Ares Lab Publications (1978-date)

(for up to the second results, search PubMed for Ares pubs)

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91. Elizabeth M. Munding, Lily Shiue, Sol Katzman, John Paul Donohue and Manuel Ares, Jr. (2013) Competition between pre-mRNAs for the splicing machinery drives global regulation of splicing. Mol Cell 51: 338-48. [AuthorAcceptedMS-preprint]

90. Effenberger KA, Perriman RJ, Bray WM, Lokey RS, Ares M Jr, Jurica MS. (2013) A High-Throughput Splicing Assay Identifies New Classes of Inhibitors of Human and Yeast Spliceosomes. J Biomol Screen. 2013 Jun 14. [Epub ahead of print][Suppl]

89. Pandit S, Zhou Y, Shiue L, Coutinho-Mansfield G, Li H, Qiu J, Huang J, Yeo GW, Ares M Jr, Fu XD. (2013) Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing. Mol Cell 50:223-35. [pdf][Suppl]

88. Hall MP, Nagel RJ, Fagg WS, Shiue L, Cline MS, Perriman RJ, Donohue JP, Ares M Jr. (2013) Quaking and PTB control overlapping splicing regulatory networks during muscle cell differentiation. RNA 19:627-38. [pdf]

87. Pistoni M, Shiue L, Cline MS, Bortolanza S, Neguembor MV, Xynos A, Ares M Jr, Gabellini D. (2013) Rbfox1 downregulation and altered calpain 3 splicing by FRG1 in a mouse model of Facioscapulohumeral muscular dystrophy (FSHD). PLoS Genet. 9(1):e1003186. doi: 10.1371/journal.pgen.1003186. Epub 2013 Jan 3. [open access journal site]

86. Beuck C, Qu S, Fagg WS, Ares M Jr, Williamson JR. (2012) Structural analysis of the quaking homodimerization interface. J Mol Biol. 423:766-81. [pdf]

85. Charizanis K, Lee KY, Batra R, Goodwin M, Zhang C, Yuan Y, Shiue L, Cline M, Scotti MM, Xia G, Kumar A, Ashizawa T, Clark HB, Kimura T, Takahashi MP, Fujimura H, Jinnai K, Yoshikawa H, Gomes-Pereira M, Gourdon G, Sakai N, Nishino S, Foster TC, Ares M Jr, Darnell RB, Swanson MS. (2012) Muscleblind-like 2-mediated alternative splicing in the developing brain and dysregulation in myotonic dystrophy. Neuron 75:437-50. [pdf]

84. Suenaga K, Lee KY, Nakamori M, Tatsumi Y, Takahashi MP, Fujimura H, Jinnai K, Yoshikawa H, Du H, Ares M Jr, Swanson MS, Kimura T. (2012) Muscleblind-like 1 knockout mice reveal novel splicing defects in the myotonic dystrophy brain. PLoS One. 7(3):e33218. Epub 2012 Mar 13. [pdf]

83. Gehman LT, Meera P, Stoilov P, Shiue L, O'Brien JE, Meisler MH, Ares M Jr, Otis TS, Black DL. (2012) The splicing regulator Rbfox2 is required for both cerebellar development and mature motor function. Genes Dev. 26:445-60. [pdf]

82. Huelga SC, Vu AQ, Arnold JD, Liang TY, Liu PP, Yan BY, Donohue JP, Shiue L, Hoon S, Brenner S, Ares M Jr, Yeo GW. (2012) Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep. 1:167-178. [link to PMC]

81. Anderson WA, Amasino RM, Ares M Jr, Banerjee U, Bartel B, Corces VG, Drennan CL, Elgin SC, Epstein IR, Fanning E, Guillette LJ Jr, Handelsman J, Hatfull GF, Hoy RR, Kelley D, Leinwand LA, Losick R, Lu Y, Lynn DG, Neuhauser C, O'Dowd DK, Olivera T, Pevzner P, Richards-Kortum RR, Rine J, Sah RL, Strobel SA, Walker GC, Walt DR, Warner IM, Wessler S, Willard HF, Zare RN. (2011) Competencies: a cure for pre-med curriculum. Science 334:760-1. [pdf]

