Multilayered Control of Alternative Splicing Regulatory Networks by Transcription Factors.
Networks of coordinated alternative splicing (AS) events play critical roles in development and disease. However, a comprehensive knowledge of the factors that regulate these networks is lacking. We describe a high-throughput system for systematically linking trans-acting factors to endogenous RNA regulatory events. Using this system, we identify hundreds of factors associated with diverse regulatory layers that positively or negatively control AS events linked to cell fate. Remarkably, more than one-third of the regulators are transcription factors. Further analyses of the zinc finger protein Zfp871 and BTB/POZ domain transcription factor Nacc1, which regulate neural and stem cell AS programs, respectively, reveal roles in controlling the expression of specific splicing regulators. Surprisingly, these proteins also appear to regulate target AS programs via binding RNA. Our results thus uncover a large "missing cache" of splicing regulators among annotated transcription factors, some of which dually regulate AS through direct and indirect mechanisms.
Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
Hong
H
Han
Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.
Ulrich
U
Braunschweig
Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.
Thomas
T
Gonatopoulos-Pournatzis
Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
Robert J
RJ
Weatheritt
Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada.
Calley L
CL
Hirsch
Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
Kevin C H
KCH
Ha
Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
Ernest
E
Radovani
Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
Syed
S
Nabeel-Shah
Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.
Tim
T
Sterne-Weiler
Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.
Juli
J
Wang
Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.
Dave
D
O'Hanlon
Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.
Qun
Q
Pan
Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.
Debashish
D
Ray
Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.
Hong
H
Zheng
Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada.
Frederick
F
Vizeacoumar
Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada.
Alessandro
A
Datti
Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON M5S 3M2, Canada.
Lilia
L
Magomedova
Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON M5S 3M2, Canada.
Carolyn L
CL
Cummins
Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
Timothy R
TR
Hughes
Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
Jack F
JF
Greenblatt
Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada.
Jeffrey L
JL
Wrana
Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
Jason
J
Moffat
Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada. Electronic address: b.blencowe@utoronto.ca.
Benjamin J
BJ
Blencowe
D017398:Alternative Splicing; D000818:Animals; D002460:Cell Line; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism; D053263:Gene Regulatory Networks; D057809:HEK293 Cells; D006801:Humans; D051379:Mice; D009474:Neurons / Q000166:cytology / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D014157:Transcription Factors / Q000378:metabolism*
D012333:RNA, Messenger; D014157:Transcription Factors
RNA interference; SPAR-seq; alternative splicing; chromatin; embryonic stem cells; high-throughput screening; neuroblastoma cells; spliceosome; splicing factors; transcription factors