Research outputs
2025
The 7SK small nuclear ribonucleoprotein links the cell responses to transcription and replication stress by promoting replication fork reversal and homologous recombination
Human RNase H2 upregulation counteracts oncogene- and chemotherapy-induced replication stress
Wilkins, R. J., Kannan, A., Plass, S. A., Wilson, C., Kelly, R. D. W., Tang, C. H. M., . . . Petermann, E. (2025). Human RNase H2 upregulation counteracts oncogene- and chemotherapy-induced replication stress. ONCOGENE, 44(35), 3255-3271. doi:10.1038/s41388-025-03489-8
Deletion of 17p in cancers: Guilt by (p53) association
van Kampen, F., Clark, A., Soul, J., Kanhere, A., Glenn, M. A., Pettitt, A. R., . . . Slupsky, J. R. (2025). Deletion of 17p in cancers: Guilt by (p53) association. Oncogene. doi:10.1038/s41388-025-03300-8
2024
Human RNase H2 upregulation counteracts oncogene- and chemotherapy-induced replication stress
Gender-different effect of Src family kinases antagonism on photophobia and trigeminal ganglion activity
Huang, Z., Yao, J., Nie, L., Nie, X., Xiong, X., Koks, S., . . . Wang, M. (2024). Gender-different effect of Src family kinases antagonism on photophobia and trigeminal ganglion activity. JOURNAL OF HEADACHE AND PAIN, 25(1). doi:10.1186/s10194-024-01875-3
Natural antisense transcripts as versatile regulators of gene expression
Werner, A., Kanhere, A., Wahlestedt, C., & Mattick, J. S. (2024). Natural antisense transcripts as versatile regulators of gene expression. NATURE REVIEWS GENETICS, 25(10), 730-744. doi:10.1038/s41576-024-00723-z
2023
Site-Directed Mutagenesis Protocol to Determine the Role of Amino Acid Residues in Polycomb Group (PcG) Protein Function.
Al-Raawi, D., & Kanhere, A. (2023). Site-Directed Mutagenesis Protocol to Determine the Role of Amino Acid Residues in Polycomb Group (PcG) Protein Function.. Methods in molecular biology (Clifton, N.J.), 2655, 79-89. doi:10.1007/978-1-0716-3143-0_7
2021
Antisense RNAs during early vertebrate development are divided in groups with distinct features
Pillay, S., Takahashi, H., Carninci, P., & Kanhere, A. (2021). Antisense RNAs during early vertebrate development are divided in groups with distinct features. GENOME RESEARCH, 31(6), 995-1010. doi:10.1101/gr.262964.120
The Missing Link Between Cancer-Associated Variants and LncRNAs
Wilson, C., & Kanhere, A. (2021). The Missing Link Between Cancer-Associated Variants and LncRNAs. TRENDS IN GENETICS, 37(5), 410-413. doi:10.1016/j.tig.2021.01.010
A long intergenic non-coding RNA regulates nuclear localization of DNA methyl transferase-1
Jones, R., Wijesinghe, S., Wilson, C., Halsall, J., Liloglou, T., & Kanhere, A. (2021). A long intergenic non-coding RNA regulates nuclear localization of DNA methyl transferase-1. ISCIENCE, 24(4). doi:10.1016/j.isci.2021.102273
8q24.21 Locus: A Paradigm to Link Non-Coding RNAs, Genome Polymorphisms and Cancer
Wilson, C., & Kanhere, A. (2021). 8q24.21 Locus: A Paradigm to Link Non-Coding RNAs, Genome Polymorphisms and Cancer. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 22(3). doi:10.3390/ijms22031094
Combined transcriptomic and phosphoproteomic analysis of BMP4 signaling in human embryonic stem cells
Papadopoulos, A., Chalmantzi, V., Mikhaylichenko, O., Hyvonen, M., Stellas, D., Kanhere, A., . . . Murphy, C. (2021). Combined transcriptomic and phosphoproteomic analysis of BMP4 signaling in human embryonic stem cells. STEM CELL RESEARCH, 50. doi:10.1016/j.scr.2020.102133
2020
Autoregulation of JARID2 through PRC2 interaction with its antisense ncRNA
Al Raawi, D., & Kanhere, A. (2020). Autoregulation of JARID2 through PRC2 interaction with its antisense ncRNA. BMC Research Notes, 13. doi:10.1186/s13104-020-05348-z
Functional annotation of human long noncoding RNAs via molecular phenotyping (vol 30, pg 1060, 2020)
Ramilowski, J. A., Yip, C. W., Agrawal, S., Chang, J. -C., Ciani, Y., Kulakovskiy, I. V., . . . Carninci, P. (2020). Functional annotation of human long noncoding RNAs via molecular phenotyping (vol 30, pg 1060, 2020). GENOME RESEARCH, 30(9), 1377. doi:10.1101/gr.270330.120
