Key publications

GENE REGULATORY MECHANISMS UNDERLYING BRAIN DEVELOPMENT AND ITS DISRUPTION IN NEUROLOGICAL DISORDERS

Dwivedi A, Mahesh A, Sanfeliu A, Larkin J, Siwicki R, Sweeney KJ, O'Brien DF, Widdess-Walsh P, Picelli S, Henshall DC, Tiwari VK. High-resolution multimodal profiling of human epileptic brain activity via explanted depth electrodes. JCI Insight. 2024 Nov 14:e184518. doi: 10.1172/jci.insight.184518. Online ahead of print. PMID: 39541170

Singh A, Del-Valle-Anton L, de Juan Romero C, Zhang Z, Ortuño EF, Mahesh A, Espinós A, Soler R, Cárdenas A, Fernández V, Lusby R, Tiwari VK*, Borrell V* (*co-corresponding authors). Gene regulatory landscape of cerebral cortex folding. Sci Adv. 2024 Jun 7;10(23):eadn1640. doi: 10.1126/sciadv.adn1640. Epub 2024 Jun 5. PMID: 38838158; PMCID: PMC11152136.

de la Fuente AG, Dittmer M, Heesbeen EJ, de la Vega Gallardo N, White JA, Young A, McColgan T, Dashwood A, Mayne K, Cabeza-Fernández S, Falconer J, Rodriguez-Baena FJ, McMurran CE, Inayatullah M, Rawji KS, Franklin RJM, Dooley J, Liston A, Ingram RJ, Tiwari VK, Penalva R, Dombrowski Y, Fitzgerald DC. Ageing impairs the regenerative capacity of regulatory T cells in mouse central nervous system remyelination. Nat Commun. 2024 Mar 11;15(1):1870. doi: 10.1038/s41467-024-45742-w. PMID: 38467607; PMCID: PMC10928230.

Sahu SK, Agirre E, Inayatullah M, Mahesh A, Tiwari N, Lavin DP, Singh A, Strand S, Diken M, Luco RF, Belmonte JCI, Tiwari VK. A complex epigenome-splicing crosstalk governs epithelial-to-mesenchymal transition in metastasis and brain development. Nat Cell Biol. 2022 Aug;24(8):1265-1277. PMID: 35941369.

Camargo Ortega G, Falk S, Johansson PA, Peyre E, Broix L, Sahu SK, Hirst W, Schlichthaerle T, Tiwari VK, et al. The centrosome protein AKNA regulates neurogenesis via microtubule organization. Nature, 2019 Mar; 567(7746):113-117. PMID: 30787442.

Basu, Amitava, Iván Mestres, Sanjeeb Kumar Sahu, Neha Tiwari, Bimola Khongwir, Jan Baumgart, Aditi Singh, Federico Calegari, and Vijay K. Tiwari. "Phf21b imprints the spatiotemporal epigenetic switch essential for neural stem cell differentiation." Genes & Development 34, no. 17-18 (2020): 1190-1209.

Noack F, Pataskar A, Schneider M, Buchholz F, Tiwari VK, Calegari F. Direct Assessment and site-specific manipulation of DNA (hydroxy-)methylation during mouse corticogenesis. Life Sci Alliance. 2019 Feb 27;2(2). e201900331. PMID: 30814272; PMCID: PMC6394126.

Tiwari N, Pataskar A, Péron S, Thakurela S, Sahu SK, Figueres-Oñate M, Marichal N, López- Mascaraque L, Tiwari VK*, Berninger B* (*co-corresponding authors). Stage-Specific Transcription Factors Drive Astrogliogenesis by Remodeling Gene Regulatory Landscapes.

Cell Stem Cell, 2018, Oct 4; 23(4):557. PMID: 30290178; PMCID: PMC6179960.

Pataskar A, Jung J, Smialowski P, Calegari F, Straub T, Tiwari VK* (*corresponding author). NeuroD1 reprograms chromatin and transcription factor landscapes to induce the neuronal program. The EMBO Journal, 2016 Jan 4;35(1):24-45. PMID: 26516211; PMCID: PMC4718003.

Thakurela S, Sahu SK, Garding A, Tiwari VK* (*corresponding author). Dynamics and function of distal regulatory elements during neurogenesis and neuroplasticity. Genome Research, 2015 Sep;25(9):1309-24. PMID: 26170447; PMCID: PMC4561490.

Thakurela S, Garding A, Jung, Schübeler D, Burger L, Tiwari VK* (*corresponding author). Gene Regulation and Priming by Topoisomerase IIα in embryonic stem cells. Nature Communications, 2013, Sep 27; 4:2478. PMID: 24072229.

Tiwari VK*, Burger L, Nikoletopoulou V, Deogracious R, Thakurela S, Wirbelauer C, Hoerner L, Barde YA, Schübeler D* (*co-corresponding authors). Target genes of Topoisomerase IIbeta regulate neuronal survival and are defined by their chromatin state. PNAS, 2012 Apr 17;109(16):E934-43. PMID: 22474351 PMCID; PMC3340998.

Tiwari VK, Stadler M, Wirbelauer C, Paro R, Beisel C, Schübeler D. A Chromatin-modifying Function of JNK during Stem Cell Differentiation. Nature Genetics, 2012 Jan 18;44(1):94-100. PMID: 22179133.

Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Schöler A, Nimwegen E, Wirebeluer C, Oakeley EJ, Gaidatzis D, Tiwari VK, Schübeler D. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature, 2011 Dec 14;480(7378):490-5. PMID: 22170606.

