Lim Lab(RNA & epi GENOMICS)
update: 2023.11.21
Selected Papers
1. Gou, L.T.*, Lim, D.H.*, Ma, W.B.*, Aubol, B.E., Hao, Y.J., Wang, X., Zhao, J., Liang, Z.Y., Shao, C.W., Zhang, X., Meng, F., Li, H.R., Zhang, X.R., Xu, R.M., Li, D.S., Rosenfeld, M.G., Mellon, P.L., Adams, J.A., Liu, M.F., and Fu, X.D. (2020) Initiation of Parental Genome Reprogramming in Fertilized Oocyte by Splicing Kinase SRPK1-Catalyzed Protamine Phosphorylation.
Cell 180(6), 1212-1227 (*co-first authors) PMID: 3216915
2. Na, D.K*, Lim, D.H.*, Hong, J.S., Lee, H.M., Cho, D.A., Yu, M.S., Shaker, B., Ren, J.,
Lee, B.M., Song, J.G., Oh, Y.N., Lee, K.G., Oh, K.S., Lee, M.Y., Choi, M.S., Choi, H.S.,
Kim, Y.H., Bui, J.M., Leem K.S., Kim, H.W., Lee, Y.S.#, and Gsponer J.# (2023)
A multi-layered network model identifies Akt1 as a common modulator of neurodegeneration.
Mol. Syst. Biol. e11801 (*co-first authors) PMID: 37984409
3. Lee, S.J.*, Kim, N.Y.*, Jang, D.G., Kim, H.K., Kim, J.I., Jeon, J.W., and Lim, D.H. (2023)
Ecdysone-induced microRNA miR-276a-3p controls developmental growth by targeting the
insulin receptor in Drosophila.
Insect Mol. Biol. 32(6):703-715 (*co-first authors) PMID: 37702106
4. Lim, D.H.*#, Choi, M.S.*, Jeon, J.W.*, and Lee, Y.S.# (2023)
MicroRNA miR-252-5p regulates the Notch signaling pathway by targeting Rab6 in Drosophila
wing development.
Insect Sci. 30(5), 1431-1444 (*co-first authors / #co-corresponding authors) PMID: 36847222
5. Kim, C.J.*, Kim, H.H.*, Kim, H.K., Lee, S.J., Jang D.G., Kim, C.H., and Lim, D.H. (2023)
MicroRNA miR-263b-5p regulates developmental growth and cell association by suppressing
Laminin A in Drosophila.
Biology 12(8), 1096 (*co-first authors) PMID: 37626982
2021 - 2023
28. Na, D.K.*, Lim, D.H.*, Hong, J.S., Lee, H.M., Cho, D.A., Yu, M.S., Shaker, B., Ren, J., Lee, B.,
Song, J.G., Oh, Y., Lee, K.G., Oh, K.S., Lee, M.Y., Choi, M.S., Choi, H. A., Kim, Y.H., Bui, J.M.,
Lee, K.S., Kim, H.W., Lee, Y.S., and Gsponer, J. (2023)
A genome-wide multi-layered network model identifies Akt1 as a common modulator of multiple
neurodegenerative diseases. Submitted 140(supplement 1) 996-997
Submission
29. Na, D.K*, Lim, D.H.*, Hong, J.S., Lee, H.M., Cho, D.A., Yu, M.S., Shaker, B., Ren, J.,
Lee, B.M., Song, J.G., Oh, Y.N., Lee, K.G., Oh, K.S., Lee, M.Y., Choi, M.S., Choi, H.S.,
Kim, Y.H., Bui, J.M., Leem K.S., Kim, H.W., Lee, Y.S.#, and Gsponer J.# (2023)
A multi-layered network model identifies Akt1 as a common modulator of neurodegeneration.
Mol. Syst. Biol. e11801 (*co-first authors) PMID: 37984409
28. Kim, H.K., Kim, C.J., Jang, D.G., and Lim, D.H. (2023)
MicroRNA miR-274-5p suppresses found-in-neurons associated with melanotic mass
formation and development growth in Drosophila.
Insects 14(8), 709 PMID: 37623419
Preprints - doi: 10.20944/preprints202306.0501.v1
27. Kim, C.J.*, Kim, H.H.*, Kim, H.K., Lee, S.J., Jang D.G., Kim, C.H., and Lim, D.H. (2023)
MicroRNA miR-263b-5p regulates developmental growth and cell association by suppressing
Laminin A in Drosophila.
Biology 12(8), 1096 (*co-first authors) PMID: 37626982
26. Lee, S.J.*, Kim, N.Y.*, Jang, D.G., Kim, H.K., Kim, J.I., Jeon, J.W., and Lim, D.H. (2023)
Ecdysone-induced microRNA miR-276a-3p controls developmental growth by targeting the
insulin receptor in Drosophila.
