Publications
GOOGLE SCHOLAR
Selected Publications:
Xhemalçe B, Miller KM and Gromak N. 2024. Epitranscriptome in action: RNA modifications in the DNA damage response. 2024.
Molecular Cell 2024 84, 3610-3626, Oct 3
Ipas H, Gouws EB, Abell NS, Chiou PC, Devanathan SK, Lee S, Mercado M, Reinsborough CW, Hervé S, Halabelian L, Arrowsmith CH and Xhemalçe B. 2024. ChemRAP uncovers specific mRNA translation regulation via RNA 5' phospho-methylation. EMBO Reports 2024 Mar;25(3):1570-1588
Reinsborough CR, Ipas H, Abell NS, Gouws EB, Williams JP, Mercado M, Van Den Berg C and Xhemalçe B. 2021. BCDIN3D RNA methyltransferase stimulates Aldolase C expression and glycolysis through let-7 microRNA in breast cancer cells. Oncogene 2021 Apr;40(13):2395-2406
Reinsborough CW, Ipas H, Abell NS, Nottingham RM, Yao J, Devanathan SK, Shelton SB, Lambowitz AM and Xhemalçe B. 2019.
BCDIN3D regulates tRNA-His 3’ fragment processing. PLOS Genetics 2019 Jul 22;15(7):e1008273
Shelton SB, Shah NM, Abell NS, Mercado M, Devanathan SK and Xhemalçe B. 2018. Crosstalk between the RNA methylation and histone binding activities of MePCE regulates P-TEFb activation on chromatin. Cell Reports 2018 Feb 6;22(6):1374-1383
Abell NS, Mercado M, Caneque T, Rodriguez R and Xhemalçe B. 2017. Click-qMS identifies PIWIL3 as a mechanistic target of RNA interference activator enoxacin in cancer cells. J Am Chem Soc 2017 Jun 1;56(23):6483-6487
Xhemalçe B, Robson SC and Kouzarides T. 2012. Human RNA methyltransferase BCDIN3D regulates microRNA processing. Cell 2012 Oct 12;151(2):278-88
Highlighted article: David R, Small RNAs: Controlling maturity. 2012. Nature Reviews Molecular Cell Biology 2012 13, 752-753
Other Publications:
Buffington JD, Kuo HC, Hu K, Chang YC, Javanmardi K, Voigt B, Li YR, Little M, Devanathan SK, Xhemalçe B, Gray R, and Finkelstein IJ. 2024. Discovery and Engineering of Retrons for Precise Genome Editing, Manuscript under review, for preprint see:
https://www.biorxiv.org/content/10.1101/2024.07.21.604473v1.
Sutjita P, Musalgaonkar S, Recchia-Rife J, Huang L, Xhemalçe B and Johnson AW. 2024. The Ribosome Assembly Factor LSG1 Interacts with Vesicle-Associated Membrane Protein-Associated Proteins (VAPs). Molecular and Cellular Biology 2024 Aug 12:1-13.
Xhemalçe B. RNA modifiers multitasking on chromatin. 2022. FASEB J, 2022, May 13; Volume 36, Issue S1
McFadden MJ, McIntyre ABR, Mourelatos H, Abell NS, Gokhale NS, Ipas H, Xhemalçe B, Mason CE, Horner SM. 2021. Post-transcriptional regulation of antiviral gene expression by N6-methyladenosine. Cell Reports 2021 March 2
Kumbhar R, Sanchez A, Perren J, Gong F, Corujo D, Medina F, Devanathan SK, Xhemalce B, Matouschek A, Buschbeck M, Buck-Koehntop B, Miller KM. 2021. Poly(ADP-ribose)-binding and macroH2A mediate recruitment and functions of KDM5A at DNA lesions. Journal of Cell Biology 2021 May 18
Xhemalçe B, 2021. Editorial of Special Issue on "Biological functions of RNA modifications". Briefings in Functional Genomics Mar 22.
