Publications by authors named "Xiang-Dong Fu"

100Publications

Active retrotransposons help maintain pericentromeric heterochromatin required for faithful cell division.

Genome Res 2020 Nov 15;30(11):1570-1582. Epub 2020 Oct 15.

Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, 100101, China.

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http://dx.doi.org/10.1101/gr.256131.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7605247PMC
November 2020

Cockayne syndrome B protein acts as an ATP-dependent processivity factor that helps RNA polymerase II overcome nucleosome barriers.

Proc Natl Acad Sci U S A 2020 10 28;117(41):25486-25493. Epub 2020 Sep 28.

Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093;

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http://dx.doi.org/10.1073/pnas.2013379117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7568279PMC
October 2020

Active RNA interference in mitochondria.

Cell Res 2020 Aug 17. Epub 2020 Aug 17.

Key Laboratory for RNA Biology, Institute of Biophysics, Chinese Academy of Science, Beijing, 100101, China.

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http://dx.doi.org/10.1038/s41422-020-00394-5DOI Listing
August 2020

RNA helicases regulate RNA condensates.

Authors:
Xiang-Dong Fu

Cell Res 2020 04;30(4):281-282

Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1038/s41422-020-0296-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118144PMC
April 2020

Author Correction: GRID-seq for comprehensive analysis of global RNA-chromatin interactions.

Nat Protoc 2020 06;15(6):2140

Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1038/s41596-020-0308-6DOI Listing
June 2020

Mechanistic Dissection of RNA-Binding Proteins in Regulated Gene Expression at Chromatin Levels.

Cold Spring Harb Symp Quant Biol 2019 3;84:55-66. Epub 2020 Jan 3.

Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1101/sqb.2019.84.039222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7332398PMC
January 2020

A tumorigenic index for quantitative analysis of liver cancer initiation and progression.

Proc Natl Acad Sci U S A 2019 Dec 16. Epub 2019 Dec 16.

Department of Pathology, Division of Biological Sciences, Moores Cancer Center, University of California San Diego, La Jolla, CA 92093;

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http://dx.doi.org/10.1073/pnas.1911193116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6936392PMC
December 2019

A Translation-Activating Function of MIWI/piRNA during Mouse Spermiogenesis.

Cell 2019 12;179(7):1566-1581.e16

State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences-University of Chinese Academy of Sciences, Shanghai 200031, China; School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.11.022DOI Listing
December 2019

[Development and application of the plant phenomics analysis platform].

Yi Chuan 2019 Nov;41(11):1060-1066

State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China.

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http://dx.doi.org/10.16288/j.yczz.19-277DOI Listing
November 2019

Nuclear miR-320 Mediates Diabetes-Induced Cardiac Dysfunction by Activating Transcription of Fatty Acid Metabolic Genes to Cause Lipotoxicity in the Heart.

Circ Res 2019 12 22;125(12):1106-1120. Epub 2019 Oct 22.

From the Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (H.L., J.F., Y.Z., B.D., J.Z., Z.Y., X.N., C.C., D.W.W.).

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http://dx.doi.org/10.1161/CIRCRESAHA.119.314898DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6903355PMC
December 2019

Author Correction: Chromatin-associated RNAs as facilitators of functional genomic interactions.

Nat Rev Genet 2019 Sep;20(9):562

Department of Cellular and Molecular Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1038/s41576-019-0155-xDOI Listing
September 2019

GRID-seq for comprehensive analysis of global RNA-chromatin interactions.

Nat Protoc 2019 07 7;14(7):2036-2068. Epub 2019 Jun 7.

Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1038/s41596-019-0172-4DOI Listing
July 2019

Chromatin-associated RNAs as facilitators of functional genomic interactions.

Nat Rev Genet 2019 09;20(9):503-519

Department of Cellular and Molecular Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.

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http://www.nature.com/articles/s41576-019-0135-1
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http://dx.doi.org/10.1038/s41576-019-0135-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7684979PMC
September 2019

R-ChIP for genome-wide mapping of R-loops by using catalytically inactive RNASEH1.

Nat Protoc 2019 05 17;14(5):1661-1685. Epub 2019 Apr 17.

Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.

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http://www.nature.com/articles/s41596-019-0154-6
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http://dx.doi.org/10.1038/s41596-019-0154-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6604627PMC
May 2019

Nexilin Is a New Component of Junctional Membrane Complexes Required for Cardiac T-Tubule Formation.

Circulation 2019 07 15;140(1):55-66. Epub 2019 Apr 15.

Department of Medicine (C.L., S.S., X.F., W.F., N.D.D., K.L.P., T.W., S.M.E., J.C.), University of California, San Diego, La Jolla.

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http://dx.doi.org/10.1161/CIRCULATIONAHA.119.039751DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6889818PMC
July 2019

RBFox2-miR-34a-Jph2 axis contributes to cardiac decompensation during heart failure.

Proc Natl Acad Sci U S A 2019 03 13;116(13):6172-6180. Epub 2019 Mar 13.

Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651;

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http://dx.doi.org/10.1073/pnas.1822176116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6442575PMC
March 2019

PTB/nPTB: master regulators of neuronal fate in mammals.

Biophys Rep 2018 28;4(4):204-214. Epub 2018 Aug 28.

1Department of Cellular and Molecular Medicine, University of California, La Jolla, San Diego, CA 92093-0651 USA.

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http://link.springer.com/10.1007/s41048-018-0066-y
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http://dx.doi.org/10.1007/s41048-018-0066-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6153489PMC
August 2018

A novel class of microRNA-recognition elements that function only within open reading frames.

Nat Struct Mol Biol 2018 11 8;25(11):1019-1027. Epub 2018 Oct 8.

State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China.

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http://www.nature.com/articles/s41594-018-0136-3
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http://dx.doi.org/10.1038/s41594-018-0136-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6219929PMC
November 2018

The RNA binding protein EWS is broadly involved in the regulation of pri-miRNA processing in mammalian cells.

Nucleic Acids Res 2017 12;45(21):12481-12495

State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.

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http://dx.doi.org/10.1093/nar/gkx912DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5716145PMC
December 2017

SRPKIN-1: A Covalent SRPK1/2 Inhibitor that Potently Converts VEGF from Pro-angiogenic to Anti-angiogenic Isoform.

Cell Chem Biol 2018 04 22;25(4):460-470.e6. Epub 2018 Feb 22.

Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S24519456183003
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http://dx.doi.org/10.1016/j.chembiol.2018.01.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5973797PMC
April 2018

The Augmented R-Loop Is a Unifying Mechanism for Myelodysplastic Syndromes Induced by High-Risk Splicing Factor Mutations.

Mol Cell 2018 02 27;69(3):412-425.e6. Epub 2018 Jan 27.

Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA; Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2017.12.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5957072PMC
February 2018

β-catenin deficiency in hepatocytes aggravates hepatocarcinogenesis driven by oncogenic β-catenin and MET.

Hepatology 2018 05 6;67(5):1807-1822. Epub 2018 Apr 6.

Department of Pathology and Division of Biological Sciences, Moores Cancer Center, University of California San Diego, La Jolla, CA.

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http://doi.wiley.com/10.1002/hep.29661
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http://dx.doi.org/10.1002/hep.29661DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5906147PMC
May 2018

R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters.

Mol Cell 2017 Nov 2;68(4):745-757.e5. Epub 2017 Nov 2.

Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2017.10.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5957070PMC
November 2017

Exploiting the Hidden Treasure of Detained Introns.

Authors:
Xiang-Dong Fu

Cancer Cell 2017 10;32(4):393-395

Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2017.09.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5967397PMC
October 2017

GRID-seq reveals the global RNA-chromatin interactome.

Nat Biotechnol 2017 Oct 18;35(10):940-950. Epub 2017 Sep 18.

Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA.

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http://dx.doi.org/10.1038/nbt.3968DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5953555PMC
October 2017

NEAT1 scaffolds RNA-binding proteins and the Microprocessor to globally enhance pri-miRNA processing.

Nat Struct Mol Biol 2017 Oct 28;24(10):816-824. Epub 2017 Aug 28.

State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China.

