Publications
2021
Debnath TK and Xhemalçe B. Deciphering RNA modifications at Base Resolution: From Chemistry to Biology. Briefings in Functional Genomics, Jan 18. doi: 10.1093/bfgp/elaa024
2020
McFadden MJ, McIntyre ABR, Mourelatos H, Abell NS, Gokhale NS, Ipas H, Xhemalçe B, Mason CE, Horner SM.
Post-Transcriptional Regulation of Antiviral Gene Expression by N6-Methyladenosine. bioRxiv 2020.08.05.238337; doi: https://doi.org/10.1101/2020.08.05.238337
Kim JJ, Lee S, Choi JH, Woo HG, Xhemalce B and Miller KM. PCAF-Mediated Histone Acetylation Promotes Replication Fork Degradation by MRE11 and EXO1 in BRCA-deficient Cells. Molecular Cell 80, 327–344, Oct 15
Highlighted article: Leuzzi G, Taglialatela A and Ciccia A. HATtracting Nucleases to stalled forks. Molecular Cell 80, Oct 15
Sriraman A, Debnath TK, Xhemalce B and Miller KM. Making it or Breaking it: DNA methylation and Genome Integrity. Essays in Biochemistry. Aug 18: Online ahead of print.
2019
Reinsborough CW, Ipas H, Abell NS, Nottingham RM, Yao J, Devanathan SK, Shelton SB, Lambowitz AM and Xhemalce B.
BCDIN3D regulates tRNA-His 3’ fragment processing. PLOS Genetics Jul 22;15(7):e1008273
Shelton SB, Xhemalce B. Antibody-Free Assay for RNA Methyltransferase Activity Analysis. J. Vis. Exp. (149), e59856
Kim JJ, Lee S, Gong F, Battenhouse AM, Boutz DR, Bashyal A, Refvik ST, Chiang CM, Xhemalce B, Paull TT, Brodbelt JS, Marcotte EM and Miller KM. 2019. Systematic Bromodomain Protein Screens Identify Homologous Recombination and R-Loop Suppression Pathways Involved in Genome Integrity, Genes & Development, 2019; 33: 1751-1774
2018
Shelton SB, Shah NM, Abell NS, Mercado M, Devanathan SK and Xhemalce B. Crosstalk between the RNA methylation and histone binding activities of MePCE regulates P-TEFb activation on chromatin. Cell Reports 2018 Feb 6
Bryant JD, Sweeney SR, Sentrandreu E, Shin M, Ipas H, Xhemalce B, Momb J, Tiziani S and Appling DR, Deletion of the neural tube defect-associated gene Mthfd1l disrupts one-carbon and central energy metabolism in mouse embryos. JBC 2018 Apr 20; 293(16):5821-5833
2017
Abell NS, Mercado M, Caneque T, Rodriguez R and Xhemalce B. Click-qMS identifies PIWIL3 as a mechanistic target of RNA interference activator enoxacin in cancer cells. J Am Chem Soc 2017 Jan 17
Zacharioudakis E, Agarwal P, Bartoli A, Abell NS, Kunalingam L, Xhemalce B, Miller KM, and Rodriguez, R. Chromatin regulates genome targeting with cisplatin. Angewandte Chemie 2017 May 5
2016
Shelton SB, Reinsborough CW and Xhemalce B, Who watches the watchmen: Roles of RNA modifications in the RNA interference Pathway, [Invited review] PLOS Genetics 2016 Jul 21;12(7)
2015
Chen W, Ebelt ND, Stracker TH, Xhemalce B, Van Den Berg CL & Miller KM, ATM regulation of IL-8 links oxidative stress to cancer cell migration and invasion, eLife 2015;10.7554/eLife.07270
2014
Spivey EC, Xhemalce B, Shear JB and Finkelstein IJ, A 3D-Printed Microfluidic Microdissector for High-Throughput Studies of Cellular Aging, Analytical Chemistry, 86(15):7406-12
2013
Xhemalce B, From histones to RNA: role of methylation in cancer, [Invited review, special issue of] Briefings in Functional Genomics on 'The Role of Epigenetics in Cancer', 12(3):244-53
2012
Xhemalce B, Robson SC and Kouzarides T, Human RNA methyltransferase BCDIN3D regulates microRNA processing, Cell: Vol. 151, Issue 2, pp. 278-288 File
Highlighted article: David R, Small RNAs: Controlling maturity (2012) Nature Reviews Molecular Cell Biology, December 2012, 13, 752-753
Dawson MA, Foster SD, Bannister AJ, Robson SC, Wang X, Xhemalce B, Wood AD, Green AR, Göttgens B and Kouzarides T. Three distinct patterns of histone H3Y41 phosphorylation mark active genes, Cell Reports: 2(3):470-7
Rodriguez R, Miller KM, Forment JV, Bradshaw CR, Nikan M, Xhemalce B, Balasubramanian S and Jackson SP, Small molecule induced DNA damage identifies druggable, alternatively-structured DNA sites, Nature Chemical Biology: 8(3):225-6
2011
Xhemalce B, Dawson MA and Bannister AJ, [Book Chapter] Histone Modifications, Epigenetic Regulation and Epigenomics, "Encyclopedia of Molecular Cell Biology and Molecular Medicine", John Wiley & Sons.
