We describe here a protocol for digital transcriptome analysis in a single mouse oocyte and blastomere using a deep-sequencing approach. In this method, individual cells are isolated and transferred into lysate buffer by mouth pipette, followed by reverse transcription carried out directly on the whole cell lysate. Free primers are removed by exonuclease I and a poly(A) tail is added to the 3' end of the first-strand cDNAs by terminal deoxynucleotidyl transferase. Single-cell cDNAs are then amplified by 20 + 9 cycles of PCR. The resulting 100-200 ng of amplified cDNAs are used to construct a sequencing library, which can be used for deep sequencing using the SOLiD system. Compared with cDNA microarray techniques, our assay can capture up to 75% more genes expressed in early embryos. This protocol can generate deep-sequencing libraries for 16 single-cell samples within 6 d.

Exoribonucleases are important enzymes for the turnover of cellular RNA species. We have isolated the first mammalian cDNA from mouse demonstrated to encode a 5′–3′ exoribonuclease. The structural conservation of the predicted protein and complementation data in Saccharomyces cerevisiae suggest a role in cytoplasmic mRNA turnover and pre-rRNA processing similar to that of the major cytoplasmic exoribonuclease Xrn1p in yeast. Therefore, a key component of the mRNA decay system in S. cerevisiae has been conserved in evolution from yeasts to mammals. The purified mouse protein (mXRN1p) exhibited a novel substrate preference for G4 RNA tetraplex–containing substrates demonstrated in binding and hydrolysis experiments. mXRN1p is the first RNA turnover function that has been localized in the cytoplasm of mammalian cells. mXRN1p was distributed in small granules and was highly enriched in discrete, prominent foci. The specificity of mXRN1p suggests that RNAs containing G4 tetraplex structures may occur in vivo and may have a role in RNA turnover.

Checkpoints, which are integral to the cellular response to DNA damage, coordinate transient cell cycle arrest and the induced expression of DNA repair genes after genotoxic stress. DNA repair ensures cellular survival and genomic stability, utilizing a multipathway network. Here we report evidence that the two systems, DNA damage checkpoint control and DNA repair, are directly connected by demonstrating that the Rad55 double-strand break repair protein of the recombinational repair pathway is a terminal substrate of DNA damage and replication block checkpoints. Rad55p was specifically phosphorylated in response to DNA damage induced by the alkylating agent methyl methanesulfonate, dependent on an active DNA damage checkpoint. Rad55p modification was also observed after gamma ray and UV radiation. The rapid time course of phosphorylation and the recombination defects identified in checkpoint-deficient cells are consistent with a role of the DNA damage checkpoint in activating recombinational repair. Rad55p phosphorylation possibly affects the balance between different competing DNA repair pathways.The SOS response in Escherichia coli provides the coordination between DNA damage sensing and the cellular responses to DNA damage (reviewed in reference 22). The primary SOS signal, single-stranded DNA (ssDNA), activates RecA in a ternary complex with ATP as a transcriptional regulator (44) and as a DNA repair protein (reviewed in reference 41). The transcriptional induction of the SOS regulon leads to increased expression of certain DNA repair genes (including RecA itself) and also elicits transient cell cycle arrest by the expression of sfiA, a cell division inhibitor (22). The activation of RecA as a repair protein leads to immediate repair of the primary damage that initiated the SOS signal. Although different in mechanism, the DNA damage checkpoints could provide a similar coordination between DNA damage sensing and repair in eukaryotes. First conceptualized as an active cell cycle control system in response to DNA damage in Saccharomyces cerevisiae (29,89), DNA damage checkpoints were later shown to control also DNA damage-induced gene expression in this organism (3). DNA damage checkpoints and DNA repair serve a common purpose to secure survival and genomic stability after DNA damage. Indirect effects of the DNA damage checkpoints on DNA repair have been discussed before (reviewed in references 18, 85, and 87), but a direct coupling of the DNA damage sensing capabilities of the checkpoint system with DNA damage repair pathways has not been identified yet.The DNA damage checkpoints in eukaryotes relay a signal in response to DNA damage to transiently delay the entry into the S or M phases, to slow down the ongoing DNA replication, or to arrest in meiotic prophase (reviewed in references 29, 62, and 87). They also elicit DNA damage-induced transcription of many genes, including some coding for DNA repair proteins (87, 93). Moreover, a related DNA replication block checkpoint ensures the dependency of M phase on a...

