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Xie Lab

Lab Members

Research

Publications

Bookmarks

Courses

Lab DATABASES:

• 1. Splice Site Matrices of >1000 Species/lineages

2. REPAG_GenomesR38R91

(Consensus of 1000 human REPAG intron ends. Credit: Aydan Wang)
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Other links:

Faculty of Graduate Studies

• Department of Physiology & Pathophysiology

College of Medicine
Faculty of Health Sciences
University of Manitoba

CONTACT:
Prof. Jiuyong Xie
Department of Physiology
University of Manitoba
440 Basic Medical Sciences Bldg
745 Bannatyne Avenue
Winnipeg, MB  CANADA
R3E 0J9
Tel  +1-204 975-7774 (O),
       +1-204 975 7740 (lab)
Email: xiej@umanitoba.ca

ZOOM Meeting ID: 626 2950 9516
(by email appointment only)

RESEARCH:     

        We are interested in understanding how the different fragments of a gene are selectively combined (spliced) to produce multiple products in biology and diseases.
       
        This process, called pre-mRNA splicing, has profound implications in the evolution and functional complexity of genes/gene products.  Its disruption is a cause of human genetic diseases by many mutations and also of the aberrant splicing in cancers. Our past research has focused on the molecular basis of adaptive splicing, likely involved in cell adaptation, neuron homeostasis and neurological diseases. This has also allowed us to discover and extend the scope to a novel class of introns/splice sites (REPA-harbouring) contributing to the evolution of alternative splicing, gene product diversity or to the prevention of aberrant splicing in human health/diseases. Here are more DETAILS. Particularly welcome to join us are students with backgrounds in biochemistry, genetics, computer science or statistics.

PUBLICATIONS:

1.    Joyce W, He K, Zhang M, Ogunsola S, Wu X, Joseph KT, Bogomolny D, Yu W, Springer MS, Xie J, Signore AV, Campbell KL: Parallel genetic excisions of the cardiac troponin I N-terminal extension in tachycardic mammals. bioRxiv, https://doi.org/10.1101/2023.05.19.541292

2.    Ogunsola S, Liu L, Das U, Xie J. 5-Aza-Cytidine Enhances Terminal Polyadenylation Site Usage for Full-Length Transcripts in Cells. Genes to Cells (2024) In revision. https://doi.org/10.1101/2024.02.22.581641

3.     Liu L, Nguyen H, Das U, Ogunsola S, Yu J, Lei L, Kung M, Pejhan S, Rastegar M, Xie J: Epigenetic Control of Adaptive or Homeostatic Splicing During Interval-Training Activities. Nucleic Acids Res. (2024)gkae311:1-14, https://doi.org/10.1093/nar/gkae311.|PDF|

4.     Xie, J., Wang, L. & Lin, RJ. Variations of intronic branchpoint motif: identification and functional implications in splicing and disease. Commun Biol 6, 1142 (2023). https://doi.org/10.1038/s42003-023-05513-7.

5.    Xie J and Friedman R, Editorial: Evolution in Neurogenomics. Front. Genet. (2023)14:1220750. doi: 10.3389/fgene.2023.1220750.

6.     Liu L, Das U, Ogunsola S, Xie J. Transcriptome-Wide Detection of Intron/Exon Definition in the Endogenous Pre-mRNA Transcripts of Mammalian Cells and its Regulation by Depolarization, Int. J. Mol. Sci. (2022) 23, 10157. https:// doi.org/10.3390/ijms231710157

7.     Tian L, Xie X, Das U, Chen Y, Sun Y, Liu F, Lu H, Peng N, Zhu Y, Gu X, Deng H, Xie J, Zhao X. Forming cytoplasmic stress granules PURα suppresses mRNA translation initiation of IGFBP3 to promote esophageal squamous cell carcinoma progression, Oncogene, 41, 4336–4348 (2022), https://www.nature.com/articles/s41388-022-02426-3.

