+ 44 28 9097 6474 V.Tiwari@qub.ac.uk
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Crosstalk of transcription factors and epigenetic mechanisms during brain development

We primarily focus on deciphering epigenetic mechanisms and transcription factors that wire the gene expression programs underlying neural development. Here we employ highly multidisciplinary approaches combining neurobiology, epigenetics, genomics and computational biology to fill-in the longstanding knowledge gap in the field, in particular to discover which players, mechanisms and principles are crucial in defining specific cell-fates at distinct stages of neural development. We uncovered a role for Topoisomerase 2α in gene regulation underlying pluripotency and developmental potential of embryonic stem cells by regulating the epigenetic state and RNA Pol II kinetics at its target genes. Subsequently, my lab revealed novel distal regulatory elements that function in concert with epigenetic mechanisms and transcription factors to generate the transcriptome underlying neuronal development and activity. My group also revealed how the transcription factor NeuroD1 functions as a pioneer transcription factor by binding its targets within repressive chromatin and inducing an open chromatin state to promote neuronal fate. In addition to revealing critical molecular switches of brain development, these studies also paved the way for translational neurosciences including regenerative therapy. Very recently, we provided the first report that the astrocyte generation involves several transcriptionally and epigenetically distinct stages and revealed transcription factors that play pivotal roles in establishing these stages by remodeling the epigenetic landscape at distal regulatory elements.

  1. A complex epigenome-splicing crosstalk governs epithelial to mesenchymal transition in metastasis and brain development. Sahu SK, Agirre E, Inayatullah M, Mahesh A, Lavin D, Singh A, Strand S, Diken M, Luco RF, Belmonte JC, Tiwari VK*.  Nature Cell Biology, 2022, Aug;24(8):1265-77. 
  2. Structural network alterations in focal and generalized epilepsy assessed in a worldwide ENIGMA study follow axes of epilepsy risk gene expression Epilepsy Consortium. Nature Communications, 2022,  Jul 27;13(1):1-6.
  3. Tcf12 and NeuroD1 cooperatively drive neuronal migration during cortical development. Singh A, Mahesh Arun, Noack F, Toledo BC, Calegari F, Tiwari VK*(*corresponding author) Development. 2022, Feb 1;149(3):dev200250.
  4. Phf21b imprints the spatiotemporal epigenetic switch essential for neural stem cell differentiation. Basu A, Mestres I, Sahu SK, Tiwari N, Khongwir B, Jan Baumgart J, Singh A, Calegari F, Tiwari VK*.(*corresponding author). Genes and Development, 2020, Sep 1;34(17-18):1190-209.
  5. Gene Regulation and Priming by Topoisomerase IIα in embryonic stem cells. Thakurela S, Garding A, Jung, Schübeler D, Burger L, Tiwari VK*(*corresponding author). Nature Communications, 2013, Sep 27; 4:2478. PMID: 24072229.
  6. Dynamics and function of distal regulatory elements during neurogenesis and neuroplasticity. Thakurela S, Sahu SK, Garding A, Tiwari VK*(*corresponding author). Genome Research, 2015 Sep;25(9):1309-24.
  7. NeuroD1 reprograms chromatin and transcription factor landscapes to induce the neuronal program. Pataskar A, Jung J, Smialowski P, Calegari F, Straub T, Tiwari VK*(*corresponding author). The EMBO Journal, 2016 Jan 4;35(1):24-45.
  8. Stage-Specific Transcription Factors Drive Astrogliogenesis by Remodeling Gene Regulatory Landscapes. 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). Cell Stem Cell, 2018,Oct 4; 23(4):557. 
  9. Direct Assessment and site-specific manipulation of DNA (hydroxy-)methylation during mouse corticogenesis. Noack F, Pataskar A, Schneider M, Buchholz F, Tiwari VK, Calegari F. Life Sci Alliance. 2019 Feb 27;2(2). e201900331.
  10. The centrosome protein AKNA regulates neurogenesis via microtubule organization. Camargo Ortega G, Falk S, Johansson PA, Peyre E, Broix L, Sahu SK, Hirst W, Schlichthaerle T, De Juan Romero C, Draganova K, Vinopal S, Chinnappa K, Gavranovic A, Karakaya T, Steininger T, Merl-Pham J, Feederle R, Shao W, Shi SH, Hauck SM, Jungmann R, Bradke F, Borrell V, Geerlof A, Reber S, Tiwari VK, Huttner WB, Wilsch-Bräuninger M, Nguyen L, Götz M. Nature, 2019 Mar; 567(7746):113-117

