Cpf1 is a CRISPR effector protein that has greater specificity than Streptococcus pyogenes Cas9 (SpCas9) in genome-editing applications. Here we show that Lachnospiraceae bacterium (Lb) and Acidaminococus sp. (As) Cpf1 orthologs have RNase activities that can excise multiple CRISPR RNAs (crRNAs) from a single RNA polymerase II-driven RNA transcript expressed in mammalian cells. This property si...

Structured non-coding RNAs have a very important functional role in the cell. They are involved in a variety of processes such as transcriptional and post-transcriptional regulation, chromosome replication, RNA processing and modification, protein degradation and translocation. Current research for annotation of eukaryotic genomes show that there is a need for novel tools that are able to ident...

We identified genomic and network properties of approximately 600 genes mutated in different cancer types. These genes tend not to duplicate but, unlike most human singletons, they encode central hubs of highly interconnected modules within the protein-protein interaction network (PIN). We find that cancer genes are fragile components of the human gene repertoire, sensitive to dosage modificati...

The histone tails on the nucleosome surface are subject to enzyme-catalyzed modifications that may, singly or in combination, form a code specifying patterns of gene expression. Recent papers provide insights into how a combinatorial code might be set and read. They show how modification of one residue can influence that of another, even when they are located on different histones, and how modi...

Performance of existing algorithms for similarity-based gene recognition in eukaryotes drops when the genomic DNA has been sequenced with errors. A modification of the spliced alignment algorithm allows for gene recognition in sequences with errors, in particular frameshifts. It tolerates up to 5% of sequencing errors without considerable drop of prediction reliability when a sufficiently close...

Directly modulating the activity of genome-editing proteins has the potential to increase their specificity by reducing activity following target locus modification. We developed Cas9 nucleases that are activated by the presence of a cell-permeable small molecule by inserting an evolved 4-hydroxytamoxifen-responsive intein at specific positions in Cas9. In human cells, conditionally active Cas9...

Histone modification by reversible lysine acetylation is a key regulatory mechanism in chromatin and nuclear signaling, whose deregulation is linked to aging, cancer, and other diseases. New work by Vazquez et al (2016) uncovers a role for the sirtuin family deacetylase SIRT7, which controls epigenetic maintenance of oncogenic gene expression programs, mitochondrial homeostasis, and ribosome bi...

5-hydroxymethylcytosine (5-hmC) is an extensively studied DNA epigenetic modification. Here we present a novel tool which combined with next generation sequencing offers new ways of analyzing 5-hmC at the genomic level. We demonstrate that the Thermo ScientificTM EpiJETTM 5-hmC Enrichment Kit is highly specific for different DNA samples containing 5-hmC modifications. Our data shows that this t...

A simplest method was followed for isolation of high quality genomic DNA form thallus of Plagiochasma appendiculatum that contained large quantities of polyphenols, terpenoids, tannins, contamination of high amount of RNA and polysaccharides. The method involved a modification of CTAB procedure using PVP (1%) and LiCl (4M) solution to remove polyphenols and RNA and some other binding proteins. ...