80. Perriman RJ, Ares M Jr. (2011) Alternative splicing variability: exactly how similar are two identical cells? Mol Syst Biol. 7:505. doi: 10.1038/msb.2011.44. [pdf]

79. Gehman LT, Stoilov P, Maguire J, Damianov A, Lin CH, Shiue L, Ares M Jr, Mody I, Black DL. (2011) The splicing regulator Rbfox1 (A2BP1) controls neuronal excitation in the mammalian brain. Nat Genet. 43:706-11. doi: 10.1038/ng.841. [pdf][Suppl]

78. Mishra SK, Ammon T, Popowicz GM, Krajewski M, Nagel RJ, Ares M, Holak TA, Jentsch S. (2011) Role of the ubiquitin-like protein Hub1 in splice-site usage and alternative splicing. Nature 474:173-8. doi: 10.1038/nature10143. [pdf][Suppl]

77. Pope WH, Jacobs-Sera D, Russell DA, Peebles CL, Al-Atrache Z, et al. (2011) Expanding the diversity of mycobacteriophages: Insights into genome architecture and evolution. PLoS ONE 6: e16329. doi:10.1371 [pdf]

76. Rio DC, Ares M Jr, Hannon GJ, Nilsen TW. (2011) RNA: A Laboratory Manual. Cold Spring Harbor Laboratory Press. 586 pp. [Buy!]

75. Munding EM, Igel AH, Shiue L, Dorighi KM, Trevi–o LR, Ares M Jr. (2010) Integration of a splicing regulatory network within the meiotic gene expression program of Saccharomyces cerevisiae. Genes Dev. 24:2693-704. [pdf]

74. Perriman RP, Ares M Jr. (2010) Invariant U2 snRNA nucleotides form a stem loop to recognize the intron early in splicing. Mol Cell. 38:416-27. [pdf]

73. Du H, Cline MS, Osborne RJ, Tuttle DL, Clark TA, Donohue JP, Hall MP, Shiue L, Swanson MS, Thornton CA, Ares M Jr. (2010) Aberrant alternative splicing and extracellular matrix gene expression in mouse models of myotonic dystrophy. Nature Struc Mol Biol 17:187-93. [pdf][Suppl]

72. Chawla G, Lin CH, Han A, Shiue L, Ares M Jr, Black DL. (2009) Sam68 regulates a set of alternatively spliced exons during neurogenesis. Mol Cell Biol. 29:201-13. [pdf]

71. Ares M Jr, Chakrabarti K. (2008) Stuttering against marginotomy. Nat Struct Mol Biol.15:18-9. [pdf]

70. Lauriat TL, Shiue L, Haroutunian V, Verbitsky M, Ares M Jr, Ospina L, McInnes LA. (2008) Developmental expression profile of quaking, a candidate gene for schizophrenia, and its target genes in human prefrontal cortex and hippocampus shows regional specificity. J Neurosci Res. 86: 785-96. [pdf]

69. Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP, Ares M Jr. (2007) Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis. RNA 13:1923-39. [pdf]

68. Boutz PL, Stoilov P, Li Q, Lin CH, Chawla G, Ostrow K, Shiue L, Ares M Jr, Black DL. (2007) A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. Genes Dev. 21:1636-52. [pdf]

67. Perriman RJ, Ares M Jr. (2007) Rearrangement of competing U2 RNA helices within the spliceosome promotes multiple steps in splicing. Genes Dev. 21:811-20. [pdf]

66. Ni JZ, Grate L, Donohue JP, Preston C, Nobida N, O'Brien G, Shiue L, Clark TA, Blume JE, Ares M Jr. (2007)Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes Dev. 21:708-18. [pdf]

