Hailing Shi

Department of Human Genetics
Assistant Professor

Health Sciences Research Building (HSRB-II)
1750 Haygood Dr NE, N650

Overview

Gene expression is extensively regulated at the RNA level in the nervous system during development and function, including RNA localization, RNA modifications, alternative splicing, etc. In addition, the dysregulation of RNA binding proteins has been observed in various neurodegenerative and neurological disorders. The brain contains diverse cellular microenvironments and complex cell morphologies, making it challenging to understand RNA biology in cell-type-specific and subcellular-compartment-resolved matter. Spatial transcriptomics offers a powerful solution by enabling high-throughput RNA profiling while retaining spatial information, opening up opportunities to characterize cellular, pathogenic, and therapeutic RNAs within their tissue context.

The Shi Lab is dedicated to uncovering the principles of context-dependent RNA regulation underlying brain physiology and malfunction and ultimately modulating gene expression in a context-dependent matter. By integrating nucleic acid chemistry, spatial genomics, and machine-learning-assisted computation, the lab is interested in the following research goals:

(1) Advancing spatial genomics tools to enable a deeper understanding of RNA regulation specific to brain tissues, cell types, and subcellular compartments.
(2) Gaining molecular insights into brain cellular and tissue functions by combining spatial genomics and reporter engineering.
(3) Modulating gene expression in a cell-state-specific manner through spatial-omics-informed rational designs of gene delivery vectors and carriers.

Academic Appointment

Assistant Professor, Human Genetics, Emory University School of Medicine

Education

Degrees

Postdoctoral Fellow from Broad Institute
PhD Chemistry from University of Chicago
B.S. Chemistry from Peking University

