Enhancers play a central role in cell-type-specific gene expression and are marked by H3K4me1/2. Active enhancers are further marked by H3K27ac. However, the methyltransferases responsible for H3K4me1/2 on enhancers remain elusive. Furthermore, how these enzymes function on enhancers to regulate cell-type-specific gene expression is unclear. In this study, we identify MLL4 (KMT2D) as a major mammalian H3K4 mono- and di-methyltransferase with partial functional redundancy with MLL3 (KMT2C). Using adipogenesis and myogenesis as model systems, we show that MLL4 exhibits cell-type- and differentiation-stage-specific genomic binding and is predominantly localized on enhancers. MLL4 co-localizes with lineage-determining transcription factors (TFs) on active enhancers during differentiation. Deletion of Mll4 markedly decreases H3K4me1/2, H3K27ac, Mediator and Polymerase II levels on enhancers and leads to severe defects in cell-type-specific gene expression and cell differentiation. Together, these findings identify MLL4 as a major mammalian H3K4 mono- and di-methyltransferase essential for enhancer activation during cell differentiation.DOI: http://dx.doi.org/10.7554/eLife.01503.001

Covalent modifications of histones, such as acetylation and methylation, play important roles in the regulation of gene expression. Histone lysine methylation has been implicated in both gene activation and repression, depending on the specific lysine (K) residue that becomes methylated and the state of methylation (mono-, di-, or trimethylation). Methylation on K4, K9, and K36 of histone H3 has been shown to be reversible and can be removed by site-specific demethylases. However, the enzymes that antagonize methylation on K27 of histone H3 (H3K27), an epigenetic mark important for embryonic stem cell maintenance, Polycombmediated gene silencing, and X chromosome inactivation have been elusive. Here we show the JmjC domain-containing protein UTX (ubiquitously transcribed tetratricopeptide repeat, X chromosome), as well as the related JMJD3 (jumonji domain containing 3), specifically removes methyl marks on H3K27 in vitro. Further, the demethylase activity of UTX requires a catalytically active JmjC domain. Finally, overexpression of UTX and JMJD3 leads to reduced di-and trimethylation on H3K27 in cells, suggesting that UTX and JMJD3 may function as H3K27 demethylases in vivo. The identification of UTX and JMJD3 as H3K27-specific demethylases provides direct evidence to indicate that similar to methylation on K4, K9, and K36 of histone H3, methylation on H3K27 is also reversible and can be dynamically regulated by site-specific histone methyltransferases and demethylases.histone methylation ͉ transcriptional regulation

PTIP, a protein with tandem BRCT domains, has been implicated in DNA damage response. However, its normal cellular functions remain unclear. Here we show that while ectopically expressed PTIP is capable of interacting with DNA damage response proteins including 53BP1, endogenous PTIP, and a novel protein PA1 are both components of a Set1-like histone methyltransferase (HMT) complex that also contains ASH2L, RBBP5, WDR5, hDPY-30, NCOA6, SET domain-containing HMTs MLL3 and MLL4, and substoichiometric amount of JmjC domain-containing putative histone demethylase UTX. PTIP complex carries robust HMT activity and specifically methylates lysine 4 (K4) on histone H3. Furthermore, PA1 binds PTIP directly and requires PTIP for interaction with the rest of the complex. Moreover, we show that hDPY-30 binds ASH2L directly. The evolutionarily conserved hDPY-30, ASH2L, RBBP5, and WDR5 likely constitute a subcomplex that is shared by all human Set1-like HMT complexes. In contrast, PTIP, PA1, and UTX specifically associate with the PTIP complex. Thus, in cells without DNA damage agent treatment, the endogenous PTIP associates with a Set1-like HMT complex of unique subunit composition. As histone H3 K4 methylation associates with active genes, our study suggests a potential role of PTIP in the regulation of gene expression.

