Publications

• 1. Lin MH
  2. Jensen MK
  3. Elrod ND
  4. Chu HF
  5. Haseley M
  6. Beam AC
  7. Huang KL
  8. Chiang W
  9. Russell WK
  10. Williams K
  11. Pröschel C
  12. Wagner EJ
  13. Tong L
  Cytoplasmic binding partners of the Integrator endonuclease INTS11 and its paralog CPSF73 are required for their nuclear function.; Molecular cell. 2024 Jul 08.
• 1. Haugen RJ
  2. Barnier C
  3. Elrod ND
  4. Luo H
  5. Jensen MK
  6. Ji P
  7. Smibert CA
  8. Lipshitz HD
  9. Wagner EJ
  10. Freddolino PL
  11. Goldstrohm AC
  Regulation of the Drosophila transcriptome by Pumilio and the CCR4-NOT deadenylase complex.; RNA (New York, N.Y.). 2024 Apr 16.
• 1. Jonnakuti VS
  2. Wagner EJ
  3. Maletić-Savatić M
  4. Liu Z
  5. Yalamanchili HK
  PolyAMiner-Bulk is a deep learning-based algorithm that decodes alternative polyadenylation dynamics from bulk RNA-seq data.; Cell reports methods. 2024 Feb 03.
• 1. Haugen RJ
  2. Barnier C
  3. Elrod ND
  4. Luo H
  5. Jensen MK
  6. Ji P
  7. Smibert CA
  8. Lipshitz HD
  9. Wagner EJ
  10. Freddolino PL
  11. Goldstrohm AC
  Regulation of the Drosophila transcriptome by Pumilio and CCR4-NOT deadenylase.; bioRxiv : the preprint server for biology. 2023 Aug 30.
• 1. Jonnakuti VS
  2. Ji P
  3. Gao Y
  4. Lin A
  5. Chu Y
  6. Elrod N
  7. Huang KL
  8. Li W
  9. Yalamanchili HK
  10. Wagner EJ
  NUDT21 alters glioma migration through differential alternative polyadenylation of LAMC1.; Journal of neuro-oncology. 2023 Jun 30.
• 1. Tepe B
  2. Macke EL
  3. Niceta M
  4. Weisz Hubshman M
  5. Kanca O
  6. Schultz-Rogers L
  7. Zarate YA
  8. Schaefer GB
  9. Granadillo De Luque JL
  10. Wegner DJ
  11. Cogne B
  12. Gilbert-Dussardier B
  13. Le Guillou X
  14. Wagner EJ
  15. Pais LS
  16. Neil JE
  17. Mochida GH
  18. Walsh CA
  19. Magal N
  20. Drasinover V
  21. Shohat M
  22. Schwab T
  23. Schmitz C
  24. Clark K
  25. Fine A
  26. Lanpher B
  27. Gavrilova R
  28. Blanc P
  29. Burglen L
  30. Afenjar A
  31. Steel D
  32. Kurian MA
  33. Prabhakar P
  34. Gößwein S
  35. Di Donato N
  36. Bertini ES
  37. Wangler MF
  38. Yamamoto S
  39. Tartaglia M
  40. Klee EW
  41. Bellen HJ
  Bi-allelic variants in INTS11 are associated with a complex neurological disorder.; American journal of human genetics. 2023 Apr 04.
• 1. de Prisco N
  2. Ford C
  3. Elrod ND
  4. Lee W
  5. Tang LC
  6. Huang KL
  7. Lin A
  8. Ji P
  9. Jonnakuti VS
  10. Boyle L
  11. Cabaj M
  12. Botta S
  13. Õunap K
  14. Reinson K
  15. Wojcik MH
  16. Rosenfeld JA
  17. Bi W
  18. Tveten K
  19. Prescott T
  20. Gerstner T
  21. Schroeder A
  22. Fong CT
  23. George-Abraham JK
  24. Buchanan CA
  25. Hanson-Khan A
  26. Bernstein JA
  27. Nella AA
  28. Chung WK
  29. Brandt V
  30. Jovanovic M
  31. Targoff KL
  32. Yalamanchili HK
  33. Wagner EJ
  34. Gennarino VA
  Alternative polyadenylation alters protein dosage by switching between intronic and 3'UTR sites.; Science advances; Vol 9(7), pp. eade4814. 2023 Feb 17.
• 1. Cui Y
  2. Arnold FJ
  3. Peng F
  4. Wang D
  5. Li JS
  6. Michels S
  7. Wagner EJ
  8. La Spada AR
  9. Li W
  Alternative polyadenylation transcriptome-wide association study identifies APA-linked susceptibility genes in brain disorders.; Nature communications; Vol 14(1), pp. 583. 2023 Feb 03.
