...is the rising use of preprints, or scientific manuscripts shared by the authors on a public server independent... their work publicly and immediately once the manuscript is drafted. Preprints were one of the key routes...same time as, or slightly before, submitting the manuscript to a journal for formal peer review. Some organizations...unpublished results at a conference? Post your working manuscript as a preprint too and you can share all the details... use your work but don’t think they’ll have subscriptions to the specialized journals in your field? Post...only way to rigorously determine or ensure a manuscript’s quality. But even journal-based peer review ...giving authors the opportunity to strengthen the manuscript prior to submission. Preprints at Addgene Preprints...

...dCas9 has focused on transcriptional activation using a fusion to a transcriptional activator such as VP64...repression of transcription through binding a promoter region to inhibit association of transcriptional activators...locus of interest, the promoter region of the transcription factor IRF-1. Immunoprecipitation, using an ...Tapscott Lab identified regulators of DUX4, a transcriptional regulator that when inappropriately expressed...CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes." Cell 154.2 (2013): 442-451. ...

... domain, such as KRAB, to prevent efficient transcription from sgRNA targets. CRISPRi is effective in ...in a narrow range around the transcription start site (TSS). The Root and Doench lab selected sgRNAs in...gene expression, dCas9 can also be used for transcriptional activation. Activation of specific genes allows... strategies have been developed to recruit transcriptional machinery to dCas9 and its RNA directed binding...include RNA domains that recruit additional transcription factors. The Root and Doench labs utilized tracrRNAs...with two PP7 stem loops to recruit additional transcription factors to the targeted region (Sanson et al.... Konermann, Silvana, et al. "Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex...

...of customizable DNA-binding domains based on transcription-activator-like effectors (TALEs) as anchors ... thaliana. The results are light-inducible transcriptional effectors (LITEs) designed to bind specific.... Genes under LITE control showed a rise in transcription in as little as 30 minutes after light stimulation... universally abundant. Second, induction of transcription occurs within minutes of light exposure. Third...really flexible and modular,” Konermann said. “Transcriptional activators are easy to expand or combine with...al. "Optical control of mammalian endogenous transcription and epigenetic states." Nature. 500, 472–476...

...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....