Focal cortical dysplasia type II (FCDII) is a sporadic developmental malformation of the cerebral cortex characterized by dysmorphic neurons, dyslamination and medically refractory epilepsy. It has been hypothesized that FCD is caused by somatic mutations in affected regions. Here, we used deep whole-exome sequencing (read depth, 412-668×) validated by site-specific amplicon sequencing (100-347,499×) in paired brain-blood DNA from four subjects with FCDII and uncovered a de novo brain somatic mutation, mechanistic target of rapamycin (MTOR) c.7280T>C (p.Leu2427Pro) in two subjects. Deep sequencing of the MTOR gene in an additional 73 subjects with FCDII using hybrid capture and PCR amplicon sequencing identified eight different somatic missense mutations found in multiple brain tissue samples of ten subjects. The identified mutations accounted for 15.6% of all subjects with FCDII studied (12 of 77). The identified mutations induced the hyperactivation of mTOR kinase. Focal cortical expression of mutant MTOR by in utero electroporation in mice was sufficient to disrupt neuronal migration and cause spontaneous seizures and cytomegalic neurons. Inhibition of mTOR with rapamycin suppressed cytomegalic neurons and epileptic seizures. This study provides, to our knowledge, the first evidence that brain somatic activating mutations in MTOR cause FCD and identifies mTOR as a treatment target for intractable epilepsy in FCD.

To investigate the role of histone H3K27 demethylase UTX in embryonic stem (ES) cell differentiation, we have generated UTX knockout (KO) and enzyme-dead knock-in male ES cells. Deletion of the X-chromosome-encoded UTX gene in male ES cells markedly decreases expression of the paralogous UTY gene encoded by Y chromosome, but has no effect on global H3K27me3 level, Hox gene expression, or ES cell self-renewal. However, UTX KO cells show severe defects in mesoderm differentiation and induction of Brachyury, a transcription factor essential for mesoderm development. Surprisingly, UTX regulates mesoderm differentiation and Brachyury expression independent of its enzymatic activity. UTY, which lacks detectable demethylase activity, compensates for the loss of UTX in regulating Brachyury expression. UTX and UTY bind directly to Brachyury promoter and are required for Wnt/β-catenin signaling-induced Brachyury expression in ES cells. Interestingly, male UTX KO embryos express normal levels of UTY and survive until birth. In contrast, female UTX KO mice, which lack the UTY gene, show embryonic lethality before embryonic day 11.5. Female UTX KO embryos show severe defects in both Brachyury expression and embryonic development of mesoderm-derived posterior notochord, cardiac, and hematopoietic tissues. These results indicate that UTX controls mesoderm differentiation and Brachyury expression independent of H3K27 demethylase activity, and suggest that UTX and UTY are functionally redundant in ES cell differentiation and early embryonic development. I n vitro, embryonic stem (ES) cells are capable of differentiating into three germ layers, ectoderm, endoderm, and mesoderm, which mimics the early stage of embryonic development in vivo (1). Transcription factor Brachyury (T) is highly expressed in the primitive streak during gastrulation and is required for mesoderm formation (2). Mutation of Brachyury gene in mice causes defective formation of posterior mesoderm, failure of notochord morphogenesis, and embryonic death around 10 d of gestation (2). Brachyury expression is directly regulated by Wnt/β-catenin signaling in mesoderm and in ES cells. Wnt/β-catenin signaling promotes de-phosphorylation of β-catenin, which enters nucleus and binds transcription factor LEF1/TCF1 to activate Brachyury expression (3, 4). Brachyury also positively regulates Wnt/β-catenin signaling. Such a positive auto-regulatory loop between Brachyury and Wnt/β-catenin signaling maintains the mesodermal progenitor cells and is essential for posterior mesoderm development in vertebrates (5).The Polycomb Repressive Complex 2 (PRC2) is critical for the proper differentiation of ES cells. PRC2 is localized on a large number of developmental regulator genes in ES cells. Disruption of PRC2 in ES cells markedly decreases the global levels of H3K27 di-and trimethylation (H3K27me2 and H3K27me3) and leads to up-regulation of many developmental regulator genes (6, 7).UTX belongs to a subfamily of JmjC domain-containing proteins that also includes UTY and JMJD3. Pr...

