RNA splicing is an essential process in the expression of genes in mammals. It is also frequently a point in regulation of gene expression via alternative splicing (AS) and through the retention of introns leading to degradation. As described below, recognition of signals for splicing such as 5'splice sites is critical for elongation by RNA polymerase and directionality of promoters. Further insights into these issues will advance the understanding of recently described long non-coding RNAs as well as many chronic, genetic, and infectious diseases. We recently found in analyzing RNA-seq data from our lab and other sources that a fraction of mammalian introns, about 6%, is more slowly spliced than their downstream introns in polyA + RNA. These """"""""detained"""""""" nuclear introns are ultimately excised before the mRNA is transported to the cytoplasm. Analysis of splicing patterns indicates an enrichment of detained introns around AS cassette exons. However, a large fraction of detained introns is considered constitutively spliced, suggesting that removal of these introns could be a rate limiting regulatory step. We propose to complete documentation of detained introns as a subgroup and to study their roles in response to stress and other conditions. We have recently found that a well-studied RNA binding protein that regulates AS, Rbfox2, binds to conserved sites adjacent to cassette exons containing nonsense codons that are important in auto-regulation of RNA binding proteins (RBP). In these cases, Rbfox2 levels set a threshold for auto-regulation by the RBP allowing variation between cell states of these RBPs. The importance of this mechanism for cross regulation of different RNA binding proteins will be investigated. Both initiation and elongation of transcription are coupled to RNA splicing. This coupling likely occurs through chromatin modifications as well as through direct interactions of splicing complexes with polymerase. We reported the wide spread (over 70%) occurrence of divergent transcription from promoter sites in mammalian cells. We recently recognized that many long non-coding RNAs originate from divergent transcription. Preliminary evidence indicates that recognition of combinations of polyadenylation sites and 5'splice sites is important in controlling termination of transcription in the upstream antisense and sense direction. We propose to further investigate this relationship and the possibility that recognition of nascent upstream RNA can mediate regulation of transcription in the sense direction and chromatin modification.

Public Health Relevance

The burden of cancer in public health is apparent in both human suffering and the cost of healthcare. The proposed research will provide the basis for new therapeutics to better treat cancer and thus improve public health.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1-MGB-E (08))
Program Officer
Bender, Michael T
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Massachusetts Institute of Technology
Internal Medicine/Medicine
Schools of Arts and Sciences
United States
Zip Code
Chow, Ryan D; Guzman, Christopher D; Wang, Guangchuan et al. (2017) AAV-mediated direct in vivo CRISPR screen identifies functional suppressors in glioblastoma. Nat Neurosci 20:1329-1341
Gosline, Sara J C; Gurtan, Allan M; JnBaptiste, Courtney K et al. (2016) Elucidating MicroRNA Regulatory Networks Using Transcriptional, Post-transcriptional, and Histone Modification Measurements. Cell Rep 14:310-9
Zhang, Xiaochang; Chen, Ming Hui; Wu, Xuebing et al. (2016) Cell-Type-Specific Alternative Splicing Governs Cell Fate in the Developing Cerebral Cortex. Cell 166:1147-1162.e15
Kuhn, Claus-D; Wilusz, Jeremy E; Zheng, Yuxuan et al. (2015) On-enzyme refolding permits small RNA and tRNA surveillance by the CCA-adding enzyme. Cell 160:644-58
Ran, F Ann; Cong, Le; Yan, Winston X et al. (2015) In vivo genome editing using Staphylococcus aureus Cas9. Nature 520:186-91
Doucet, Aurélien J; Wilusz, Jeremy E; Miyoshi, Tomoichiro et al. (2015) A 3' Poly(A) Tract Is Required for LINE-1 Retrotransposition. Mol Cell 60:728-741
Boutz, Paul L; Bhutkar, Arjun; Sharp, Phillip A (2015) Detained introns are a novel, widespread class of post-transcriptionally spliced introns. Genes Dev 29:63-80
Jangi, Mohini; Boutz, Paul L; Paul, Prakriti et al. (2014) Rbfox2 controls autoregulation in RNA-binding protein networks. Genes Dev 28:637-51
Jangi, Mohini; Sharp, Phillip A (2014) Building robust transcriptomes with master splicing factors. Cell 159:487-98
Zamudio, Jesse R; Kelly, Timothy J; Sharp, Phillip A (2014) Argonaute-bound small RNAs from promoter-proximal RNA polymerase II. Cell 156:920-34

Showing the most recent 10 out of 59 publications