Debnath TK and Xhemalçe B. 2021. Deciphering RNA modifications at Base Resolution: From Chemistry to Biology. Briefings in Functional Genomics Jan 18.
Devanathan SK, Debnath TK and Xhemalçe B. 2021. Facile detection of RNA phospho-methylation in cells and tissues. Methods in Enzymology: RNA modification enzymes.
Kim JJ, Lee S, Choi JH, Woo HG, Xhemalçe B and Miller KM. 2020. 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, Xhemalçe B and Miller KM. 2020. Making it or Breaking it: DNA methylation and Genome Integrity. Essays in Biochemistry Oct 26;64(5):687-703.
Shelton SB, Xhemalçe B. Antibody-Free Assay for RNA Methyltransferase Activity Analysis. 2019. J. Vis. Exp. (149), e59856
Kim JJ, Lee S, Gong F, Battenhouse AM, Boutz DR, Bashyal A, Refvik ST, Chiang CM, Xhemalçe 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 33: 1751-1774
Bryant JD, Sweeney SR, Sentrandreu E, Shin M, Ipas H, Xhemalçe B, Momb J, Tiziani S and Appling DR. 2018. 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
Zacharioudakis E, Agarwal P, Bartoli A, Abell NS, Kunalingam L, Xhemalçe B, Miller KM, and Rodriguez, R. 2017. Chromatin regulates genome targeting with cisplatin. Angewandte Chemie 2017 May 5
Shelton SB, Reinsborough CW and Xhemalçe B. 2016. Who watches the watchmen: Roles of RNA modifications in the RNA interference Pathway, [Invited review] PLOS Genetics 2016 Jul 21;12(7)
Chen W, Ebelt ND, Stracker TH, Xhemalçe B, Van Den Berg CL & Miller KM. 2015. ATM regulation of IL-8 links oxidative stress to cancer cell migration and invasion, eLife 2015;10.7554/eLife.07270
Spivey EC, Xhemalçe B, Shear JB and Finkelstein IJ. 2014. A 3D-Printed Microfluidic Microdissector for High-Throughput Studies of Cellular Aging, Analytical Chemistry, 86(15):7406-12
Xhemalçe B. 2013. 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
Dawson MA, Foster SD, Bannister AJ, Robson SC, Wang X, Xhemalçe B, Wood AD, Green AR, Göttgens B and Kouzarides T. 2012. Three distinct patterns of histone H3Y41 phosphorylation mark active genes, Cell Reports 2012 2(3):470-7
Rodriguez R, Miller KM, Forment JV, Bradshaw CR, Nikan M, Xhemalçe B, Balasubramanian S and Jackson SP. 2012. Small molecule induced DNA damage identifies druggable, alternatively-structured DNA sites, Nature Chemical Biology 8(3):225-6
Xhemalçe B, Dawson MA and Bannister AJ. 2011. [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
Bartke T, Vermeulen M, Xhemalçe B, Robson SC, Mann M, Kouzarides T, Nucleosome-Interacting Proteins Regulated by DNA and Histone Methylation. 2010. Cell Vol. 143, Issue 3, pp. 470-484
Xhemalçe B and Kouzarides T. 2010. 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
Xhemalçe B, Miller KM, Driscoll R, Masumoto H, Jackson SP, Kouzarides T, Verreault A and Arcangioli B. 2007. Regulation of histone H3 lysine 56 acetylation in Schizosaccharomyces pombe, JBC: 282: 15040-15047
Xhemalçe B, Madi Riising E, Baumann P, Thon G, Dejean A, Arcangioli B and Seeler JS. 2007. Role of SUMO in the Dynamics of Telomere Maintenance in Fission Yeast, PNAS: 104(3): 893-8
Xhemalçe B, Seeler JS, Thon G, Dejean A and Arcangioli B. 2004. Role of the Fission Yeast SUMO E3 Ligase Pli1p in Centromere and Telomere Maintenance, EMBO Journal: 23, 3844-3853
Selected Publications:
Xhemalçe B, Miller KM and Gromak N. 2024. Epitranscriptome in action: RNA modifications in the DNA damage response. 2024.