Functional annotation of human long noncoding RNAs via molecular phenotyping
Ramilowski, J. A., Yip, C. W., Agrawal, S., Chang, J. -C., Ciani, Y., Kulakovskiy, I. V., . . . Carninci, P. (2020). Functional annotation of human long noncoding RNAs via molecular phenotyping. GENOME RESEARCH, 30(7), 1060-1072. doi:10.1101/gr.254219.119
A long intergenic non-coding RNA regulates nuclear localisation of DNA methyl transferase-1
Jones, R., Wijesinghe, S., Halsall, J., & Kanhere, A. (2020). A long intergenic non-coding RNA regulates nuclear localisation of DNA methyl transferase-1. doi:10.1101/2020.03.11.985705
Antisense ncRNAs during early vertebrate development are divided in groups with distinct features
Pillay, S., Takahashi, H., Carninci, P., & Kanhere, A. (2020). Antisense ncRNAs during early vertebrate development are divided in groups with distinct features. doi:10.1101/2020.02.08.940148
2019
Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping
Ramilowski, J. A., Yip, C. W., Agrawal, S., Chang, J. -C., Ciani, Y., Kulakovskiy, I. V., . . . Carninci, P. (2019). Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping. doi:10.1101/700864
A novel form of JARID2 is required for differentiation in lineage-committed cells
Al-Raawi, D., Jones, R., Wijesinghe, S., Halsall, J., Petric, M., Roberts, S., . . . Kanhere, A. (2019). A novel form of JARID2 is required for differentiation in lineage-committed cells. The EMBO Journal, 38(3). doi:10.15252/embj.201798449
2018
Regulation of Leukocytes by TspanC8 Tetraspanins and the "Molecular Scissor" ADAM10
Matthews, A. L., Koo, C. Z., Szyroka, J., Harrison, N., Kanhere, A., & Tomlinson, M. G. (2018). Regulation of Leukocytes by TspanC8 Tetraspanins and the "Molecular Scissor" ADAM10. FRONTIERS IN IMMUNOLOGY, 9. doi:10.3389/fimmu.2018.01451
2017
Exercise and high-fat feeding remodel transcript-metabolite interactive networks in mouse skeletal muscle
Perez-Schindler, J., Kanhere, A., Edwards, L., Allwood, J. W., Dunn, W. B., Schenk, S., & Philp, A. (2017). Exercise and high-fat feeding remodel transcript-metabolite interactive networks in mouse skeletal muscle. SCIENTIFIC REPORTS, 7. doi:10.1038/s41598-017-14081-w
2016
Exon junction complex proteins bind nascent transcripts independently of pre-mRNA splicing in Drosophila melanogaster
Choudhury, S. R., Singh, A. K., McLeod, T., Blanchette, M., Jang, B., Badenhorst, P., . . . Brogna, S. (2016). Exon junction complex proteins bind nascent transcripts independently of pre-mRNA splicing in Drosophila melanogaster. Elife, 5. doi:10.7554/eLife.19881
Identification of RNA-Protein Interactions Through In Vitro RNA Pull-Down Assays
Barnes, C., & Kanhere, A. (2016). Identification of RNA-Protein Interactions Through In Vitro RNA Pull-Down Assays. POLYCOMB GROUP PROTEINS: METHODS AND PROTOCOLS, 1480, 99-113. doi:10.1007/978-1-4939-6380-5_9
2013
Genome-Wide Regulatory Analysis Reveals That T-bet Controls Th17 Lineage Differentiation through Direct Suppression of IRF4
Goekmen, M. R., Dong, R., Kanhere, A., Powell, N., Perucha, E., Jackson, I., . . . Lord, G. M. (2013). Genome-Wide Regulatory Analysis Reveals That T-bet Controls Th17 Lineage Differentiation through Direct Suppression of IRF4. JOURNAL OF IMMUNOLOGY, 191(12), 5925-5932. doi:10.4049/jimmunol.1202254
Modulation of Enhancer Looping and Differential Gene Targeting by Epstein-Barr Virus Transcription Factors Directs Cellular Reprogramming
McClellan, M. J., Wood, C. D., Ojeniyi, O., Cooper, T. J., Kanhere, A., Arvey, A., . . . West, M. J. (2013). Modulation of Enhancer Looping and Differential Gene Targeting by Epstein-Barr Virus Transcription Factors Directs Cellular Reprogramming. PLOS PATHOGENS, 9(9). doi:10.1371/journal.ppat.1003636
2012
T-bet and GATA3 orchestrate Th1 and Th2 differentiation through lineage-specific targeting of distal regulatory elements.
