Characterizing Pathogenic Enhancer Activity at Single-cell Resolution
DOI:
https://doi.org/10.47611/jsrhs.v12i1.4022Keywords:
Pathogenic, Disease, Enhancers, DNA, Mutation, Transcription, UMAP, Single-Celled SequencingAbstract
The ZRS enhancer, a regulatory sequence found in numerous organisms, plays an important role in early embryonic limb development. ZRS controls the expression of the Sonic Hedgehog gene (Shh), and therefore early limb development in an organism as Shh has been shown to control the width of the limb bud by stimulating mesenchyme cell proliferation due to its ability to regulate the anterior-posterior length of the apical ectodermal ridge. Several transcription factors, acting as repressors or activators of the Shh gene, coordinate this limb development process in tandem with the ZRS enhancer. While the significance of normal ZRS activity is evident, this study looks deeper into the effects of pathogenic changes to the ZRS enhancer and the development of associated limb disorders such as preaxial polydactyly (PPD) by focusing on several aspects of ZRS regulation and its relation to Shh expression. This was accomplished by characterizing the expression of Shh and mCherry, an introduced luminescence gene regulated by ZRS, through single-cell RNA sequenced cells from a developing limb bud of a mouse embryo. Additionally, this study characterized specific transcription factors as potential repressors or activators of ZRS by determining TF enrichment or depletion in highly expressive Shh and mCherry cells. Classifying such TFs is vital in identifying the regulatory elements that control the formation of limb malformation disorders such as preaxial polydactyly and aid in the development of future therapeutic interventions.
Downloads
References or Bibliography
Arnold I. Caplan. “Mesenchymal stem cells”. In: Journal of Orthopaedic Research 9.5 (Sept. 1991), pp. 641–650. doi: 10.1002/jor.1100090504.
Katherine Q Chen et al. “Development of the Proximal-Anterior Skeletal Elements in the Mouse Hindlimb Is Regulated by a Transcriptional and Signaling Network Controlled by Sall4 ”. In: Genetics 215.1 (May 1, 2020), pp. 129–141. doi: 10.1534/genetics.120.303069.
Eileen E. M. Furlong and Michael Levine. “Developmental enhancers and chromosome topology”. In: Science 361.6409 (Sept. 28, 2018), pp. 1341– 1345. doi: 10.1126/science.aau0320. (Visited on 06/30/2021).
Linh Huynh and Fereydoun Hormozdiari. “TAD fusion score: discovery and ranking the contribution of deletions to genome structure”. In: Genome Biology 20.1 (Mar. 21, 2019), p. 60. doi: 10.1186/s13059-019-1666-7.
Evgeny Z. Kvon et al. “Comprehensive In Vivo Interrogation Reveals Phenotypic Impact of Human Enhancer Variants”. In: Cell 180.6 (Mar. 2020), 1262–1271.e15. doi: 10.1016/j.cell.2020.02.031.
Evgeny Z. Kvon et al. “Enhancer redundancy in development and disease”. In: Nature Reviews Genetics 22.5 (May 2021), pp. 324–336. doi: 10.1038/ s41576-020-00311-x.
L. A. Lettice. “A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly”. In: Human Molecular Genetics 12.14 (July 15, 2003), pp. 1725–1735. doi: 10.1093/hmg/ddg180. (Visited on 06/30/2021).
Hannah K. Long, Sara L. Prescott, and Joanna Wysocka. “Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution”. In: Cell 167.5 (Nov. 2016), pp. 1170–1187. doi: 10.1016/j.cell.2016. 09.018. (Visited on 06/30/2021).
Dar´ıo G. Lupi´a˜nez et al. “Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions”. In: Cell 161.5 (May 2015), pp. 1012–1025. doi: 10.1016/j.cell.2015.04.004.
S. Malik. “Polydactyly: phenotypes, genetics and classification”. In: Clinical Genetics 85.3 (Mar. 2014), pp. 203–212. doi: 10.1111/cge.12276.
S´ebastien Mella et al. “Expression patterns of the coe/ebf transcription factor genes during chicken and mouse limb development”. In: Gene Expression Patterns 4.5 (Sept. 2004), pp. 537–542. doi: 10.1016/j.modgep.2004. 02.005. 24
Yanling Peng and Yubo Zhang. “Enhancer and super-enhancer: Positive regulators in gene transcription”. In: Animal Models and Experimental Medicine 1.3 (Sept. 2018), pp. 169–179. doi: 10 . 1002 / ame2 . 12032. (Visited on 06/30/2021).
Len A. Pennacchio et al. “Enhancers: five essential questions”. In: Nature Reviews Genetics 14.4 (Apr. 2013), pp. 288–295. doi: 10.1038/nrg3458.
Florence Petit, Karen E. Sears, and Nadav Ahituv. “Limb development: a paradigm of gene regulation”. In: Nature Reviews Genetics 18.4 (Apr. 2017), pp. 245–258. doi: 10.1038/nrg.2016.167. (Visited on 06/30/2021).
Sandrine Pizette and L Niswander. “BMPs negatively regulate structure and function of limb apical ectodermal ridge”. In: Development (Cambridge, England) 126 (Mar. 1999), pp. 883–94.
Valerie Reinke. “Transcriptional regulation of gene expression in C. elegans”. In: WormBook (June 4, 2013), pp. 1–31. doi: 10.1895/wormbook.1.45.2.
Michael I. Robson, Alessa R. Ringel, and Stefan Mundlos. “Regulatory Landscaping: How Enhancer-Promoter Communication Is Sculpted in 3D”. In: Molecular Cell 74.6 (June 2019), pp. 1110–1122. doi: 10 . 1016 / j . molcel.2019.05.032. (Visited on 06/30/2021).
Tomoko Sagai et al. “Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression and truncation of the mouse limb”. In: Development 132.4 (Feb. 15, 2005), pp. 797–803. doi: 10.1242/dev.01613.
Stefan Schoenfelder and Peter Fraser. “Long-range enhancer–promoter contacts in gene expression control”. In: Nature Reviews Genetics 20.8 (Aug. 2019), pp. 437–455. doi: 10.1038/s41576-019-0128-0. (Visited on 06/30/2021).
Fran¸cois Spitz and Eileen E. M. Furlong. “Transcription factors: from enhancer binding to developmental control”. In: Nature Reviews Genetics 13.9 (Sept. 2012), pp. 613–626. doi: 10 . 1038 / nrg3207. (Visited on 06/30/2021).
Leila Taher et al. “Global Gene Expression Analysis of Murine Limb Development”. In: PLoS ONE 6.12 (Dec. 9, 2011). Ed. by Costanza Emanueli, e28358. doi: 10.1371/journal.pone.0028358.
Cheryll Tickle and Matthew Towers. “Sonic Hedgehog Signaling in Limb Development”. In: Frontiers in Cell and Developmental Biology 5 (Feb. 28, 2017). doi: 10.3389/fcell.2017.00014.
Itai Tzchori et al. “LIM homeobox transcription factors integrate signaling events that control three-dimensional limb patterning and growth”. In: Development 136.8 (Apr. 15, 2009), pp. 1375–1385. doi: 10.1242/dev. 026476.
Shigetoshi Yokoyama et al. “Analysis of transcription factors expressed at the anterior mouse limb bud”. In: PLOS ONE 12.5 (May 3, 2017). Ed. by Michael Schubert, e0175673. doi: 10.1371/journal.pone.0175673.
Published
How to Cite
Issue
Section
Copyright (c) 2023 Arul Loomba, Sohum Mehta
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
Copyright holder(s) granted JSR a perpetual, non-exclusive license to distriute & display this article.