65. Ares M Jr. (2007) Sing the genome electric: excited cells adjust their splicing. (2007) PLoS Biol. 5:e55. [pdf]

64. Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares M Jr, Vanderhaeghen P, Haussler D. (2006) An RNA gene expressed during cortical development evolved rapidly in humans. Nature 443:167-72. [pdf]

63. Davis C, and Ares M. (2006) Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae. Proc. Nat'l. Acad. Sci 103:3262-7. [pdf] [Suppl]

62. Li C, Kato M, Shiue L, Shively JE, Ares M, and Lin R-J. (2006) Cell type and culture condition-dependent alternative splicing in human breast cancer cells revealed by splicing-sensitive microarrays. Cancer Research 66:1990-9. [pdf] [Suppl]

61. Sugnet CW, Srinivasan K, Clark TA, O'Brien G, Cline MS, Wang H, Williams A, Kulp D, Blume JE, Haussler D, Ares M. (2006) Unusual Intron Conservation near Tissue-Regulated Exons Found by Splicing Microarrays. PLoS Comput Biol. 2:e4. [pdf] [Suppl]

60. Combs DJ, Nagel RJ, Ares M Jr, Stevens SW. (2006) Prp43p is a DEAH-box spliceosome disassembly factor essential for ribosome biogenesis. Mol Cell Biol. 26:523-34. [pdf]

59. Srinivasan K, Shiue L, Hayes JD, Centers R, Fitzwater S, Loewen R, Edmondson LR, Bryant J, Smith M, Rommelfanger C, Welch V, Clark TA, Sugnet CW, Howe KJ, Mandel-Gutfreund Y, Ares M Jr. (2005) Detection and measurement of alternative splicing using splicing-sensitive microarrays. Methods 37:345-59. [pdf]

58. Burckin T, Nagel R, Mandel-Gutfreund Y, Shiue L, Clark T, Chong J-L, Chang T-H, Squazzo S, Hartzog G, and Ares, M. (2005) Exploring functional relationships between components of the gene expression machinery. Nature Struc Mol Biol. 12:175-18. [pdf][Suppl]

57. Ares, M, and Proudfoot, N. (2005) The Spanish Connection: Transcription and mRNA Processing Get Even Closer.  Cell 120: 163-166. (Meeting Review) [pdf]

56. Robertson MP, Igel H, Baertsch R, Haussler D, Ares M, and Scott W. G. (2005) The structure of a rigorously conserved RNA element within the SARS virus genome. PLoS Biol 3(1): e5. [pdf]

55. Ares M. (2004) Interdisciplinary research and the undergraduate biology student. Nat Struct Mol Biol 11:1170-2. (Commentary) [pdf]

54. Schattner P, Decatur WA, Davis CA, Ares M Jr, Fournier MJ, Lowe TM. (2004) Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome.  Nucleic Acids Res. 32:4281-4289. [pdf]

53. Leulliot N, Quevillon-Cheruel S, Graille M, Van Tilbeurgh H, Leeper TC, Godin KS, Edwards TE, Sigurdsson ST, Rozenkrants N, Nagel RJ, Ares M, Varani G. (2004)  A new alpha-helical extension promotes RNA binding by the dsRBD of Rnt1p RNAse III.  EMBO J. 23:2468-2477. [pdf]

52. Sugnet, C., Kent, W. J., Ares, M., and Haussler, D. (2004) Transcriptome and genome conservation of alternative splicing events in humans and mice. Pac Symp Biocomput. 2004:66-77. [pdf]

51. Spingola M, Armisen J, Ares M Jr. (2004)  Mer1p is a modular splicing factor whose function depends on the conserved U2 snRNP protein Snu17p. Nucleic Acids Res. 32:1242-50. [pdf]