Kanhere, A. S. (2012). T-bet and GATA3 orchestrate Th1 and Th2 differentiation through lineage-specific targeting of distal regulatory elements.. Nature Communications. doi:10.1038/ncomms2260
Genome-Wide Analyses of Zta Binding to the Epstein-Barr Virus Genome Reveals Interactions in both Early and Late Lytic Cycles and an Epigenetic Switch Leading to an Altered Binding Profile
Ramasubramanyan, S., Kanhere, A., Osborn, K., Flower, K., Jenner, R. G., & Sinclair, A. J. (2012). Genome-Wide Analyses of Zta Binding to the Epstein-Barr Virus Genome Reveals Interactions in both Early and Late Lytic Cycles and an Epigenetic Switch Leading to an Altered Binding Profile. JOURNAL OF VIROLOGY, 86(23), 12494-12502. doi:10.1128/JVI.01705-12
Downregulation of Integrin Receptor-Signaling Genes by Epstein-Barr Virus EBNA 3C via Promoter-Proximal and -Distal Binding Elements
McClellan, M. J., Khasnis, S., Wood, C. D., Palermo, R. D., Schlick, S. N., Kanhere, A. S., . . . West, M. J. (2012). Downregulation of Integrin Receptor-Signaling Genes by Epstein-Barr Virus EBNA 3C via Promoter-Proximal and -Distal Binding Elements. JOURNAL OF VIROLOGY, 86(9), 5165-5178. doi:10.1128/JVI.07161-11
Noncoding RNA localisation mechanisms in chromatin regulation.
Kanhere, A., & Jenner, R. G. (2012). Noncoding RNA localisation mechanisms in chromatin regulation.. Silence, 3(1), 2. doi:10.1186/1758-907x-3-2
T-bet and GATA3 orchestrate Th1 and Th2 differentiation through lineage-specific targeting of distal regulatory elements
Kanhere, A., Hertweck, A., Bhatia, U., Goekmen, M. R., Perucha, E., Jackson, I., . . . Jenner, R. G. (2012). T-bet and GATA3 orchestrate Th1 and Th2 differentiation through lineage-specific targeting of distal regulatory elements. NATURE COMMUNICATIONS, 3. doi:10.1038/ncomms2260
2011
IL-2 Regulates Expression of <i>C</i>-<i>MAF</i> in Human CD4 T Cells
Rani, A., Afzali, B., Kelly, A., Tewolde-Berhan, L., Hackett, M., Kanhere, A. S., . . . John, S. (2011). IL-2 Regulates Expression of <i>C</i>-<i>MAF</i> in Human CD4 T Cells. JOURNAL OF IMMUNOLOGY, 187(7), 3721-3729. doi:10.4049/jimmunol.1002354
2010
Short RNAs Are Transcribed from Repressed Polycomb Target Genes and Interact with Polycomb Repressive Complex-2
Kanhere, A., Viiri, K., Araujo, C. C., Rasaiyaah, J., Bouwman, R. D., Whyte, W. A., . . . Jenner, R. G. (2010). Short RNAs Are Transcribed from Repressed Polycomb Target Genes and Interact with Polycomb Repressive Complex-2. MOLECULAR CELL, 38(5), 675-688. doi:10.1016/j.molcel.2010.03.019
2009
CpG-depleted promoters harbor tissue-specific transcription factor binding signals-implications for motif overrepresentation analyses
Roider, H. G., Lenhard, B., Kanhere, A., Haas, S. A., & Vingron, M. (2009). CpG-depleted promoters harbor tissue-specific transcription factor binding signals-implications for motif overrepresentation analyses. NUCLEIC ACIDS RESEARCH, 37(19), 6305-6315. doi:10.1093/nar/gkp682
Horizontal Gene Transfers in prokaryotes show differential preferences for metabolic and translational genes
Kanhere, A., & Vingron, M. (2009). Horizontal Gene Transfers in prokaryotes show differential preferences for metabolic and translational genes. BMC EVOLUTIONARY BIOLOGY, 9. doi:10.1186/1471-2148-9-9
2007
Predicting transcription factor affinities to DNA from a biophysical model
Roider, H. G., Kanhere, A., Manke, T., & Vingron, M. (2007). Predicting transcription factor affinities to DNA from a biophysical model. BIOINFORMATICS, 23(2), 134-141. doi:10.1093/bioinformatics/btl565
2005
Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes
Kanhere, A., & Bansal, M. (2005). Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes. NUCLEIC ACIDS RESEARCH, 33(10), 3165-3175. doi:10.1093/nar/gki627
A novel method for prokaryotic promoter prediction based on DNA stability - art. no. 1
Kanhere, A., & Bansal, M. (2005). A novel method for prokaryotic promoter prediction based on DNA stability - art. no. 1. BMC BIOINFORMATICS, 6. doi:10.1186/1471-2105-6-1
2003
Identification of the domains for DNA binding and transactivation function of C protein from bacteriophage Mu
Paul, B. D., Kanhere, A., Chakraborty, A., Bansal, M., & Nagaraja, V. (2003). Identification of the domains for DNA binding and transactivation function of C protein from bacteriophage Mu. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 52(2), 272-282. doi:10.1002/prot.10413
An assessment of three dinucleotide parameters to predict DNA curvature by quantitative comparison with experimental data
Kanhere, A., & Bansal, M. (2003). An assessment of three dinucleotide parameters to predict DNA curvature by quantitative comparison with experimental data. NUCLEIC ACIDS RESEARCH, 31(10), 2647-2658. doi:10.1093/nar/gkg362