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Disease-Causing Mutations in SF3B1 Alter Splicing by Disrupting Interaction with SUGP1.

Zhang J, Ali AM, Lieu YK, Liu Z, Gao J, Rabadan R, Raza A, Mukherjee S, Manley JL.

Mol Cell. 2019 Aug 9. pii: S1097-2765(19)30547-7. doi: 10.1016/j.molcel.2019.07.017. [Epub ahead of print]


TCF3 Mutually Exclusive Alternative Splicing Is Controlled by Long Range Cooperative Actions between hnRNPH1 and PTBP1.

Yamazaki T, Liu L, Manley JL.

RNA. 2019 Aug 7. pii: rna.072298.119. doi: 10.1261/rna.072298.119. [Epub ahead of print]


Corrigendum: TCF3 alternative splicing controlled by hnRNP H/F regulates E-cadherin expression and hESC pluripotency.

Yamazaki T, Liu L, Lazarev D, Al-Zain A, Fomin V, Yeung PL, Chambers SM, Lu CW, Studer L, Manley JL.

Genes Dev. 2019 Jun 1;33(11-12):733-736. doi: 10.1101/gad.326983.119. No abstract available.


C9orf72 and triplet repeat disorder RNAs: G-quadruplex formation, binding to PRC2 and implications for disease mechanisms.

Wang X, Goodrich KJ, Conlon EG, Gao J, Erbse AH, Manley JL, Cech TR.

RNA. 2019 Aug;25(8):935-947. doi: 10.1261/rna.071191.119. Epub 2019 May 2.


Consensus report of the 8 and 9th Weinman Symposia on Gene x Environment Interaction in carcinogenesis: novel opportunities for precision medicine.

Carbone M, Amelio I, Affar EB, Brugarolas J, Cannon-Albright LA, Cantley LC, Cavenee WK, Chen Z, Croce CM, Andrea A, Gandara D, Giorgi C, Jia W, Lan Q, Mak TW, Manley JL, Mikoshiba K, Onuchic JN, Pass HI, Pinton P, Prives C, Rothman N, Sebti SM, Turkson J, Wu X, Yang H, Yu H, Melino G.

Cell Death Differ. 2018 Nov;25(11):1885-1904. doi: 10.1038/s41418-018-0213-5. Epub 2018 Oct 15. Review.


The C9ORF72 Gene, Implicated in Amyotrophic Lateral Sclerosis and Frontotemporal Dementia, Encodes a Protein That Functions in Control of Endothelin and Glutamate Signaling.

Fomin V, Richard P, Hoque M, Li C, Gu Z, Fissore-O'Leary M, Tian B, Prives C, Manley JL.

Mol Cell Biol. 2018 Oct 29;38(22). pii: e00155-18. doi: 10.1128/MCB.00155-18. Print 2018 Nov 15.


TCF3 alternative splicing controlled by hnRNP H/F regulates E-cadherin expression and hESC pluripotency.

Yamazaki T, Liu L, Lazarev D, Al-Zain A, Fomin V, Yeung PL, Chambers SM, Lu CW, Studer L, Manley JL.

Genes Dev. 2018 Sep 1;32(17-18):1161-1174. doi: 10.1101/gad.316984.118. Epub 2018 Aug 16. Erratum in: Genes Dev. 2019 Jun 1;33(11-12):733-736.


Unexpected similarities between C9ORF72 and sporadic forms of ALS/FTD suggest a common disease mechanism.

Conlon EG, Fagegaltier D, Agius P, Davis-Porada J, Gregory J, Hubbard I, Kang K, Kim D; New York Genome Center ALS Consortium, Phatnani H, Kwan J, Sareen D, Broach JR, Simmons Z, Arcila-Londono X, Lee EB, Van Deerlin VM, Shneider NA, Fraenkel E, Ostrow LW, Baas F, Zaitlen N, Berry JD, Malaspina A, Fratta P, Cox GA, Thompson LM, Finkbeiner S, Dardiotis E, Miller TM, Chandran S, Pal S, Hornstein E, MacGowan DJ, Heiman-Patterson T, Hammell MG, Patsopoulos NA, Dubnau J, Nath A, Phatnani H, Shneider NA, Manley JL.

Elife. 2018 Jul 13;7. pii: e37754. doi: 10.7554/eLife.37754.


NRDE-2, the human homolog of fission yeast Nrl1, prevents DNA damage accumulation in human cells.