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http://dx.doi.org/10.1038/nsmb.3455DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5766049PMC
October 2017

Ubiquitination-Deficient Mutations in Human Piwi Cause Male Infertility by Impairing Histone-to-Protamine Exchange during Spermiogenesis.

Cell 2017 Jun 25;169(6):1090-1104.e13. Epub 2017 May 25.

State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China; School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China; Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674173048
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http://dx.doi.org/10.1016/j.cell.2017.04.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5985145PMC
June 2017

Both sides of the same coin: Rac1 splicing regulating by EGF signaling.

Authors:
Xiang-Dong Fu

Cell Res 2017 04 10;27(4):455-456. Epub 2017 Feb 10.

Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA.

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http://dx.doi.org/10.1038/cr.2017.19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5385611PMC
April 2017

JMJD6 and U2AF65 co-regulate alternative splicing in both JMJD6 enzymatic activity dependent and independent manner.

Nucleic Acids Res 2017 04;45(6):3503-3518

Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China.

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http://nar.oxfordjournals.org/content/early/2016/11/29/nar.g
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http://dx.doi.org/10.1093/nar/gkw1144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389685PMC
April 2017

SPOP-containing complex regulates SETD2 stability and H3K36me3-coupled alternative splicing.

Nucleic Acids Res 2017 01 9;45(1):92-105. Epub 2016 Sep 9.

Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China

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http://dx.doi.org/10.1093/nar/gkw814DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5224501PMC
January 2017

MicroRNA-21 Lowers Blood Pressure in Spontaneous Hypertensive Rats by Upregulating Mitochondrial Translation.

Circulation 2016 Sep 19;134(10):734-51. Epub 2016 Aug 19.

From Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (H.L., F.W., L.Z., Z.Y., J.F., X.N., P.W., C.C., D.W.W.); Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China (X.Z., X.-D.F.); and Department of Cellular and Molecular Medicine and Institute of Genomic Medicine, University of California, San Diego, La Jolla (X.-D.F.).

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http://dx.doi.org/10.1161/CIRCULATIONAHA.116.023926DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5515592PMC
September 2016

Release of SR Proteins from CLK1 by SRPK1: A Symbiotic Kinase System for Phosphorylation Control of Pre-mRNA Splicing.

Mol Cell 2016 07 7;63(2):218-228. Epub 2016 Jul 7.

Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2016.05.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4941815PMC
July 2016

CELF RNA binding proteins promote axon regeneration in C. elegans and mammals through alternative splicing of Syntaxins.

Elife 2016 06 2;5. Epub 2016 Jun 2.

Section of Neurobiology, University of California, San Diego, Division of Biological Sciences, San Diego, United States.

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http://dx.doi.org/10.7554/eLife.16072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4946901PMC
June 2016

RBFox2 Binds Nascent RNA to Globally Regulate Polycomb Complex 2 Targeting in Mammalian Genomes.

Mol Cell 2016 06 19;62(6):875-889. Epub 2016 May 19.

Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA; Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2016.04.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5515591PMC
June 2016

Sequential regulatory loops as key gatekeepers for neuronal reprogramming in human cells.

Nat Neurosci 2016 06 25;19(6):807-15. Epub 2016 Apr 25.

Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA.

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http://dx.doi.org/10.1038/nn.4297DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4882254PMC
June 2016

Diabetic Insult-Induced Redistribution of MicroRNA in Spatially Organized Mitochondria in Cardiac Muscle.

Circ Cardiovasc Genet 2015 Dec;8(6):747-8

From the Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla.

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http://dx.doi.org/10.1161/CIRCGENETICS.115.001258DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4683416PMC
December 2015

Context-dependent modulation of Pol II CTD phosphatase SSUP-72 regulates alternative polyadenylation in neuronal development.

Genes Dev 2015 Nov;29(22):2377-90

Neurobiology Section, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093, USA; Howard Hughes Medical Institute, University of California at San Diego, La Jolla, California 92093, USA; Department of Cellular and Molecular Medicine, School of Medicine, University of California at San Diego, La Jolla, California 92093, USA;

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http://dx.doi.org/10.1101/gad.266650.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691892PMC
November 2015

Widespread JNK-dependent alternative splicing induces a positive feedback loop through CELF2-mediated regulation of MKK7 during T-cell activation.