Gene regulatory mechanisms underlying epithelial to mesenchymal transition

As a second branch in my lab, we also study molecular mechanisms underlying epithelial to mesenchymal transition. The epithelial to mesenchymal transition (EMT) is a biological process in which cells lose cell-cell contacts and become motile. EMT is used during development, for example, in triggering neural crest migration, and in cancer metastasis. Despite progress, the dynamics and function of signaling pathways, transcription factors and epigenetic mechanisms driving the transcriptional program underlying EMT remained poorly understood. I contributed to a study that discovered how the transcription Sox4acts as a master regulator of EMT by controlling the expression of Ezh2, encoding the Polycomb group histone methyltransferase, and downstream epigenetic reprogramming. My team identified a role for JNK pathway in breast cancer metastasis by regulating a distinct gene expression program, at the same time revealed epigenetic mechanisms and a new repertoire of transcription factors that mediate these responses. This study also guided for novel therapeutic avenues in breast cancer. Extending these findings, we showed a kinetically different function of ERK pathway during EMT and showed how it modulates epigenome at distal elements to promote this process. Recently, we discovered FBXO32 as a novel critical regulator of EMT by mediating epigenetic remodeling and transcriptional induction of a specific set of genes, which create a suitable microenvironment for EMT progression. Lastly, linking the two branches within my lab, we made several illustrations how cortical development involves an EMT-like process and may involve similar gene regulatory programs and players.

 
  1. A complex epigenome-splicing crosstalk governs epithelial to mesenchymal transition in metastasis and brain development. Sahu SK, Agirre E, Inayatullah M, Mahesh A, Lavin D, Singh A, Strand S, Diken M, Luco RF, Belmonte JC, Tiwari VK*.  Nature Cell Biology, 2022, Aug;24(8):1265-77. 
  2. Mnt Represses Epithelial Identity To Promote Epithelial-to-Mesenchymal Transition. Lavin DP, Abassi L, Inayatullah M, Tiwari VK*(*corresponding author). Molecular and Cellular Biology. 2021 Oct 26;41(11):e0018321. 
  3. Unresolved Complexity in the Gene Regulatory Network Underlying EMT. Lavin DP, Tiwari VK*(*corresponding author). Frontiers in Oncology, 2020,May; 10:554.
  4. Sox4 Is a Master Regulator of Epithelial-Mesenchymal Transition by Controlling Ezh2 Expression and Epigenetic Reprogramming. Tiwari N, Tiwari VK, Waldmeier L, Balwierz P, Arnold P, Meyer-Schaller N, Schübeler D, van Nimwegen E, Christofori G. Cancer Cell, 2013 23, 768-783.
  5. JNK-dependent gene regulatory circuitry governs mesenchymal fate. Sahu SK, Garding A, Tiwari N, Thakurela S, Toedling J, Gebhard S, Ortega F, Berninger B, Nitsch R, Schmidt M, Tiwari VK*(*corresponding author). The EMBO Journal, 2015 Aug 13;34(16):2162-81.
  6. ERK signaling modulates epigenome to drive epithelial to mesenchymal transition. Navandar M, Garding A, Sahu SK, Pataskar A, Schick S, Tiwari VK*(*corresponding author). Oncotarget, 2017Apr 25;8(17):29269-29281. PMID: 28418928.
  7. FBXO32 promotes microenvironment underlying Epithelial-Mesenchymal Transition via CtBP1 during tumor metastasis and brain development. Sahu S, Tiwari N, Pataskar A,Diken M, Tiwari VK*(*corresponding author). Nature Communications, 2017Nov 15;8(1):1523.

