Functional elucidation of causal genetic variants and elements requires precise genome editing technologies. The type II prokaryotic CRISPR (clustered regularly interspaced short palindromic repeats)/Cas adaptive immune system has been shown to facilitate RNA-guided site-specific DNA cleavage. We engineered two different type II CRISPR/Cas systems and demonstrate that Cas9 nucleases can be directed by short RNAs to induce precise cleavage at endogenous genomic loci in human and mouse cells. Cas9 can also be converted into a nicking enzyme to facilitate homology-directed repair with minimal mutagenic activity. Lastly, multiple guide sequences can be encoded into a single CRISPR array to enable simultaneous editing of several sites within the mammalian genome, demonstrating easy programmability and wide applicability of the RNA-guided nuclease technology.

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The phosphorylation status of the myocyte enhancer factor 2 (MEF2) transcriptional regulator is a critical determinant of its tissue-specific functions. However, due to the complexity of its phosphorylation pattern in vivo, a systematic inventory of MEF2A phosphorylation sites in mammalian cells has been difficult to obtain. We employed modern affinity purification techniques, combined with mass spectrometry, to identify several novel MEF2 phosphoacceptor sites. These include an evolutionarily conserved KSP motif, which we show is important in regulating the stability and function of MEF2A. Also, an indirect pathway in which a protein kinase casein kinase 2 phosphoacceptor site is phosphorylated by activation of p38 MAPK signaling was documented. Together, these findings identify several novel aspects of MEF2 regulation that may prove important in the control of gene expression in neuronal and muscle cells. Myocyte enhancer factor 2 (MEF2)1 is a transcriptional regulatory complex mediating diverse cellular functions in neurons (1, 2), skeletal (reviewed in Ref.3) and cardiac muscle (4 -6), and T cells (7,8). It is now well established that MEF2 plays a role in the differentiation of these cell types as well as functioning in a protective role against neuronal apoptosis.To respond to diverse developmental and physiological cues, MEF2 is structurally organized to receive and respond to multiple signals from several intracellular signaling pathways (reviewed in Refs. 3 and 9). In this regard, perhaps the best characterized is the p38 MAPK-MEF2 axis, in mammals (10, 11) and in yeast (12), although other kinase-catalyzed cascades mediated by big MAP kinase (13,14), protein kinase C (10), and protein kinase CK2 (15) are known to target MEF2. Moreover, consistent with its role as a signal sensor, putative phosphoacceptor motifs in the carboxyl terminal MEF2 transactivation domain may prove to further modulate MEF2 function in response to extracellular cues.Given that MEF2, and the biological processes it regulates, are intrinsically governed by MEF2 phosphorylation status, we undertook to systematically document MEF2 phosphorylation patterns in mammalian cells; previous phosphopeptide mapping studies used in vitro phosphorylated MEF2 protein. The purpose thus being to detect physiologically relevant, and possibly novel, in vivo MEF2 phosphorylation sites. To accomplish this we used several state-of-the-art mass spectrometric techniques to detect phosphorylation sites from MEF2 expressed in mammalian cells. To this end, we have made use of a mammalian tandem affinity purification (TAP) method (16, 17) for low-abundance nuclear transcription factors that allows purification to homogeneity and provides amounts compatible with mass spectrometric analysis of phosphorylation sites.In these studies, we have identified two important and novel aspects of MEF2 regulation. One is a highly conserved phosphoacceptor motif that regulates MEF2 stability and function. The second is an indirect pathway of MEF2 regulation by p38 MAPK me...

The role of activating protein-1 (AP-1) in muscle cells is currently equivocal. While some studies propose that AP-1 is inhibitory for myogenesis, others implicate a positive role in this process. We tested whether this variation may be due to different properties of the AP-1 subunit composition in differentiating cells. Using Western analysis we show that c-Jun, Fra-2, and JunD are expressed throughout the time course of differentiation. Phosphatase assays indicate that JunD and Fra-2 are phosphorylated in muscle cells and that at least two isoforms of each are expressed in muscle cells. Electrophoretic mobility shift assays combined with antibody supershifts indicate the appearance of Fra-2 as a major component of the AP-1 DNA binding complex in differentiating cells. In this context it appears that Fra-2 heterodimerizes with c-Jun and JunD. Studying the c-jun enhancer in reporter gene assays we observed that the muscle transcription factors MEF2A and MyoD can contribute to robust transcriptional activation of the c-jun enhancer. In differentiating muscle cells mutation of the MEF2 site reduces transactivation of the c-jun enhancer and MEF2A is the predominant MEF2 isoform binding to this cis element. Transcriptional activation of an AP-1 site containing reporter gene (TRE-Luc) is enhanced under differentiation conditions compared with growth conditions in C2C12 muscle cells. Further studies indicate that Fra-2 containing AP-1 complexes can transactivate the MyoD enhancer/promoter. Thus, an AP-1 complex containing Fra-2 and c-Jun or JunD is consistent with muscle differentiation, indicating that AP-1 function during myogenesis is dependent on its subunit composition.

Acoustic ejection mass spectrometry is a recently developed concept in which low nanolitervolume sample droplets are acoustically dispensed from microtiter plate wells into a continuous fluid transfer open-port interface for subsequent ionization at atmospheric pressure. This manuscript focuses on the acoustic droplet dispensing component of a prototype system, in particular the well-to-well sampling speed, droplet volume calibration, precision, reproducibility, and various modes of operation this device enables. A new method to measure the volume of individually dispensed droplets is presented to both aid method validation and potentially assist in the tuning of acoustic dispense parameters for samples having a wide range of viscosities and surface tensions. Acoustic dispensing modes of operation discussed are high-speed, well-to-well dispensing of individual nanoliter-scale droplets from microtiter plates, including the first demonstration of 1536-well compatibility using this approach. Multiple nanoliter-volume droplets per sampling event to increase detection dynamic range is described, and a "continuous infusion" mode to provide a low sample consumption sustained steady-state signal for analyte detection optimization, improved ion statistics and signal-to-noise ratio (S/N), or time for in-depth tandem mass spectrometry of the components in a sample is presented. The concept of "bar coding" using combinations of dispensed droplet patterns to register well-plate position to specific mass spectral signals is introduced, as well as judicious well-plate sample layout to enable assay "multiplexing" as a means to maximize well-to-well sample analysis throughput, is also demonstrated.

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