Interest in CRISPR-Cas12 and CRISPR-Cas13 detection continues to increase as these detection schemes enable the specific recognition of nucleic acids. The fundamental sensitivity limits of these schemes (and their applicability in amplification-free assays) are governed by kinetic rates. However, these kinetic rates remain poorly understood, and their reporting has been inconsistent. We quantify kinetic parameters for several enzymes (LbCas12a, AsCas12a, AapCas12b, LwaCas13a, and LbuCas13a) and their corresponding limits of detection (LoD). Collectively, we present quantification of enzyme kinetics for 14 guide RNAs (gRNAs) and nucleic acid targets for a total of 50 sets of kinetic rate parameters and 25 LoDs. We validate the self-consistency of our measurements by comparing trends and limiting behaviors with a Michaelis−Menten trans-cleavage reaction kinetics model. For our assay conditions, activated Cas12 and Cas13 enzymes exhibit trans-cleavage catalytic efficiencies between order 10 5 and 10 6 M −1 s −1 . For assays that use fluorescent reporter molecules (ssDNA and ssRNA) for target detection, the kinetic rates at the current assay conditions result in an amplification-free LoD in the picomolar range. The results suggest that successful detection of target requires cleavage (by an activated CRISPR enzyme) of the order of at least 0.1% of the fluorescent reporter molecules. This fraction of reporters cleaved is required to differentiate the signal from the background, and we hypothesize that this required fraction is largely independent of the detection method (e.g., endpoint vs reaction velocity) and detector sensitivity. Our results demonstrate the fundamental nature by which kinetic rates and background signal limit LoDs and thus highlight areas of improvement for the emerging field of CRISPR diagnostics.

. trans phosphorylation by Rad53 does not require the Dun1 kinase activity and is likely to involve only a transient interaction between the two kinases. The checkpoint functions of Dun1 kinase in DNA damage-induced transcription, G 2 /M cell cycle arrest, and Rad55 phosphorylation are severely compromised in an FHA domain mutant of Dun1. As a consequence, the Dun1 FHA domain mutant displays enhanced sensitivity to genotoxic stress induced by UV, methyl methanesulfonate, and the replication inhibitor hydroxyurea. We show that the Dun1 FHA domain is critical for direct kinase-to-kinase signaling from Rad53 to Dun1 in the DNA damage checkpoint pathway.DNA damage checkpoints coordinate the cellular responses to genotoxic stress and ensure genomic integrity (31,40,55,60). Besides cell cycle transitions, DNA damage checkpoints in the yeast Saccharomyces cerevisiae control damage-induced transcription; DNA replication; DNA repair and genomic stability; deoxynucleoside triphosphate metabolism; the relocalization of the Sir3/4, Ku80, and Rap1 proteins; and possibly other physiological responses to genotoxic stress (5,20,35,55,58,60,61).Central to the DNA damage checkpoints in S. cerevisiae is a branched kinase cascade consisting of five protein kinases (Mec1, Tel1, Rad53, Chk1, and Dun1) (55, 60). Mec1 and Tel1 are both high-molecular-weight phosphoinositide 3-kinase-related protein kinases that are activated by unknown mechanisms. Their human counterparts, ATM and ATR, are also essential for the human DNA damage checkpoints. Rad53 and Dun1 are related forkhead-associated (FHA) domain kinases (see Fig. 1) and have counterparts in other organisms, including fission yeast Cds1 and human Chk2 (40, 60). Finally, Chk1 kinase, as well as its fission yeast and human homologs, is critical for the G 2 cell cycle arrest in response to DNA damage (41). Genetic analysis of S. cerevisiae established that Mec1 controls the activities of the three downstream kinases Rad53, Dun1, and Chk1 (4,38,41,42,61). Under certain conditions, Tel1 controls the activation of Rad53 kinase in a Mec1-independent fashion (52). The exact mechanisms of how DNA damage checkpoints are activated and how the checkpoint kinases transmit and possibly amplify the signal, as well as control the effector pathways, are only beginning to be understood.Dun1 kinase functions in DNA damage-induced transcription of a subset of damage-inducible genes, including the RNR genes, by controlling the inactivating phosphorylation of the Crt1 transcriptional repressor (26,27,61). Mutations in DUN1 cause sensitivity to DNA damaging-agents and the replication inhibitor hydroxyurea (HU). This sensitivity can be partly suppressed by elevating the deoxynucleoside triphosphate pools through deletion of the ribonucleotide reductase inhibitor Sml1 or by overexpression of RNR1, the gene encoding the large subunit of ribonucleotide reductase (58, 61). In addition, Dun1 functions in one pathway with Rad53 kinase to cause a G 2 /M arrest in response to DNA damage by negatively regulating ...