HSLS MolBio Workshops

This workshop provides an overview of resources and search strategies on transcriptional regulation. Emphasis will be given to HSLS-licensed TRANSFAC/Match and Correlation Engine software, as well as open-access tools such as the UCSC genome browser and Cistrome data browser. 

Participants will learn to

• retrieve information linked with a transcription factor
• retrieve the promoter sequence for a gene of interest
• extract transcription regulatory elements--promoters, enhancers, and silencers associated with a gene of interest
• identify the transcription factor binding site(s) present in a DNA sequence
• identify transcription factor binding sites present in a ChIP-Seq dataset (motif discovery)
• identify upstream regulatory transcription factors for a differentially expressed gene data set
• start with a gene expression data set and find correlated studies with gene perturbation experiments (knock-out, knock-down, etc.) available in the GEO database
• start with a ChIP-Seq data set and find factors that have a significant binding overlap with the ChIP-Seq peak set

Target Audience

Experimental biologists seeking to analyze bulk RNA-Seq data generated through experiments or retrieved from a repository such as GEO. The software covered in the workshop operates through a user-friendly, point-and-click graphical user interface, so neither programming experience nor familiarity with the command-line interface is required.

Powerpoint

• Slides 

Lecture Video

• Part1 - morning session offered on February 03, 2021
• Part2 - afternoon session offered on February 03, 2021

Data Download

• Myc_human - generic promoter sequence for human myc
• CD274_human - generic promoter sequence for CD247
• RUNX1_ChIPseq - RUNX1 transcription factor binding peaks in .bed format
• AI-10-49 vs DMSO RNA_Seq - differentially expressed genes between AI-10-49 treatment vs. DMSO (control) formatted for IPA upload
• AI-10-49 vs DMSO RNA-seq - differentially expressed genes between AI-10-49 treatment vs. DMSO (control) formatted for Correlation Engine upload
• Practice Exercise (SARSCov-2 vs mock_Calu3) - a dataset with the differentially expressed genes between SARS-CoV2 infected vs. mock-infected Calu3 cells for practice
• CD47_UCSCGB - UCSC Browser displaying  Myc binding sites on CD47 promoter region 

Software Registration

• Register for Transfac & Match- database of eukaryotic transcription factors, their genomic binding sites, and DNA-binding profiles.
• Register for Correlation Engine -support research to identify mechanisms of disease, drug targets, and prognostic or predictive biomarkers.

• GeneExplain Portal - provides bioinformatics, systems biology, and cheminformatics software and databases for life science and medical research.
• UCSC Genome Browser 
• UCSC GB_CD47 - UCSC genome browser displaying CD47 promoter sequence
• BLAT - Paste in a query sequence to find its location in the genome.
• Jasper - contains a curated, non-redundant set of profiles, derived from published and experimentally defined transcription factor binding sites for eukaryotes. 
• GeneCards - a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. 
• Cistrome Data Browser - Check what factors regulate your gene of interest, what factors bind in your interval or have a significant binding overlap with your peak set.
• Cistrome ToolKit - allows users to quickly examine their hypothesis regarding gene regulation through public ChIP-seq (protein factors and histone marks), chromatin accessibility (DNase-seq and ATAC-seq) data.
• Illumina Correlation Engine - support research to identify mechanisms of disease, drug targets, and prognostic or predictive biomarkers.
• BioRender - Scientific illustrations creating tool

Key References

• Pulikkan JA, Hegde M, Ahmad HM, et al. CBFβ-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia. Cell. 2018;174(1):172-186.e21. doi:10.1016/j.cell.2018.05.048
• Casey, S. C. et al. MYC regulates the antitumor immune response through CD47 and PD-L1. Science (2016). doi:10.1126/science.aac9935
• Andersson R, Sandelin A. Determinants of enhancer and promoter activities of regulatory elements. Nat Rev Genet. October 2019. doi:10.1038/s41576-019-0173-8
• Gasperini M, Tome JM, Shendure J. Towards a comprehensive catalogue of validated and target-linked human enhancers. Nat Rev Genet. January 2020. doi:10.1038/s41576-019-0209-0
• Fishilevich, S., Nudel, R., Rappaport, N., Hadar, R., Plaschkes, I., Iny Stein, T., … Cohen, D. (2017). GeneHancer: genome-wide integration of enhancers and target genes in GeneCards. Database: The Journal of Biological Databases and Curation, 2017. doi:1
• Kel AE, Gößling E, Reuter I, Cheremushkin E, Kel-Margoulis OV, Wingender E. (2003) MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res 31:3576-3579.
• Schmitt, A. D., Hu, M. & Ren, B. Genome-wide mapping and analysis of chromosome architecture. Nat Rev Mol Cell Biol 17, 743–755 (2016).
• 3D Genome - Nature Reviews 

Publications citing GeneXplain/Biobase/Transfac from Pitt researchers

Attribution

Please include the following statement in the acknowledgments section for all publications, posters, and presentations: 

[Software name] licensed through the Molecular Biology Information Service of the Health Sciences Library System, University of Pittsburgh (RRID:SCR_011975) was used for data analysis.

Feedback

•  Class Evaluation

Support

• HSLS-MBIS - request for Consultation