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    Epigenetics & RNA Processing Lab

    IISER Bhopal

    Publications

    Our contributions to understanding RNA splicing, cancer epigenetics, and tumor metabolism.

    40of 40 results

    1. PKM2-DNMT3A-SMAD2 Axis Regulates Cell Proliferation via Histone Lactylation in Breast Cancer

      2026

      Authors: *

      Published in: Molecular and Cellular Biology, 46(5), 584–595

    2. PRMT5 regulates alternative splicing of TCF3 under hypoxia to promote EMT and invasion in breast cancer

      2025

      Authors: Shruti AgrawalAtul Samaiya*

      Published in: PLOS Biology

    3. Interplay of YEATS2 and GCDH regulates histone crotonylation and drives EMT in head and neck cancer

      2025

      Authors: Shruti AgrawalAtul Samaiya*

      Published in: eLife

    4. Identification of SRSF9 through pooled shRNA screening links BNIP3 splicing to autophagy and metabolic reprogramming in breast cancer

      2025

      Authors: Atul Samaiya*

      Published in: Journal of Biological Chemistry, 301(8), 110482

    5. Hypoxia induced ATF3 escalates breast cancer invasion by increasing collagen deposition via P4HA1

      2025

      Authors: Shruti AgrawalAtul Samaiya*

      Published in: Cell Death & Disease, 16, 142

    6. Hypoxia-induced CTCF mediates alternative splicing via coupling chromatin looping and RNA Pol II pause to promote EMT in breast cancer

      2025

      Authors: Sachin MishraDimple Notani*

      Published in: Cell Reports, 44(2)

    7. Hypoxia-induced CTCF promotes EMT in breast cancer

      2024

      Authors: Jharna MishraAtul Samaiya*

      Published in: Cell Reports, 43(7)

    8. CTCF and BORIS-mediated autophagy regulation via alternative splicing of BNIP3L in breast cancer

      2024

      Authors: *

      Published in: Journal of Biological Chemistry, 300(7)

    9. ROS production by mitochondria: Function or dysfunction

      2024

      Authors: Flavio R. PalmaBenjamin N. GantnerMarcelo J. SakiyamaCezar KayzukaRiccardo LacchiniBrian CunniffMarcelo G. Bonini

      Published in: Oncogene

    10. PKM2 dictates the poised chromatin state of PFKFB3 promoter to enhance breast cancer progression

      2023

      Authors: Kajal BiswasJharna MishraAtul SamaiyaTyler MalysAlexander Y MitrophanovShyam K Sharan*

      Published in: NAR Cancer

    11. Oncometabolite lactate enhances breast cancer progression by orchestrating histone lactylation-dependent c-Myc expression

      2023

      Authors: Atul Samaiya*

      Published in: Translational Oncology

    12. Hypoxia-induced loss of SRSF2-dependent DNA methylation promotes CTCF-mediated alternative splicing of VEGFA in breast cancer

      2023

      Authors: Atul SamaiyaJharna Mishra*

      Published in: iScience

    13. Human behavior inspired linchpin directed catalysis for traceless precision labeling of lysine in native proteins

      2022

      Authors: Kalyani ThakurSajeev T. K.Shivam KumarRagendu V.Dattatraya Gautam RawaleSrinivasa Rao AdusumalliNeetu KalraRam Kumar MishraVishal Rai*

      Published in: Bioconjugate Chemistry

    14. Traceless cysteine-linchpin enables precision engineering of lysine in native proteins

      2022

      Authors: Neelesh C. ReddyRajib MollaPralhad Namdev JoshiSajeev T. K.Ipsita BasuJyotsna KawadkarNeetu KalraRam Kumar MishraSuman ChakrabartyVishal Rai*

      Published in: Nature Communications

    15. The role of SARS CoV-2 spike NTD mutations in determining neutralization susceptibility and virion infectivity

      2022

      Authors: Tarun MishraRishikesh DalaviGarima JoshiAtul KumarPankajRam K MishraAjit Chande

      Published in: Life Science Alliance

    16. Improved loss-of-function CRISPR/Cas9 genome editing in human cells concomitant with inhibition of TGFβ signaling

      2022

      Authors: Tarun MishraVipin BhardwajPallavi GadgilPavitra RamdasAjit Chande

      Published in: Molecular Therapy-Nucleic Acids, 28, 202–218

    17. Unfolding the role of autophagy in the cancer metabolism

      2021

      Authors: *

      Published in: Biochemical & Biophysical Reports, 28, 1–18

    18. ERK1/2-EGR1-SRSF10 axis mediated alternative splicing plays a critical role in head and neck cancer

      2021

      Authors: Atul SamaiyaNeetu KalraSanjay Gupta*

      Published in: Frontiers in Cell and Developmental Biology, 9, 1–13

    19. E2F1 and epigenetic modifiers orchestrate breast cancer progression by regulating oxygen-dependent ESRP1 expression

      2021

      Authors: Jharna MishraAtul Samaiya*

      Published in: Oncogenesis, 10(58), 1–10

    20. Interplay within tumor microenvironment orchestrates neoplastic RNA metabolism and transcriptome diversity

      2021

      Authors: *

      Published in: WIREs RNA

    21. Oxygen gradient and tumor heterogeneity: The chronicle of a toxic relationship

      2021

      Authors: *

      Published in: BBA Reviews on Cancer

    22. Tumor suppressor SMAR1 regulates PKM alternative splicing by HDAC6-mediated deacetylation of PTBP1

      2021

      Authors: Arpankumar ChoksiApoorva ParulekarRichaVibhuti Kumar ShahRamakrishna NimmaPriyanka FirmalGopal C. KunduSamit Chattopadhyay*

