...our AAV preparations. We recently published a description of the VGS process and use cases in Human Gene...addition, we wrote an open-source custom Python script that uses the VGS data to determine the percent...recombination present in Cre-dependent vectors and a script that can confirm the serotype of AAV preparations...use this to our advantage by designing a Python script that looks for pre-defined serotype specific signature...parallel and provide serotype data in minutes and the scripts  can be easily customized to detect other sequences...are excited to share the procedures and Python scripts with laboratories and viral vector cores routinely...

...non-exclusive gene silencing pathways: transcriptional and post-transcriptional gene silencing (PTGS). In either...silence the target gene(s) either transcriptionally or post-transcriptionally. In plants, different dicer-like...alternative start codons, and/or the phenomenon of transcriptional adaptation (Smits et al., 2019; Sztal and Stainier...can be easily scored. However, determining the transcript or protein abundance of your specific target ...s41592-019-0614-5 Sztal TE, Stainier DYR (2020) Transcriptional adaptation: a mechanism underlying genetic ...

...nomenclature of the plasmid backbone is meant to be descriptive of the components found within the backbone. ... Pol Precursor protein containing Reverse Transcriptase and Integrase components. Transfer cPPT... WPRE Woodchuck hepatitis virus post‐transcriptional regulatory element; sequence that stimulates...necessary for activation of viral genomic RNA transcription. R; Repeat region found within both the 5' and... 5’ LTR Acts as an RNA pol II promoter. The transcript begins, by definition, at the beginning of R,...rest of the provirus. 3’ LTR Terminates transcription started by 5' LTR by the addition of a poly ...

...fused to a transcriptional repressor to your gene of interest. It will inhibit transcription instead of...stranded RNA molecules that degrade target mRNA transcripts. When transiently introduced, they can deplete...that, too! CRISPR activators (CRISPRa) are transcriptional activators fused to a dead Cas9. The system...tetracycline or one of its analogs will induce these transcriptional changes, and expression is tunable by titration...expression goes back to baseline) and occurs at the transcriptional level.     Fig. 2 Tetracycline...

...affect transcription independent of their enzymatic activity. They interact with transcriptional machinery...specifically edit methylation sites.  Step aside, transcriptionally active dioxygenase  When I started to work...by distinct proteins and result in unclear transcriptional consequences (Sprujit 2013). Enzymatic domains...in the genome and directly interacting with transcription machinery.   Well, I’ve got some good news...Hydroxylation, Active DNA Demethylation, Gene Transcription, and Memory Formation. Neuron 79, 6 P1086-1093...

...a protein that regulated its own transcription, or the transcription of another gene? Now you have a genetic...hierarchical levels: individual DNA parts, transcriptional units, and multigene constructs. Let’s start...start by examining individual parts and transcriptional units. Individual parts are defined DNA sequences...selected, individual units can be combined into… Transcription units (TUs), which are functional units composed... with DNA, and these complexes regulate the transcription of specific genes. What if one of those genes...

...xCas9 for transcriptional regulation and base editing Hu et al. also engineered transcriptional activators...activating transcription. Sites containing NG, GAA, or GAT PAMs averaged 56-91% transcriptional activation...subunit ω. This construct is designed to activate transcription from the accessory plasmid (AP) encoding phage...could recognize a library PAM, it would induce transcription of gene III, permitting phage propagation and...

...They rely on a viral protein called reverse transcriptase to convert their RNA genomes into DNA to be ... larger protein: PR (protease), RT (reverse transcriptase), and IN (integrase). These viral packaging ...the retroviral life cycle for a more detailed description). Since the integrated portion does not contain... cycle initially proceeds as usual. Reverse transcription of the transgene occurs in the cytoplasm, then... McCray, 2010). However, IDLV genomes are transcriptionally active, leading to transient expression of...Lentiviral vectors tend to integrate into transcriptionally active regions of the genome (Schröder et ...

... modulating gene expression at the level of transcription – CRISPRa (activation) and CRISPRi (inhibition...most-efficacious to target a ~100nt window upstream of the transcription start site (TSS), while for CRISPRi, a ~100nt...of producing the guide (synthetic, in vitro transcription, or lentiviral delivery) can affect the accuracy...examined whenever possible when using knockout or transcriptional modulation approaches. Avoiding off-target ...improves the efficiency of CRISPR/dCas9-mediated transcriptional repression. Nucleic Acids Res 44:e141–e141 ...editing: precision chemistry on the genome and transcriptome of living cells. Nat Rev Genet 19:770–788 . ...