Insect Mol. Biol. 32(6):703-715 (*co-first authors) PMID: 37702106
25. Lim, D.H.*#, Choi, M.S.*, Jeon, J.W.*, and Lee, Y.S.# (2023)
MicroRNA miR-252-5p regulates the Notch signaling pathway by targeting Rab6 in Drosophila
wing development.
Insect Sci. 30(5), 1431-1444 (*co-first authors / #co-corresponding authors) PMID: 36847222
24. Jayne, N, Liu, M.D., Chen, B.S., Liang, Z.Y., Lim, D.H., Ren, B., Fu, X.D., Zhang, D.E. (2022)
Pathogenic RUNX1 C-Terminal Truncation Mutations Contribute to Differentiation Block and
Result in Unique Changes in Transcription and Chromatin Organization.
Blood 140(supplement 1), 996-997 DOI:10.1182/blood-2022-163838
23. Chen, J.Y.*, Lim, D.H.*, Chen, L., Zhou, Y.L., Zhang, F.L., Shao, C.W., Zhang, X., Li, H.R.,
Wang, D., Zhang, D.E., and Fu, X.D. (2022)
Systematic Evaluation of Different R-loop Mapping Methods: Achieving Consensus,
Resolving Discrepancies and Uncovering Distinct Types of RNA:DNA Hybrids.
BioRxiv. DOI:10.1101/2022.02.18.480986 (*co-first authors)
22. Li, L.X., Luo, H.F., Lim, D.H., Han, L., Li, Y., Fu, X.D., and Qi, Y.J. (2021)
Global profiling of RNA-chromatin interactions reveals co-regulatory gene expression
networks in Arabidopsis.
Nature Plants. 7(10), 1364-1378 PMID:34650265
~2020
21. Hao, Y.J., Wang, D.P., Wu, S.H., Li, X., Shao, C.W., Zhang, P., Chen, J.Y., Lim, D.H., Fu, X.D., He, S.M., and Chen,
R.S. (2020) Active Retrotransposons Help Maintain Pericentromeric Heterochromatin Required for Faithful Cell Division.
Genome Res. 30(11), 1570-1582. PMID:33060173
20. Lee, S.J., Hong, J.S., Lim, D.H., and Lee, Y.S. (2020) Roles for Drosophila Cap1 2’-O-ribose methyltransferase in the
small RNA silencing pathway associated with Argonaute 2. Insect Biochem. Mol. Biol. 123, 103415. PMID: 32504809
19. Lim, D.H.*, Lee, S.J.*, Chou, M.S., Han, J.Y., Seong, Y.M., Na, D.K., Kwon, Y.S., and Lee, Y.S. (2020) The conserved
microRNA miR-8-3p coordinates the expression of V-ATPase subunits to regulate ecdysone biosynthesis for Drosophila
metamorphosis. FASEB J. 34(5), 6449-6465 (*co-first authors). PMID: 32196731
18. Gou, L.T.*, Lim, D.H.*, Ma, W.B.*, Aubol, B.E., Hao, Y.J., Wang, X., Zhao, J., Liang, Z.Y., Shao, C.W., Zhang, X., Meng,
F., Li, H.R., Zhang, X.R., Xu, R.M., Li, D.S., Rosenfeld, M.G., Mellon, P.L., Adams, J.A., Liu, M.F., and Fu, X.D. (2020)
Initiation of Parental Genome Reprogramming in Fertilized Oocyte by Splicing Kinase SRPK1-Catalyzed Protamine
Phosphorylation. Cell 180(6), 1212-1227 (*co-first authors). PMID: 3216915
17. Chen, J.Y., Lim, D.H., and Fu, X.D. (2020) Mechanistic Dissection of RNA Binding Proteins in Regulated Gene
Expression at Chromatin Levels. Cold Spring Harb. Symp. Quant. Biol. 84, 55-66. PMID: 31900328
16. Zhou, B., Li, X., Luo, D., Lim, D.H., Zhou, Y., and Fu, X.D. (2019). GRID-seq for comprehensive analysis of global RNA-
chromatin interactions. Nature Protocols. 14(7), 2036-2068. PMID: 31175345
15. Lim, D.H.*, Lee, S.*, Han, J.Y.*, Choi, M.S., Hong, J.S., and Lee, Y.S. (2019). MicroRNA miR-252 targets mbt to control
the developmental growth of Drosophila. Insect Mol. Biol. 28(3), 444-454. (*co-first authors). PMID: 30582233
14. Lim, D.H.*, Lee, S.*, Han, J.Y., Choi, M.S., Hong, J.S., Seong, Y., Kwon, Y.S., and Lee, Y.S. (2018). Ecdysone-
responsive microRNA-252-5p controls the cell cycle by targeting Abi in Drosophila. FASEB J. 32(8), 4519-4533. (*co-
first authors). PMID: 29543534
13. Bao, X., Guo, X., Yin, M., Tariq, M., Lai, Y., Kanwal, S., Zhou, J., Li, N., Lv, Y., Pulido-Quetglas, C., Wang, X., Ji, L.,
Khan, M.J., Zhu, X., Luo, Z., Shao, C., Lim, D.H., Liu, X., Li, N., Wang, W., He, M.H., Liu, Y.L., Ward, C., Wang, T. ,
Zhang, G., Wang, D.Y., Yang, J.H., Chen, Y.W., Zhang, C.L., Jauch, R., Yang, Y.G., Wang, Y.M., Qin, B.M., Anko, M.L.,
Hutchins, A.P., Sun, H., Wang, H.T., Fu, X.D., Zhang, B.L., and Esteban, M.A. (2018). Capturing the interactome of
newly transcribed RNA. Nature Methods. 15(3), 213-220. PMID: 29431736
12. Lim, J.H., Kim, D.J., Lee, D.E., Han, J.Y., Chung, J.H., Ahn, H.K., Lee, S.W., Lim, D.H., Lee, Y.S., Park, S.Y., and Ryu,
H.M. (2015). Genome-wide microRNA expression profiling in placentas of fetuses with Down syndrome. Placenta.
