The paper identifies a HNRNPU-CHD2 RNA-processing axis linked to neurodevelopmental disease by showing HNRNPU depletion causes splicing changes in CHD2 that may lead to nonsense-mediated decay.

bioRxiv · Nov 3, 2026 · PreprintCell Biology

SALL2 constrains TEAD4 by maintaining repressive chromatin to restrict trophectoderm identity

Yu Qiao, Jianfei Xu, Lin Zheng, Zhen Xiao, Zhuoqi Huang, Zhangting Liang, Xuemeng Zhou, Gang Ma, Guoqing Tong, Miguel Angel Esteban, Andrew P. Hutchins

This study shows SALL2 restricts trophectoderm identity by maintaining repressive chromatin at TEAD4-bound loci, preventing TE lineage commitment in human pluripotent stem cells.

bioRxiv · Jul 10, 2026 · PreprintCell Biology

Dissecting the Contribution of Transposable Elements to Interphase Chromosome Structure

Liyang Shi, Zhen Xiao, Isaac A. Babarinde, Fu Xiuling, Gang Ma, Zhouqi Huang, Li Sun, Xuemeng Zhou, Jiangping He, Alexander V. Strunnikov, Andrew P. Hutchins

This study shows transposable elements contribute significantly to 3D genome structure by mediating chromatin contacts through specific transcription factors.

Genome biology · Jan 20, 2026Peer-reviewedCell Biology

Transposable Element Expression and Sub-cellular Dynamics During hPSC Differentiation to Endoderm, Mesoderm, and Ectoderm Lineages

Isaac A. Babarinde, Xiuling Fu, Gang Ma, Yuhao Li, Zhangting Liang, Jianfei Xu, Zhen Xiao, Yu Qiao, Lin Zheng, Katerina Oleynikova, Mobolaji T. Akinwole, Xuemeng Zhou, Alexey S. Ruzov, Andrew P. Hutchins

This study examines TE expression and sub-cellular dynamics during hPSC differentiation to endoderm, mesoderm, and ectoderm lineages, revealing lineage-specific TE expression patterns and chromatin associations.

Nature Communications · Aug 18, 2025Peer-reviewedGenomics

Thioredoxin-1 inhibits granulosa cell ferroptosis to rescue ovarian aging through mitophagy-dependent activation of BNIP3L

Wenting Yang, Xiaorui Zhang, Rui Xu, Zhuoqi Huang, Yanmin Ma, Jiao Yang, Lin Zheng, Gang Ma, Jianfei Xu, Yu Qiao, Zhen Xiao, Jing Cao, Shan Li, Xinyu Zhang, Andrew P. Hutchins, Guoqing Tong

This study shows that Thioredoxin-1 prevents granulosa cell ferroptosis by promoting mitophagy, thereby improving ovarian aging and fertility in mice.

bioRxiv · Jul 12, 2025 · PreprintCell Biology

BRD8 guards the pluripotent state by sensing and maintaining histone acetylation

Li Sun, Xiuling Fu, Zhen Xiao, Gang Ma, Yibin Zhou, Haoqing Hu, Liyang Shi, Dongwei Li, Ralf Jauch, Andrew P. Hutchins

This study shows BRD8 maintains pluripotency by sensing and maintaining histone acetylation, preventing the conversion of primed EpiSCs to naive ESCs.

Advanced Science · Dec 10, 2024Peer-reviewedCell Biology

Human embryos arrest in a quiescent-like state characterized by metabolic and zygotic genome activation problems

Yang Yang, Liyang Shi, Xiuling Fu, Gang Ma, Zhongzhou Yang, Yuhao Li, Yibin Zhou, Lihua Yuan, Ye Xia, Xiufang Zhong, Ping Yin, Li Sun, Wuwen Zhang, Isaac A. Babarinde, Yongjun Wang, , Guoqing Tong

This study identifies a quiescent-like state in arrested IVF embryos and shows that modulating metabolic pathways can rescue the arrest.

bioRxiv · Dec 19, 2021 · PreprintDevelopmental Biology

Unveiling transposable element expression heterogeneity in cell fate regulation at the single-cell level

Jiangping He, Isaac A. Babarinde, Li Sun, Shuyang Xu, Ruhai Chen, Junjie Shi, Yuanjie Wei, Yuhao Li, Gang Ma, Qiang Zhuang, Andrew P. Hutchins, Jiekai Chen

The paper develops a single-cell TE analysis pipeline, scTE, and shows TEs are dynamically expressed in various cell states and can be used for cell type discrimination.

Nature Communications · Mar 5, 2021Peer-reviewedBioinformatics

Transposable Element-Gene Splicing Modulates the Transcriptional Landscape of Human Pluripotent Stem Cells

Isaac A. Babarinde, Gang Ma, Yuhao Li, Boping Deng, Zhiwei Luo, Hao Liu, Mazid Md. Abdul, Carl Ward, Minchun Chen, Xiuling Fu, Martha Duttlinger, Jiangping He, Li Sun, Wenjuan Li, Qiang Zhuang, , Andrew P. Hutchins

This study shows that transposable elements contribute to the transcriptome of human pluripotent stem cells by being spliced into coding and non-coding transcripts, affecting gene expression and generating novel peptides.

bioRxiv · Jul 26, 2020 · PreprintGenomics