• 1. Jonnakuti VS
  2. Wagner EJ
  3. Maletić-Savatić M
  4. Liu Z
  5. Yalamanchili HK
  PolyAMiner-Bulk: A Machine Learning Based Bioinformatics Algorithm to Infer and Decode Alternative Polyadenylation Dynamics from bulk RNA-seq data.; bioRxiv : the preprint server for biology. 2023 Jan 24.
• 1. Fongang B
  2. Wadop YN
  3. Zhu Y
  4. Wagner EJ
  5. Kudlicki A
  6. Rowicka M
  Coevolution combined with molecular dynamics simulations provides structural and mechanistic insights into the interactions between the integrator complex subunits.; Computational and structural biotechnology journal; Vol 21, pp. 5686-5697. 2023 Jan 19.
• 1. Liu S
  2. Baeg GH
  3. Yang Y
  4. Goh FG
  5. Bao H
  6. Wagner EJ
  7. Yang X
  8. Cai Y
  The Integrator complex desensitizes cellular response to TGF-β/BMP signaling.; Cell reports; Vol 42(1), pp. 112007. 2023 Jan 14.
• 1. Wagner EJ
  2. Tong L
  3. Adelman K
  Integrator is a global promoter-proximal termination complex.; Molecular cell. 2023 Jan 04.
• 1. Lin MH
  2. Jensen MK
  3. Elrod ND
  4. Huang KL
  5. Welle KA
  6. Wagner EJ
  7. Tong L
  Inositol hexakisphosphate is required for Integrator function.; Nature communications; Vol 13(1), pp. 5742. 2022 Sep 30.
• 1. Tseng V
  2. Collum SD
  3. Allawzi A
  4. Crotty K
  5. Yeligar S
  6. Trammell A
  7. Ryan Smith M
  8. Kang BY
  9. Sutliff RL
  10. Ingram JL
  11. Jyothula SSSK
  12. Thandavarayan RA
  13. Huang HJ
  14. Nozik ES
  15. Wagner EJ
  16. Michael Hart C
  17. Karmouty-Quintana H
  3'UTR shortening of HAS2 promotes hyaluronan hyper-synthesis and bioenergetic dysfunction in pulmonary hypertension.; Matrix biology : journal of the International Society for Matrix Biology; Vol 111, pp. 53-75. 2022 Jun 04.
• 1. Wilson C
  2. Mertens TC
  3. Shivshankar P
  4. Bi W
  5. Collum SD
  6. Wareing N
  7. Ko J
  8. Weng T
  9. Naikawadi RP
  10. Wolters PJ
  11. Maire P
  12. Jyothula SS
  13. Thandavarayan RA
  14. Ren D
  15. Elrod ND
  16. Wagner EJ
  17. Huang HJ
  18. Dickey BF
  19. Ford HL
  20. Karmouty-Quintana H
  Sine oculis homeobox homolog 1 plays a critical role in pulmonary fibrosis.; JCI insight; Vol 7(10). 2022 May 23.
• 1. LaForce GR
  2. Farr JS
  3. Liu J
  4. Akesson C
  5. Gumus E
  6. Pinkard O
  7. Miranda HC
  8. Johnson K
  9. Sweet TJ
  10. Ji P
  11. Lin A
  12. Coller J
  13. Philippidou P
  14. Wagner EJ
  15. Schaffer AE
  Suppression of premature transcription termination leads to reduced mRNA isoform diversity and neurodegeneration.; Neuron. 2022 Feb 04.
• 1. Stein CB
  2. Field AR
  3. Mimoso CA
  4. Zhao C
  5. Huang KL
  6. Wagner EJ
  7. Adelman K
  Integrator endonuclease drives promoter-proximal termination at all RNA polymerase II-transcribed loci.; Molecular cell. 2022 Jan 28.
• 1. Mascibroda LG
  2. Shboul M
  3. Elrod ND
  4. Colleaux L
  5. Hamamy H
  6. Huang KL
  7. Peart N
  8. Singh MK
  9. Lee H
  10. Merriman B
  11. Jodoin JN
  12. Sitaram P
  13. Lee LA
  14. Fathalla R
  15. Al-Rawashdeh B
  16. Ababneh O
  17. El-Khateeb M
  18. Escande-Beillard N
  19. Nelson SF
  20. Wu Y
  21. Tong L
  22. Kenney LJ
  23. Roy S
  24. Russell WK
  25. Amiel J
  26. Reversade B
  27. Wagner EJ
  INTS13 variants causing a recessive developmental ciliopathy disrupt assembly of the Integrator complex.; Nature communications; Vol 13(1), pp. 6054. 2022 Jan 13.