MOLECULAR MECHANISMS OF CANCER METASTASIS AND THERAPY RESISTANCE

Inayatullah M, Mahesh A, Turnbull AK, Dixon JM, Natrajan R, Tiwari VK. Basal-epithelial subpopulations underlie and predict chemotherapy resistance in triple-negative breast cancer. EMBO Mol Med. 2024 Apr;16(4):823-853. doi: 10.1038/s44321-024-00050-0. Epub 2024 Mar 13. PMID: 38480932; PMCID: PMC11018633.

Lusby R, Zhang Z, Mahesh A, Tiwari VK. Decoding gene regulatory circuitry underlying TNBC chemoresistance reveals biomarkers for therapy response and therapeutic targets. NPJ Precis Oncol. 2024 Mar 12;8(1):64. doi: 10.1038/s41698-024-00529-6. PMID: 38472332; PMCID: PMC10933292.

Sahu S, Tiwari N, Pataskar A, Diken M, Tiwari VK* (*corresponding author). FBXO32 promotes microenvironment underlying Epithelial-Mesenchymal Transition via CtBP1 during tumor metastasis and brain development.

Nature Communications, 2017 Nov 15;8(1):1523. PMID: 29142217; PMCID: PMC5688138.

Navandar M, Garding A, Sahu SK, Pataskar A, Schick S, Tiwari VK* (*corresponding author).

ERK signaling modulates epigenome to drive epithelial to mesenchymal transition.

Oncotarget, 2017 Apr 25;8(17):29269-29281. PMID: 28418928; PMCID: PMC5438729.

Sahu SK, Garding A, Tiwari N, Thakurela S, Toedling J, Gebhard S, Ortega F, Berninger B, Nitsch R, Schmidt M, Tiwari VK* (*corresponding author). JNK-dependent gene regulatory circuitry governs mesenchymal fate. The EMBO Journal, 2015 Aug 13;34(16):2162-81. PMID: 26157010; PMCID: PMC4557668.

Tiwari N, Tiwari VK, Waldmeier L, Balwierz P, Arnold P, Meyer-Schaller N, Schübeler D, van Nimwegen E, Christofori G. Sox4 Is a Master Regulator of Epithelial-Mesenchymal Transition by Controlling Ezh2 Expression and Epigenetic Reprogramming. Cancer Cell, 2013 23, 768-783. PMID: 23764001.

Tiwari VK, McGarvey KM, Licchesi J, Ohm JE, Herman JG, Schübeler D, Baylin SB. PcG Proteins. DNA methylation and gene repression by chromatin looping. PLoS Biology, 2008 Dec 2; 6(12):2911-27. PMID: 19053175; PMCID: PMC2592355.

Tiwari VK, Cope L, McGarvey KM, Ohm JE, Baylin SB. A Novel 6C assay uncovers polycomb-mediated higher order chromatin conformations. Genome Research, 2008 Jul; 18(7): 1171-9. PMID: 18502945; PMCID: PMC2493406.

CROSSTALK OF TRANSCRIPTION FACTORS AND EPIGENETIC MECHANSISMS IN EPITHELIAL TO MESENCHYMAL TRANSITIO

Navandar M, Garding A, Sahu SK, Pataskar A, Schick S, Tiwari VK* (*corresponding author). ERK signaling modulates epigenome to drive epithelial to mesenchymal transition. Oncotarget, 2017 Apr 25;8(17):29269-29281. PMID: 28418928; PMCID: PMC5438729.

EPIGENETIC REGULATION OF HIGHER ORDER CHROMATIN CONFIRMATION AND ITS FUNCTION IN DEVELOPMENT

Tiwari VK#, Kurukuti S#, Tavoosidana G#, Pugacheva E, Murrell A, Zhao Z, Lobanenkov V, Reik W and Ohlsson R. CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2. PNAS, 2006 103, 10684-10689. PMID: 16815976; PMCID: PMC1484419.

Zhao Z, Tavoosidana G, Sjolinder M, Gondor A, Mariano P, Wang S, Kanduri C, Lezcano M, Singh Sandhu K, Singh U, Pant V, Tiwari VK, Kurukuti S and Ohlsson R (2006). Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nature Genetics, 2006 38, 1341-1347. PMID: 17033624.

Tiwari VK#, Thakur N#, Thomassin H, Pandey RR, Kanduri M, Gondor A, Grange T, Ohlsson R and Kanduri C. An antisense RNA regulates the bidirectional silencing property of the Kcnq1 imprinting control region. Mol Cell Biol, 2004 24, 7855-62. PMID: 15340049 PMCID: PMC515059.

Pugacheva EM, Tiwari VK, Abdullaev Z, Vostrov AA, Flanagan PT, Quitschke WW, Loukinov DI, Ohlsson R and Lobanenkov VV. Familial cases of point mutations in the XIST promoter reveal a correlation between CTCF binding and pre-emptive choices of X chromosome inactivation. Hum Mol Genet, 2005 14, 953-65. PMID: 15731119.

Key publications

GENE REGULATORY MECHANISMS UNDERLYING BRAIN DEVELOPMENT AND ITS DISRUPTION IN NEUROLOGICAL DISORDERS

MOLECULAR MECHANISMS OF CANCER METASTASIS AND THERAPY RESISTANCE

CROSSTALK OF TRANSCRIPTION FACTORS AND EPIGENETIC MECHANSISMS IN EPITHELIAL TO MESENCHYMAL TRANSITIO

EPIGENETIC REGULATION OF HIGHER ORDER CHROMATIN CONFIRMATION AND ITS FUNCTION IN DEVELOPMENT

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