Molecular Cell 2024 84, 3610-3626, Oct 3
Ipas H, Gouws EB, Abell NS, Chiou PC, Devanathan SK, Lee S, Mercado M, Reinsborough CW, Hervé S, Halabelian L, Arrowsmith CH and Xhemalçe B. 2024. ChemRAP uncovers specific mRNA translation regulation via RNA 5' phospho-methylation. EMBO Reports 2024 Mar;25(3):1570-1588
Reinsborough CR, Ipas H, Abell NS, Gouws EB, Williams JP, Mercado M, Van Den Berg C and Xhemalçe B. 2021. BCDIN3D RNA methyltransferase stimulates Aldolase C expression and glycolysis through let-7 microRNA in breast cancer cells. Oncogene 2021 Apr;40(13):2395-2406
Reinsborough CW, Ipas H, Abell NS, Nottingham RM, Yao J, Devanathan SK, Shelton SB, Lambowitz AM and Xhemalçe B. 2019.
BCDIN3D regulates tRNA-His 3’ fragment processing. PLOS Genetics 2019 Jul 22;15(7):e1008273
Shelton SB, Shah NM, Abell NS, Mercado M, Devanathan SK and Xhemalçe B. 2018. Crosstalk between the RNA methylation and histone binding activities of MePCE regulates P-TEFb activation on chromatin. Cell Reports 2018 Feb 6;22(6):1374-1383
Abell NS, Mercado M, Caneque T, Rodriguez R and Xhemalçe B. 2017. Click-qMS identifies PIWIL3 as a mechanistic target of RNA interference activator enoxacin in cancer cells. J Am Chem Soc 2017 Jun 1;56(23):6483-6487
Xhemalçe B, Robson SC and Kouzarides T. 2012. Human RNA methyltransferase BCDIN3D regulates microRNA processing. Cell 2012 Oct 12;151(2):278-88
Highlighted article: David R, Small RNAs: Controlling maturity. 2012. Nature Reviews Molecular Cell Biology 2012 13, 752-753
Other Publications:
Buffington JD, Kuo HC, Hu K, Chang YC, Javanmardi K, Voigt B, Li YR, Little M, Devanathan SK, Xhemalçe B, Gray R, and Finkelstein IJ. 2024. Discovery and Engineering of Retrons for Precise Genome Editing, Manuscript under review, for preprint see:
https://www.biorxiv.org/content/10.1101/2024.07.21.604473v1.
Sutjita P, Musalgaonkar S, Recchia-Rife J, Huang L, Xhemalçe B and Johnson AW. 2024. The Ribosome Assembly Factor LSG1 Interacts with Vesicle-Associated Membrane Protein-Associated Proteins (VAPs). Molecular and Cellular Biology 2024 Aug 12:1-13.
Xhemalçe B. RNA modifiers multitasking on chromatin. 2022. FASEB J, 2022, May 13; Volume 36, Issue S1
McFadden MJ, McIntyre ABR, Mourelatos H, Abell NS, Gokhale NS, Ipas H, Xhemalçe B, Mason CE, Horner SM. 2021. Post-transcriptional regulation of antiviral gene expression by N6-methyladenosine. Cell Reports 2021 March 2
Kumbhar R, Sanchez A, Perren J, Gong F, Corujo D, Medina F, Devanathan SK, Xhemalce B, Matouschek A, Buschbeck M, Buck-Koehntop B, Miller KM. 2021. Poly(ADP-ribose)-binding and macroH2A mediate recruitment and functions of KDM5A at DNA lesions. Journal of Cell Biology 2021 May 18
Xhemalçe B, 2021. Editorial of Special Issue on "Biological functions of RNA modifications". Briefings in Functional Genomics Mar 22.