Genes Dev 2015 Oct;29(19):2054-66

Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennysylvania 19104, USA.

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http://dx.doi.org/10.1101/gad.267245.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4604346PMC
October 2015

Global analysis of physical and functional RNA targets of hnRNP L reveals distinct sequence and epigenetic features of repressed and enhanced exons.

RNA 2015 Dec 5;21(12):2053-66. Epub 2015 Oct 5.

Department of Biochemistry and Biophysics Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.

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http://rnajournal.cshlp.org/lookup/doi/10.1261/rna.052969.11
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http://dx.doi.org/10.1261/rna.052969.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4647460PMC
December 2015

TRAP150 interacts with the RNA-binding domain of PSF and antagonizes splicing of numerous PSF-target genes in T cells.

Nucleic Acids Res 2015 Oct 10;43(18):9006-16. Epub 2015 Aug 10.

Department of Biochemistry and Biophysics Perelman, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA

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http://dx.doi.org/10.1093/nar/gkv816DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4605305PMC
October 2015

SRSF2 Is Essential for Hematopoiesis, and Its Myelodysplastic Syndrome-Related Mutations Dysregulate Alternative Pre-mRNA Splicing.

Mol Cell Biol 2015 Sep 29;35(17):3071-82. Epub 2015 Jun 29.

Moores UCSD Cancer Center, University of California, San Diego, La Jolla, California, USA Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA Department of Pathology, University of California, San Diego, La Jolla, California, USA

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http://dx.doi.org/10.1128/MCB.00202-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4525309PMC
September 2015

Molecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex.

Nature 2015 Jul 29;523(7562):621-5. Epub 2015 Jun 29.

Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/nature14482DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4521995PMC
July 2015

Oncogenic miR-17/20a Forms a Positive Feed-forward Loop with the p53 Kinase DAPK3 to Promote Tumorigenesis.

J Biol Chem 2015 Aug 27;290(32):19967-75. Epub 2015 Jun 27.

From the State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China and Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093-0651

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http://dx.doi.org/10.1074/jbc.M115.661504DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528155PMC
August 2015

Transcription Factor PAX6 (Paired Box 6) Controls Limbal Stem Cell Lineage in Development and Disease.

J Biol Chem 2015 Aug 4;290(33):20448-54. Epub 2015 Jun 4.

the State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China, the Department of Ophthalmology, Biomaterials and Tissue Engineering Center, Institute for Engineering in Medicine.

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http://www.jbc.org/content/290/33/20448.full.pdf
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http://www.jbc.org/lookup/doi/10.1074/jbc.M115.662940
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http://dx.doi.org/10.1074/jbc.M115.662940DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4536450PMC
August 2015

Genomic functions of U2AF in constitutive and regulated splicing.

RNA Biol 2015 ;12(5):479-85

a Department of Medicine ; University of California, San Diego ; La Jolla , CA USA.

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http://dx.doi.org/10.1080/15476286.2015.1020272DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615725PMC
February 2016

Induced transcription and stability of CELF2 mRNA drives widespread alternative splicing during T-cell signaling.

Proc Natl Acad Sci U S A 2015 Apr 13;112(17):E2139-48. Epub 2015 Apr 13.

Departments of Biochemistry and Biophysics and Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and

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http://dx.doi.org/10.1073/pnas.1423695112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4418860PMC
April 2015

Non-coding RNA: a new frontier in regulatory biology.

Authors:
Xiang-Dong Fu

Natl Sci Rev 2014 Jun;1(2):190-204

Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA.

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http://dx.doi.org/10.1093/nsr/nwu008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374487PMC
June 2014

Yes, SiR.

Authors:
Xiang-Dong Fu

RNA 2015 Apr;21(4):619-21

Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093-0651, USA

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http://dx.doi.org/10.1261/rna.049858.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4371306PMC
April 2015

An evolutionarily conserved DNA architecture determines target specificity of the TWIST family bHLH transcription factors.

Genes Dev 2015 Mar 11;29(6):603-16. Epub 2015 Mar 11.

