Sundarraj J., Patel M., Aziz H., Brooke G., Tummala H., Pradeepa MM* PSIP1/LEDGF reduces R-loops at transcription sites to maintain genome integrity Nature Communications 15, 361(2024) https://doi.org/10.1038/s41467-023-44544-w
Pal, D., Patel M., Boulet F., Sundarraj J., Grant OA., Branco MR., Basu S., Santos S., Zabet, N R., Scaffidi, P., Pradeepa, MM* H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function Nature Struct. Mol. Biol. 2023 https://rdcu.be/deluI
Patel MB, Maniati E, Atanur SS, Pal D, Rio-Machin A, Heward J, Fitzgibbon J, Pradeepa MM* & Wang J* Non-coding mutations at enhancer clusters contribute to pancreatic ductal adenocarcinoma BioRxiv 2023.06.28.546873; doi: https://doi.org/10.1101/2023.06.28.546873
De Vas MG, Boulet F. Garstang MG, Joshi SS, Khan TN, Atla G, Parry D, Moore D, Cebola I, Zhang S, Cui W, Lampe A K, Lam WW, Genomics England Consortium, Ferrer J, Pradeepa MM*, Atanur SS* Regulatory de novo mutations underlying intellectual disability Life Science Alliance 2023. DOI:10.26508/lsa.202201843.
· Tummala H, Walne A, Buccafusca R, Alnajar J, Szabo A, Robinson P, McConkie-Rosell A, Wilson M, Crowley S, Kinsler V, Ewins AM, Pradeepa MM, Patel M, Pontikos N, Codd V, Vulliamy T, Dokal I. Germline thymidylate synthase deficiency impacts nucleotide metabolism and causes dyskeratosis congenita. Am J Hum Genet. 2022 Aug 4;109(8):1472-1483.
· Rodriguez-Algarra F, Seaborne RAE, Danson AF, Yildizoglu S, Yoshikawa H, Law PP, Ahmad Z, Maudsley VA, Brew A, Holmes N, Ochôa M, Hodgkinson A, Marzi SJ, Pradeepa MM, Loose M, Holland ML, Rakyan VK. Genetic variation at mouse and human ribosomal DNA influences associated epigenetic states. Genome Biol. 2022 Feb 14;23(1):54.
· Olley G, Pradeepa MM, Grimes GR, Piquet S, Polo SE, FitzPatrick DR, Bickmore WA, Boumendil C. Cornelia de Lange syndrome-associated mutations cause a DNA damage signalling and repair defect. Nat Commun. 2021 May 25;12(1):3127.
· Olley G, Ansari M, Bengani H, Grimes GR, Rhodes J, Kriegsheim AV, Blatnik A, Stewart F J, Ross A, Bickmore WA*, Pradeepa MM*, and FitzPatrick DR*. BRD4 interacts with NIPBL and is mutated in a Cornelia de Lange-like syndrome. Nature Genet. 2018. 50 (3), 329-332
· Marin R#, Cortez D#, Lamanna F#, Pradeepa MM#, Leushkin E, Julien P, Liechti A, Halbert J, Kerver HN, Wade J, Tschopp P and Kaessmann H (2017) Convergent origination of a Drosophila-like dosage compensation mechanism in a reptile lineage Genome Res, 27 (12), 1974-1987
· Pradeepa MM*, Taylor GCA, and Kriegsheim AV. Proteomic analysis of H3K36me3 and PSIP1/p75 (LEDGF) complexes show their wider role in DNA repair 2017 Wellcome Open Res https://doi.org/10.12688/wellcomeopenres.11589.2
· Pradeepa M M*, McKenna F, Taylor GCA, Bengani H, Grimes GR, Wood A, Bhatia S, and Bickmore W A*. (2017) Psip1/p52 regulates distal Hoxa genes through activation of lncRNA Hottip PLoS Genet 13, e1006677 (2017).
· A perspective article highlighting this work is published in PLoS Genet 13(6): e1006797.
· Pradeepa M M*, Grimes G, Kumar Y, Taylor G, Olley G, Schneider R and Bickmore W A* (2016) Histone H3 globular domain acetylation identifies a new class of enhancers. Nature Genet. 48, 681–686 doi:10.1038/ng.3550.
· Illingworth R S, Moffat M, Mann A R, Read D, Hunter C J, Pradeepa M M, Adams I R & Bickmore W A (2015) The E3 ubiquitin ligase activity of Ring1B is not essential for early mouse development Genes and Dev 29: 1897-1902.
· Gupta N, Pradeepa M M, Bhat U A, Rao M R S (2015) Mapping of post-translational modifications of transition Proteins, TP1 and TP2, and identification of protein arginine methyltransferase 4 and lysine Methyltransferase 7 as methyltransferase for TP2. J Biol Chem. 290 (19), 12101-22.
· Pradeepa M M*, Grimes G, Taylor G, Sutherland H & Bickmore W A*. (2014) Psip1/p75 restrains expression of Hox genes by recruiting both trithorax and polycomb proteins. Nucleic Acid Res. DOI: 10.1093/nar/gku647.
· Taylor G, Eskeland R. Balkan B H, Pradeepa M M* & Bickmore W A*. (2013) H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction. Genome Res. doi: 10.1101/gr.155028.113.
· Pradeepa, M M., Sutherland, H. G., Ule, J., Grimes, G. R., & Bickmore, W. A. (2012). Psip1/Ledgf p52 binds methylated histone H3K36 and splicing factors and contributes to the regulation of alternative splicing. PLoS genetics, 8(5), e1002717. doi:10.1371.
· Ullas K S#, Pradeepa M M#, Nikhil G, Rammohan N, & Rao M R. (2009). Spatiotemporal organization of AT and GC rich DNA and their association with transition proteins TP1 and TP2 in rat condensing spermatids. J Histochem Cytochem. DOI:10.1369/jhc.2009.953414.
· Pradeepa M M, Nikhil G, Hari Kishore A, Bharath G N, Kundu T K, & Rao M R. (2009) Acetylation of transition protein 2 (TP2) by KAT3B (p300) alters its DNA condensation property and interaction with putative histone chaperone NPM3. J Biol Chem. 284(43):29956-67.
· Pradeepa M M, Manjunatha S, Sathish V, Agrawal S, & Rao M R. (2008). Involvement of importin-4 in the transport of transition protein 2 into the spermatid nucleus. Mol Cell Biol. 2008; 28(1):4331-41.
· Reviews
· Garstang M and Pradeepa MM (2018) An Enhancer-Derived RNA Muscles In to Regulate Myogenin In trans Molecular Cell 71 (1), 3-5
· Pradeepa M M (2017) Histone modifications and their importance in enhancer function, Transcription invited review, 8 (1), 40-47
· Pradeepa M M, & Rao M R. Chromatin remodeling during mammalian spermatogenesis: role of testis specific histone variants and transition proteins. Soc Reprod Fertl Suppl. 2007;63:1-10. (book chapter)