36(3), 322-328.
11. Seong, Y., Lim, D.H., Kim, A., Seo, J.H., Lee, Y.S., Song, H., and Kwon, Y.S. (2014). Global identification of target
recognition and cleavage by the Microprocessor in human ES cells. Nucleic Acids Res. 42(20), 12806-12821.
10. Lim, D.H., Oh, C.T., Han, S.J., and Lee, Y.S. (2014). Methods for studying the biological consequences of endo-siRNA
deficiency in Drosophila melanogaster. Methods Mol. Biol. 1173, 51-58.
9. Joo, J.Y., Lee, J., Ko, H.Y., Lee, Y.S., Lim, D.H., Kim, E.Y., Cho, S., Hong, K.S., Ko, J.J., Lee, S., Lee, Y.S., Choi, Y.S.,
Lee, K.A., and Kim, S.H. (2014). Microinjection free delivery of miRNA inhibitor into zygotes. Sci. Rep. 4, 5417.
8. Lim, D.H., Lee, L., Oh, C.T., Kim, N.H., Hwang, S., Han, S.J., and Lee, Y.S. (2013). Microarray analysis of Drosophila
dicer-2 mutants reveals potential regulation of mitochondrial metabolism by endogenous siRNAs. J. Cell. Biochem.
114(2), 418-427.
7. Kwak, G.H., Lim, D.H., Han, J.Y., Lee, Y.S., and Kim, H.Y. (2012). Methionine sulfoxide reductase B3 protects from
endoplasmic reticulum stress in Drosophila and in mammalian cells. Biochem. Biophys. Res. Commun. 420(1), 130-
135.
6. Lim, D.H., Han, J.Y., Kim, J.R., Lee, Y.S., and Kim, H.Y. (2012). Methionine sulfoxide reductase B in the endoplasmic
reticulum is critical for stress resistance and aging in Drosophila. Biochem. Biophys. Res. Commun. 419(1), 20-26.
5. Lim, D.H.*, Oh, C.T.*, Lee, L., Hong, J.S., Noh, S.H., Hwang, S., Kim, S., Han, S.J., and Lee, Y.S. (2011). The
endogenous siRNA pathway in Drosophila impacts stress resistance and lifespan by regulating metabolic homeostasis.
FEBS Lett. 585(19), 3079-3085. (*co-first authors)
4. Cho, I.S., Kim, J., Seo, H.Y., Lim, D.H., Hong, J.S., Park, Y.H., Park, D.C., Hong, K.C., Whang, K.Y., and Lee, Y.S.
(2010). Cloning and characterization of microRNAs from porcine skeletal muscle and adipose tissue. Mol. Biol. Rep.
37(7), 3567-3574.
3. Lee, Y.S., Pressman, S., Andress, A.P., Kim, K., White, J.L., Cassidy, J.J., Li, X., Lubell, K., Lim, D.H., Cho, I.S.,
Nakahara, K., Preall, J.B., Bellare, P., Sontheimer, E.J., and Carthew, R.W. (2009). Silencing by small RNAs is linked to
endosomal trafficking. Nature Cell Biology 11(9), 1150-1156.
2. Cho, I.S., Kim, J., Lim, D.H., Ahn, H.C., Kim, H., Lee, K.B., and Lee, Y.S. (2008). Improved serum stability and
biophysical properties of siRNAs following chemical modifications. Biotechnol. Lett. 30(11), 1901-1908.
1. Lim, D.H.*, Kim, J.*, Kim, S.U., Carthew, R.W., and Lee, Y.S. (2008). Functional analysis of dicer-2 missense mutations in the siRNA pathway of Drosophila. Biochem. Biophys. Res. Commun. 371(3), 525-530. (*co-first authors)