MBNL proteins repress ES-cell-specific alternative splicing and reprogramming

• Published in: Nature (London) Vol. 498; no. 7453; pp. 241 - 245
• Main Authors: Han, Hong, Irimia, Manuel, Ross, P. Joel, Sung, Hoon-Ki, Alipanahi, Babak, David, Laurent, Golipour, Azadeh, Gabut, Mathieu, Michael, Iacovos P., Nachman, Emil N., Wang, Eric, Trcka, Dan, Thompson, Tadeo, O’Hanlon, Dave, Slobodeniuc, Valentina, Barbosa-Morais, Nuno L., Burge, Christopher B., Moffat, Jason, Frey, Brendan J., Nagy, Andras, Ellis, James, Wrana, Jeffrey L., Blencowe, Benjamin J.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 13.06.2013; Nature Publishing Group
• Subjects: 631/136/532; 631/208/200; 631/337/1645/1946; 631/337/2019; Alternative Splicing - genetics; Amino Acid Motifs; Animals; Binding proteins; Binding sites; Biology; Cell Differentiation - genetics; Cell Line; Cellular Reprogramming; Cloning; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - deficiency; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; Embryonic stem cells; Embryonic Stem Cells - cytology; Embryonic Stem Cells - metabolism; Fibroblasts - cytology; Fibroblasts - metabolism; Forkhead Transcription Factors - metabolism; Gene expression; Gene Knockdown Techniques; Genetic aspects; Genetic engineering; Genetic regulation; HEK293 Cells; HeLa Cells; Humanities and Social Sciences; Humans; Identification and classification; Induced Pluripotent Stem Cells - cytology; Induced Pluripotent Stem Cells - metabolism; Kinases; Kinetics; letter; Mice; multidisciplinary; Physiological aspects; Proteins; Repressor Proteins - metabolism; RNA splicing; RNA-Binding Proteins - chemistry; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism; Science; Testing; Canada
• ISSN: 0028-0836; 1476-4687; 1476-4687
• DOI: 10.1038/nature12270

This study identifies MBNL proteins as negative regulators of alternative splicing events that are differentially regulated between ES cells and other cell types; several lines of evidence show that these proteins repress an ES cell alternative splicing program and the reprogramming of somatic cells to induced pluripotent stem cells. MBNL proteins and pluripotency Ben Blencowe and colleagues identify the muscleblind-like RNA binding proteins MBNL1 and MBNL2 as negative regulators of alternative splicing events that are differentially regulated between embryonic stem cells and other cell types. Several lines of evidence show that they are involved in the regulation of embryonic-stem-cell-like alternative splicing patterns. The authors also identify a regulatory role during the reprogramming of fibroblasts to induced pluripotent stem (iPS) cells. Previous investigations of the core gene regulatory circuitry that controls the pluripotency of embryonic stem (ES) cells have largely focused on the roles of transcription, chromatin and non-coding RNA regulators 1 , 2 , 3 . Alternative splicing represents a widely acting mode of gene regulation 4 , 5 , 6 , 7 , 8 , yet its role in regulating ES-cell pluripotency and differentiation is poorly understood. Here we identify the muscleblind-like RNA binding proteins, MBNL1 and MBNL2, as conserved and direct negative regulators of a large program of cassette exon alternative splicing events that are differentially regulated between ES cells and other cell types. Knockdown of MBNL proteins in differentiated cells causes switching to an ES-cell-like alternative splicing pattern for approximately half of these events, whereas overexpression of MBNL proteins in ES cells promotes differentiated-cell-like alternative splicing patterns. Among the MBNL-regulated events is an ES-cell-specific alternative splicing switch in the forkhead family transcription factor FOXP1 that controls pluripotency 9 . Consistent with a central and negative regulatory role for MBNL proteins in pluripotency, their knockdown significantly enhances the expression of key pluripotency genes and the formation of induced pluripotent stem cells during somatic cell reprogramming.