Identification of oil palm cis-regulatory elements based on DNA free energy and single nucleotide polymorphism density.

Transcription control through cis-regulatory elements (CREs) is one of important regulators of gene expression. This study aimed to identify the location of CREs in oil palm (Elaeis guineensis Jacq.) using the combination of DNA free energy and single nucleotide polymorphism (SNP) density approaches. Promoter region sequences were extracted oil palm genome spanning from 1500 nucleotides (nt) upstream to 1000 nt downstream of every annotated transcription start sites (TSS). Free energy profiles of each promoter region were calculated using PromPredict software. Raw reads from the deep sequencing of 59 oil palm origins were used to calculate SNP density of each promoter region. The result showed that the average free energy (AFE) on the upstream region of TSS is about 1.5 kcal/mol higher compared to the downstream region. Using DNA free energy method, 16,281 regions of CREs were predicted. Most of predicted CREs was located between 1 and 500 nt upstream of TSS. Anti-correlation pattern between free energy and SNP density was observed on the predicted regions of CREs. This anti-correlated pattern was also observed on an experimentally determined promoter of the oil palm metallothionein gene, EgMSP1. Considering the increasing use of promoter information on plant biotechnology, an easy and accurate promoter prediction using the combination of free energy and SNP density method could be recommended.

CROP: a CRISPR/Cas9 guide selection program based on mapping guide variants.

The off-target effect, in which DNA cleavage was conducted outside the targeted region, is a major problem which limits the applications of CRISPR/Cas9 genome editing system. CRISPR Off-target Predictor (CROP) is standalone program developed to address this problem by predicting off-target propensity of guide RNAs and thereby allowing the user to select the optimum guides. The approach used by CROP involves generating substitution, deletion and insertion combinations which are then mapped into the reference genome. Based on these mapped variants, scoring and alignment are conducted and then reported as a table comprising the off-target propensity of all guide RNAs from a given gene sequence. The Python script for this program is freely available from: https://github.com/vaprilyanto/crop .