• 1. Cao J
  2. Verma SK
  3. Jaworski E
  4. Mohan S
  5. Nagasawa CK
  6. Rayavara K
  7. Sooter A
  8. Miller SN
  9. Holcomb RJ
  10. Powell MJ
  11. Ji P
  12. Elrod ND
  13. Yildirim E
  14. Wagner EJ
  15. Popov V
  16. Garg NJ
  17. Routh AL
  18. Kuyumcu-Martinez MN
  RBFOX2 is critical for maintaining alternative polyadenylation patterns and mitochondrial health in rat myoblasts.; Cell reports; Vol 37(5). 2021 Nov 02.
• 1. Li L
  2. Huang KL
  3. Gao Y
  4. Cui Y
  5. Wang G
  6. Elrod ND
  7. Li Y
  8. Chen YE
  9. Ji P
  10. Peng F
  11. Russell WK
  12. Wagner EJ
  13. Li W
  An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability.; Nature genetics; Vol 53(7). 2021 Jul.
• 1. Enwerem III
  2. Elrod ND
  3. Chang CT
  4. Lin A
  5. Ji P
  6. Bohn JA
  7. Levdansky Y
  8. Wagner EJ
  9. Valkov E
  10. Goldstrohm AC
  Human Pumilio proteins directly bind the CCR4-NOT deadenylase complex to regulate the transcriptome.; RNA (New York, N.Y.); Vol 27(4). 2021 Apr.
• 1. Lin A
  2. Ji P
  3. Niu X
  4. Zhao X
  5. Chen Y
  6. Liu W
  7. Liu Y
  8. Fan W
  9. Sun Y
  10. Miao C
  11. Zhang S
  12. Tan W
  13. Lin D
  14. Wagner EJ
  15. Wu C
  CstF64-Induced Shortening of the BID 3'UTR Promotes Esophageal Squamous Cell Carcinoma Progression by Disrupting ceRNA Cross-talk with ZFP36L2.; Cancer research; Vol 81(22), pp. 5638-5651. 2021 Jan 04.
• 1. Jensen MK
  2. Elrod ND
  3. Yalamanchili HK
  4. Ji P
  5. Lin A
  6. Liu Z
  7. Wagner EJ
  Application and design considerations for 3'-end sequencing using click-chemistry.; Methods in enzymology; Vol 655. 2021.
• 1. Yalamanchili HK
  2. Elrod ND
  3. Jensen MK
  4. Ji P
  5. Lin A
  6. Wagner EJ
  7. Liu Z
  A computational pipeline to infer alternative poly-adenylation from 3' sequencing data.; Methods in enzymology; Vol 655. 2021.
• 1. Yuan F
  2. Hankey W
  3. Wagner EJ
  4. Li W
  5. Wang Q
  Alternative polyadenylation of mRNA and its role in cancer.; Genes & diseases; Vol 8(1). 2021 Jan.
• 1. Yalamanchili HK
  2. Alcott CE
  3. Ji P
  4. Wagner EJ
  5. Zoghbi HY
  6. Liu Z
  PolyA-miner: accurate assessment of differential alternative poly-adenylation from 3'Seq data using vector projections and non-negative matrix factorization.; Nucleic acids research; Vol 48(12). 2020 Jul 09.
• 1. Alcott CE
  2. Yalamanchili HK
  3. Ji P
  4. van der Heijden ME
  5. Saltzman A
  6. Elrod N
  7. Lin A
  8. Leng M
  9. Bhatt B
  10. Hao S
  11. Wang Q
  12. Saliba A
  13. Tang J
  14. Malovannaya A
  15. Wagner EJ
  16. Liu Z
  17. Zoghbi HY
  Partial loss of CFIm25 causes learning deficits and aberrant neuronal alternative polyadenylation.; eLife; Vol 9. 2020 Apr 22.
• 1. Weng T
  2. Huang J
  3. Wagner EJ
  4. Ko J
  5. Wu M
  6. Wareing NE
  7. Xiang Y
  8. Chen NY
  9. Ji P
  10. Molina JG
  11. Volcik KA
  12. Han L
  13. Mayes MD
  14. Blackburn MR
  15. Assassi S
  Downregulation of CFIm25 amplifies dermal fibrosis through alternative polyadenylation.; The Journal of experimental medicine; Vol 217(2). 2020 Feb 03.