Department of Pharmacology, University of California at San Diego, La Jolla, California, 92093, USA; Department of Pediatrics, University of California at San Diego, La Jolla, California, 92093, USA

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http://dx.doi.org/10.1101/gad.242842.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4378193PMC
March 2015

Repression of the Central Splicing Regulator RBFox2 Is Functionally Linked to Pressure Overload-Induced Heart Failure.

Cell Rep 2015 Mar 5;10(9):1521-1533. Epub 2015 Mar 5.

Department of Cellular and Molecular Medicine University of California, San Diego, La Jolla, CA 92093-0651, USA; Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.02.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4559494PMC
March 2015

MIWI and piRNA-mediated cleavage of messenger RNAs in mouse testes.

Cell Res 2015 Feb 13;25(2):193-207. Epub 2015 Jan 13.

Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.

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http://dx.doi.org/10.1038/cr.2015.4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4650574PMC
February 2015

Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate.

Genes Dev 2014 Dec;28(23):2663-76

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA;

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http://dx.doi.org/10.1101/gad.252106.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4248296PMC
December 2014

Mechanisms for U2AF to define 3' splice sites and regulate alternative splicing in the human genome.

Nat Struct Mol Biol 2014 Nov 19;21(11):997-1005. Epub 2014 Oct 19.

State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China.

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http://dx.doi.org/10.1038/nsmb.2906DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4429597PMC
November 2014

Direct reprogramming of Huntington's disease patient fibroblasts into neuron-like cells leads to abnormal neurite outgrowth, increased cell death, and aggregate formation.

PLoS One 2014 2;9(10):e109621. Epub 2014 Oct 2.

Division of Basic Biomedical Sciences, University of South Dakota Sanford School of Medicine, Vermillion, South Dakota, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0109621PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4183653PMC
December 2015

Context-dependent control of alternative splicing by RNA-binding proteins.

Nat Rev Genet 2014 Oct 12;15(10):689-701. Epub 2014 Aug 12.

Center for Molecular Biology of RNA, and Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA.

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http://www.nature.com/articles/nrg3778
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http://dx.doi.org/10.1038/nrg3778DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4440546PMC
October 2014

MicroRNA directly enhances mitochondrial translation during muscle differentiation.

Cell 2014 Jul;158(3):607-19

State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA; Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674140080
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http://dx.doi.org/10.1016/j.cell.2014.05.047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4119298PMC
July 2014

WNT7A and PAX6 define corneal epithelium homeostasis and pathogenesis.

Nature 2014 Jul 2;511(7509):358-61. Epub 2014 Jul 2.

1] State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China [2] Department of Ophthalmology, and Biomaterial and Tissue Engineering Center of Institute of Engineering in Medicine, University of California San Diego, La Jolla, California 92093, USA [3] Molecular Medicine Research Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Sichuan 610041, China [4] Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92093, USA [5] Veterans Administration Healthcare System, San Diego, California 92093, USA.

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http://dx.doi.org/10.1038/nature13465DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4610745PMC
July 2014

N-terminus of the protein kinase CLK1 induces SR protein hyperphosphorylation.

Biochem J 2014 Aug;462(1):143-52

*Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093-0636, U.S.A.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5056641PMC
http://dx.doi.org/10.1042/BJ20140494DOI Listing
August 2014

Pachytene piRNAs instruct massive mRNA elimination during late spermiogenesis.

Cell Res 2014 Jun 2;24(6):680-700. Epub 2014 May 2.

1] Center for RNA Research, State Key Laboratory of Molecular Biology-University of Chinese Academy of Sciences, Shanghai 200031, China [2] Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.

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http://dx.doi.org/10.1038/cr.2014.41DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4042167PMC
June 2014

Both decreased and increased SRPK1 levels promote cancer by interfering with PHLPP-mediated dephosphorylation of Akt.

Mol Cell 2014 May 3;54(3):378-91. Epub 2014 Apr 3.

Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA; Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2014.03.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4019712PMC
May 2014

Multiplex analysis of polyA-linked sequences (MAPS): an RNA-seq strategy to profile poly(A+) RNA.