Epigenetic regulation of cell-fate specification and its misregulation in cancer

My postdoctoral work was focused on addressing a longstanding challenge of how signaling pathways and transcription factors crosstalk with chromatin during cellular differentiation and how this communication goes wrong in diseases. During my first postdoc, I showed for the first time how different epigenetic mechanisms cooperate to mediate chromatin compaction for silencing tumor suppressor genes in cancer cells. I then invented a novel technique and showed that protein complexes that control epigenetic gene regulation mediate physical proximity between distant chromosomal elements. This study also showed that epigenetic machineries could be shared by various loci to simultaneously co-regulate genes. My second postdoctoral work provided the first evidence that a MAP kinase, JNK, directly modifies chromatin at promoters of neuronal genes to induce their transcription during neurogenesis. This finding challenged the classical view that MAP kinases alter gene expression only via activating a downstream set of cytosolic proteins. In another study, we noticed that a specific isoform of Topoisomerase 2, Top2β, was expressed specifically in neurons. We next revealed that it binds promoters of neuronal differentiation genes to induce their expression during neurogenesis. This was a move away from the classical view as Topoisomerases were primarily known to relieve the torsional strain in DNA.

  1. PcG Proteins, DNA methylation and gene repression by chromatin looping. Tiwari VK, McGarvey KM, Licchesi J, Ohm JE, Herman JG, Schübeler D, Baylin SB. PLoS Biology, 2008 Dec 2; 6(12):2911-27. PMID: 19053175; PMCID: PMC2592355.
  2. A Novel 6C assay uncovers polycomb-mediated higher order chromatin conformations. Tiwari VK, Cope L, McGarvey KM, Ohm JE, Baylin SB. Genome Research, 2008 Jul; 18(7): 1171-9.PMID: 18502945; PMCID: PMC2493406.
  3. DNA-binding factors shape the mouse methylome at distal regulatory regions. Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Schöler A, Nimwegen E,Wirebeluer C, Oakeley EJ, Gaidatzis D, Tiwari VK, Schübeler D. Nature,2011 Dec 14;480(7378):490-5.PMID: 22170606
  4. Target genes of Topoisomerase IIbeta regulate neuronal survival and are defined by their chromatin state. Tiwari VK*,Burger L, Nikoletopoulou V, Deogracious R, Thakurela S, Wirbelauer C, Hoerner L, Barde YA, Schübeler D*(*co-corresponding authors). PNAS,2012 Apr 17;109(16):E934-43.PMID: 22474351 PMCID; PMC3340998.
  5. A Chromatin-modifying Function of JNK during Stem Cell Differentiation. Tiwari VK, Stadler M, Wirbelauer C, Paro R, Beisel C, Schübeler D. Nature Genetics,2012 Jan 18;44(1):94-100.PMID: 22179133.

Epigenetic regulation of higher order chromatin confirmation and its function in development

My early work was primarily centered on investigating epigenetic regulation of higher order chromatin conformation and its impact on embryonic development. When I began asking these questions, no labs in the world had previously investigated how chromatin looping contributes to genomic imprinting regulation and, consequently, to proper development. My studies revealed that CTCF controls imprinting at the Igf2-H19 locus by regulating its epigenetic state and higher-order chromatin structure. Interestingly, both CTCF binding and dependent chromatin higher order structures were maintained in mitotic chromatin. We also revealed networks of epigenetically regulated intra- and interchromosomal interactions and showed how these interactions influence epigenetic state of the interacting loci. Second part of my studies uncovered role for a specific non-coding RNA in the imprinted gene expression at the Kcnq1 locus and also showed how mutations in the XIST promoter influence CTCF binding and X chromosome inactivation.

  1. CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2. Tiwari VK#, Kurukuti S#, Tavoosidana G#, Pugacheva E, Murrell A, Zhao Z, Lobanenkov V, Reik W and Ohlsson R. PNAS, 2006 103, 10684-10689.  PMID: 16815976; PMCID: PMC1484419.                                                                                                   
  2. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. 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). Nature Genetics, 2006 38, 1341-1347. PMID: 17033624.
  3. An antisense RNA regulates the bidirectional silencing property of the Kcnq1 imprinting control region. Tiwari VK#, Thakur N#, Thomassin H, Pandey RR, Kanduri M, Gondor A, Grange T, Ohlsson R and Kanduri C. Mol Cell Biol, 2004 24, 7855-62. PMID: 15340049 PMCID: PMC515059.
  4. Familial cases of point mutations in the XIST promoter reveal a correlation between CTCF binding and pre-emptive choices of X chromosome inactivation. Pugacheva EM, Tiwari VK, Abdullaev Z, Vostrov AA, Flanagan PT, Quitschke WW, Loukinov DI, Ohlsson R and Lobanenkov VV. Hum Mol Genet, 2005 14, 953-65.  PMID: 15731119.