8.     Ling Liu, Jinghua Feng, Julian Polimeni, Manli Zhang, Hai Nguyen, Urmi Das, Xu Zhang, Harminder Singh, Xiao-Jian Yao, Etienne Leygue, Sam K.P. Kung, and Xie J. Characterization of cell free plasma methyl-DNA from xenografted tumours to guide the selection of diagnostic markers for early-stage cancers. Frontiers in Oncology, 11:615821 (2021) Feb. 5. DOI: 10.3389/fonc.2021.615821.

9.     Xie J, Weiskirchen R. What does the 'AKT' stand for in the name 'AKT kinase'?: some historical comments. Frontiers in Oncology, 10:1329. June, 2020, https://www.frontiersin.org/articles/10.3389/fonc.2020.01329/full.

10.  Nguyen H, Das U, Xie J. Genome-wide evolution of wobble base-pairing nucleotides of branchpoint motifs with increasing organismal complexity. RNA Biology, 17:3, 311-324, Dec. 2019, http://dx.doi.org/10.1080/15476286.2019.1697548. 

11.  Nguyen H, Xie J. Widespread separation of the polypyrimidine tract from 3' AG by G tracts in association with alternative exons in metazoa and plants. Frontiers in Genetics, 9:741, published: 14 January 2019, doi: 10.3389/fgene.2018.00741. |PDF|

12.  Das U, Nguyen H, Xie J. Transcriptome protection by the expanded family of hnRNPs. RNA Biology, 16:2, 155-159, 2018 Dec 30. PMID: 30596342 DOI: 10.1080/15476286.2018.1564617.

13.  Lei L, Cao W, Liu L, Das U, Wu Y, Liu G, Sohail M, Chen Y, Xie J. Multi-level differential control of hormone gene expression programs by hnRNP L and LL in pituitary cells. Mol. Cell. Biol., 2018 May 29;38(12):e00651-17.(MCB Most-Read'04-05'18). |PDF|

14.  Nguyen H, Das U, Wang B, Xie J. The matrices and constraints of GT/AG splice sites of more than 1000 species/lineages. Gene, 2018, 660:92-101. ------ *UPDATE splice site matrices/constraints from recent Ensembl releases. **A list of alternative exons differentially spliced between male and hermaphrodite ('female') C. elegans ('sex'-specific alternative splicing in C. elegans)  from this study (Raw RNA-seq reads from 'Kramer et al, Genetics 204 (2016) 355-69' in the NCBI SRA database).

• More

Keywords: molecular biology, RNA, processing, alternative splicing, cryptic splicing, transcriptome integrity, hnRNP, gene regulation, gene expression, evolution, proteomic diversity, complexity, splicing factors, protein kinases, cell signaling, neurons, endocrine cells, SNP, mutation, cancer, GWAS, human health/genetic diseases

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A new group of introns: REPA element 'inserted' between the Py and 3'AG and its effects on alternative splicing.



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Misce. links:

1. WES, EXON, Exome and Protein-Coding Regions, Non-coding regions, UTR
2. Eradication of Polio in China
3. RNA Meeting in Winnipeg, June 23-26, 2019 Some RNA/DNA literature/history:
4. Why are the snRNAs in splicing called U1, U2, U4, U5, U6 snRNAs? Here is the original paper that describes the use of Us in the names for some of the small nuclear RNAs that are Uridylic acid-rich, by James L. Hodnett and Harris Busch of the Baylor University College of Medicine in 1968: Hodnett JL, Busch H. Isolation and characterization of uridylic acid-rich 7 S ribonucleic acid of rat liver nuclei. J Biol Chem. 1968 Dec 25;243(24):6334-42. |PDF|
5. 125 Questions in Science, which ones are related to Alternative Splicing?
6. How to present a clean, highlight revision text without the deleted words in the text or balloons after tracking changes in WORD?
7. Albert Einstein the mediocre: Why the h-index is a bogus measure of academic impact (Reader discretion is advised).
8. Sequencing RNA and its modifications Webinar

9. Opinions about the term non-coding RNA
10. 谁 翻译了基 因一词？维 基百科
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