Publications

† Co-corresponding, * Co-first authorship

Highlighted publication

Dileep V †*, Boix CA*, Mathys H, Marco A, Welch GM, Meharena HS, Loon A, Jeloka R, Peng Z, Bennett DA, Kellis M†, Tsai LH†. Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration. Cell (2023) [PDF]

Disruption of genome stability and 3D genome organization by DNA double- strand breaks in neurons are pathological steps in the progression of neurodegeneration.

Highlights:

  • Increased somatic mosaic gene fusions in excitatory neurons in Alzheimer’s disease

  • DNA double-strand breaks lead to mosaic gene fusions and genome structural variations

  • Changes in 3D genome organization in neurons enriched for DNA double-strand breaks

  • 3D genome changes align with differential gene expression in neurodegeneration

List of all publications:​

Full Bibliography: https://scholar.google.com/citations?user=250qpw4AAAAJ&hl=en)

  1. Dileep V †*, Boix CA*, Mathys H, Marco A, Welch GM, Meharena HS, Loon A, Jeloka R, Peng Z, Bennett DA, Kellis M†, Tsai LH†. Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration. Cell (2023) [PDF]

  2. Xiong X*, James BT*, Boix CA*, Park YP, Galani K, Victor MB, Sun N, Hou L, Dileep V, Ho L-L, Mantero J, Ni Scannail A, Mathys H, Bennett DA, Tsai LH†, Kellis M†. Epigenomic dissection of Alzheimer's disease pinpoints causal variants and reveals epigenome erosion. Cell (2023) [PDF]

  3. Penney J, Ralvenius WT, Loon AR, Cerit O, Dileep V, Milo M, Woolf H, Tsai LH. Distinct effects of disease-associated TREM2 R47H/+ and T66M mutations on iPSC-derived microglia. Glia (2023) [PDF]

  4. Welch GM, Boix CA, Schmauch E, Davila-Velderrain J, Victor MB, Dileep V, Bozzelli PL, Su Q, Cheng JD, Lee A, Leary NS, Pfenning AR, Kellis M, Tsai LH. Neurons burdened by DNA double-strand breaks incite microglia activation through antiviral-like signaling in neurodegeneration. Science Advances (2022) [PDF]

  5. Meharena HS, Marco A, Dileep V, Lockshin ER, Akatsu GY, Mullahoo J, Watson LA, Ko T, Guerin LN, Abdurrob F, Rengarajan S, Papanastasiou M, Jaffe JD, Tsai LH. Down-syndrome-induced senescence disrupts the nuclear architecture of neural progenitors. Cell Stem Cell (2022) [PDF]

  6. Bartlett DA, Dileep V, Baslan T, Gilbert DM. Mapping Replication Timing in Single Mammalian Cells. Current Protocols (2022) [PDF]

  7. Dileep V, Tsai LH. Neuronal enhancers get a break. Neuron (2021) (Opinion Article) [PDF]                      

  8. Dileep V, Tsai LH. Three-dimensional chromatin organization in brain function and dysfunction. Current Opinion in Neurobiology (2021) (Review Article) [PDF]

  9. Bartlett DA, Dileep V, Handa T, Ohkawa Y, Kimura H, Henikoff S, Gilbert DM. High-throughput single-cell epigenomic profiling by targeted insertion of promoters (TIP-seq). Journal of Cell Biology (2021) [PDF]

  10. Marco A, Meharena HS, Dileep V, Raju RM, Davila-Velderrain J, Zhang AL, Adaikkan C, Young JZ, Gao F, Kellis M, Tsai LH. Mapping the epigenomic and transcriptomic interplay during memory formation and recall in the hippocampal engram ensemble. Nature Neuroscience (2020) [PDF]

  11. Zhang J, Lee D, Dhiman V,….., Dileep V,.…, Gerstein M. An integrative ENCODE resource for cancer genomics. Nature Communication (2020) [PDF]

  12. ENCODE Project Consortium, Moore JE, Purcaro MJ, et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature (2020) [PDF]

