A global regulatory mechanism for activating an exon network required for neurogenesis.

Mol. Cell. 2014 Oct 02;56(1):90-103. Epub 2014 Sep 11

Bushra Raj ¹ , Manuel Irimia ² , Ulrich Braunschweig ² , Timothy Sterne-Weiler ² , Dave O'Hanlon ² ,

Bushra Raj ¹ , Manuel Irimia ² , Ulrich Braunschweig ² , Timothy Sterne-Weiler ² , Dave O'Hanlon ² , Zhen-Yuan Lin ³ , Ginny I Chen ³ , Laura E Easton ⁴ , Jernej Ule ⁵ , Anne-Claude Gingras ⁶ , Eduardo Eyras ⁷ , Benjamin J Blencowe ⁸

+ et al

Author information

¹ Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
² Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.
³ Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada.
⁴ MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
⁵ MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK.
⁶ Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada.
⁷ Computational Genomics Group, Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain.
⁸ 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.

摘要

The vertebrate and neural-specific Ser/Arg (SR)-related protein nSR100/SRRM4 regulates an extensive program of alternative splicing with critical roles in nervous system development. However, the mechanism by which nSR100 controls its target exons is poorly understood. We demonstrate that nSR100-dependent neural exons are associated with a unique configuration of intronic cis-elements that promote rapid switch-like regulation during neurogenesis. A key feature of this configuration is the insertion of specialized intronic enhancers between polypyrimidine tracts and acceptor sites that bind nSR100 to potently activate exon inclusion in neural cells while weakening 3' splice site recognition and contributing to exon skipping in nonneural cells. nSR100 further operates by forming multiple interactions with early spliceosome components bound proximal to 3' splice sites. These multifaceted interactions achieve dominance over neural exon silencing mediated by the splicing regulator PTBP1. The results thus illuminate a widespread mechanism by which a critical neural exon network is activated during neurogenesis.

原始数据

保存测序数据

Sample name	Organism	Experiment title	Sample type	Library instrument	Attributes
Sample name	Organism	Experiment title	Sample type	Library instrument	antibody	cell line	construct	shRNA/sirna	source name
nSR100-iCLIP-hs	Homo sapiens	GSM1486179: nSR100-iCLIP-hs; Homo sapiens; OTHER	OTHER	Illumina HiSeq 2500	FLAG	293T	dox-inducible lentiviruses expressing Flag-nSR100		293T, dox-inducible
PTBP1-iCLIP_ plus nSR100	Homo sapiens	GSM1486178: PTBP1-iCLIP_ plus nSR100; Homo sapiens; OTHER	OTHER	Illumina HiSeq 2500	PTBP1	293T	dox-inducible lentiviruses expressing Flag-nSR100		293T, dox-inducible
PTBP1-iCLIP_no nSR100	Homo sapiens	GSM1486177: PTBP1-iCLIP_no nSR100; Homo sapiens; OTHER	OTHER	Illumina HiSeq 2500	PTBP1	293T	dox-inducible lentiviruses expressing Flag-nSR100		293T, dox-inducible
nSR100-PAR-iCLIP-mm_rep2	Mus musculus	GSM1486176: nSR100-PAR-iCLIP-mm_rep2; Mus musculus; OTHER	OTHER	Illumina HiSeq 2500	FLAG	N2A	dox-inducible lentiviruses expressing Flag-nSR100		N2A, dox-inducible
nSR100-PAR-iCLIP-mm_rep1	Mus musculus	GSM1486175: nSR100-PAR-iCLIP-mm_rep1; Mus musculus; OTHER	OTHER	Illumina HiSeq 2500	FLAG	N2A	dox-inducible lentiviruses expressing Flag-nSR100		N2A, dox-inducible