A5028041228- RNA Research and Splicing
- Genomics and Chromatin Dynamics
- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- Bacteriophages and microbial interactions
- Glycosylation and Glycoproteins Research
- Single-cell and spatial transcriptomics
- Neurobiology and Insect Physiology Research
Fred Hutch Cancer Center
2000-2025
Howard Hughes Medical Institute
2000
Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa
1998
We describe a new primer design strategy for PCR amplification of unknown targets that are related to multiply-aligned protein sequences. Each consists short 3′ degenerate core region and longer 5′ consensus clamp region. Only 3–4 highly conserved amino acid residues necessary the core, which is stabilized by during annealing template molecules. During later rounds amplification, non-degenerate permits stable product demonstrate practical utility this hybrid method detection diverse reverse...
The Blocks Database WWW (http://blocks.fhcrc.org ) and Email (blocks@blocks.fhcrc.org servers provide tools to search DNA protein queries against the Blocks+ of multiple alignments, which represent conserved regions. nearly doubles number families included in database by adding from Pfam-A, ProDom Domo databases those PROSITE PRINTS. Other new features include improved Block Searcher statistics, searching with NCBI's IMPALA program 3D display blocks on PDB structures.
Genome-wide hypertranscription is common in human cancer and predicts poor prognosis. To understand how might drive cancer, we applied our formalin-fixed paraffin-embedded (FFPE)–cleavage under targeted accessible chromatin method for mapping RNA polymerase II (RNAPII) genome-wide FFPE sections. We demonstrate global RNAPII elevations mouse gliomas assorted tumors small clinical samples discover regional corresponding to de novo HER2 amplifications punctuated by likely selective sweeps....
Abstract For more than a century, formalin-fixed paraffin-embedded (FFPE) sample preparation has been the preferred method for long-term preservation of biological material. However, use FFPE samples epigenomic studies difficult because chromatin damage from long exposure to high concentrations formaldehyde. Previously, we introduced Cleavage Under Targeted Accessible Chromatin (CUTAC), an antibody-targeted accessibility mapping protocol based on CUT&Tag. Here show that simple...
Hypertranscription is common in human cancers and predicts poor prognosis. However detection of hypertranscription indirect, relying on accurately quantifying mRNA levels estimating cell numbers. Previously, we introduced FFPE-CUTAC, a genome-wide method for mapping RNA Polymerase II (RNAPII) formalin-fixed paraffin-embedded (FFPE) sections. Here use FFPE-CUTAC to demonstrate both transgene-driven mouse gliomas assorted tumors at active regulatory elements replication-coupled histone genes...