Cover of Epigenetic Regulation and Epigenomics Book
2010
Bartke T, Vermeulen M, Xhemalce B, Robson SC, Mann M, Kouzarides T, Nucleosome-Interacting Proteins Regulated by DNA and Histone Methylation, Cell: Vol. 143, Issue 3, pp. 470-484
Xhemalce B and Kouzarides T, A chromodomain switch mediated by Histone H3 Lysine 4 Acetylation regulates heterochromatin assembly, Genes & Development: 24(7): 647-52
Highlighted article: Kim JH and Workman JL, Histone acetylation in heterochromatin assembly (2010) Genes & Development, 2010 Apr 15; 24(7): 738-40
2007
Xhemalce B, Miller KM, Driscoll R, Masumoto H, Jackson SP, Kouzarides T, Verreault A and Arcangioli B, Regulation of histone H3 lysine 56 acetylation in Schizosaccharomyces pombe, JBC: 282: 15040-15047
Xhemalce B, Madi Riising E, Baumann P, Thon G, Dejean A, Arcangioli B and Seeler JS, Role of SUMO in the Dynamics of Telomere Maintenance in Fission Yeast, PNAS: 104(3): 893-8
2004
Xhemalce B, Seeler JS, Thon G, Dejean A and Arcangioli B, Role of the Fission Yeast SUMO E3 Ligase Pli1p in Centromere and Telomere Maintenance, EMBO Journal: 23, 3844-3853
Debnath TK and Xhemalçe B. Deciphering RNA modifications at Base Resolution: From Chemistry to Biology. Briefings in Functional Genomics, Jan 18. doi: 10.1093/bfgp/elaa024
2020
McFadden MJ, McIntyre ABR, Mourelatos H, Abell NS, Gokhale NS, Ipas H, Xhemalçe B, Mason CE, Horner SM.
Post-Transcriptional Regulation of Antiviral Gene Expression by N6-Methyladenosine. bioRxiv 2020.08.05.238337; doi: https://doi.org/10.1101/2020.08.05.238337
Kim JJ, Lee S, Choi JH, Woo HG, Xhemalce B and Miller KM. PCAF-Mediated Histone Acetylation Promotes Replication Fork Degradation by MRE11 and EXO1 in BRCA-deficient Cells. Molecular Cell 80, 327–344, Oct 15
Highlighted article: Leuzzi G, Taglialatela A and Ciccia A. HATtracting Nucleases to stalled forks. Molecular Cell 80, Oct 15
Sriraman A, Debnath TK, Xhemalce B and Miller KM. Making it or Breaking it: DNA methylation and Genome Integrity. Essays in Biochemistry. Aug 18: Online ahead of print.
2019
Reinsborough CW, Ipas H, Abell NS, Nottingham RM, Yao J, Devanathan SK, Shelton SB, Lambowitz AM and Xhemalce B.
