Ravi K. Singh Lab
Muscle-powered movements govern lifespan and overall quality of human life. Our research aims to better understand how gene expression programs in cardiac and skeletal muscle respond to biological, nutritional, and environmental cues to grow and mature after birth, and to identify mechanisms contributing to aging-associated decline in muscle function (cardiac dysfunction and sarcopenia).
It is now clear that multiple mechanisms regulate gene expression soon after transcription including alternative pre-mRNA splicing and processing, mRNA export, localization, stability and control of translation. These post-transcriptional mechanisms increase proteomic diversity, or cause a change in protein abundance/distribution, ultimately affecting cellular or tissue function. It is not well understood how these mechanisms affect muscle function in the context of development, aging and disease.
What is alternative splicing and why is it important?
Alternative splicing is a process where pre-mRNA from a single gene selects different sets of exons (protein-coding segments) to generate multiple mRNAs (encoding different protein isoforms), and significantly increases proteomic diversity in mammals. RNA-sequencing studies indicate that >90% of human protein-coding genes are alternatively spliced and a majority of alternative splicing occurs in tissue-specific manner including brain, heart, and skeletal muscle. On the other hand, disruption in alternative splicing is also known to cause human diseases (Singh RK and Cooper TA, Trends Mol Med. 2012, (8):472). A major focus of our lab is to better understand how alternative splicing is regulated and integrates with other gene expression programs and cellular processes to optimize cardiac and skeletal function.
RNA binding proteins (or RBPs) regulate nearly all aspects of post-transcriptional gene expression including alternative splicing. Current projects in our lab stems from our and others’ finding that highly conserved RBPs of the RNA binding fox-1 homolog (Rbfox) family is important for regulating alternative splicing in cardiac and skeletal muscle. Of the three Rbfox genes, Rbfox1 and Rbfox2 are expressed in heart and skeletal muscle. Double knockout of Rbfox1 and Rbfox2 in adult skeletal muscle causes a ~50% reduction in muscle mass within 4 weeks (Singh et al. Cell Rep. 2018, 24(1):197), lack of Rbfox2 in developing mouse and human heart causes cardiomyopathy (Wei et al., Cell Reports 2015, (10)1521; Homsy et al., Science. 2015, 350(6265):1262; and our preliminary observation), and lack of RBFOX2 in myoblasts inhibits myogenesis (Singh et al. Mol Cell. 2014,55(4):592), emphasizing the importance of regulated splicing in cardiac and skeletal muscle function. Recent studies also suggest that alternative splicing, RBPs and other post-transcriptional gene regulatory mechanisms play a role in in aging-associated decline in muscle function. The objectives of research in our lab are:
- To identify the functional consequences of alternative splicing in modulation of gene expression programs and cellular processes to optimize heart and skeletal muscle function.
- To determine the role of RBPs and alternative splicing in promoting gender-biased functional differences in heart and skeletal muscle biology.
- To identify gene expression programs contributing to aging-associated decline in cardiac and skeletal muscle function.
We are using mouse genetics (classical and CRISPR-Cas9 tools), cell/molecular biology approaches, transcriptome-wide experimental and bioinformatic methods to address these questions.
We are interested in motivated and discovery-driven individuals to join our group. Please contact us to initiate the conversation.
- Sushil Kumar, Postdoctoral Fellow
- Jacob Besler, Research Technologist I
(Graetz D, Crews KR, Azzato EM, Singh RK, Raimondi S, Mason J, Valentine M, Mullighan CG, Holland A, Inaba H, Leventaki V.) Haematologica. 2019 May;104(5):e218-e221.
(Singh RK, Kolonin AM, Fiorotto ML, Cooper TA.) Cell Rep. 2018 07 03;24(1):197-208.
(Comiskey DF Jr, Jacob AG, Singh RK, Tapia-Santos AS, Chandler DS.) Nucleic Acids Res. 2015 Apr 30;43(8):4202-18.
(Pedrotti S, Giudice J, Dagnino-Acosta A, Knoblauch M, Singh RK, Hanna A, Mo Q, Hicks J, Hamilton S, Cooper TA.) Hum Mol Genet. 2015 Apr 15;24(8):2360-74.
(Gennarino VA, Singh RK, White JJ, De Maio A, Han K, Kim JY, Jafar-Nejad P, di Ronza A, Kang H, Sayegh LS, Cooper TA, Orr HT, Sillitoe RV, Zoghbi HY.) Cell. 2015 Mar 12;160(6):1087-98.
(Singh RK, Xia Z, Bland CS, Kalsotra A, Scavuzzo MA, Curk T, Ule J, Li W, Cooper TA.) Mol Cell. 2014 Aug 21;55(4):592-603.
(Jacob AG, Singh RK, Mohammad F, Bebee TW, Chandler DS.) J Biol Chem. 2014 Jun 20;289(25):17350-64.
(Kalsotra A, Singh RK, Gurha P, Ward AJ, Creighton CJ, Cooper TA.) Cell Rep. 2014 Jan 30;6(2):336-45.
(Jacob AG, Singh RK, Comiskey DF Jr, Rouhier MF, Mohammad F, Bebee TW, Chandler DS.) PLoS One. 2014;9(8):e104444.
(Jacob AG, O'Brien D, Singh RK, Comiskey DF Jr, Littleton RM, Mohammad F, Gladman JT, Widmann MC, Jeyaraj SC, Bolinger C, Anderson JR, Barkauskas DA, Boris-Lawrie K, Chandler DS.) Neoplasia. 2013 Sep;15(9):1049-63.
(Singh RK, Cooper TA.) Trends Mol Med. 2012 Aug;18(8):472-82.
(Singh RK, Tapia-Santos A, Bebee TW, Chandler DS.) Exp Cell Res. 2009 Nov 15;315(19):3419-32.