• 1. Huang KL
  2. Jee D
  3. Stein CB
  4. Elrod ND
  5. Henriques T
  6. Mascibroda LG
  7. Baillat D
  8. Russell WK
  9. Adelman K
  10. Wagner EJ
  Integrator Recruits Protein Phosphatase 2A to Prevent Pause Release and Facilitate Transcription Termination.; Molecular cell; Vol 80(2). 2020 Jan 15.
• 1. Chu Y
  2. Elrod N
  3. Wang C
  4. Li L
  5. Chen T
  6. Routh A
  7. Xia Z
  8. Li W
  9. Wagner EJ
  10. Ji P
  Nudt21 regulates the alternative polyadenylation of Pak1 and is predictive in the prognosis of glioblastoma patients.; Oncogene; Vol 38(21). 2019 May.
• 1. Weng T
  2. Ko J
  3. Masamha CP
  4. Xia Z
  5. Xiang Y
  6. Chen NY
  7. Molina JG
  8. Collum S
  9. Mertens TC
  10. Luo F
  11. Philip K
  12. Davies J
  13. Huang J
  14. Wilson C
  15. Thandavarayan RA
  16. Bruckner BA
  17. Jyothula SS
  18. Volcik KA
  19. Li L
  20. Han L
  21. Li W
  22. Assassi S
  23. Karmouty-Quintana H
  24. Wagner EJ
  25. Blackburn MR
  Cleavage factor 25 deregulation contributes to pulmonary fibrosis through alternative polyadenylation.; The Journal of clinical investigation; Vol 129(5). 2019 May 01.
• 1. Wagner EJ
  2. Goldstrohm AC
  Biochemical and Next Generation Sequencing Approaches to Study RNA Regulation.; Methods (San Diego, Calif.); Vol 155. 2019 Feb 15.
• 1. Elrod ND
  2. Jaworski EA
  3. Ji P
  4. Wagner EJ
  5. Routh A
  Development of Poly(A)-ClickSeq as a tool enabling simultaneous genome-wide poly(A)-site identification and differential expression analysis.; Methods (San Diego, Calif.); Vol 155. 2019 Feb 15.
• 1. Matera AG
  2. Raimer AC
  3. Schmidt CA
  4. Kelly JA
  5. Droby GN
  6. Baillat D
  7. Ten Have S
  8. Lamond AI
  9. Wagner EJ
  10. Gray KM
  Composition of the Survival Motor Neuron (SMN) Complex in Drosophila melanogaster.; G3 (Bethesda, Md.); Vol 9(2). 2019 Feb 07.
• 1. Elrod ND
  2. Henriques T
  3. Huang KL
  4. Tatomer DC
  5. Wilusz JE
  6. Wagner EJ
  7. Adelman K
  The Integrator Complex Attenuates Promoter-Proximal Transcription at Protein-Coding Genes.; Molecular cell; Vol 76(5). 2019 Jan 05.
• 1. Tatomer DC
  2. Elrod ND
  3. Liang D
  4. Xiao MS
  5. Jiang JZ
  6. Jonathan M
  7. Huang KL
  8. Wagner EJ
  9. Cherry S
  10. Wilusz JE
  The Integrator complex cleaves nascent mRNAs to attenuate transcription.; Genes & development; Vol 33(21-22). 2019 Jan 01.
• 1. Yoshimi A
  2. Lin KT
  3. Wiseman DH
  4. Rahman MA
  5. Pastore A
  6. Wang B
  7. Lee SC
  8. Micol JB
  9. Zhang XJ
  10. de Botton S
  11. Penard-Lacronique V
  12. Stein EM
  13. Cho H
  14. Miles RE
  15. Inoue D
  16. Albrecht TR
  17. Somervaille TCP
  18. Batta K
  19. Amaral F
  20. Simeoni F
  21. Wilks DP
  22. Cargo C
  23. Intlekofer AM
  24. Levine RL
  25. Dvinge H
  26. Bradley RK
  27. Wagner EJ
  28. Krainer AR
  29. Abdel-Wahab O
  Coordinated alterations in RNA splicing and epigenetic regulation drive leukaemogenesis.; Nature; Vol 574(7777). 2019 Jan.
• 1. Park HJ
  2. Ji P
  3. Kim S
  4. Xia Z
  5. Rodriguez B
  6. Li L
  7. Su J
  8. Chen K
  9. Masamha CP
  10. Baillat D
  11. Fontes-Garfias CR
  12. Shyu AB
  13. Neilson JR
  14. Wagner EJ
  15. Li W
  3' UTR shortening represses tumor-suppressor genes in trans by disrupting ceRNA crosstalk.; Nature genetics; Vol 50(6). 2018 Jun.