50. Perriman, R., Barta, I., Voeltz, G. K., Abelson, J., and Ares, M. (2003) ATP requirement for Prp5p function is determined by Cus2p and the structure of U2 snRNA. PNAS 100:13857-13862. [pdf]

49. Howe, K. J., Kane, C. M., and Ares, M. (2003) Perturbation of transcription elongation influences the fidelity of internal exon inclusion in Saccharomyces cerevisiae. RNA 9:993-1006. [pdf]

48. Wang, H., Hubbell, E., Hu, J.-S., Mei, G., Cline, M., Lu, G., Clark, T., Siani-Rose, M., Ares, M., Kulp, D., and Haussler, D. (2003) Gene structure-based splice variant deconvolution using a microarray platform.  Bioinformatics 19:Suppl1:I315-I322. [pdf]

47. Clark, T., Sugnet, C., and Ares, M. (2002) Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 296:907-10. [pdf] [Suppl]

46. Burns, C. G., Ohi, R., Mehta, S., O'Toole, E. T., Winey, M., Clark, T. A., Sugnet, C. W., Ares, M., and Gould, K. L. (2002) Removal of a single a-tubulin gene intron suppresses cell cycle arrest phenotypes of splicing factor mutations in S. cerevisiae. Mol Cell Biol. 22:801-15. [pdf]

45. Grate, L., and Ares, M. (2002) Searching Yeast Intron Data at the Areslab Website. (In Guide to Yeast Genetics and Molecular and Cell Biology, Part B, C. Guthrie and G. Fink, eds) Methods Enz. 350: 380-392. [pdf]

44. Perriman, R. Circular mRNA coding for monomeric and polymeric GFP protein. (2002) In: Methods in Molecular Biology, 183:69-85.[pdf]

43. Giorgi, C., Fatica, A., Nagel, R., and Bozzoni, I. (2001) The release of U18 snoRNA from its host-intron requires the interaction between Nop1p and the Rnt1p endonuclease. EMBO J 20:6856-65. [pdf]

42. Spingola, M. and Ares, M. (2000) A yeast intronic splicing enhancer and Nam8p are required for Mer1p-activated splicing. Molecular Cell 6:329-338. [pdf]

41. Nagel, R. and Ares, M. (2000) Substrate recognition by a eukaryotic RNase III: the double stranded RNA binding domain of Rnt1p selectively binds RNA containing a 5'-AGNN-3' loop. RNA 6:1142-1156. [pdf]

40. Davis, C., Grate L., Spingola, M., and Ares, M. (2000) Test of intron predictions reveals novel splice sites, alternatively spliced mRNAs and new introns in meiotically regulated genes of yeast. Nucl. Acids Res. 28:1700-1706. [pdf]

39. Wells, S., Hughes, J., Igel, H., and Ares, M. (2000) Use of dimethylsulfate to probe RNA structure in vivo.  Methods. Enz 318:479-493. [pdf]

38. Pauling, M. H., McPheeters, D., and Ares, M. (2000) Functional Cus1p is found with Hsh155p in a multiprotein splicing factor associated with U2 snRNA. Molec. Cell. Biol. 20:2176-2185. [pdf]

37. Brown, M., Grundy, W., Lin, D., Cristianini, N., Sugnet, C., Furey, T., Ares, M., and Haussler, D. (2000) Knowledge-based Analysis of Microarray Gene Expression Data Using Support Vector Machines. Proc. Nat'l. Acad. Sci. 97:262-267. [pdf]

36. Perriman, R., and Ares, M. (2000) ATP can be dispensable for prespliceosome formation in yeast.  Genes & Development 14:97-107. [pdf]

35. Ares, M., Grate, L., and Pauling, M. H. (1999) A handful of intron-containing genes produce the lion's share of yeast mRNA. RNA 5:1138-1139. (Letter to the Editor) [pdf] [Suppl]