      Published in: BMC Cancer & Metabolism

    23. Hypoxia-induced alternative splicing in human diseases: The pledge, the turn, and the prestige

      2021

      Authors: *

      Published in: Cellular and Molecular Life Sciences

    24. Hypoxia-induced TGFβ-RBFOX2-ESRP1 axis regulates human MENA alternative splicing and promotes EMT in breast cancer

      2020

      Authors: Anna CherianVishnuS.S.Jharna MishraAtul Samaiya*

      Published in: NAR Cancer

    25. HNRNP2B1-MST1R-AKT axis contributes to the EMT in head and neck cancer

      2020

      Authors: Jharna MishraAtul SamaiyaRajendra Kumar Panday*

      Published in: Laboratory Investigation

    26. Chemoselective and site-selective lysine-directed lysine modification enables single-site labeling of native proteins

      2020

      Authors: Srinivasa Rao AdusumalliDattatraya Gautam RawaleKalyani ThakurLanda PurushottamNeelesh C. ReddyNeetu KalraVishal Rai

      Published in: Angewandte Chemie International Edition, 59, 10332–10336

    27. Hypoxia-induced changes in intragenic DNA methylation correlate with alternative splicing in breast cancer

      2020

      Authors: Nagarjun Vijay**

      Published in: Journal of Biosciences, 45(3)

    28. Dietary-phytochemical mediated reversion of cancer-specific splicing inhibits Warburg effect in head and neck cancer

      2019

      Authors: Somnath D. BhagatAtul SamaiyaAasheesh Srivastava*

      Published in: BMC Cancer, 19, 1031

    29. Single-site labeling of native proteins enabled by a chemoselective and site-selective chemical technology

      2018

      Authors: Srinivasa Rao AdusumalliDattatraya Gautam Rawale, UshaPrabhanshu TripathiRajesh PaulNeetu KalraRam Kumar MishraVishal Rai

      Published in: Journal of the American Chemical Society, 140(44), 15114–15123

    30. PAK2-c-MYC-PKM2 axis plays an essential role in head and neck oncogenesis via regulating Warburg effect

      2018

      Authors: AjithRajendra Kumar PandayAtul Samaiya*

      Published in: Cell Death & Disease, 9, 825

    31. Single-site labeling of lysine in proteins through a metal-free multicomponent approach

      2018

      Authors: Maheshwerreddy ChilamariNeetu KalraVishal Rai

      Published in: Chemical Communications

    32. Intragenic DNA methylation and BORIS-mediated cancer-specific splicing contributes to Warburg effect

      2017

      Authors: Kajal BiswasRajendra Kumar PandayAtul SamaiyaShyam K. Sharan*

      Published in: Proceedings of the National Academy of Sciences, 114(43), 11440–11445

    33. A saga of cancer epigenetics: Linking epigenetics to alternative splicing

      2017

      Authors: *

      Published in: Biochemical Journal, 474(6), 885–896

    34. TET-catalyzed oxidation of intragenic 5-methylcytosine regulates CTCF-dependent alternative splicing

      2016

      Authors: Ryan J MarinaDavid SturgillMarc A BaillyMorgan ThenozGarima VarmaMaria F PriggeKyster K NananNazmul HaqueShalini Oberdoerffer

      Published in: EMBO Journal, 35(3), 335–355

    35. Integrated genomic analyses identify KDM1A's role in cell proliferation via modulating E2F signaling activity and associate with poor clinical outcome in oral cancer

      2015

      Authors: Shree Ram**

      Published in: Cancer Letters, 367, 162–172

    36. Prognostic utility of autoantibodies to alpha-enolase and Hsp70 for cancer of the gingivobuccal complex using immunoproteomics

      2013

      Authors: Aditi PranayS. KannanS. A. MalgundkarRajiv B. GovekarA. PatilSudhir V. KanePankaj ChaturvediAnil K. D'CruzSudhir M. Zingde

      Published in: Proteomics Clinical Applications, 7(5–6), 392–402

    37. Co-transcriptional regulation of alternative pre-mRNA splicing

      2012

      Authors: Shalini Oberdoerffer

      Published in: BBA-Gene Regulatory Mechanisms, 1819(7), 673–683

    38. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

      2011

      Authors: Ersen KavakMelissa GregoryMasahiko ImashimizuBojan ShutinoskiMikhail KashlevPhilipp OberdoerfferRickard SandbergShalini Oberdoerffer

      Published in: Nature, 479, 74–79

    39. Immunoproteomics reveals that cancer of the tongue and the gingivo-buccal complex exhibit differential autoantibody response

      2009

      Authors: Aditi PranayAnil K. D'CruzPankaj ChaturvediSudhir V. KaneSudhir M. Zingde

      Published in: Cancer Biomarkers, 5(3), 127–135

    40. Tumor antigens eliciting autoantibody response in cancer of gingivo-buccal complex

      2007

      Authors: Rajiv B. GovekarRaghunath SirdeshmukhChandra S. SundaramAnil K. D'CruzK. A. PathakSudhir V. KaneSudhir M. Zingde

      Published in: Proteomics Clinical Applications, 1(12), 1592–1604

    IP

    Patent

    A METHOD AND COMPOSITION FOR THE TREATMENT OF CANCER

    Inventors: Dr. Sanjeev Shukla

    Patent Application Filed
    Details pending

    *Corresponding author · Source: sshuklagroup.iiserb.ac.in