Showing papers on "Transcription (biology) published in 2022"
TL;DR: In this paper, the results from molecular docking and dynamics simulations as the primary determinative factor as well as the observed reliable binding modes have demonstrated that Nicotinamide Riboside and its active metabolite NMN can target human ACE2 and IMPDH, along with the viral Spro, Mpro, PLpro, and on top of all, RdRp as a potential competitive inhibitor.
17 citations
TL;DR: In this paper, a modified Intacellular Antibilinear Antibody (mintbody) was used to detect the sites of RNAP2 Ser2ph-mintbody foci.
Abstract: In eukaryotic nuclei, most genes are transcribed by RNA polymerase II (RNAP2), whose regulation is a key to understanding the genome and cell function. RNAP2 has a long heptapeptide repeat (Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7), and Ser2 is phosphorylated on an elongation form. To detect RNAP2 Ser2 phosphorylation (RNAP2 Ser2ph) in living cells, we developed a genetically encoded modification-specific intracellular antibody (mintbody) probe. The RNAP2 Ser2ph-mintbody exhibited numerous foci, possibly representing transcription "factories," and foci were diminished during mitosis and in a Ser2 kinase inhibitor. An in vitro binding assay using phosphopeptides confirmed the mintbody's specificity. RNAP2 Ser2ph-mintbody foci were colocalized with proteins associated with elongating RNAP2 compared with factors involved in the initiation. These results support the view that mintbody localization represents the sites of RNAP2 Ser2ph in living cells. RNAP2 Ser2ph-mintbody foci showed constrained diffusional motion like chromatin, but they were more mobile than DNA replication domains and p300-enriched foci, suggesting that the elongating RNAP2 complexes are separated from more confined chromatin domains.
10 citations
TL;DR: It is demonstrated that this construct of CRISPRa system (dCas9 protein fused with transcriptional activator VP64) could alter efficiently gene expression in N. ocanica and will open new avenue for genome engineering of Nannochloropsis.
7 citations
01 Jan 2022
TL;DR: In this article, the authors have highlighted various approaches and strategies for the development of antiviral drugs using the computation tools has been highlighted for the main targets of SARS-CoV-2.
Abstract: The well-established structure of SARS-CoV-2 proteins has opened the door for the drug development of the potent inhibitors. The interaction of spike proteins of the virus with human angiotensin converting enzyme (ACE-2) via receptor binding domain start the journey of the virus in the host cell. The entry of corona virus by endocytosis is followed by genomic replication, transcription and formation of the positive sense RNA. The assembling of genomic material with viral structure proteins, endoplasmic reticulum & golgi intermediate forms mature viron, which on exocytosis completes the SARS-CoV-2 life cycle. The entire cycle highlights the importance of different proteins involved in functioning and virulence of the virus. Targeting some of these proteins such as spike proteins, 3C like protease (3CL pro), papaine like protease (PL pro), helicase, RNA dependent RNA polymerase (RdRp) and N protein plays important role in the development of the antiviral drugs. Using computational approach the researchers are investigating important targets interaction with ligands (novel or existing) for the development of potent antiviral drugs. Number of existing FDA approved drug molecules are repurposed against 3CL pro, PL pro, RdRp and few of them, e.g. remdisivir, favipiravir and lvermectin, are currently used in clinical application against SARS-CoV-2. Numbers of small molecules libraries are also high through output screened for the identification of novel ligand molecule for new drug development. In the present chapter various approaches and strategies for the development of antiviral drugs using the computation tools has been highlighted for the main targets of SARS-CoV-2.
3 citations
TL;DR: In this paper, the authors describe how to characterize Cas13 nucleases from Type VI CRISPR-Cas systems using cell-free transcription-translation (TXTL) assays.
Abstract: Cell-free transcription-translation (TXTL) systems produce RNAs and proteins from added DNA. By coupling their production to a biochemical assay, these biomolecules can be rapidly and scalably characterized without the need for purification or cell culturing. Here, we describe how TXTL can be applied to characterize Cas13 nucleases from Type VI CRISPR-Cas systems. These nucleases employ guide RNAs to recognize complementary RNA targets, leading to the nonspecific collateral cleavage of nearby RNAs. In turn, RNA targeting by Cas13 has been exploited for numerous applications, including in vitro diagnostics, programmable gene silencing in eukaryotes, and sequence-specific antimicrobials. As part of the described method, we detail how to set up TXTL assays to measure on-target and collateral RNA cleavage by Cas13 as well as how to assay for putative anti-CRISPR proteins. Overall, the method should be useful for the characterization of Type VI CRISPR-Cas systems and their use in ranging applications.
2 citations
TL;DR: A series of hybrid compounds that incorporated anthranilic acid with activated 1H-indoles through a glyoxylamide linker were designed to target bacterial RNA polymerase holoenzyme formation using computational docking.
2 citations
TL;DR: The Drosophila Keap1 homolog (dKeap1) is conserved with mammalian Keap 1 except that dKeap 1 contains a 156 aa C-terminal tail (CTD) as discussed by the authors.
2 citations
TL;DR: It could be concluded that the transcription activity of CYP19 gene was activated by transcriptional factors in its proximal region of promoter to promote the synthesis of estrogens, regulating the selection of pre-hierarchical into hierarchical follicle in goose.
1 citations
TL;DR: Time-resolved transcriptomics by thiol (SH)-linked alkylation for the metabolic sequencing of RNA (SLAMseq) provides accurate information on transcript half-lives across annotated features in the genome, including by-products of transcription, such as introns as discussed by the authors.
Abstract: Gene expression is controlled at multiple levels, including RNA transcription and turnover. But determining the relative contributions of RNA biogenesis and decay to the steady-state abundance of cellular transcripts remains challenging because conventional transcriptomics approaches do not provide the temporal resolution to derive the kinetic parameters underlying steady-state gene expression.Here, we describe a protocol that combines metabolic RNA labeling by 4-thiouridine with chemical nucleoside conversion and whole-transcriptome sequencing followed by bioinformatics analysis to determine RNA stability in cultured cells at a genomic scale. Time-resolved transcriptomics by thiol (SH)-linked alkylation for the metabolic sequencing of RNA (SLAMseq) provides accurate information on transcript half-lives across annotated features in the genome, including by-products of transcription, such as introns. We provide a step-by-step instruction for time-resolved transcriptomics, which enhances traditional RNA sequencing protocols to acquire the temporal resolution required to directly measure the cellular kinetics of RNA turnover under physiological conditions.