Richard P, Ogami K, Chen Y, Feng S, Moresco JJ, Yates JR 3rd, Manley JL.

RNA Biol. 2018;15(7):868-876. doi: 10.1080/15476286.2018.1467180. Epub 2018 Aug 2.


RNA surveillance by the nuclear RNA exosome: mechanisms and significance.

Ogami K, Chen Y, Manley JL.

Noncoding RNA. 2018;4(1). pii: 8. doi: 10.3390/ncrna4010008. Epub 2018 Mar 11.


MPK1/SLT2 Links Multiple Stress Responses with Gene Expression in Budding Yeast by Phosphorylating Tyr1 of the RNAP II CTD.

Yurko N, Liu X, Yamazaki T, Hoque M, Tian B, Manley JL.

Mol Cell. 2017 Dec 7;68(5):913-925.e3. doi: 10.1016/j.molcel.2017.11.020.


Molecular basis for the recognition of the human AAUAAA polyadenylation signal.

Sun Y, Zhang Y, Hamilton K, Manley JL, Shi Y, Walz T, Tong L.

Proc Natl Acad Sci U S A. 2018 Feb 13;115(7):E1419-E1428. doi: 10.1073/pnas.1718723115. Epub 2017 Dec 5.


Erratum: RNA-binding proteins in neurodegeneration: mechanisms in aggregate.

Conlon EG, Manley JL.

Genes Dev. 2017 Oct 1;31(19):2015. doi: 10.1101/gad.308205.117. No abstract available.


Mtr4/ZFC3H1 protects polysomes through nuclear RNA surveillance.

Ogami K, Manley JL.

Cell Cycle. 2017;16(21):1999-2000. doi: 10.1080/15384101.2017.1377501. Epub 2017 Sep 29. No abstract available.


Comparative analysis of alternative polyadenylation in S. cerevisiae and S. pombe.

Liu X, Hoque M, Larochelle M, Lemay JF, Yurko N, Manley JL, Bachand F, Tian B.

Genome Res. 2017 Oct;27(10):1685-1695. doi: 10.1101/gr.222331.117. Epub 2017 Sep 15.


RNA-binding proteins in neurodegeneration: mechanisms in aggregate.

Conlon EG, Manley JL.

Genes Dev. 2017 Aug 1;31(15):1509-1528. doi: 10.1101/gad.304055.117. Review. Erratum in: Genes Dev. 2017 Oct 1;31(19):2015.


The RNA polymerase II CTD "orphan" residues: Emerging insights into the functions of Tyr-1, Thr-4, and Ser-7.

Yurko NM, Manley JL.

Transcription. 2018;9(1):30-40. doi: 10.1080/21541264.2017.1338176. Epub 2017 Oct 4. Review.


An Mtr4/ZFC3H1 complex facilitates turnover of unstable nuclear RNAs to prevent their cytoplasmic transport and global translational repression.

Ogami K, Richard P, Chen Y, Hoque M, Li W, Moresco JJ, Yates JR 3rd, Tian B, Manley JL.

Genes Dev. 2017 Jun 15;31(12):1257-1271. doi: 10.1101/gad.302604.117. Epub 2017 Jul 21.


Roles of Sumoylation in mRNA Processing and Metabolism.

Richard P, Vethantham V, Manley JL.

Adv Exp Med Biol. 2017;963:15-33. doi: 10.1007/978-3-319-50044-7_2. Review.


SRSF10 Connects DNA Damage to the Alternative Splicing of Transcripts Encoding Apoptosis, Cell-Cycle Control, and DNA Repair Factors.

Shkreta L, Toutant J, Durand M, Manley JL, Chabot B.

Cell Rep. 2016 Nov 15;17(8):1990-2003. doi: 10.1016/j.celrep.2016.10.071.


Alternative polyadenylation of mRNA precursors.

Tian B, Manley JL.

Nat Rev Mol Cell Biol. 2017 Jan;18(1):18-30. doi: 10.1038/nrm.2016.116. Epub 2016 Sep 28. Review.


The C9ORF72 GGGGCC expansion forms RNA G-quadruplex inclusions and sequesters hnRNP H to disrupt splicing in ALS brains.

Conlon EG, Lu L, Sharma A, Yamazaki T, Tang T, Shneider NA, Manley JL.

Elife. 2016 Sep 13;5. pii: e17820. doi: 10.7554/eLife.17820.


