An expression vector capable of disrupting the silencing of cell cycle genes in adult cells, such as adult cardiac myocytes and other quiescent cells in terminally differentiated tissues, comprising: (a) a nucleic acid sequence encoding lysine-specific demethylase 4D (KDM4D); (b) a promoter that induces or effects overexpression of KDM4D, wherein the promoter is operably linked to the nucleic acid sequence; and (c) a regulatory element that inducibly represses the overexpression of KDM4D. The vector can be administered to a subject in a method for inducing tissue-specific hyperplasia in a mammal, including cardiomyocyte proliferation. The method provides for regenerative therapy, including improving cardiac function after myocardial infarct and other forms of cardiac damage.

Provided is a method for detecting the chemical modification of a target RNA site X, comprising the steps as follows: (1) acquiring an RNA sample and selecting in the RNA sample a target RNA segment comprising the target RNA site X; (2) SELECT; (3) PCR amplification; (4) comprising the PCR cycle threshold value with a reference PCR cycle threshold value, or comparing the PCR amplification product quantity with a reference PCR amplification product quantity, so as to determine whether there is a target chemical modification in the target RNA site X. Further provided are a method for identifying a substrate target site of RNA modification enzyme or RNA demodification enzyme and a method for quantifying an RNA modification rate in a transcript.

Methods and constructs for RNA-guided targeting of heterologous functional domains such as transcriptional activators to specific genomic loci.

Engineered CRISPR from Prevotella and Francisella 1 (Cpf1) nucleases with altered and improved target specificity and their use in genomic engineering, epigenomic engineering, genome targeting, genome editing, and in vitro diagnostics.

Provided are transgenic organisms, such as plants and plant parts, cells, and related compositions and methods for producing and monitoring the genotype for enhanced production of montbretin A and/or its precursors. For example, provided is a transgenic organism comprising at least one heterologous nucleic acid operatively linked to a promoter, wherein the heterologous nucleic acid encodes at least one enzyme in a montbretin A (MbA) metabolic pathway. The organisms can be a plant, plant part, or plant cell, or a microorganism such as a yeast. Also provided is a method for producing at least one montbretin A (MbA) precursor and/or MbA, comprising permitting the expression of the at least one heterologous nucleic acid in the transgenic organism. The disclosure also provides isolated nucleic acid molecules that comprise sequence encoding at least one enzyme in a montbretin A (MbA) metabolic pathway and vectors comprising the nucleic acids.

A method for identifying any of the presence, location and phasing of modified cytosines (C) in long stretches of nucleic acids is provided. In some embodiments, the method may comprise (a) reacting a first portion of a nucleic acid sample containing at least one C and/or at least one modified C with a DNA glucosyltransferase and a cytidine deaminase to produce a first product and/or reacting a second portion of the sample with a dioxygenase, optionally a DNA glucosyltransferase and a cytidine deaminase to produce a second product and; (b) comparing the sequences from the first and optionally the second product obtained in (a), or amplification products thereof, with each other and/or an untreated reference sequence to determine which Cs in the initial nucleic acid fragment are modified. A modified TET methylcytosine dioxygenase with improved efficiency compared to unmodified TET2 at converting methylcytosine to carboxymethylcytosine is also provided.

Many studies have shown that CRISPR-Cas nucleases can tolerate up to five mismatches and still cleave; it is hard to predict the effects of any given single or combination of mismatches on activity. Taken together, these nucleases can show significant off-target effects but it can be challenging to predict these sites. Described herein are methods for increasing the specificity of genome editing using the CRISPR/Cas system, e.g., using RNA-guided FokI Nucleases (RFNs), e.g., FokI-Cas9 or FokI-dCas9-based fusion proteins.

Provided herein are composition and process for using an electrochemical device for the reduction of the oxidized state of phosphorylated or non-phosphorylated nicotinamide adenine dinucleotide to the reduced state in which unwanted products of the electrochemical reduction are recovered as the oxidized state of the phosphorylated or non-phosphorylated nicotinamide adenine dinucleotide and returned to the electrochemical device for reduction.

Disclosed are compositions and methods that use lysine demethylase inhibitors for inhibiting the growth of cancer stem cells or tumor initiating cells, for enhancing the biological effects of chemotherapeutic drugs or irradiation on cancer cells and/or for preventing cancer recurrence.

Methods for increasing specificity of RNA-guided genome editing, e.g., editing using CRISPR/Cas9 systems.