Research

Publications

Spatial omics advances for in situ RNA biology.
Mol Cell Volume: 84 Page(s): 3737 - 3757
10/03/2024 Authors: Ren J; Luo S; Shi H; Wang X
Publisher Correction: Spatial atlas of the mouse central nervous system at molecular resolution.
Nature Volume: 625 Page(s): E6
01/01/2024 Authors: Shi H; He Y; Zhou Y; Huang J; Maher K; Wang B; Tang Z; Luo S; Tan P; Wu M
FMRP phosphorylation modulates neuronal translation through YTHDF1.
Mol Cell Volume: 83 Page(s): 4304 - 4317.e8
12/07/2023 Authors: Zou Z; Wei J; Chen Y; Kang Y; Shi H; Yang F; Shi Z; Chen S; Zhou Y; Sepich-Poore C
Spatial atlas of the mouse central nervous system at molecular resolution.
Nature Volume: 622 Page(s): 552 - 561
10/01/2023 Authors: Shi H; He Y; Zhou Y; Huang J; Maher K; Wang B; Tang Z; Luo S; Tan P; Wu M
Spatially resolved single-cell translatomics at molecular resolution.
Science Volume: 380 Page(s): eadd3067
06/30/2023 Authors: Zeng H; Huang J; Ren J; Wang CK; Tang Z; Zhou H; Zhou Y; Shi H; Aditham A; Sui X
Multimodal charting of molecular and functional cell states via in situ electro-sequencing.
Cell Volume: 186 Page(s): 2002 - 2017.e21
04/27/2023 Authors: Li Q; Lin Z; Liu R; Tang X; Huang J; He Y; Sui X; Tian W; Shen H; Zhou H
Chemically Modified mocRNAs for Highly Efficient Protein Expression in Mammalian Cells.
ACS Chem Biol Volume: 17 Page(s): 3352 - 3366
12/16/2022 Authors: Aditham A; Shi H; Guo J; Zeng H; Zhou Y; Wade SD; Huang J; Liu J; Wang X
ClusterMap for multi-scale clustering analysis of spatial gene expression.
Nat Commun Volume: 12 Page(s): 5909
10/08/2021 Authors: He Y; Tang X; Huang J; Ren J; Zhou H; Chen K; Liu A; Shi H; Lin Z; Li Q
Exposure to constant light impairs cognition with FTO inhibition and m6A-dependent TrB repression in mouse hippocampus.
Environ Pollut Volume: 283 Page(s): 117037
08/15/2021 Authors: Yang Y; Feng Y; Hu Y; Liu J; Shi H; Zhao R
EGFR/SRC/ERK-stabilized YTHDF2 promotes cholesterol dysregulation and invasive growth of glioblastoma.
Nat Commun Volume: 12 Page(s): 177
01/08/2021 Authors: Fang R; Chen X; Zhang S; Shi H; Ye Y; Shi H; Zou Z; Li P; Guo Q; Ma L
YTHDF3 Induces the Translation of m6A-Enriched Gene Transcripts to Promote Breast Cancer Brain Metastasis.
Cancer Cell Volume: 38 Page(s): 857 - 871.e7
12/14/2020 Authors: Chang G; Shi L; Ye Y; Shi H; Zeng L; Tiwary S; Huse JT; Huo L; Ma L; Ma Y
Publisher Correction: Recognition of RNA N6-methyladenosine by IGF2BP proteins enhances mRNA stability and translation.
Nat Cell Biol Volume: 22 Page(s): 1288
10/01/2020 Authors: Huang H; Weng H; Sun W; Qin X; Shi H; Wu H; Zhao BS; Mesquita A; Liu C; Yuan CL
Genetic analyses support the contribution of mRNA N6-methyladenosine (m6A) modification to human disease heritability.
Nat Genet Volume: 52 Page(s): 939 - 949
09/01/2020 Authors: Zhang Z; Luo K; Zou Z; Qiu M; Tian J; Sieh L; Shi H; Zou Y; Wang G; Morrison J
m6A mRNA methylation controls autophagy and adipogenesis by targeting Atg5 and Atg7.
Autophagy Volume: 16 Page(s): 1221 - 1235
07/01/2020 Authors: Wang X; Wu R; Liu Y; Zhao Y; Bi Z; Yao Y; Liu Q; Shi H; Wang F; Wang Y
Molecular biology of oral cavity squamous cell carcinoma.
Oral Oncol Volume: 102 Page(s): 104552
03/01/2020 Authors: Hsu PJ; Yan K; Shi H; Izumchenko E; Agrawal N
The RNA-binding protein FMRP facilitates the nuclear export of N6-methyladenosine-containing mRNAs.
J Biol Chem Volume: 294 Page(s): 19889 - 19895
12/27/2019 Authors: Hsu PJ; Shi H; Zhu AC; Lu Z; Miller N; Edens BM; Ma YC; He C
Regulation of Co-transcriptional Pre-mRNA Splicing by m6A through the Low-Complexity Protein hnRNPG.
Mol Cell Volume: 76 Page(s): 70 - 81.e9
10/03/2019 Authors: Zhou KI; Shi H; Lyu R; Wylder AC; Matuszek ; Pan JN; He C; Parisien M; Pan T
Where, When, and How: Context-Dependent Functions of RNA Methylation Writers, Readers, and Erasers.
Mol Cell Volume: 74 Page(s): 640 - 650
05/16/2019 Authors: Shi H; Wei J; He C
Single base resolution mapping of 2'-O-methylation sites in human mRNA and in 3' terminal ends of small RNAs.
Methods Volume: 156 Page(s): 85 - 90
03/01/2019 Authors: Hsu PJ; Fei Q; Dai Q; Shi H; Dominissini D; Ma L; He C
Transcriptome-wide reprogramming of N6-methyladenosine modification by the mouse microbiome.