R Loops and Links to Human Disease.

Richard P, Manley JL.

J Mol Biol. 2017 Oct 27;429(21):3168-3180. doi: 10.1016/j.jmb.2016.08.031. Epub 2016 Sep 4. Review.


XRN2 Links Transcription Termination to DNA Damage and Replication Stress.

Morales JC, Richard P, Patidar PL, Motea EA, Dang TT, Manley JL, Boothman DA.

PLoS Genet. 2016 Jul 20;12(7):e1006107. doi: 10.1371/journal.pgen.1006107. eCollection 2016 Jul.


cFLIP expression is altered in severe corticosteroid-resistant asthma.

Lazarev D, Miller RL, Dimango E, Fu XD, Li HR, Logan CJ, Manley JL.

Genom Data. 2014 May 23;2:99-104. doi: 10.1016/j.gdata.2014.05.003. eCollection 2014 Dec.


Disease-associated mutation in SRSF2 misregulates splicing by altering RNA-binding affinities.

Zhang J, Lieu YK, Ali AM, Penson A, Reggio KS, Rabadan R, Raza A, Mukherjee S, Manley JL.

Proc Natl Acad Sci U S A. 2015 Aug 25;112(34):E4726-34. doi: 10.1073/pnas.1514105112. Epub 2015 Aug 10.


ALS mutations in TLS/FUS disrupt target gene expression.

Coady TH, Manley JL.

Genes Dev. 2015 Aug 15;29(16):1696-706. doi: 10.1101/gad.267286.115. Epub 2015 Aug 6.


Mutant p53 cooperates with the SWI/SNF chromatin remodeling complex to regulate VEGFR2 in breast cancer cells.

Pfister NT, Fomin V, Regunath K, Zhou JY, Zhou W, Silwal-Pandit L, Freed-Pastor WA, Laptenko O, Neo SP, Bargonetti J, Hoque M, Tian B, Gunaratne J, Engebraaten O, Manley JL, Børresen-Dale AL, Neilsen PM, Prives C.

Genes Dev. 2015 Jun 15;29(12):1298-315. doi: 10.1101/gad.263202.115. Epub 2015 Jun 16.


SUMOylation Is an Inhibitory Constraint that Regulates the Prion-like Aggregation and Activity of CPEB3.

Drisaldi B, Colnaghi L, Fioriti L, Rao N, Myers C, Snyder AM, Metzger DJ, Tarasoff J, Konstantinov E, Fraser PE, Manley JL, Kandel ER.

Cell Rep. 2015 Jun 23;11(11):1694-702. doi: 10.1016/j.celrep.2015.04.061. Epub 2015 Jun 11.


The end of the message: multiple protein-RNA interactions define the mRNA polyadenylation site.

Shi Y, Manley JL.

Genes Dev. 2015 May 1;29(9):889-97. doi: 10.1101/gad.261974.115. Review.


Systematic profiling of poly(A)+ transcripts modulated by core 3' end processing and splicing factors reveals regulatory rules of alternative cleavage and polyadenylation.

Li W, You B, Hoque M, Zheng D, Luo W, Ji Z, Park JY, Gunderson SI, Kalsotra A, Manley JL, Tian B.

PLoS Genet. 2015 Apr 23;11(4):e1005166. doi: 10.1371/journal.pgen.1005166. eCollection 2015 Apr.


A journey to the end of the message.

Manley JL.

RNA. 2015 Apr;21(4):538-40. doi: 10.1261/rna.050724.115. No abstract available.


Sumoylation controls the timing of Tup1-mediated transcriptional deactivation.

Ng CH, Akhter A, Yurko N, Burgener JM, Rosonina E, Manley JL.

Nat Commun. 2015 Mar 13;6:6610. doi: 10.1038/ncomms7610.


RBBP6 isoforms regulate the human polyadenylation machinery and modulate expression of mRNAs with AU-rich 3' UTRs.

Di Giammartino DC, Li W, Ogami K, Yashinskie JJ, Hoque M, Tian B, Manley JL.

Genes Dev. 2014 Oct 15;28(20):2248-60. doi: 10.1101/gad.245787.114.


CPSF30 and Wdr33 directly bind to AAUAAA in mammalian mRNA 3' processing.

Chan SL, Huppertz I, Yao C, Weng L, Moresco JJ, Yates JR 3rd, Ule J, Manley JL, Shi Y.

