URMC / Labs / Wagner Lab / Publications

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.