Sujin Kim

Ph.D. Candidate @ BNAL in KAIST

I'm a Ph.D. Candidate at Bio Network Analysis Lab, advised by Prof. Yoosik Kim at Korea Advanced Institute of Science and Technology (KAIST). My research keywords are epitranscriptomics, endogenous double-stranded RNA (dsRNA), mitochondria, and degenerative disease.

Contact: kuki430@kaist.ac.kr
You can also use this email: ksj55605690@gmail.com

Education

2019.02 - Present
Ph.D. in Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
Advisor: Professor Yoosik Kim
Dissertation title: Mitochondrial double-stranded RNA: Discovery, Regulation, and Function
2017.02 - 2019.02
M.S. in Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
Advisor: Professor Yoosik Kim
Thesis title: Establishing mitochondrial RNAs as a pathophysiological marker for arthritis

2013.03 - 2017.02
B.S. in Biosystem and Biomedical Science, Korea University, Seoul, Republic of Korea

RESEARCH INTEREST

Epitranscriptomics (RNA modification)
Non-coding RNA
Endogenous double-stranded RNA
Regulation of mitochondrial dsRNA strands
Degenerative disease

PUBLICATIONS

Mitochondrial double-stranded RNAs govern the stress response in chondrocytes to promote osteoarthritis development

Sujin Kim*, Keonyong Lee*, Yong Seok Choi, Jayoung Ku, Hyeonkyeong Kim, Raisa Kharbash, Jimin Yoon, Yong Seuk Lee, Jin Hong Kim, Yun Jong Lee#, and Yoosik Kim#

Cell reports. 40, 111178 (2022)

Keywords: Mitochondrial double-stranded RNA; Protein kinase R; Toll-like receptor 3; Autophagy; Osteoarthritis

https://doi.org/10.1016/j.celrep.2022.111178

PKR Senses Nuclear and Mitochondrial Signals by Interacting with Endogenous Double-Stranded RNAs

Yoosik Kim*#, Joha Park*, Sujin Kim*, MinA Kim, Myeong-Gyun Kang, Chulhwan Kwak, Minjeong Kang, Baekgyu Kim, Hyun-Woo Rhee, and V. Narry Kim#

Molecular Cell. 71, 1051-1063 (2018)

Keywords: cellular dsRNAs; mitochondrial RNAs; PKR; Alu; retrotransposons; mitochondria; cell cycle; stress response; high-throughput sequencing; fCLIP-seq

https://doi.org/10.1016/j.molcel.2018.07.029.

Highlighted in Nature Chemical Biology. https://www.nature.com/articles/s41589-018-0159-4

Analysis of mitochondrial double-stranded RNAs in human cells

Sujin Kim*, Jimin Yoon*, Keonyong Lee, and Yoosik Kim#

STAR Protocol. In revision

Keywords: Mitochondrial double-stranded RNA; Immunocytochemistry; Small-molecule RNA fluorescence in situ hybridization; Strand-specific RT-qPCR

Mitochondrial double-stranded RNAs as a pivotal mediator in the pathogenesis of Sjӧgren's syndrome

Jimin Yoon, Minseok Lee, Ahsan Ausaf Ali, Ye Rim Oh, Yong Seok Choi, Sujin Kim, Namseok Lee, Se Gwang Jang, Seonghyeon Park, Jin-Haeng Chung, Seung-Ki Kwok, Joon Young Hyon, Seunghee Cha, Yun Jong Lee, Sung Gap Im, and Yoosik Kim#

Molecular Therapy Nucleic Acids. 30, 257-269 (2022)

Keywords: Mitochondrial double-stranded RNA; Protein kinase R; Autoimmunity; Sjӧgren's syndrome

https://doi.org/10.1016/j.omtn.2022.09.020

Evidence of Aberrant Immune Response by Endogenous Double-Stranded RNAs: Attack from Within

Sujin Kim, Yongsuk Ku, Jayoung Ku, and Yoosik Kim#

BioEssays. 41, e1900023 (2019)

Keywords: Alu; double-stranded RNA; endogenous retroviral element; innate immune responses; long interspersed nuclear element; mitochondrial RNA

https://doi.org/10.1002/bies.201900023

Studying RNA interactors of protein kinase RNA-activated during the mammalian cell cycle

Sujin Kim, Minjeong Kang, and Yoosik Kim#

J. Vis. Exp. 145, e59215 (2019)

Keywords: double-stranded RNA; protein kinase RNA-activated (PKR); RNA-binding protein; cell cycle; high-throughput sequencing

https://www.jove.com/t/59215/studying-rna-interactors-protein-kinase-rna-activated-during

Biophysical and biochemical approaches in the analysis of Argonaute-microRNA complexes

Sujin Kim and Yoosik Kim#

Springer, New York, NY. 167-188 (2019)

