Research 

Those bacteria that constantly adapt due to the rapid and continuous changes in the ecological environment have more pseudogenes. Traditionally considered non-functional remnants, pseudogenes are increasingly recognized for their potential roles in cellular processes. Recent some studies have revealed that pseudogenification can affect the metabolism of the prokaryote genomes and certain pseudogenes can be transcribed and even translated (somehow).

My research aims to integrate computational method (currently used probability model-based tool LAST, which designed by Dr. Martin Frith) to identify and characterize pseudogenes and its functions (evolution, antiviral, biosynthetic and metabolism) in prokaryotes.

Future:

• Combine different computational methods (classical alignment tools and ML/DL)

• Analyze different data (DNA, RNA, assembled genomes from different tool)

• Willing to construct a tool or framework to analyze the pseudogene in prokaryotes

Repeat elements, which make up 55% of the human genome (e.g., LINE1, SINE, ERV), play essential roles in human genome, beyond being genetic fossils. Integrating into host genomes, some of repeat elements have been repurposed by the host for some specific functions, for instance, gene regulation or encoding "extra" protein.

Current:

• (Collaborative) Utilize interactions detected biotechnology: RADICL-seq (from RIKEN), to analyze the repeats involved possible regulation in breast cancer estrogen-independence cell transition, from MCF7 to Long term estrogen deprivation (LTED) cells. (under preparing for journal, a rough speech in GIW-2023)

Future:

• To be honest, I am not very sure now. Next new research should one focus on a certain repeat or a certain type of species...

1. Frith M C, Ni S. DNA conserved in diverse animals since the Precambrian controls genes for embryonic development. Molecular Biology and Evolution. (2023).

2. Zhang H*, Ni S* and Frith M C. An immune-suppressing protein in human endogenous retroviruses. Bioinformatics Advances (2023, GIW ISCB-Asia 2022 associated).

1. Ni S*, Shu S*, Kato M, Saitoh N and Frith M C. Repeat elements enriched in cis-regulatory regions act in cancer cell transition to estrogen-independence. Oral Presentation.  GIW ISCB-Asia 2023 (recommend to NAR Genomics and Bioinformatics).

2. Ni S*, Shu S*, Kato M, Saitoh N and Frith M C. Investigating the role of repeat elements in promoting the transition of MCF7 cells to LTED cells. Oral Presentation. The 11th IIBMP (2022).

3. Ni S* and Frith M C. K The protein fossil record in prokaryote genomes: a hidden treasure. Oral Presentation. The 11th IIBMP (2022).

1. Ni S*, Shu S*, Kato M, Saitoh N, Frith M C, Palihati M, Carninci P. Repeat elements enriched in cis-regulatory regions act in cancer cell transition to estrogen-independence. Poster. Cold Spring Harbor Asia meeting on Chromatin, Epigenetics & Transcription (2024)

2. Ni S*, Shu S*, Kato M, Saitoh N and Frith M C. Investigating the role of repeat elements in promoting the transition of MCF-7 cells to LTED cells. Poster. The 46rd annual meeting of MBSJ (2023).

3. Ni S*, Shu S*, Kato M, Saitoh N and Frith M C. Investigating the role of repeat elements in promoting the transition of MCF-7 cells to LTED cells. Poster. The 68th HGA (2023). 

4. Ni S* and Ui-Tei K. Design and validation of antiviral siRNAs for targeting the conserved regions in coronavirus. Poster. The 43rd annual meeting of MBSJ (2020).

5. Ni S* and Ui-Tei K. Design and validation of antiviral siRNAs for targeting the conserved regions in coronavirus. Poster. The 25th annual meeting of RNA Biology (2020).