Cell Res Volume: 29 Page(s): 167 - 170
02/01/2019 Authors: Wang X; Li Y; Chen W; Shi H; Eren AM; Morozov A; He C; Luo G-Z; Pan T
mRNA m6A plays opposite role in regulating UCP2 and PNPLA2 protein expression in adipocytes.
Int J Obes (Lond) Volume: 42 Page(s): 1912 - 1924
11/01/2018 Authors: Wang X; Sun B; Jiang Q; Wu R; Cai M; Yao Y; Liu Q; Shi H; Feng J; Wang Y
m6A facilitates hippocampus-dependent learning and memory through YTHDF1.
Nature Volume: 563 Page(s): 249 - 253
11/01/2018 Authors: Shi H; Zhang X; Weng Y-L; Lu Z; Liu Y; Lu Z; Li J; Hao P; Zhang Y; Zhang F
Author Correction: Suppression of m6A reader Ythdf2 promotes hematopoietic stem cell expansion.
Cell Res Volume: 28 Page(s): 1042
10/01/2018 Authors: Li Z; Qian P; Shao W; Shi H; He XC; Gogol M; Yu Z; Wang Y; Qi M; Zhu Y
Differential m6A, m6Am, and m1A Demethylation Mediated by FTO in the Cell Nucleus and Cytoplasm.
Mol Cell Volume: 71 Page(s): 973 - 985.e5
09/20/2018 Authors: Wei J; Liu F; Lu Z; Fei Q; Ai Y; He PC; Shi H; Cui X; Su R; Klungland A
Author Correction: Recognition of RNA N6-methyladenosine by IGF2BP proteins enhances mRNA stability and translation.
Nat Cell Biol Volume: 20 Page(s): 1098
09/01/2018 Authors: Huang H; Weng H; Sun W; Qin X; Shi H; Wu H; Zhao BS; Mesquita A; Liu C; Yuan CL
Suppression of m6A reader Ythdf2 promotes hematopoietic stem cell expansion.
Cell Res Volume: 28 Page(s): 904 - 917
09/01/2018 Authors: Li Z; Qian P; Shao W; Shi H; He XC; Gogol M; Yu Z; Wang Y; Qi M; Zhu Y
Mettl14 Is Essential for Epitranscriptomic Regulation of Striatal Function and Learning.
Neuron Volume: 99 Page(s): 283 - 292.e5
07/25/2018 Authors: Koranda JL; Dore L; Shi H; Patel MJ; Vaasjo LO; Rao MN; Chen K; Lu Z; Yi Y; Chi W
Ythdf2-mediated m6A mRNA clearance modulates neural development in mice.
Genome Biol Volume: 19 Page(s): 69
05/31/2018 Authors: Li M; Zhao X; Wang W; Shi H; Pan Q; Lu Z; Perez SP; Suganthan R; He C; Bjrs M
Recognition of RNA N6-methyladenosine by IGF2BP proteins enhances mRNA stability and translation.
Nat Cell Biol Volume: 20 Page(s): 285 - 295
03/01/2018 Authors: Huang H; Weng H; Sun W; Qin X; Shi H; Wu H; Zhao BS; Mesquita A; Liu C; Yuan CL
Phasing Gene Expression: mRNA N6-Methyladenosine Regulates Temporal Progression of Mammalian Cortical Neurogenesis.
Biochemistry Volume: 57 Page(s): 1055 - 1056
02/20/2018 Authors: Shi H; He C
METTL14 Inhibits Hematopoietic Stem/Progenitor Differentiation and Promotes Leukemogenesis via mRNA m6A Modification.
Cell Stem Cell Volume: 22 Page(s): 191 - 205.e9
02/01/2018 Authors: Weng H; Huang H; Wu H; Qin X; Zhao BS; Dong L; Shi H; Skibbe J; Shen C; Hu C
Epitranscriptomic influences on development and disease.
Genome Biol Volume: 18 Page(s): 197
10/23/2017 Authors: Hsu PJ; Shi H; He C
N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis.
Nat Struct Mol Biol Volume: 24 Page(s): 870 - 878
10/01/2017 Authors: Edupuganti RR; Geiger S; Lindeboom RGH; Shi H; Hsu PJ; Lu Z; Wang S-Y; Baltissen MPA; Jansen PWTC; Rossa M
Ythdc2 is an N6-methyladenosine binding protein that regulates mammalian spermatogenesis.
Cell Res Volume: 27 Page(s): 1115 - 1127
09/01/2017 Authors: Hsu PJ; Zhu Y; Ma H; Guo Y; Shi X; Liu Y; Qi M; Lu Z; Shi H; Wang J
m6A RNA Methylation Regulates the Self-Renewal and Tumorigenesis of Glioblastoma Stem Cells.
Cell Rep Volume: 18 Page(s): 2622 - 2634
03/14/2017 Authors: Cui Q; Shi H; Ye P; Li L; Qu Q; Sun G; Sun G; Lu Z; Huang Y; Yang C-G
YTHDF3 facilitates translation and decay of N6-methyladenosine-modified RNA.
Cell Res Volume: 27 Page(s): 315 - 328
03/01/2017 Authors: Shi H; Wang X; Lu Z; Zhao BS; Ma H; Hsu PJ; Liu C; He C
m6A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition.
Nature Volume: 542 Page(s): 475 - 478
02/23/2017 Authors: Zhao BS; Wang X; Beadell AV; Lu Z; Shi H; Kuuspalu A; Ho RK; He C
A glance at N(6)-methyladenosine in transcript isoforms.
Nat Methods Volume: 13 Page(s): 624 - 625
07/28/2016 Authors: Shi H; He C
N(6)-methyladenosine Modulates Messenger RNA Translation Efficiency.
Cell Volume: 161 Page(s): 1388 - 1399
06/04/2015 Authors: Wang X; Zhao BS; Roundtree IA; Lu Z; Han D; Ma H; Weng X; Chen K; Shi H; He C

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