High Activity Target-Site Identification Using Phenotypic Independent CRISPR-Cas9 Core Functionality

The activity of CRISPR-Cas9 target sites can be measured experimentally through phenotypic assays or mutation rate and used to build computational models to predict activity of novel target sites. However, currently published models have been reported to perform poorly in situations other than their training conditions. In this study, we hence investigate how different sources of data influence predictive power and identify the best data set for the most robust predictive model. We use the activity of 28,606 target sites and a machine learning approach to train a predictive model of CRISPR-Cas9 activity, outperforming other published methods by an average increase in accuracy of 80% for prediction of the degree of activity and 13% for classification into active and inactive categories. We find that using data sets that measure CRISPR-Cas9 activity through sequencing provides more accurate predictions of activity. Our model, dubbed TUSCAN, is highly scalable, predicting the activity of 5000 target sites in under 7 s, making it suitable for genome-wide screens. We conclude that sophisticated machine learning methods can classify binary CRISPR-Cas9 activity; however, predicting fine-scale activity scores will require larger data sets directly measuring Indel insertion rate.

Resistant starches protect against colonic DNA damage and alter microbiota and gene expression in rats fed a Western diet

Resistant starch (RS), fed as high amylose maize starch (HAMS) or butyrylated HAMS (HAMSB), opposes dietary protein-induced colonocyte DNA damage in rats. In this study, rats were fed Western-type diets moderate in fat (19%) and protein (20%) containing digestible starches [low amylose maize starch (LAMS) or low amylose whole wheat (LAW)] or RS [HAMS, HAMSB, or a whole high amylose wheat (HAW) generated by RNA interference] for 11 wk (n = 10/group). A control diet included 7% fat, 13% protein, and LAMS. Colonocyte DNA single-strand breaks (SSB) were significantly higher (by 70%) in rats fed the Western diet containing LAMS relative to controls. Dietary HAW, HAMS, and HAMSB opposed this effect while raising digesta levels of SCFA and lowering ammonia and phenol levels. SSB correlated inversely with total large bowel SCFA, including colonic butyrate concentration (R(2) = 0.40; P = 0.009), and positively with colonic ammonia concentration (R(2) = 0.40; P = 0.014). Analysis of gut microbiota populations using a phylogenetic microarray revealed profiles that fell into 3 distinct groups: control and LAMS; HAMS and HAMSB; and LAW and HAW. The expression of colonic genes associated with the maintenance of genomic integrity (notably Mdm2, Top1, Msh3, Ung, Rere, Cebpa, Gmnn, and Parg) was altered and varied with RS source. HAW is as effective as HAMS and HAMSB in opposing diet-induced colonic DNA damage in rats, but their effects on the large bowel microbiota and colonocyte gene expression differ, possibly due to the presence of other fiber components in HAW.