• 1. Albrecht TR
  2. Shevtsov SP
  3. Wu Y
  4. Mascibroda LG
  5. Peart NJ
  6. Huang KL
  7. Sawyer IA
  8. Tong L
  9. Dundr M
  10. Wagner EJ
  Integrator subunit 4 is a 'Symplekin-like' scaffold that associates with INTS9/11 to form the Integrator cleavage module.; Nucleic acids research; Vol 46(8). 2018 May 04.
• 1. Gray KM
  2. Kaifer KA
  3. Baillat D
  4. Wen Y
  5. Bonacci TR
  6. Ebert AD
  7. Raimer AC
  8. Spring AM
  9. Have ST
  10. Glascock JJ
  11. Gupta K
  12. Van Duyne GD
  13. Emanuele MJ
  14. Lamond AI
  15. Wagner EJ
  16. Lorson CL
  17. Matera AG
  Self-oligomerization regulates stability of survival motor neuron protein isoforms by sequestering an SCFSlmb degron.; Molecular biology of the cell; Vol 29(2). 2018 Jan 15.
• 1. Masamha CP
  2. Wagner EJ
  The contribution of alternative polyadenylation to the cancer phenotype.; Carcinogenesis; Vol 39(1). 2018 Jan 12.
• 1. Feng X
  2. Li L
  3. Wagner EJ
  4. Li W
  TC3A: The Cancer 3' UTR Atlas.; Nucleic acids research; Vol 46(D1). 2018 Jan 04.
• 1. Peart N
  2. Wagner EJ
  A distal auxiliary element facilitates cleavage and polyadenylation of Dux4 mRNA in the pathogenic haplotype of FSHD.; Human genetics; Vol 136(9). 2017 Sep.
• 1. Oegema R
  2. Baillat D
  3. Schot R
  4. van Unen LM
  5. Brooks A
  6. Kia SK
  7. Hoogeboom AJM
  8. Xia Z
  9. Li W
  10. Cesaroni M
  11. Lequin MH
  12. van Slegtenhorst M
  13. Dobyns WB
  14. de Coo IFM
  15. van den Berg D
  16. Verheijen FW
  17. Kremer A
  18. van der Spek PJ
  19. Heijsman D
  20. Wagner EJ
  21. Fornerod M
  22. Mancini GMS
  Correction: Human mutations in integrator complex subunits link transcriptome integrity to brain development.; PLoS genetics; Vol 13(8). 2017 Aug.
• 1. Routh A
  2. Ji P
  3. Jaworski E
  4. Xia Z
  5. Li W
  6. Wagner EJ
  Poly(A)-ClickSeq: click-chemistry for next-generation 3΄-end sequencing without RNA enrichment or fragmentation.; Nucleic acids research; Vol 45(12). 2017 Jul 07.
• 1. Oegema R
  2. Baillat D
  3. Schot R
  4. van Unen LM
  5. Brooks A
  6. Kia SK
  7. Hoogeboom AJM
  8. Xia Z
  9. Li W
  10. Cesaroni M
  11. Lequin MH
  12. van Slegtenhorst M
  13. Dobyns WB
  14. de Coo IFM
  15. Verheijen FW
  16. Kremer A
  17. van der Spek PJ
  18. Heijsman D
  19. Wagner EJ
  20. Fornerod M
  21. Mancini GMS
  Human mutations in integrator complex subunits link transcriptome integrity to brain development.; PLoS genetics; Vol 13(5). 2017 May.
• 1. Wu Y
  2. Albrecht TR
  3. Baillat D
  4. Wagner EJ
  5. Tong L
  Molecular basis for the interaction between Integrator subunits IntS9 and IntS11 and its functional importance.; Proceedings of the National Academy of Sciences of the United States of America; Vol 114(17). 2017 Apr 25.
• 1. Peart N
  2. Wagner EJ
  Genome-Wide RNAi Screens for RNA Processing Events in Drosophila melanogaster S2 Cells.; Methods in molecular biology (Clifton, N.J.); Vol 1648. 2017.
• 1. Masamha CP
  2. Xia Z
  3. Peart N
  4. Collum S
  5. Li W
  6. Wagner EJ
  7. Shyu AB
  CFIm25 regulates glutaminase alternative terminal exon definition to modulate miR-23 function.; RNA (New York, N.Y.); Vol 22(6). 2016 Jun.
• 1. Masamha CP
  2. Albrecht TR
  3. Wagner EJ
  Discovery and characterization of a novel CCND1/MRCK gene fusion in mantle cell lymphoma.; Journal of hematology & oncology; Vol 9. 2016 Mar 29.