Embodiments disclosed herein provide a general, scalable, high-throughput, and high-resolution approach for experimental dissection of regulatory regions and driver nucleotides in the context of human biology and disease. Applicants present HiDRA, a novel high-resolution global screen for transcriptional regulatory activity in accessible chromatin regions, enabling high-efficiency, high-throughput, and high-resolution inference of regulatory activity.

Provided are constructs and methods useful for the screening and identification of polynucleotide sequences of interest, in particular promoters, RNA stability modifying sequences and transcriptional modifying sequences.

A method for identifying and characterizing biological parts based on omics datasets and a dual-fluorescent reporter gene system, and a biological part library constructed thereon are provided, relating to a technical filed of biology. The method includes steps of: identifying the biological parts using the omics datasets; constructing a single-fluorescent reporter gene system using a shuttle vector pEZ15Asp as a skeleton for screening and determining fluorescent reporter genes; obtaining a dual-fluorescent reporter gene system skeleton; constructing recombinant plasmids, and finally transforming into competent cells for quantitative analysis of fluorescence intensities. The present invention is convenient and quick, and can screen and identify different biological parts such as RBS, UTRs, promoters, and terminators of different intensities in batch quantitatively in a relatively short time. Moreover, the present invention can quickly expand the biological part library of Z. mobilis, so as to be applied in metabolic engineering of different demands.

Nucleic acid constructs that allow insertion and/or expression of a sequence of interest, such as a transgene, are provided. Compositions and methods of using such constructs for expression of a polypeptide or therapeutic agent, for example, are also provided.

Disclosed are compositions, methods, and kits for performing cell-free RNA transcription and/or cell-free protein synthesis (CFPS). The disclosed compositions, methods, and kits include or utilize components prepared from a species of Clostridia such as cellular extracts from Clostridium autoethanogenum.

Described herein is a method for identifying synthetic inducible promoters that have specified induction and/or repression for DNA binding proteins such as an allosteric transcription factor and an inducer molecule. The method includes an in vitro selection from an unselected polynucleotide library comprising a plurality of random degeneracies, and an in vivo selection to produce an induced promoter library. Produced is an induction table, which allows the selection of a promoter with specific induction and/or repression properties. Also included are biosensors containing the synthetic inducible promoters.

Described herein is a method for identifying synthetic inducible promoters that have specified induction and/or repression for DNA binding proteins such as an allosteric transcription factor and an inducer molecule. The method includes an in vitro selection from an unselected polynucleotide library comprising a plurality of random degeneracies, and an in vivo selection to produce an induced promoter library. Produced is an induction table, which allows the selection of a promoter with specific induction and/or repression properties. Also included are biosensors containing the synthetic inducible promoters.

Provided are constructs and methods useful for the screening and identification of polynucleotide sequences of interest, in particular promoters, RNA stability modifying sequences and transcriptional modifying sequences.

The disclosure provides artificial nucleic acid introns configured for selective splicing in cells with aberrant RNA splicing activity, e.g., neoplastic cells. The artificial intron can comprise a 5 splice site, a canonical 3 splice site, at least one cryptic 3 splice site, a pyrimidine-rich domain, and at least one branchpoint. Also provided are constructs integrating the artificial introns with exons in a configuration that, when the artificial intron is spliced out by the aberrant RNA splicing factors, encode a functional protein. Also disclosed are methods that employ the disclosed platform of selective expression, including, targeted gene therapy methods (e.g., in cancers), diagnostics and imaging, and drug screening.

The present invention provides methods for identifying a factor which modulates gene expression comprising providing a library of at least 110.sup.6 nucleic acid molecules each comprising a stochastic sequence of at least 50 nucleotides, introducing said nucleic acid molecules into nucleic acid constructs which comprise a reporter sequence and which do not comprise a further separate sequence upstream of the reporter sequence that can modulate expression of the reporter sequence to generate test constructs, introducing test constructs into host cells and assessing expression of the reporter sequence, thereby to identify a factor which modulates gene expression. Libraries of nucleic acid molecules, test constructs and host cells for use in such methods are also provided.