Keywords: MicroRNA; Argonaute; RISC; Protein structure; Single-molecule experiment; Speed-stability paradox

https://doi.org/10.1007/978-1-4939-9726-8_8

Honors and awards

RNA 2022 Poster Prize Winner, The 27th Annual Meeting of the RNA Society (USA), 2022
KSMCB Young Investigator Research Award, Korean Society for Molecular and Cellular Biology (KSMCB), 2020
Graduate Students in Biomedical Research Fellowship, ASAN foundation (KRW 40,000,000/2 years), 2020-2021
Best Poster Award at 2018 KAIST CBE Graduate Student Symposium, Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST CBE), 2018

GRANT

Research Subsidies for Ph.D. Candidates, National Research Foundation of Korea (KRW 40,000,000/2 years) (2020.06 - 2022.05)
Title: Investigation on pathophysiological function of endogenous double-stranded RNAs in osteoarthritis
Research Program for Graduate and PhD Students, Korea Advanced Institute of Science and Technology (KAIST) (KRW 9,000,000/8 months) (2017.05 - 2017.12)
Title: Development of double-stranded RNA based prediction software for osteoarthritis

PATENT

Yoosik Kim, Ahsan Ausaf Ali, Raisa Kharbash, Minjeong Kang, Sujin Kim. "Method for providing information on diagnosing cancer using analyzing dsRNA expression" (Patent number: 10-2341059, Application number: 10-2019-0127999), Korea

Conference

2022 Oral/Poster Presentation
NSUN4-mediated RNA 5-methylcytosine Promotes Degradation of Mitochondrial Double-stranded RNA, Epigenetics and Epigenomics in Health and Disease (Belgium, Brussels)
2022 Oral Presentation
NSUN4-mediated RNA 5-methylcytosine Promotes Degradation of Mitochondrial Double-stranded RNA, Invited talk, KAIST RNA Club
2022 Poster
RNA methylation by NSUN4 marks mitochondrial double-stranded RNAs for degradation, Poster Prize Winner, The 27th Annual Meeting of the RNA Society (USA)
2021 Poster
CRISPR Screening of Mitochondrial RNA-binding Proteins Reveals Dynamic Regulation of Mitochondrial Double-stranded RNAs, 2021 International Conference Korean society for molecular and cellular biology (KSMCB)
2021 Oral Presentation
Release of mitochondrial double-stranded RNAs aggravates chondrocyte damage during osteoarthritis development, 2021 IBS-SNU MINI-SYMPOSIA ON RNA BIOLOGY & THERAPEUTICS
2020 Oral Presentation
Mitochondrial dsRNAs activate PKR and TLR3 to promote chondrocyte degeneration in osteoarthritis, Young Investigator's Session 1, 2020 International Conference: Korean Society for Molecular and Cellular Biology (KSMCB)
2019 Poster
Investigation on Establishing PKR and Mitochondrial dsRNAs as Pathophysiological Markers for Osteoarthritis, 84th Cold Spring Harbor Symposium (RNA control & regulation CSH)
2018 Poster
Regulation of PKR Activation by Mitochondrial Double-Stranded RNAs, RNA Biology meetings on CSH-Asia
2018 Poster
Establishing Mitochondrial RNAs as Novel Functional Markers for Arthritis, Best Poster Award, The 8th Graduate Students Symposium in the Department of Chemical and Biomolecular Engineering

Teaching experience

2022 Fall
Teaching Assistant, Engineering Principles in Biological Systems (CBE463)
2020 Summer/Fall
Teaching Assistant, Summer/Fall semester URP Program, Development of effective cancer treatment by CRISPR-Cas9 screening of novel mitochondrial dsRNAs regulatory factors (Stephanie Tan), 2nd Prize
2020 Spring
Teaching Assistant, Chemical and Biomolecular Engineering Laboratory (CBE301, Topic: Kinetics of Free and Immobilized Enzyme Systems)
2019 Summer/Fall
Teaching Assistant, Summer/Fall semester URP Program, Establishing engineered osteoarthritis mimic platform to identify RNA based marker of the disease (Keonyong Lee), 2nd Prize
2019 Fall
Teaching Assistant, Chemical and Biomolecular Engineering Laboratory (CBE301, Topic: Purification and electrophoresis analysis of plasmid DNA & proteins from Escherichia coli), Excellent TA
2019 Spring
Teaching Assistant, Molecular Reaction Engineering (CBE311)
2018 Winter/Spring
Co-teaching Assistant with a student from prof. Shang Li's lab, Winter/Spring semester URP Program, Development of autophagy inducer material for prevention and treatment of osteoarthritis (Namseok Lee)
2018 Fall
Teaching Assistant, Understanding religious studies
2018 Spring
Teaching Assistant, Molecular Reaction Engineering (CBE311)