...from the event can be found below along with a description of the program beneath it. You can jump to the...the different time stamps in the description to watch any sections you’re particularly interested in, ...abbreviated methods section found within a published manuscript. Luckily, many organizations have been working...JoVe, and Bio-protocol all work to provide more descriptive and interactive protocols that make it much easier...would get in-principle acceptance of the final manuscript regardless of whether the ultimate results were...Minisymposium on Reproducibility Booklet - Including descriptions of many organizations promoting reproducibility...

...pluripotent stem cells) through the expression of transcription factors OCT3/4, SOX2, KLF4, and c-MYC is the... method for generating iPSCs to express the transcription factors from a polycistronic cassette. However...beautifully demonstrate light-dependent Gal4 transcriptional activation and Cre recombination. Find PhoCl...podcast segment on the B. subtilis libraries Transcription factor fusions elucidate iPSC reprogramming ...fusion protein, the authors show that the VP16 transcription activation domain fusion increases the efficiency...eliminates reprogramming. These results argue that transcription activation by SOX2 leads to its reprogramming... KLF4, SOX2 and OCT4 DNA binding domain and transcription activation domain fusion constructs. This is...

...activation of transcription in bacteria by co-opting σ54-based transcription. Transcription from σ54 promoters... PMID: 31366908 Adapting sigma54-dependent transcription for CRISPR activation in bacteria Article contributed...UAS via the dCas9-gRNA complex which allows transcription from the promoter.  They found that the system...

...Students Writing Scientific Manuscripts Tips for Improving Your Next Manuscript...learned a lot from listening to others' alt text descriptions, and we’d love to hear yours as well.  More ... You can use them to help you write an entire manuscript, or you could use them to write alt text for ...accept alt text, so you can submit it with your manuscript and help make your paper accessible to even more...

...tRNAs contain internal transcriptional elements that enhance pol III transcription, potentially increasing...base Csy4 recognition sites from a polycistronic transcript. Although this method shortens construct size...coexpression of Csy4 with Cas9 and the polycistronic transcript. As nucleases may have off-target effects and...matching traditional gRNA-expressing constructs, transcript levels of PTG1 and PTG2 were 3 and 31 times higher...

...synthetic promoters. Legend: TSS: transcription start site. TFBS: transcription factor binding site. Image from...conserved sequences that are upstream of the transcription initiation sites of at least two genes with ...promoters by repeating mouse cell type specific transcription factor binding sites interspaced with random...designed using stretches of DNA that were transcriptionally active in retinal cell types in mice. ...

...publication in Science describing the development of “transcriptors,” transistor-like digital genetic switches that...cellular computing. These logic gates built from transcriptors are now available at Addgene through the Biobrick...kit comprised of well-characterized bacterial transcription and translation initiation elements. Open science...with the central dogma - replication of DNA, transcription of DNA to make RNA, translation of RNA to make...Precise and reliable gene expression via standard transcription and translation initiation." Nature Methods....

...(or host cell) by the viral protein reverse transcriptase (RT). In the case of a natural virus, both the...the protein and the genetic code for reverse transcriptase are packaged (Wu et al., 1997) inside of the...viral vectors, only the protein for reverse transcriptase (RT) is present in the capsid, as the engineered...cell’s genome and then use cell machinery for transcription and translation. Here, we will discuss several...during uncoating. After uncoating, reverse transcription follows the release of the two strands of viral...

...you can use to study these genes! Groucho, a transcriptional co-repressor The first conference room, that...Addgenies, was named after the protein Groucho, a transcriptional co-repressor important in development. Groucho.... It binds to a specific set of DNA-binding transcription factors to repress the expression of genes primarily...Ish-Horowicz. "The Groucho/TLE/Grg family of transcriptional co-repressors." Genome biology 9.1 (2008): ... Jiang, Jianqiao, and Helen White-Cooper. "Transcriptional activation in Drosophila spermatogenesis involves...

...create secondary structures in RNA transcripts Effects on transcription (remember, it’s not all about translation...locations or fail to make it through the entire transcript resulting in the production of nonfunctional ...translation - e.g. codon choice may interrupt transcription factor binding sites) As you might imagine,...algorithms and DNA synthesis companies such as IDT and GenScript host online codon optimization tools. Keep in ...

...independently of their position relative to a transcription start site. In STARR-seq, randomly sheared genomic...contain an enhancer, it will activate its own transcription from the minimal promoter and its strength can... Receptor-ome Expression and Screening via Transcriptional Output-TANGO (PRESTO-TANGO) to screen the NCC...RAS signaling pathway and includes 180 unique transcripts. Each gene was chosen to represent the primary...variant in 38 types of human cancer. Many of the transcripts are not available from other existing sources...Available at Addgene: Lab Plasmids Dan Carlson RCIscript-GoldyTALEN, pC-GoldyTALEN Tom Ellis pTAL5-BB...targeting vectors that encode both a guide RNA transcript and a repair template for an individual tagging...