Muhammad Shuaib

Research Scientists

Research Scientist





He obtained Ph.D in Molecular and Cellular Biology from the University of Strasbourg in 2012, and continued his postdoctoral work at the Institute of Genetics and Molecular and Cellular Biology (IGBMC), where he studied the role of histone variants in the epigenetic specification of centromeric chromatin. After joining KAUST in 2014 as a research scientist, he first pioneered in establishing epigenomic laboratory with Prof. Valerio Orlando. In his research at KAUST, he has been using genome-wide approaches combined with biochemical and molecular biology tools to investigate the role of long non-coding RNAs and RNAi proteins in 3D genome organization and gene expression regulation. He joined the Pathogen Genomic Laboratory (Prof. Arnab Pain group) on July 1, 2020. His current research interests include:

  1. Host-pathogen epigenomic interactions
  2. Host 3D genome and transcriptome remodeling upon infection
  3. Role of non-coding RNAs and RNA-protein interactions in Apicomplexan parasites

Research Interests

Dr. Shuaib's current research interests include host-pathogen epigenomic interactions, functional genomics, and non-coding RNA. 

Selected Publications

  • SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load (2022). Mourier T*Shuaib M* Hala S*, Mfarrej S*, Alofi F, Naeem R, Alsomali A, Jorgensen D, Subudhi AM, Rached FB, Guan Q, Salunke RP, Ooi A, Esau L, Douvropoulou O, Nugmanova R, Perumal S, Zhang H, Rajan I, Al-Omari A, Salih S, Shamsan A, Mutair A A, Taha J, Alahmadi A, Khotani N, Alhamss A, Mahmoud A, Alquthami A, Dageeg A, Khogeer A, Hashem AM, Moraga P, Volz E, Almontashiri N, Pain A. Nature Communication,13:601 | (*Equal first author)
  • Ago1 controls myogenic differentiation by regulating eRNA mediated CBP guided epigenome reprogramming (2021). Fallatah B*, Shuaib M*, Adroub S.A, Paytuví-Gallart A, Della Valle F, Nadeef S, Lanzuolo C, Orlando V. Cell Report. 37 (9): 110066 (*Equal first author)
  • Nuclear AGO1 Regulates Gene Expression by Affecting Chromatin Architecture in Human Cells. (2019)Shuaib M, Parsi K.M, Adroub SA, Thimma M, Hideya K, Seridi L, Carninci P, Orlando V. Cell Systems.9 (5): 446-458.e6. 
  • Ubiquitin ligases HUWE1 and NEDD4 cooperatively control signal dependent PRC2-Ezh1 a/b mediated adaptive stress response pathway in skeletal muscle cells (2019). Liu P, Shuaib M,Zhang H, Nadeef S, Orlando V.Epigenetics & Chromatin12,78 (2019) doi:10.1186/s13072-019-0322-5. 
  • AGO1 in association with NEAT1 lncRNA contributes to nuclear and 3D chromatin architecture in human cells (2019). Shuaib M,Parsi K.M, Kawaji H, Fort A, Adroub S.A, Thimma M, Ghosheh Y, Yamazaki T, Mannen T, Seridi L, Fallatah B, Carninci P, Hirose T, and Orlando V. BioRxivdoi:
  • The Flexible Ends of CENP-A Nucleosome Are Required for Mitotic Fidelity. (2016).Roulland Y, Ouararhni K, Naidenov M, Ramos L, Shuaib M,Syed SH, Lone IN, Boopathi R, Fontaine E, Papai G, Tachiwana H, Gautier T, Skoufias D, Padmanabhan K, Bednar J, Kurumizaka H, Schultz P, Angelov D, Hamiche A, Dimitrov S. Molecular Cell63 (4): 674-85.
  • Phosphorylation of the CENP-A amino-terminus in mitotic centromeric chromatin is required for kinetochore function. (2013).  Goutte-Gattat* D, Shuaib M*,Ouararhni K*, Gautier T, Skoufias D.A, Hamiche A, Dimitrov S. Proc Natl Acad Sci USA. 110 (21): 8579-8584.(*Equal first author). 
  • Chaperoning the histone H3 family. (2012).Hamiche A and Shuaib M. BBA-Gene Regulatory Mechanisms. 1819 (3-4): 230-237. 
  • HJURP binds CENP-A via a highly conserved N-terminal domain and mediates its deposition at centromeres. (2010)Shuaib M,Ouararhni K, Dimitrov S, Hamiche A. Proc Natl Acad Sci USA. 107(4): 1349-1354.
  • The death-associated protein DAXX is a novel histone chaperone involved in the replication-independent deposition of H3.3. (2010).  Drané P, Ouararhni K, Depaux A, Shuaib M,Hamiche A. Genes & Development. 24(12): 1253-1265.


Ph.D in Molecular and Cellular Biology from the University of Strasbourg, 2012

Research Interests Keywords

Host-pathogen interactions epigenetics functional genomics Non-coding RNAs