Methods Mol Biol 2014 ;1125:169-78

Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, University of California, Room 239, San Diego, La Jolla, CA, 92093-0651, USA.

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http://dx.doi.org/10.1007/978-1-62703-971-0_15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4445727PMC
November 2014

De novo prediction of PTBP1 binding and splicing targets reveals unexpected features of its RNA recognition and function.

PLoS Comput Biol 2014 Jan 30;10(1):e1003442. Epub 2014 Jan 30.

Department of Bioengineering, University of California at Los Angeles, Los Angeles, California, United States of America ; Department of Microbiology, Immunology and Molecular Genetics, University of California at Los Angeles, Los Angeles, California, United States of America ; Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, California, United States of America.

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http://dx.plos.org/10.1371/journal.pcbi.1003442
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http://dx.doi.org/10.1371/journal.pcbi.1003442DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3907290PMC
January 2014

The splicing regulator PTBP2 controls a program of embryonic splicing required for neuronal maturation.

Elife 2014 21;3:e01201. Epub 2014 Jan 21.

Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States.

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http://dx.doi.org/10.7554/eLife.01201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3896118PMC
February 2016

Efficient generation of human iPSCs by a synthetic self-replicative RNA.

Cell Stem Cell 2013 Aug;13(2):246-54

Department of Cellular & Molecular Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0686, USA.

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http://dx.doi.org/10.1016/j.stem.2013.06.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3845961PMC
August 2013

Partitioning RS domain phosphorylation in an SR protein through the CLK and SRPK protein kinases.

J Mol Biol 2013 Aug 23;425(16):2894-909. Epub 2013 May 23.

Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093-0636, USA.

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http://dx.doi.org/10.1016/j.jmb.2013.05.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3860265PMC
August 2013

SR proteins collaborate with 7SK and promoter-associated nascent RNA to release paused polymerase.

Cell 2013 May;153(4):855-68

State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China.

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http://dx.doi.org/10.1016/j.cell.2013.04.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103662PMC
May 2013

Hepatitis B viral RNA directly mediates down-regulation of the tumor suppressor microRNA miR-15a/miR-16-1 in hepatocytes.

J Biol Chem 2013 Jun 6;288(25):18484-93. Epub 2013 May 6.

State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China.

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http://www.jbc.org/lookup/doi/10.1074/jbc.M113.458158
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http://dx.doi.org/10.1074/jbc.M113.458158DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689990PMC
June 2013

Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing.

Mol Cell 2013 Apr 4;50(2):223-35. Epub 2013 Apr 4.

Department of Cellular and Molecular Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA.

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http://dx.doi.org/10.1016/j.molcel.2013.03.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3640356PMC
April 2013

Regulation of splicing by SR proteins and SR protein-specific kinases.

Chromosoma 2013 Jun 24;122(3):191-207. Epub 2013 Mar 24.

Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA.

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http://dx.doi.org/10.1007/s00412-013-0407-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3660409PMC
June 2013

Alternative Splicing of a Novel Inducible Exon Diversifies the CASK Guanylate Kinase Domain.

J Nucleic Acids 2012 12;2012:816237. Epub 2012 Sep 12.

Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.

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http://dx.doi.org/10.1155/2012/816237DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3447378PMC
September 2012

Regulation of the Hippo-YAP pathway by G-protein-coupled receptor signaling.

Cell 2012 Aug 2;150(4):780-91. Epub 2012 Aug 2.

Department of Pharmacology and Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1016/j.cell.2012.06.037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3433174PMC
August 2012

SRSF1 regulates the assembly of pre-mRNA processing factors in nuclear speckles.

Mol Biol Cell 2012 Sep 1;23(18):3694-706. Epub 2012 Aug 1.

Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

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http://dx.doi.org/10.1091/mbc.E12-03-0206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3442416PMC
September 2012

The Akt-SRPK-SR axis constitutes a major pathway in transducing EGF signaling to regulate alternative splicing in the nucleus.

Mol Cell 2012 Aug 21;47(3):422-33. Epub 2012 Jun 21.

Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA.

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http://dx.doi.org/10.1016/j.molcel.2012.05.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418396PMC
August 2012