scholarly journals Complete guide RNA design for CRISPR-mediated regulation of human long noncoding RNA transcription

2018 ◽  
Author(s):  
Amir Saberi ◽  
Renjun Zhu ◽  
Chulan Kwon
Keyword(s):  
Noncoding Rna ◽  
Large Fraction ◽  
Guide Rna ◽  
Transcription Start Sites ◽  
Common Reference ◽  
Functional Studies ◽  
Short Palindromic Repeat ◽  
Genome Annotations ◽  
Rna Design ◽  
Genome Scale

AbstractTranscription inhibition and activation of long noncoding RNAs (lncRNAs) mediated by clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 technology provides potential advantages in high-throughput functional genomics studies over RNA interference or overexpression platforms. In this work, we identify over 90,000 lncRNA transcription start sites (TSSs) based on the MiTranscriptome human genome annotation and design single guide RNA (sgRNA) libraries with strong predicted activities and low off-target effects for CRISPR-mediated inhibition and activation (CRISPRi/a) of their transcription. A large fraction of these TSSs correspond to putative genes that are not annotated in common reference genome annotations and have never been functionally studied. Our CRISPRi/a libraries, or their context-dependent subsets, are potentially useful in genome-scale functional studies of human lncRNAs.

scholarly journals Optimized CRISPR guide RNA design for two high-fidelity Cas9 variants by deep learning

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Daqi Wang ◽  
Chengdong Zhang ◽  
Bei Wang ◽  
Bin Li ◽  
Qiang Wang ◽  
...  
Keyword(s):  
Design Tool ◽  
High Fidelity ◽  
Design Tools ◽  
Wild Type ◽  
Activity Prediction ◽  
Guide Rna ◽  
Biological Features ◽  
A Genome ◽  
Rna Design ◽  
Genome Scale

Abstract Highly specific Cas9 nucleases derived from SpCas9 are valuable tools for genome editing, but their wide applications are hampered by a lack of knowledge governing guide RNA (gRNA) activity. Here, we perform a genome-scale screen to measure gRNA activity for two highly specific SpCas9 variants (eSpCas9(1.1) and SpCas9-HF1) and wild-type SpCas9 (WT-SpCas9) in human cells, and obtain indel rates of over 50,000 gRNAs for each nuclease, covering ~20,000 genes. We evaluate the contribution of 1,031 features to gRNA activity and develope models for activity prediction. Our data reveals that a combination of RNN with important biological features outperforms other models for activity prediction. We further demonstrate that our model outperforms other popular gRNA design tools. Finally, we develop an online design tool DeepHF for the three Cas9 nucleases. The database, as well as the designer tool, is freely accessible via a web server, http://www.DeepHF.com/.

Flexible guide-RNA design for CRISPR applications using Protospacer Workbench

2015 ◽  
Vol 33 (8) ◽  
pp. 805-806 ◽  
Author(s):  
Cameron Ross MacPherson ◽  
Artur Scherf
Keyword(s):  
Guide Rna ◽  
Rna Design

scholarly journals BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree

2019 ◽  
Author(s):  
Charles J Norsigian ◽  
Neha Pusarla ◽  
John Luke McConn ◽  
James T Yurkovich ◽  
Andreas Dräger ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Knowledge Base ◽  
The Past ◽  
Scale Models ◽  
Metabolic Models ◽  
New Community ◽  
Genome Annotations ◽  
Genome Scale ◽  
High Quality Genome ◽  
Strain Genome

Abstract The BiGG Models knowledge base (http://bigg.ucsd.edu) is a centralized repository for high-quality genome-scale metabolic models. For the past 12 years, the website has allowed users to browse and search metabolic models. Within this update, we detail new content and features in the repository, continuing the original effort to connect each model to genome annotations and external databases as well as standardization of reactions and metabolites. We describe the addition of 31 new models that expand the portion of the phylogenetic tree covered by BiGG Models. We also describe new functionality for hosting multi-strain models, which have proven to be insightful in a variety of studies centered on comparisons of related strains. Finally, the models in the knowledge base have been benchmarked using Memote, a new community-developed validator for genome-scale models to demonstrate the improving quality and transparency of model content in BiGG Models.

Guide RNA Design for CRISPR/Cas9-Mediated Potato Genome Editing

2018 ◽  
Vol 479 (1) ◽  
pp. 90-94 ◽  
Author(s):  
A. V. Khromov ◽  
V. A. Gushchin ◽  
V. I. Timerbaev ◽  
N. O. Kalinina ◽  
M. E. Taliansky ◽  
...  
Keyword(s):  
Genome Editing ◽  
Potato Genome ◽  
Guide Rna ◽  
Rna Design

scholarly journals Lysine Propionylation is a Widespread Post-Translational Modification Involved in Regulation of Photosynthesis and Metabolism in Cyanobacteria

2019 ◽  
Vol 20 (19) ◽  
pp. 4792 ◽  
Author(s):  
Mingkun Yang ◽  
Hui Huang ◽  
Feng Ge
Keyword(s):  
Large Fraction ◽  
Bioinformatic Analysis ◽  
High Light ◽  
Site Directed Mutagenesis ◽  
Oxygenic Photosynthesis ◽  
Post Translational Modification ◽  
Functional Studies ◽  
Photosynthetic Organisms ◽  
Model Combining ◽  
And Function