Programmed genetic rearrangements in lymphocytes require transcription at antigen receptor genes to promote accessibility for initiating double-strand break (DSB) formation critical for DNA recombination and repair. Here, we showed that activated B cells deficient in the PTIP component of the MLL3 (mixed-lineage leukemia 3)-MLL4 complex display impaired trimethylation of histone 3 at lysine 4 (H3K4me3) and transcription initiation of downstream switch regions at the immunoglobulin heavy-chain (Igh) locus, leading to defective immunoglobulin class switching. We also showed that PTIP accumulation at DSBs contributes to class switch recombination (CSR) and genome stability independently of Igh switch transcription. These results demonstrate that PTIP promotes specific chromatin changes that control the accessibility of the Igh locus to CSR and suggest a nonredundant role for the MLL3-MLL4 complex in altering antibody effector function.

We demonstrate the conditional reversal of a weak (partial-collapse) quantum measurement on a photonic qubit. The weak quantum measurement causes a nonunitary transformation of a qubit which is subsequently reversed to the original state after a successful reversing operation. Both the weak measurement and the reversal operation are implemented linear optically. The state recovery fidelity, determined by quantum process tomography, is shown to be over 94% for partial-collapse strength up to 0.9. We also experimentally study information gain due to the weak measurement and discuss the role of the reversing operation as an information erasure.PACS numbers: 03.65.Wj, 42.50.Dv, The projection postulate states that measurement of a variable of a quantum system irrevocably collapses the initial state to one of the eigenstates (corresponding to the measurement outcome) of the measurement operator and is one of the basic postulates of the standard quantum theory [1,2]. The initial state can never be recovered after a projection measurement on a quantum system.If the measurement is not sharp (i.e., non-projective measurement), however, the situation is different. It is possible to reverse the measurement-induced state collapse and the unsharpness of a measurement has been shown to be related to the probabilistic nature of the reversing operation which can serve as a probabilistic quantum error correction [3]. In particular, practical schemes for reversing the state collapse due to a weak (or partialcollapse) measurement in a solid-state qubit have been proposed in Ref.[4] and one of the schemes has recently been demonstrated using a superconducting phase qubit in Ref. [5].Since single-photon states and linear optics play important roles in quantum communication and quantum computing research [6,7,8,9], it is of interest and importance to investigate how the measurement-induced state collapse due to a weak measurement can be reversed for a photonic qubit. In this letter, we report a linear optical implementation of conditional reversal of weak (or partial-collapse) quantum measurements on a photonic qubit. We demonstrate experimentally that a nonunitary transformation of a photonic qubit, caused by a weak quantum measurement, can be reversed by applying an appropriately designed reversing operation. We also quantify and experimentally study information gain due to the weak measurement and discuss the role of the reversing operation as an information erasure.Consider the initial state of a qubit represented in the computational basis, |ψ o = α|0 + β|1 , where * Electronic address: yskim25@postech.ac.kr † Electronic address: yoonho@postech.ac.kr |α| 2 + |β| 2 = 1. Ordinary projection measurement in the computational basis would collapse the state into |0 (or |1 ) with the probability equal to |α| 2 (or |β| 2 ). The projection measurement cannot be reversed because the projection operators P 0 = |0 0| = ( 1 0 0 0 ) and P 1 = |1 1| = ( 0 0 0 1 ) do not have mathematical inverse. An unsharp measurement on the qubit, however, ...

In eukaryotes, cyclin B-bound cyclin-dependent protein kinase 1 promotes mitotic entry but is held in check, in part, by Wee1 protein kinase. Timely mitotic entry in budding yeast requires inactivation of Swe1 (Wee1 ortholog). Perturbations of the septin collar at the bud neck lead to Swe1 stabilization, delaying the G2͞M transition. Swe1 is recruited to the neck and hyperphosphorylated before ubiquitin-mediated degradation. Hsl1 kinase (Nim1 ortholog), a negative regulator of Wee1, is required for efficient Swe1 localization at the neck but seems not to phosphorylate Swe1. Here, we show that two other kinases targeted sequentially to the neck, Cla4͞PAK and Cdc5͞Polo, are responsible for stepwise phosphorylation and down-regulation of Swe1. This mechanism links assembly of a cellular structure to passage into mitosis.Cdk1 regulation ͉ mitotic progression ͉ G2͞M transition ͉ Saccharomyces cerevisiae