Journal: Molecular cell

Article Title: Alternative splicing is a developmental switch for hTERT expression

doi: 10.1016/j.molcel.2021.03.033

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal Anti-SON Novus Biologicals NBP1-88706 Mouse monoclonal GAPDH (0411) Santa Cruz Biotech. sc-47724 Mouse monoclonal SSEA-4 (MC-813–70) R&D Systems MAB1435 Mouse monoclonal COL1A1 (3G3) Santa Cruz Biotech. sc-293182 Bacterial and virus strains Cytotune iPS Sendai Reprogramming kit ThermoFisher A16517 One Shot Stbl3 Chemically Competent E. coli ThermoFisher C737303 Biological samples Patient derived PBMCs Dr. Savage, NIH NCT-00027274 Chemicals, peptides, and recombinant proteins Y-27632 2HCl SelleckChem S1049 Isoginkgetin Tocris 6483 Critical commercial assays Dual-Luciferase® Reporter Assay System Promega E1910 Nano-Glo® Dual-Luciferase® Reporter Assay System Promega N1610 DNA Prep Kit, Tagmentation Illumina 20018704 Deposited data Raw and analyzed sequencing data This paper GEO accession: GSE168193 Human reference genome NCBI build 37, GRCh37 Genome Reference Consortium https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/ Raw data at Mendeley This paper https://dx.doi.org/10.17632/jfmsvxnpbg.1 Experimental models: cell lines Human: BJ Fibroblast ATCC CRL-2522 Human: ARPE-19 ATCC CRL-2302 Human: HeLa ATCC CCL-2 Human: TREx-HeLa Invitrogen R71407 Human: H7 ESC Dr. Lei Bu WA07 Oligonucleotides See Table S1 This paper N/A Recombinant DNA pRF-HCV Maria Barna n/a pNL1.1 Promega N1001 pcDNA5/FRT/TO ThermoFisher V652020 Software and algorithms 4C-ker Raviram et al., 2016 https://github.com/rr1859/R.4Cker Oligostan Tsanov et al., 2016 https://bitbucket.org/muellerflorian/fish_quant ImageJ Schneider et al., 2012 https://imagej.nih.gov/ij/ Bowtie2 Langmead and Salzberg, 2012 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Samtools Li et al., 2009 http://samtools.sourceforge.net/ Open in a separate window KEY RESOURCES TABLE Enhancers have a minor role in regulating telomerase during development Alternative splicing of exon 2 is a major determinant of hTERT levels Exon 2 skipping triggers hTERT mRNA decay in somatic cells SON regulates hTERT splicing, and its mutation manifests in telomerase insufficiency

Techniques: Virus, Derivative Assay, Recombinant, Reporter Assay, Sequencing, Software

Journal: Nucleic Acids Research

Article Title: Tracing the molecular basis of transcriptional dynamics in noisy data by using an experiment-based mathematical model

doi: 10.1093/nar/gku1272

Figure Lengend Snippet: Re-fitting the model can indicate the perturbation in the system. Human HepG2 cells were pre-incubated with 100 μM isoginkgetin for 16 h and subsequently treated with PPARδ ligand for the indicated time periods. qPCR was performed in order to measure pre-mRNA ( A ) and mature mRNA levels ( B ) and copy numbers were calculated. Small filled circles represent all data points from at least four biological experiments corrected for outlier and empty circles indicate their mean. All the individual data points are reported in Supplementary Tables S9. The mathematical model (adjusted for apparent fold induction) was fitted to the data by changing a single constant at a time and the quality of the fit was compared for pre-mRNA (grey) and mature mRNA (green) time courses ( C ). The best model obtained by lowering the splicing rate constant was further tested for fit improvement by changing the remaining constants ( D ). The best fit given by adjusting both splicing and degradation constants is also shown for the pre-mRNA (A) and mature mRNA (B) time courses.

Article Snippet: The splicing inhibitor isoginkgetin (kindly provided by the Dr Willmar, Schwabe GmbH & Co. KG, Karlsruhe, Germany) was added after 24 h to a final concentration of 50 μM.

Techniques: Incubation