Volume 35, Issue 1, Pages 1-10 (July 2009) SR Proteins in Vertical Integration of Gene Expression from Transcription to RNA Processing to Translation  Xiang-Yang Zhong, Pingping Wang, Joonhee Han, Michael G. Rosenfeld, Xiang-Dong Fu  Molecular Cell  Volume 35, Issue 1, Pages 1-10 (July 2009) DOI: 10.1016/j.molcel.2009.06.016 Copyright © 2009 Elsevier Inc. Terms and Conditions

Figure 1 The SR Protein B52/SRp55 on Actively Transcribed Genes (A) The SR protein B52/SRp55 brackets Pol II on induced Hsp70 puffs on Drosophila polytene chromosomes. Picture is reproduced with permission from Champlin et al. (1991). (B) Structure of “classic,” mAb104 reactive SR proteins, which are characterized by one or two RNA Recognition Motifs (RRM) at the N-terminus and the signature RS domain at the C terminus. Molecular Cell 2009 35, 1-10DOI: (10.1016/j.molcel.2009.06.016) Copyright © 2009 Elsevier Inc. Terms and Conditions

Figure 2 A Working Model for SR Protein-Mediated Dynamic Coupling between Transcription and Cotranscriptional mRNA Splicing Events SR protein may be first recruited at the initial Pol II pausing site after pTEFb-mediated Pol II phosphorylation at its CTD. The recruitment of pTEFb and SR proteins may mutually benefit one another. When a splicing signal emerges from nascent RNA, SR protein is switched from Pol II to the RNA (step 1) to nucleate spliceosome assembly, which may be accompanied by transient pausing of the Pol II complex, resulting in elevated H3K36 methylation (step 2). Altered chromatin may also enhance the recruitment of additional SR proteins to Pol II (step 3) to continue transcriptional elongation. Molecular Cell 2009 35, 1-10DOI: (10.1016/j.molcel.2009.06.016) Copyright © 2009 Elsevier Inc. Terms and Conditions

Figure 3 Potential Mechanism for SR Proteins to Prevent R-Loop Formation during Transcriptional Elongation The Pol II-associated SR proteins may help displace nascent RNA from the template DNA to suppress R-loop formation during transcriptional elongation. The absence of SR proteins may introduce positive and negative DNA supercoiling in front and back of induced R-loops, thereby retarding the movement of the Pol II complex. Prolonged RNA loops may potentiate DNA breaks, and initial ssDNA breaks may be further converted to dsDNA breaks by both DNA replication-dependent and -independent mechanisms. Recognition of DSBs by the MRN complex recruits ATM to trigger the S phase checkpoint. DSBs may be further trimmed by the exonuclease activity of the MRN to produce excessive single-stranded 3′ overhangs, which induces the binding of the single-strand DNA binding protein RPA and recruits ATR. The activated ATM/ATR pathway triggers a cascade of events, leading to cell-cycle arrest or apoptosis. Molecular Cell 2009 35, 1-10DOI: (10.1016/j.molcel.2009.06.016) Copyright © 2009 Elsevier Inc. Terms and Conditions

Figure 4 The Spatial Relationship between SR Protein Localization and Gene Networks in the Nucleus Two estrogen-responsive genes, TFF1 and GREB1, do not exhibit interaction with one another nor show any spatial relationship with the speckled SC35 domains in the absence of ligand (−E2). The estrogen treatment (+E2) induces specific interchromosomal interactions between these two genes, which also become intermediately associated with nuclear speckles marked by anti-SC35. Pictures are reproduced from Hu et al. (2008). The diagram on the right illustrates the induction of gene networks at or near a nuclear speckle enriched with mRNPs. Molecular Cell 2009 35, 1-10DOI: (10.1016/j.molcel.2009.06.016) Copyright © 2009 Elsevier Inc. Terms and Conditions