DNA methylation generally functions as a repressive transcriptional signal, but it is also known to activate gene expression. In either case, the downstream factors remain largely unknown. By using comparative interactomics, we isolated proteins in Arabidopsis thaliana that associate with methylated DNA. Two SU(VAR)3–9 homologs, the transcriptional anti-silencing factor SUVH1, and SUVH3, were among the methyl reader candidates. SUVH1 and SUVH3 bound methylated DNA in vitro, were associated with euchromatic methylation in vivo, and formed a complex with two DNAJ domain-containing homologs, DNAJ1 and DNAJ2. Ectopic recruitment of DNAJ1 enhanced gene transcription in plants, yeast, and mammals. Thus, the SUVH proteins bind to methylated DNA and recruit the DNAJ proteins to enhance proximal gene expression, thereby counteracting the repressive effects of transposon insertion near genes.

Long noncoding RNAs (lncRNAs) have emerged as a major regulator of cell physiology, but many of which have no known function. CDKN1A/p21 is an important inhibitor of the cell-cycle, regulator of the DNA damage response and effector of the tumor suppressor p53, playing a crucial role in tumor development and prevention. In order to identify a regulator for tumor progression, we performed an siRNA screen of human lncRNAs required for cell proliferation, and identified a novel lncRNA, APTR, that acts in trans to repress the CDKN1A/p21 promoter independent of p53 to promote cell proliferation. APTR associates with the promoter of CDKN1A/p21 and this association requires a complementary-Alu sequence encoded in APTR. A different module of APTR associates with and recruits the Polycomb repressive complex 2 (PRC2) to epigenetically repress the p21 promoter. A decrease in APTR is necessary for the induction of p21 after heat stress and DNA damage by doxorubicin, and the levels of APTR and p21 are anti-correlated in human glioblastomas. Our data identify a new regulator of the cell-cycle inhibitor CDKN1A/p21 that acts as a proliferative factor in cancer cell lines and in glioblastomas and demonstrate that Alu elements present in lncRNAs can contribute to targeting regulatory lncRNAs to promoters.

The pairing of 59 and 39 splice sites across an intron is a critical step in spliceosome formation and its regulation. Interactions that bring the two splice sites together during spliceosome assembly must occur with a high degree of specificity and fidelity to allow expression of functional mRNAs and make particular alternative splicing choices. Here, we report a new interaction between stem-loop 4 (SL4) of the U1 snRNA, which recognizes the 59 splice site, and a component of the U2 small nuclear ribonucleoprotein particle (snRNP) complex, which assembles across the intron at the 39 splice site. Using a U1 snRNP complementation assay, we found that SL4 is essential for splicing in vivo. The addition of free U1-SL4 to a splicing reaction in vitro inhibits splicing and blocks complex assembly prior to formation of the prespliceosomal A complex, indicating a requirement for a SL4 contact in spliceosome assembly. To characterize the interactions of this RNA structure, we used a combination of stable isotope labeling by amino acids in cell culture (SILAC), biotin/Neutravidin affinity pull-down, and mass spectrometry. We show that U1-SL4 interacts with the SF3A1 protein of the U2 snRNP. We found that this interaction between the U1 snRNA and SF3A1 occurs within prespliceosomal complexes assembled on the pre-mRNA. Thus, SL4 of the U1 snRNA is important for splicing, and its interaction with SF3A1 mediates contact between the 59 and 39 splice site complexes within the assembling spliceosome.[Keywords: RNA-protein interaction; alternative splicing; gene expression; pre-mRNA splicing; ribonucleoprotein; snRNA; spliceosome] Supplemental material is available for this article. Intron removal is catalyzed by an ;40S RNP complex called the spliceosome, which consists of five small nuclear ribonucleoprotein particles (snRNPs) (U1, U2, U4, U5, and U6) and ;150 auxiliary proteins . In vitro, the spliceosome assembles onto an intron through the sequential binding of the snRNPs Hoskins et al. 2011). The 59 splice site is recognized by the U1 snRNP through base-pairing between the pre-mRNA and the snRNA. At the 39 end of the intron, the U2 auxiliary factor (U2AF) and splicing factor 1 (SF1) bind to the 39 splice site and branch point sequence, respectively. Initial association of the U2 snRNP can be ATP-independent and has been proposed to occur through interactions with the U2AF65 protein (Gozani et al. 1998;Das et al. 2000). This ATP-independent complex is referred to as the E complex. However, the stable association of U2 with the pre-mRNA requires ATP hydrolysis and formation of a base-pairing interaction between U2 snRNA and the branch point sequence with displacement of SF1. This pre-mRNP complex containing both the U1 and U2 snRNPs is called the prespliceosomal A complex. Recruitment of the U4/U6-U5 tri-snRNP forms the precatalytic B complex. In another mode of B complex formation, the U4/U6-U5 trisnRNP binds with the U2 snRNP to the 39 splice site, Ó 2014 Sharma et al. This article is distributed exclusively by Cold Spring...

