Dr. Douglas Black's lab works on a range of projects related to the control of pre-mRNA splicing and its role in gene regulation. They study the mechanisms of action of splicing regulators, as well as how these regulators affect biological processes such as neuronal development, tumor progression and the inflammatory response in macrophages. They have long-standing projects examining two families of regulatory factors: the polypyrimidine tract binding proteins (PTBP1 and PTBP2) and the Rbfox proteins (1, 2 and 3).
In mechanistic studies, Black's lab uses biochemical methods and in vitro systems to examine the molecular interactions of these proteins and analyze how they can alter spliceosome assembly. In biological studies, they have shown that each of these RNA binding proteins alters the splicing of a specific set of gene transcripts in neurons, and each can induce different splicing outcomes depending on the target exon. The PTB proteins control regulatory transitions during early and late neuronal differentiation, and are required for proper neuronal development and synaptogenesis. The Rbfox proteins control the expression and isoform choice of many synaptic proteins determining neuronal activity in mature cells, such as ion channels, neurotransmitter receptors and proteins involved in calcium signaling. These efforts use whole transcriptome sequencing, crosslinking-immunoprecipitation and other genomic methods in ES and primary cell culture models and in conditional mutant mice to understand how these proteins, and their particular splicing targets, affect development and cellular phenotype.
More recent projects apply nascent RNA sequencing to understand the role of splicing kinetics in the innate immune response and combine RNA sequencing of defined cell culture and mouse models with broad analyses of sequence databases to identify tumor-specific spliced isoforms. This work has brought Black's lab into collaborative projects with numerous other groups at UCLA and outside, who specialize in proteomics, bioinformatics, structure determination, molecular neuroscience, physiology, immunology, cancer biology and other fields.
Ying Y, Wang XJ, Vuong CK, Lin CH, Damianov A, Black DL. Splicing Activation by Rbfox Requires Self-Aggregation through Its Tyrosine-Rich Domain. Cell. 2017 Jul 13;170(2):312-323.e10. doi: 10.1016/j.cell.2017.06.022.
Wongpalee SP, Vashisht A, Sharma S, Chui D, Wohlschlegel JA, Black DL. Large-scale remodeling of a repressed exon ribonucleoprotein to an exon definition complex active for splicing. Elife. 2016 Nov 24;5. pii: e19743. doi: 10.7554/eLife.19743.
Damianov A, Ying Y, Lin CH, Lee JA, Tran D, Vashisht AA, Bahrami-Samani E, Xing Y, Martin KC, Wohlschlegel JA, Black DL. Rbfox Proteins Regulate Splicing as Part of a Large Multiprotein Complex LASR. Cell. 2016 Apr 21;165(3):606-19. doi: 10.1016/j.cell.2016.03.040.
Lee JA, Damianov A, Lin CH, Fontes M, Parikshak NN, Anderson ES, Geschwind DH, Black DL, Martin KC. Cytoplasmic Rbfox1 Regulates the Expression of Synaptic and Autism-Related Genes. Neuron. 2016 Jan 6;89(1):113-28. doi: 10.1016/j.neuron.2015.11.025. Epub 2015 Dec 10.
Linares AJ, Lin CH, Damianov A, Adams KL, Novitch BG, Black DL. The splicing regulator PTBP1 controls the activity of the transcription factor Pbx1 during neuronal differentiation. Elife. 2015 Dec 24;4:e09268. doi: 10.7554/eLife.09268.