysine methylation of non-histone proteins, and we propose
that lysine methylation, like phosphorylation and acetylation, is a common PTM that regulates proteins in diverse cellular
processes.
In Drosophila ovaries, distinct Piwi-interacting RNA (piRNA) pathways defend against transposons in somatic and germline cells. Germline piRNAs predominantly arise from bidirectional clusters and are amplified by the ping-pong cycle. In this study, we characterize a novel Drosophila gene, kumo and show that it encodes a conserved germline piRNA pathway component. Kumo contains five tudor domains and localizes to nuage, a unique structure present in animal germline cells, which is considered to be the processing site for germline piRNAs. Transposons targeted by the germline piRNA pathway are derepressed in kumo mutant females. Moreover, germline piRNA production is significantly reduced in mutant ovaries, thereby indicating that kumo is required to generate germline piRNAs. Kumo localizes to the nuage as well as to nucleus early female germ cells, where it is required to maintain cluster transcript levels. Our data suggest that kumo facilitates germline piRNA production by promoting piRNA cluster transcription in the nucleus and piRNA processing at the nuage.