Dr Saima Shahid
School of Biosciences
Lecturer
+44 114 2224318
Full contact details
School of Biosciences
Alfred Denny Building
Western Bank
Sheffield
S10 2TN
- Profile
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- 2024 ‒ present: Lecturer, University of Sheffield, UK
- 2022 ‒ 2024: Assistant professor, Department of Plant Biology, Ecology and Evolution, Oklahoma State University, USA
- 2019 ‒ 2022: Simons Fellow for the Life Sciences Research Foundation, Donald Danforth Plant Science Center, USA
- 2018 ‒ 2022: Postdoctoral Research Associate, Donald Danforth Plant Science Center, USA
- 2017‒ 2018: Postdoctoral Research Associate, Dept. of Molecular Genetics, Ohio State University, USA
- 2017: PhD, The Pennsylvania State University, USA
- 2010 – 2011: Bioinformatician, Bangladesh Jute Research Institute & University of Dhaka, Bangladesh
- 2009: MS, Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
- 2008: BSc, Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
- Research interests
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Mobile small RNAs in interspecies communication:
Small RNA-mediated gene silencing is a powerful mechanism conserved across diverse eukaryotes including plants, fungi, and animals. Emerging evidence suggests that small RNAs function not only within an organism but can also be trafficked to other interacting organisms where they regulate ‘non-self’ gene expression. Using the parasitic plant Cuscuta, we demonstrated for the first time the evidence of such interspecies regulatory small RNAs in plant - plant communication (Shahid et al., 2018, Nature). Our goal is to understand how interspecies small RNA trafficking influences diverse host – parasite/symbiont interactions, and develop RNA-based solutions for improved parasite resistance in crops.
De novo chromatin modification and epigenetic memory in plant parasitism:
Genomes harbour many hidden regulatory elements that can influence gene expression and reshape genome structure. These include transposable elements (TEs) which are ubiquitous DNA fragments that can move within and across genomes, thereby causing structural variations/mutation. Host genomes usually repress TE activity through chromatin modifications and RNA silencing pathways. However, TEs often escape this silencing during biotic/abiotic stress and certain developmental transitions. We are interested in how TE activity and chromatin modifications shape host – parasite interactions, trigger epigenetic memory, and facilitate host/parasite adaptation.We use bioinformatics, genomics, molecular and synthetic biology approaches to address the above research questions. For detailed information on current research projects and available positions, please visit the lab website: https://shahidlab.github.io/.
- Publications
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Journal articles
- The Epigenetic Control of the Transposable Element Life Cycle in Plant Genomes and Beyond. Annual Review of Genetics, 56(1), 63-87.
- Sorghum anthracnose resistance: One MITE to rule them all. The Plant Cell, 34(5), 1429-1430.
- Hunting for TEs: MicroRNAs switch targets in developing pollen. The Plant Cell, 34(2), 710-711.
- The making and unmaking of the silenced chromatin. The Plant Cell, 33(4), 786-787.
- A DNA Methylation Reader with an Affinity for Salt Stress. The Plant Cell, 32(11), 3380-3381.
- On UPF Proteins, Baking Cookies, and the Many Targets of Nonsense-Mediated RNA Decay. The Plant Cell, 32(9), 2665-2666.
- Soybean aphids adapted to host-plant resistance by down regulating putative effectors and up regulating transposable elements. Insect Biochemistry and Molecular Biology, 121, 103363-103363.
- The Rules of Attachment: REC8 Cohesin Connects Chromatin Architecture and Recombination Machinery in Meiosis. The Plant Cell, 32(4), 808-809.
- The current revolution in transposable element biology enabled by long reads. Current Opinion in Plant Biology, 54, 49-56.
- To Be or Not To Be Pathogenic: Transcriptional Reprogramming Dictates a Fungal Pathogen’s Response to Different Hosts. The Plant Cell, 32(2), 289-290.
- Convergent horizontal gene transfer and cross-talk of mobile nucleic acids in parasitic plants.. Nat Plants, 5(9), 991-1001.
- The RNA Export Factor ALY1 Enables Genome-Wide RNA-Directed DNA Methylation. The Plant Cell, 31(4), 759-774.
- MicroRNAs from the parasitic plant Cuscuta campestris target host messenger RNAs. Nature, 553(7686), 82-85.
- Comparative genomics of two jute species and insight into fibre biogenesis.. Nat Plants, 3, 16223.
- Variability in amylose content of Bangladeshi rice cultivars due to unique SNPs in Waxy allele. Journal of Cereal Science, 71, 1-9.
- Comprehensive Annotation of Physcomitrella patens Small RNA Loci Reveals That the Heterochromatic Short Interfering RNA Pathway Is Largely Conserved in Land Plants. The Plant Cell, 27(8), 2148-2162.
- A stable RNA G-quadruplex within the 5′-UTR of Arabidopsis thaliana ATR mRNA inhibits translation. Biochemical Journal, 467(1), 91-102.
- Seeing the forest for the trees: annotating small RNA producing genes in plants. Current Opinion in Plant Biology, 18, 87-95.
- Identification and annotation of small RNA genes using ShortStack. Methods, 67(1), 20-27.
- The
Amborella
Genome and the Evolution of Flowering Plants. Science, 342(6165).
- Prediction of plant promoters based on hexamers and random triplet pair analysis. Algorithms for Molecular Biology, 6(1).
- Physiology and gene expression of the rice landrace Horkuch under salt stress. Functional Plant Biology, 38(4), 282-282.
- READS - a resource for plant non-coding regulatory sequence analysis. Plant Tissue Culture and Biotechnology, 20(2), 211-223.
Chapters
- Deciphering comparative and structural variation that regulates abiotic stress response, Bioinformatics in Agriculture (pp. 561-586). Elsevier
- The Epigenetic Control of the Transposable Element Life Cycle in Plant Genomes and Beyond. Annual Review of Genetics, 56(1), 63-87.
- Research group
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- Megan Adler (PBEE MS student, Oklahoma State University)
- Professional activities and memberships
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- 2023 - present: Reviewing Editor for the Frontiers in Plant Physiology journal
- 2019 - 2021: Assistant Features Editor for The Plant Cell journal