The ability to target epigenetic marks like DNA methylation to specific loci is important in both basic research and in crop plant engineering. However, heritability of targeted DNA methylation, how it impacts gene expression, and which epigenetic features are required for proper establishment are mostly unknown. Here, we show that targeting the CG-specific methyltransferase M.SssI with an artificial zinc finger protein can establish heritable CG methylation and silencing of a targeted locus in Arabidopsis. In addition, we observe highly heritable widespread ectopic CG methylation mainly over euchromatic regions. This hypermethylation shows little effect on transcription while it triggers a mild but significant reduction in the accumulation of H2A.Z and H3K27me3. Moreover, ectopic methylation occurs preferentially at less open chromatin that lacks positive histone marks. These results outline general principles of the heritability and interaction of CG methylation with other epigenomic features that should help guide future efforts to engineer epigenomes.

Highlights d Caenorhabditis elegans MORC-1 traps DNA loops d Recruitment of additional MORC-1s cause further loop trapping and DNA compaction d MORC-1 assemblages become topologically entrapped on DNA d MORC-1 forms discrete foci in vivo and can phase transition in vitro

Polypyrimidine-tract binding protein PTBP1 can repress splicing during the exon definition phase of spliceosome assembly, but the assembly steps leading to an exon definition complex (EDC) and how PTBP1 might modulate them are not clear. We found that PTBP1 binding in the flanking introns allowed normal U2AF and U1 snRNP binding to the target exon splice sites but blocked U2 snRNP assembly in HeLa nuclear extract. Characterizing a purified PTBP1-repressed complex, as well as an active early complex and the final EDC by SILAC-MS, we identified extensive PTBP1-modulated changes in exon RNP composition. The active early complex formed in the absence of PTBP1 proceeded to assemble an EDC with the eviction of hnRNP proteins, the late recruitment of SR proteins, and binding of the U2 snRNP. These results demonstrate that during early stages of splicing, exon RNP complexes are highly dynamic with many proteins failing to bind during PTBP1 arrest.DOI: http://dx.doi.org/10.7554/eLife.19743.001

Transcription by RNA polymerase V (Pol V) in plants is required for RNA-directed DNA methylation, leading to transcriptional gene silencing. Global chromatin association of Pol V requires components of the DDR complex DRD1, DMS3 and RDM1, but the assembly process of this complex and the underlying mechanism for Pol V recruitment remain unknown. Here we show that all DDR complex components co-localize with Pol V, and we report the cryoEM structures of two complexes associated with Pol V recruitment—DR (DMS3-RDM1) and DDR′ (DMS3-RDM1-DRD1 peptide), at 3.6 Å and 3.5 Å resolution, respectively. RDM1 dimerization at the center frames the assembly of the entire complex and mediates interactions between DMS3 and DRD1 with a stoichiometry of 1 DRD1:4 DMS3:2 RDM1. DRD1 binding to the DR complex induces a drastic movement of a DMS3 coiled-coil helix bundle. We hypothesize that both complexes are functional intermediates that mediate Pol V recruitment.

Introduction: Murdannia loriformis (hassk) Rolla Roa et Kammathy, family Commelinaceae, is used by Chinese practitioners as a remedy for cancer in an early stage, and also for treating other diseases including colds, throat infections, pneumonia, diabetes mellitus, flu and inflammation. Although anticancer as well as other pharmacological effects of M. loriformis have been reported, its anti-inflammatory and other activities related to inflammation are still limited. Methods: The anti-inflammatory activity was evaluated using carrageenan- and arachidonic acid-induced paw edema in rats, and cotton pellet-induced granuloma formation in rats. The analgesic and antipyretic activities were determined by formalin test in mice and yeast-induced hyperthermia in rats, respectively. Results: The ethanol extract of the aerial part of M. loriformis exhibited anti-inflammatory activity on the rat paw edema induced by carrageenan and arachidonic acid. It also showed an inhibitory effect on the granuloma and the transudative formation of the rat implanted with cotton pellets as well as lowered the elevated serum alkaline phosphatase activity to normal level. It exerted potent analgesic effect on both the early and late phase of formalin test as well as the antipyretic effect on yeast-induced hyperthermic rats. The oral single high dose of the extract of 5,000 mg/Kg did not produce death or any abnormalities or changes of the internal organs of rats during 14 days of the observed period. Conclusion: The results obtained from this study support the use of the plant in traditional medicine for inflammatory ailments.