34. Spingola, M., Grate, L., Haussler, D., and Ares, M. (1999)  Genome-wide bioinformatic and molecular analysis of yeast introns. RNA 5:221-34. [pdf]

33. Perriman, R. and Ares, M.  (1998) Engineered circular mRNA can direct the synthesis of extremely long repeating sequence proteins in vivo. RNA 4:1047-1054. [pdf]

32. Yan, D., Perriman, R., Igel, H., Howe, K., Neville, M., and Ares, M.  (1998) CUS2, a yeast homolog of human Tat-SF1, rescues function of misfolded U2 through an unusual RNA recognition motif (RRM). Molec. Cell. Biol. 18:5000-5009. [pdf]

31. Abou Elela, S., and Ares, M. (1998) Depletion of yeast RNase III blocks correct U2 3' end formation and results in polyadenylated but functional U2 snRNA. EMBO J 17:3738-3746. [pdf]

30. Ares, M. (1998) The 1997 Genetics Society of America Medal. Christine Guthrie. Genetics 148:3-5 (A review of Guthrie's contributions upon her receipt of this award) [pdf]

29. Igel, H., Wells, S., Perriman, R. and Ares, M. (1998) Conservation of structure and subunit interactions in yeast homologs of Splicing Factor 3b (SF3b) subunits. RNA  4:1-10. [pdf]

28. Howe, K. and Ares, M. (1997) Intron self-complementarity enforces exon inclusion in a yeast pre-mRNA. Proc. Nat'l Acad. Sci. USA 94:12467-12472. [pdf]

27. Chanfreau, G., Abou Elela, S., Ares, M., and Guthrie, C. (1997) Alternative 3'-end processing of U5 snRNA by RNase III. Genes & Development  11: 2741-2751. [pdf]

26. Abou Elela, S., Igel, H., and Ares, M. (1996) RNase III cleaves eukaryotic pre-ribosomal RNA at a U3 snoRNP-dependent site. Cell 85: 115-124. [pdf]

25. Yan, D., and Ares, M. (1996) Invariant U2 sequences bordering the branchpoint interaction region are essential for interaction with SF3a and SF3b subunits. Mol. Cell. Biol. 16: 818-828. [pdf]

24. Wells, S., Neville, M., Haynes, M., Wang, J., Igel, H., and Ares, M. (1996) CUS1, a suppressor of cold sensitive U2 snRNA mutations, is a novel yeast splicing factor homologous to SAP 145. Genes & Development 10: 220-232. [pdf]

23. Ares, M. and Weiser, B. (1995) Rearrangement of snRNA structure during assembly and function of the spliceosome. Progress in Nucleic Acid Research and Molecular Biology 50: 131-159. [pdf]

22. Wells, S. and Ares, M. (1994) Interaction between distinct U2 snRNA structures and the PRP5, PRP9, PRP11, and PRP21 proteins is required to ensure integrity of the U2 snRNP. Mol. Cell. Biol. 14: 6337-6349. [pdf]

21. Ford, E. and Ares, M. (1994) Synthesis of circular RNA in bacteria and yeast using RNA cyclase ribozymes derived from a group I intron of phage T4. Proc. Nat'l Acad. Sci. USA 91:3117-3121. [pdf]

20. Zavanelli, M., Britton, J., Igel, H. and Ares, M. (1994) Mutations in an essential U2 snRNA structure cause cold sensitive U2 snRNP function by favoring competing alternative U2 RNA structures. Mol. Cell. Biol.14: 1689-1697. [pdf]

19. Zavanelli, M., and Ares, M. (1991) Efficient association of U2 snRNPs with premessenger RNA requires an essential U2 snRNA structural element. Genes & Development 5 :2521-2533. [pdf]

18. Hughes, J., and Ares, M. (1991) Depletion of U3 small nucleolar RNA inhibits cleavage in the 5' external transcribed spacer of yeast pre-ribosomal RNA and impairs formation of 18S ribosomal RNA. EMBO J 10 : 4231-4239. [pdf]