  13. Sima J, Chakraborty A, Dileep V, Michalski M, Rivera-Mulia JC, Trevilla-Garcia C, Klein KN, Bartlett D, Washburn BK, Paulsen MT, Vera D, Nora EP, Kraft K, Mundlos S, Bruneau BG, Ljungman M, Fraser P, Ay F, Gilbert DM. Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication. Cell (2019) [PDF]                            

  14. Dileep V*, Wilson K*, Marchal C, Lyu X, Zhao PA, Li B, Axel P, Bartlett DA, Qin Z, Robins AJ, Schulz TC, Kulik KJ, Dalton S, Corces VG, Gilbert DM. Rapid lineage determination of human embryonic stem cells is accompanied by discordant changes in replication timing and chromatin compartment. Stem Cell Reports (2019) [PDF]

  15. Dixon J†*, Xu J*, Dileep V*, Zhan Y*, Song F*, Le VT, Yardimci GG, Chakraborty A, Bann DV, Wang Y, Clark R, Zhang L, Yang H, Liu T, Iyyanki S, An L, Pool C, Sasaki T, Rivera-Mulia JC, …, Ay F†, Noble WS†, Dekker J†, Gilbert DM†, Yue F†. Integrative detection and analysis of structural variation in cancer genomes. Nature Genetics (2018) [PDF] 

  16. Dileep V, Gilbert DM. Single-cell replication profiling reveals stochastic regulation of the mammalian replication-timing program. Nature Communication (2018) [PDF]

  17. Foti R, Gnan S, Cornacchia D, Dileep V, Bulut-Karslioglu A, Diehl S, Buness A, Klein FA, Huber W, Johnstone E, Loos R, Bertone P, Gilbert DM, Manke T, Jenuwein T, Buonomo SC. Nuclear Architecture Organized by Rif1 Underpins the Replication-Timing Program. Molecular Cell (2016) [PDF]

  18. Dileep V, Rivera-Mulia JC, Sima J, Gilbert DM. Large-Scale Chromatin Structure-Function Relationships during the Cell Cycle and Development: Insights from Replication Timing. Cold Spring Harb Symp Quant Biol (2015) (Review Article) [PDF]

  19. Dileep V, Ay F, Sima J, Vera DL, Noble WS, Gilbert DM. Topologically-associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication timing program. Genome Research (2015) [PDF]

  20. Pope BD*, Ryba T*, Dileep V, Yue F, Wu W, Denas O, Vera DL, Wang Y, Hansen RS, Canfield TK, Thurman RE, Cheng Y, Gülsoy G, Dennis JH, Snyder MP, Stamatoyannopoulos JA, Taylor J, Hardison RC, Kahveci T, Ren B, Gilbert DM. Topologically associating domains are stable units of replication-timing regulation. Nature (2014) [PDF]

  21. Takebayashi S, Lei I, Ryba T, Sasaki T, Dileep V, Battaglia D, Gao X, Fang P, Fan Y, Esteban MA, Tang J, Crabtree GR, Wang Z, Gilbert DM. Murine esBAF chromatin remodeling complex subunits BAF250a and Brg1 are necessary to maintain and reprogram pluripotency-specific replication timing of select replication domains. Epigenetics & Chromatin (2013) [PDF]

  22. Cornacchia D, Dileep V, Quivy JP, Foti R, Tili F, Santarella-Mellwig R, Antony C, Almouzni G, Gilbert DM, Buonomo SB. Mouse Rif1 is a key regulator of the replication-timing programme in mammalian cells. EMBO Journal (2012) [PDF]

  23. Takebayashi S, Dileep V, Ryba T, Dennis JH, Gilbert DM. Chromatin-interaction compartment switch at developmentally regulated chromosomal domains reveals an unusual principle of chromatin folding. PNAS (2012) [PDF]

  24. Dileep V, Didier R, Gilbert DM. Genome-wide analysis of replication timing in mammalian cells: troubleshooting problems encountered when comparing different cell types. Methods (2012) [PDF]

  25. Dileep V. The place and function of non-coding DNA in the evolution of variability. Hypothesis (2009) (Opinion Article) [PDF]

     

​Thesis: 
​Replication Timing Regulation and Chromatin Structure Dynamics during the Cell Cycle and Development (2017). [PDF]