Lysine propionylation is a reversible and widely distributed post-translational modification that is known to play a regulatory role in both eukaryotes and prokaryotes. However, the extent and function of lysine propionylation in photosynthetic organisms remains unclear. Cyanobacteria are the most ancient group of Gram-negative bacteria capable of oxygenic photosynthesis, and are of great importance to global carbon and nitrogen cycles. Here, we carried out a systematic study of lysine propionylaiton in cyanobacteria where we used Synechocystis sp. PCC 6803 (Synechocystis) as a model. Combining high-affinity anti-propionyllysine pan antibodies with high-accuracy mass spectrometry (MS) analysis, we identified 111 unique lysine propionylation sites on 69 proteins in Synechocystis. Further bioinformatic analysis showed that a large fraction of the propionylated proteins were involved in photosynthesis and metabolism. The functional significance of lysine propionylation on the enzymatic activity of fructose-1,6-bisphosphatase (FbpI) was studied by site-directed mutagenesis and biochemical studies. Further functional studies revealed that the propionylation level of subunit II of photosystem I (PsaD) was obviously increased after high light (HL) treatment, suggesting that propionylation may be involved in high light adaption in Synechocystis. Thus, our findings provide novel insights into the range of functions regulated by propionylation and reveal that reversible propionylation is a functional modification with the potential to regulate photosynthesis and carbon metabolism in Synechocystis, as well as in other photosynthetic organisms.

scholarly journals Ecological divergence and hybridization of Neotropical Leishmania parasites

2020 ◽  
Vol 117 (40) ◽  
pp. 25159-25168 ◽  
Author(s):  
Frederik Van den Broeck ◽  
Nicholas J. Savill ◽  
Hideo Imamura ◽  
Mandy Sanders ◽  
Ilse Maes ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Ecological Niche Modeling ◽  
Nuclear Genome ◽  
Leishmania Braziliensis ◽  
Tropical Andes ◽  
Structural Variations ◽  
Evolutionary Pattern ◽  
Guide Rna ◽  
History Of ◽  
Genome Scale

The tropical Andes are an important natural laboratory to understand speciation in many taxa. Here we examined the evolutionary history of parasites of the Leishmania braziliensis species complex based on whole-genome sequencing of 67 isolates from 47 localities in Peru. We first show the origin of Andean Leishmania as a clade of near-clonal lineages that diverged from admixed Amazonian ancestors, accompanied by a significant reduction in genome diversity and large structural variations implicated in host–parasite interactions. Within the Andean species, patterns of population structure were strongly associated with biogeographical origin. Molecular clock and ecological niche modeling suggested that the history of diversification of the Andean lineages is limited to the Late Pleistocene and intimately associated with habitat contractions driven by climate change. These results suggest that changes in forestation over the past 150,000 y have influenced speciation and diversity of these Neotropical parasites. Second, genome-scale analyses provided evidence of meiotic-like recombination between Andean and Amazonian Leishmania species, resulting in full-genome hybrids. The mitochondrial genome of these hybrids consisted of homogeneous uniparental maxicircles, but minicircles originated from both parental species. We further show that mitochondrial minicircles—but not maxicircles—show a similar evolutionary pattern to the nuclear genome, suggesting that compatibility between nuclear-encoded mitochondrial genes and minicircle-encoded guide RNA genes is essential to maintain efficient respiration. By comparing full nuclear and mitochondrial genome ancestries, our data expand our appreciation on the genetic consequences of diversification and hybridization in parasitic protozoa.

scholarly journals DeepCRISPR: optimized CRISPR guide RNA design by deep learning

2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Guohui Chuai ◽  
Hanhui Ma ◽  
Jifang Yan ◽  
Ming Chen ◽  
Nanfang Hong ◽  
...  
Keyword(s):  
Deep Learning ◽  
Guide Rna ◽  
Rna Design

scholarly journals CRISPR-offinder: a CRISPR guide RNA design and off-target searching tool for user-defined protospacer adjacent motif

2017 ◽  
Vol 13 (12) ◽  
pp. 1470-1478 ◽  
Author(s):  
Changzhi Zhao ◽  
Xiaoguo Zheng ◽  
Wubin Qu ◽  
Guanglei Li ◽  
Xinyun Li ◽  
...  
Keyword(s):  
Guide Rna ◽  
Protospacer Adjacent Motif ◽  
Target Searching ◽  
Rna Design

scholarly journals GuideScan software for improved single and paired CRISPR guide RNA design

2017 ◽  
Vol 35 (4) ◽  
pp. 347-349 ◽  
Author(s):  
Alexendar R Perez ◽  
Yuri Pritykin ◽  
Joana A Vidigal ◽  
Sagar Chhangawala ◽  
Lee Zamparo ◽  
...  
Keyword(s):  
Guide Rna ◽  
Rna Design
Sign in / Sign up

Export Citation Format

Share Document