17. Miraglia, L., Seiwert, S., Igel, H., and Ares, M. (1991) Limited functional equivalence of phylogenetic variation in small nuclear RNA: Yeast U2 RNA with altered branchpoint complementarity inhibits splicing and produces a dominant lethal phenotype. Proc. Natl. Acad. Sci. USA  88: 7061-7065. [pdf]

16. Ares, M., and Igel, H. (1990) Lethal and temperature sensitive mutations identify an essential structural element in U2 small nuclear RNA. Genes and Development 4:2132-2145. [pdf]

15. Ares M Jr, Igel AH. (1990) Mutations define essential and nonessential U2 RNA structures. Mol Biol Rep. 14:131-2. [pdf]

14. Ares, M., and Igel, H. (1989) Phylogenetic comparisons of U2 small nuclear RNA sequences suggest a pseudoknot structure. In: Molecular Biology of RNA, UCLA Symposium on Molecular and Cellular Biology, New Series, Vol. 94, (T. Cech, ed.) pp13-23. [pdf]

13. Igel, H., and Ares, M. (1988) Internal sequences that distinguish yeast from metazoan U2 are unnecessary for pre-mRNA splicing. Nature 334:450-453. [pdf]

12. Gerbi, S., Jeppessen, C., Stebbins-Boaz, B., and Ares, M. (1987) Evolution of eukaryotic rRNA: Constraints imposed by RNA interactions. Cold Spring Harbor Symposia on Quantitative Biology 52: 709-719. [pdf]

11. Ares, M., Chung, J.-S., Giglio, L., and Weiner, A. (1987) Distinct factors with Sp1 and NFA specificities bind to adjacent functional elements of the human U2 enhancer. Genes & Development 1:808-817. [pdf]

10. Ares, M. (1986) U2 RNA from yeast is unexpectedly large and contains homology to vertebrate U4, U5, and U6 small nuclear RNAs. Cell 47: 49-59. [pdf]

9. Mangin, M., Ares, M., and Weiner, A. (1986) Human U2 small nuclear RNA genes contain an upstream enhancer. EMBO J 5: 987-995. [pdf]

8. Yuo, C.-Y., Ares, M., and Weiner, A. (1985) Sequences required for 3' end formation of human small nuclear RNA. Cell 42: 193-202. [pdf]

7. Mangin, M., Ares, M., and Weiner, A. (1985) U1 genes are subject to dosage compensation in mouse cells. Science 229: 272-275. [pdf]

6. Ares, M., Mangin, M., and Weiner, A. (1985) Orientation-dependent  transcriptional activator upstream of a human U2 small nuclear RNA gene. Mol. Cell. Biol. 5: 1560-1570. [pdf]

5. Lindgren, V., Ares, M., Weiner, A., and Francke, U. (1985) Human genes for U2 small nuclear RNA map to a major adenovirus modification site on chromosome 17. Nature 314: 115-116. [pdf]

4. Dallman, T., Ares, M., and Howell, S. (1983) Analysis of transcription during the cell cycle in toluenized Chlamydomonas reinhardi cells. Mol. Cell. Biol. 3: 1537-1539. [pdf]

3. Ares, M. and Howell, S. (1982) Cell cycle stage-specific accumulation of mRNAs encoding tubulin and other polypeptides in Chlamydomonas. Proc. Natl. Acad. Sci. USA 79: 5577-5581. [pdf]

2. Sutton, C., Ares, M., and Hallberg, R. (1978) Cycloheximide resistance can be mediated through either ribosomal subunit. Proc. Natl. Acad. Sci. USA 75: 3158-3162. [pdf]

1. Ares, M., and Bruns, P. (1978) Isolation and genetic characterization of a mutation affecting ribosomal resistance to cycloheximide in Tetrahymena. Genetics 90: 463-474. [pdf]