Debnath TK and Xhemalçe B. 2021. Deciphering RNA modifications at Base Resolution: From Chemistry to Biology. Briefings in Functional Genomics Jan 18.
Devanathan SK, Debnath TK and Xhemalçe B. 2021. Facile detection of RNA phospho-methylation in cells and tissues. Methods in Enzymology: RNA modification enzymes.
Kim JJ, Lee S, Choi JH, Woo HG, Xhemalçe B and Miller KM. 2020. 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, Xhemalçe B and Miller KM. 2020. Making it or Breaking it: DNA methylation and Genome Integrity. Essays in Biochemistry Oct 26;64(5):687-703.
Shelton SB, Xhemalçe B. Antibody-Free Assay for RNA Methyltransferase Activity Analysis. 2019. J. Vis. Exp. (149), e59856
Kim JJ, Lee S, Gong F, Battenhouse AM, Boutz DR, Bashyal A, Refvik ST, Chiang CM, Xhemalçe 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 33: 1751-1774
Bryant JD, Sweeney SR, Sentrandreu E, Shin M, Ipas H, Xhemalçe B, Momb J, Tiziani S and Appling DR. 2018. 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
Zacharioudakis E, Agarwal P, Bartoli A, Abell NS, Kunalingam L, Xhemalçe B, Miller KM, and Rodriguez, R. 2017. Chromatin regulates genome targeting with cisplatin. Angewandte Chemie 2017 May 5
Shelton SB, Reinsborough CW and Xhemalçe B. 2016. Who watches the watchmen: Roles of RNA modifications in the RNA interference Pathway, [Invited review] PLOS Genetics 2016 Jul 21;12(7)
Chen W, Ebelt ND, Stracker TH, Xhemalçe B, Van Den Berg CL & Miller KM. 2015. ATM regulation of IL-8 links oxidative stress to cancer cell migration and invasion, eLife 2015;10.7554/eLife.07270
Spivey EC, Xhemalçe B, Shear JB and Finkelstein IJ. 2014. A 3D-Printed Microfluidic Microdissector for High-Throughput Studies of Cellular Aging, Analytical Chemistry, 86(15):7406-12
Xhemalçe B. 2013. 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
Dawson MA, Foster SD, Bannister AJ, Robson SC, Wang X, Xhemalçe B, Wood AD, Green AR, Göttgens B and Kouzarides T. 2012. Three distinct patterns of histone H3Y41 phosphorylation mark active genes, Cell Reports 2012 2(3):470-7
Rodriguez R, Miller KM, Forment JV, Bradshaw CR, Nikan M, Xhemalçe B, Balasubramanian S and Jackson SP. 2012. Small molecule induced DNA damage identifies druggable, alternatively-structured DNA sites, Nature Chemical Biology 8(3):225-6
Xhemalçe B, Dawson MA and Bannister AJ. 2011. [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
Bartke T, Vermeulen M, Xhemalçe B, Robson SC, Mann M, Kouzarides T, Nucleosome-Interacting Proteins Regulated by DNA and Histone Methylation. 2010. Cell Vol. 143, Issue 3, pp. 470-484
Xhemalçe B and Kouzarides T. 2010. 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
Xhemalçe B, Miller KM, Driscoll R, Masumoto H, Jackson SP, Kouzarides T, Verreault A and Arcangioli B. 2007. Regulation of histone H3 lysine 56 acetylation in Schizosaccharomyces pombe, JBC: 282: 15040-15047
Xhemalçe B, Madi Riising E, Baumann P, Thon G, Dejean A, Arcangioli B and Seeler JS. 2007. Role of SUMO in the Dynamics of Telomere Maintenance in Fission Yeast, PNAS: 104(3): 893-8
Xhemalçe B, Seeler JS, Thon G, Dejean A and Arcangioli B. 2004. Role of the Fission Yeast SUMO E3 Ligase Pli1p in Centromere and Telomere Maintenance, EMBO Journal: 23, 3844-3853