2022

Uppala, J. K., Ghosh, C., Sabat, G. and Dey, M. (2022). Pull-down of Biotinylated RNA and Associated Proteins. Bio-protocol 12(4): e4331. DOI: 10.21769/BioProtoc.4331.

Uppala JK, Sathe L, Chakraborty A, Bhattacharjee S, Pulvino AT, Dey M. The cap-proximal RNA secondary structure inhibits pre-initiation complex formation on HAC1 mRNA. J Biol Chem. 2022 Jan 28:101648. doi: 10.1016/j.jbc.2022.101648. Epub ahead of print. PMID: 35101452.
Uppala JK, Dey M. Detection of HAC1 mRNA Splicing by RT-PCR in Saccharomyces cerevisiae. Methods Mol Biol. 2022;2378:101-110. doi: 10.1007/978-1-0716-1732-8_7. PMID: 34985696.

2021

George J, Li Y, Kadamberi IP, Parashar D, Tsaih SW, Gupta P, Geethadevi A, Chen C, Ghosh C, Sun Y, Mittal S, Ramchandran R, Rui H, Lopez-Berestein G, Rodriguez-Aguayo C, Leone G, Rader JS, Sood AK, Dey M, Pradeep S, Chaluvally-Raghavan P. RNA-binding protein FXR1 drives cMYC translation by recruiting eIF4F complex to the translation start site. Cell Rep. 2021 Nov 2;37(5):109934. doi: 10.1016/j.celrep.2021.109934. PMID: 34731628; PMCID: PMC8675433.

Uppala JK, Bhattacharjee S, Dey M. Vps34 and TOR Kinases Coordinate HAC1 mRNA Translation in the Presence or Absence of Ire1-Dependent Splicing. Mol Cell Biol. 2021 Jun 23;41(7):e0066220. doi: 10.1128/MCB.00662-20. Epub 2021 Jun 23. PMID: 33972394; PMCID: PMC8224233.

Ghosh C, Uppala JK, Sathe L, Hammond CI, Anshu A, Pokkuluri PR, Turk BE, Dey M. Phosphorylation of Pal2 by the protein kinases Kin1 and Kin2 modulates HAC1 mRNA splicing in the unfolded protein response in yeast. Sci Signal. 2021 May 25;14(684):eaaz4401. doi: 10.1126/scisignal.aaz4401. PMID: 34035143; PMCID: PMC8285061.

2018

Ghosh C, Sathe L, Paprocki JD, Raicu V, Dey M. Adaptation to Endoplasmic Reticulum Stress Requires Transphosphorylation within the Activation Loop of Protein Kinases Kin1 and Kin2, Orthologs of Human Microtubule Affinity-Regulating Kinase. Mol Cell Biol. 2018 Nov 13;38(23):e00266-18. doi: 10.1128/MCB.00266-18. PMID: 30201804; PMCID: PMC6234288.

Uppala JK, Ghosh C, Sathe L, Dey M. Phosphorylation of translation initiation factor eIF2α at Ser51 depends on site- and context-specific information. FEBS Lett. 2018 Sep;592(18):3116-3125. doi: 10.1002/1873-3468.13214. Epub 2018 Sep 19. PMID: 30070006; PMCID: PMC6167009.

2015

Sathe L, Bolinger C, Mannan MA, Dever TE, Dey M. Evidence That Base-pairing Interaction between Intron and mRNA Leader Sequences Inhibits Initiation of HAC1 mRNA Translation in Yeast. J Biol Chem. 2015 Sep 4;290(36):21821-32. doi: 10.1074/jbc.M115.649335. Epub 2015 Jul 14. PMID: 26175153; PMCID: PMC4571938.

Anshu A, Mannan MA, Chakraborty A, Chakrabarti S, Dey M. A novel role for protein kinase Kin2 in regulating HAC1 mRNA translocation, splicing, and translation. Mol Cell Biol. 2015 Jan;35(1):199-210. doi: 10.1128/MCB.00981-14. Epub 2014 Oct 27. PMID: 25348718; PMCID: PMC4295377.

2014

Dey M, Mann BR, Anshu A, Mannan MA. Activation of protein kinase PKR requires dimerization-induced cis-phosphorylation within the activation loop. J Biol Chem. 2014 Feb 28;289(9):5747-57. doi: 10.1074/jbc.M113.527796. Epub 2013 Dec 13. PMID: 24338483; PMCID: PMC3937647.

2013

Mannan MA, Shadrick WR, Biener G, Shin BS, Anshu A, Raicu V, Frick DN, Dey M. An ire1-phk1 chimera reveals a dispensable role of autokinase activity in endoplasmic reticulum stress response. J Mol Biol. 2013 Jun 26;425(12):2083-99. doi: 10.1016/j.jmb.2013.02.036. Epub 2013 Mar 27. PMID: 23541589.

2011

Dey M, Velyvis A, Li JJ, Chiu E, Chiovitti D, Kay LE, Sicheri F, Dever TE. Requirement for kinase-induced conformational change in eukaryotic initiation factor 2alpha (eIF2alpha) restricts phosphorylation of Ser51. Proc Natl Acad Sci U S A. 2011 Mar 15;108(11):4316-21. doi: 10.1073/pnas.1014872108. Epub 2011 Feb 28. PMID: 21368187; PMCID: PMC3060252.

2009

Dev K, Santangelo TJ, Rothenburg S, Neculai D, Dey M, Sicheri F, Dever TE, Reeve JN, Hinnebusch AG. Archaeal aIF2B interacts with eukaryotic translation initiation factors eIF2alpha and eIF2Balpha: Implications for aIF2B function and eIF2B regulation. J Mol Biol. 2009 Sep 25;392(3):701-22. doi: 10.1016/j.jmb.2009.07.030. Epub 2009 Jul 17. PMID: 19616556; PMCID: PMC2937263.

2008

Gárriz A, Qiu H, Dey M, Seo EJ, Dever TE, Hinnebusch AG. A network of hydrophobic residues impeding helix alphaC rotation maintains latency of kinase Gcn2, which phosphorylates the alpha subunit of translation initiation factor 2. Mol Cell Biol. 2009 Mar;29(6):1592-607. doi: 10.1128/MCB.01446-08. Epub 2008 Dec 29. PMID: 19114556; PMCID: PMC2648240.

Rothenburg S, Deigendesch N, Dey M, Dever TE, Tazi L. Double-stranded RNA-activated protein kinase PKR of fishes and amphibians: varying the number of double-stranded RNA binding domains and lineage-specific duplications. BMC Biol. 2008 Mar 3;6:12. doi: 10.1186/1741-7007-6-12. PMID: 18312693; PMCID: PMC2291453.

Lee KP, Dey M, Neculai D, Cao C, Dever TE, Sicheri F. Structure of the dual enzyme Ire1 reveals the basis for catalysis and regulation in nonconventional RNA splicing. Cell. 2008 Jan 11;132(1):89-100. doi: 10.1016/j.cell.2007.10.057. PMID: 18191223; PMCID: PMC2276645.