BCDIN3D regulates tRNA-His 3’ fragment processing. PLOS Genetics Jul 22;15(7):e1008273
Shelton SB, Xhemalce B. Antibody-Free Assay for RNA Methyltransferase Activity Analysis. J. Vis. Exp. (149), e59856
Kim JJ, Lee S, Gong F, Battenhouse AM, Boutz DR, Bashyal A, Refvik ST, Chiang CM, Xhemalce B, Paull TT, Brodbelt JS, Marcotte EM and Miller KM. 2019. Systematic Bromodomain Protein Screens Identify Homologous Recombination and R-Loop Suppression Pathways Involved in Genome Integrity, Genes & Development, 2019; 33: 1751-1774
2018
Shelton SB, Shah NM, Abell NS, Mercado M, Devanathan SK and Xhemalce B. Crosstalk between the RNA methylation and histone binding activities of MePCE regulates P-TEFb activation on chromatin. Cell Reports 2018 Feb 6
Bryant JD, Sweeney SR, Sentrandreu E, Shin M, Ipas H, Xhemalce B, Momb J, Tiziani S and Appling DR, Deletion of the neural tube defect-associated gene Mthfd1l disrupts one-carbon and central energy metabolism in mouse embryos. JBC 2018 Apr 20; 293(16):5821-5833
2017
Abell NS, Mercado M, Caneque T, Rodriguez R and Xhemalce B. Click-qMS identifies PIWIL3 as a mechanistic target of RNA interference activator enoxacin in cancer cells. J Am Chem Soc 2017 Jan 17
Zacharioudakis E, Agarwal P, Bartoli A, Abell NS, Kunalingam L, Xhemalce B, Miller KM, and Rodriguez, R. Chromatin regulates genome targeting with cisplatin. Angewandte Chemie 2017 May 5
2016
Shelton SB, Reinsborough CW and Xhemalce B, Who watches the watchmen: Roles of RNA modifications in the RNA interference Pathway, [Invited review] PLOS Genetics 2016 Jul 21;12(7)
2015
Chen W, Ebelt ND, Stracker TH, Xhemalce B, Van Den Berg CL & Miller KM, ATM regulation of IL-8 links oxidative stress to cancer cell migration and invasion, eLife 2015;10.7554/eLife.07270
2014
Spivey EC, Xhemalce B, Shear JB and Finkelstein IJ, A 3D-Printed Microfluidic Microdissector for High-Throughput Studies of Cellular Aging, Analytical Chemistry, 86(15):7406-12
2013
Xhemalce B, From histones to RNA: role of methylation in cancer, [Invited review, special issue of] Briefings in Functional Genomics on 'The Role of Epigenetics in Cancer', 12(3):244-53
2012
Xhemalce B, Robson SC and Kouzarides T, Human RNA methyltransferase BCDIN3D regulates microRNA processing, Cell: Vol. 151, Issue 2, pp. 278-288 File
Highlighted article: David R, Small RNAs: Controlling maturity (2012) Nature Reviews Molecular Cell Biology, December 2012, 13, 752-753
Dawson MA, Foster SD, Bannister AJ, Robson SC, Wang X, Xhemalce B, Wood AD, Green AR, Göttgens B and Kouzarides T. Three distinct patterns of histone H3Y41 phosphorylation mark active genes, Cell Reports: 2(3):470-7
Rodriguez R, Miller KM, Forment JV, Bradshaw CR, Nikan M, Xhemalce B, Balasubramanian S and Jackson SP, Small molecule induced DNA damage identifies druggable, alternatively-structured DNA sites, Nature Chemical Biology: 8(3):225-6
2011
Xhemalce B, Dawson MA and Bannister AJ, [Book Chapter] Histone Modifications, Epigenetic Regulation and Epigenomics, "Encyclopedia of Molecular Cell Biology and Molecular Medicine", John Wiley & Sons.
Cover of Epigenetic Regulation and Epigenomics Book
2010
Bartke T, Vermeulen M, Xhemalce B, Robson SC, Mann M, Kouzarides T, Nucleosome-Interacting Proteins Regulated by DNA and Histone Methylation, Cell: Vol. 143, Issue 3, pp. 470-484
Xhemalce B and Kouzarides T, A chromodomain switch mediated by Histone H3 Lysine 4 Acetylation regulates heterochromatin assembly, Genes & Development: 24(7): 647-52
Highlighted article: Kim JH and Workman JL, Histone acetylation in heterochromatin assembly (2010) Genes & Development, 2010 Apr 15; 24(7): 738-40
2007
Xhemalce B, Miller KM, Driscoll R, Masumoto H, Jackson SP, Kouzarides T, Verreault A and Arcangioli B, Regulation of histone H3 lysine 56 acetylation in Schizosaccharomyces pombe, JBC: 282: 15040-15047
Xhemalce B, Madi Riising E, Baumann P, Thon G, Dejean A, Arcangioli B and Seeler JS, Role of SUMO in the Dynamics of Telomere Maintenance in Fission Yeast, PNAS: 104(3): 893-8
2004
Xhemalce B, Seeler JS, Thon G, Dejean A and Arcangioli B, Role of the Fission Yeast SUMO E3 Ligase Pli1p in Centromere and Telomere Maintenance, EMBO Journal: 23, 3844-3853