Genes Dev. 2014 Nov 1;28(21):2370-80. doi: 10.1101/gad.250993.114. Epub 2014 Oct 9.


New links between mRNA polyadenylation and diverse nuclear pathways.

Di Giammartino DC, Manley JL.

Mol Cells. 2014 Sep;37(9):644-9. doi: 10.14348/molcells.2014.0177. Epub 2014 Aug 1. Review.


Threonine-4 of the budding yeast RNAP II CTD couples transcription with Htz1-mediated chromatin remodeling.

Rosonina E, Yurko N, Li W, Hoque M, Tian B, Manley JL.

Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):11924-31. doi: 10.1073/pnas.1412802111. Epub 2014 Jul 28.


SETX sumoylation: A link between DNA damage and RNA surveillance disrupted in AOA2.

Richard P, Manley JL.

Rare Dis. 2014 Jan 21;2:e27744. doi: 10.4161/rdis.27744. eCollection 2014.


RNAP II CTD tyrosine 1 performs diverse functions in vertebrate cells.

Hsin JP, Li W, Hoque M, Tian B, Manley JL.

Elife. 2014 May 8;3:e02112. doi: 10.7554/eLife.02112.


Function and control of RNA polymerase II C-terminal domain phosphorylation in vertebrate transcription and RNA processing.

Hsin JP, Xiang K, Manley JL.

Mol Cell Biol. 2014 Jul;34(13):2488-98. doi: 10.1128/MCB.00181-14. Epub 2014 Apr 21.


Delineating the structural blueprint of the pre-mRNA 3'-end processing machinery.

Xiang K, Tong L, Manley JL.

Mol Cell Biol. 2014 Jun;34(11):1894-910. doi: 10.1128/MCB.00084-14. Epub 2014 Mar 3. Review.


In vitro analysis of transcriptional activators and polyadenylation.

Nagaike T, Manley JL.

Methods Mol Biol. 2014;1125:65-74. doi: 10.1007/978-1-62703-971-0_6.


Kub5-Hera, the human Rtt103 homolog, plays dual functional roles in transcription termination and DNA repair.

Morales JC, Richard P, Rommel A, Fattah FJ, Motea EA, Patidar PL, Xiao L, Leskov K, Wu SY, Hittelman WN, Chiang CM, Manley JL, Boothman DA.

Nucleic Acids Res. 2014 Apr;42(8):4996-5006. doi: 10.1093/nar/gku160. Epub 2014 Mar 3.


Transcriptome analysis of alternative splicing events regulated by SRSF10 reveals position-dependent splicing modulation.

Zhou X, Wu W, Li H, Cheng Y, Wei N, Zong J, Feng X, Xie Z, Chen D, Manley JL, Wang H, Feng Y.

Nucleic Acids Res. 2014 Apr;42(6):4019-30. doi: 10.1093/nar/gkt1387. Epub 2014 Jan 17.


Misregulation of pre-mRNA alternative splicing in cancer.

Zhang J, Manley JL.

Cancer Discov. 2013 Nov;3(11):1228-37. doi: 10.1158/2159-8290.CD-13-0253. Epub 2013 Oct 21. Review.


How bidirectional becomes unidirectional.

Richard P, Manley JL.

Nat Struct Mol Biol. 2013 Sep;20(9):1022-4. doi: 10.1038/nsmb.2657. No abstract available.


Target specificity among canonical nuclear poly(A) polymerases in plants modulates organ growth and pathogen response.

Vi SL, Trost G, Lange P, Czesnick H, Rao N, Lieber D, Laux T, Gray WM, Manley JL, Groth D, Kappel C, Lenhard M.

Proc Natl Acad Sci U S A. 2013 Aug 20;110(34):13994-9. doi: 10.1073/pnas.1303967110. Epub 2013 Aug 5.


Far upstream element-binding protein 1 and RNA secondary structure both mediate second-step splicing repression.

Li H, Wang Z, Zhou X, Cheng Y, Xie Z, Manley JL, Feng Y.

Proc Natl Acad Sci U S A. 2013 Jul 16;110(29):E2687-95. doi: 10.1073/pnas.1310607110. Epub 2013 Jul 1.


Alternative cleavage and polyadenylation: the long and short of it.

Tian B, Manley JL.

Trends Biochem Sci. 2013 Jun;38(6):312-20. doi: 10.1016/j.tibs.2013.03.005. Epub 2013 Apr 27. Review.

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