1
|
Ali S, Abrar M, Hussain I, Batool F, Raza RZ, Khatoon H, Zoia M, Visel A, Shubin NH, Osterwalder M, Abbasi AA. Identification of ancestral gnathostome Gli3 enhancers with activity in mammals. Dev Growth Differ 2024; 66:75-88. [PMID: 37925606 PMCID: PMC10841732 DOI: 10.1111/dgd.12901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/01/2023] [Accepted: 10/23/2023] [Indexed: 11/06/2023]
Abstract
Abnormal expression of the transcriptional regulator and hedgehog (Hh) signaling pathway effector Gli3 is known to trigger congenital disease, most frequently affecting the central nervous system (CNS) and the limbs. Accurate delineation of the genomic cis-regulatory landscape controlling Gli3 transcription during embryonic development is critical for the interpretation of noncoding variants associated with congenital defects. Here, we employed a comparative genomic analysis on fish species with a slow rate of molecular evolution to identify seven previously unknown conserved noncoding elements (CNEs) in Gli3 intronic intervals (CNE15-21). Transgenic assays in zebrafish revealed that most of these elements drive activities in Gli3 expressing tissues, predominantly the fins, CNS, and the heart. Intersection of these CNEs with human disease associated SNPs identified CNE15 as a putative mammalian craniofacial enhancer, with conserved activity in vertebrates and potentially affected by mutation associated with human craniofacial morphology. Finally, comparative functional dissection of an appendage-specific CNE conserved in slowly evolving fish (elephant shark), but not in teleost (CNE14/hs1586) indicates co-option of limb specificity from other tissues prior to the divergence of amniotes and lobe-finned fish. These results uncover a novel subset of intronic Gli3 enhancers that arose in the common ancestor of gnathostomes and whose sequence components were likely gradually modified in other species during the process of evolutionary diversification.
Collapse
Affiliation(s)
- Shahid Ali
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, 45320, Islamabad Pakistan
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL 60637, USA
| | - Muhammad Abrar
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, 45320, Islamabad Pakistan
| | - Irfan Hussain
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, 45320, Islamabad Pakistan
| | - Fatima Batool
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, 45320, Islamabad Pakistan
| | - Rabail Zehra Raza
- Department of Biological Sciences, Faculty of Multidisciplinary Studies, National University of Medical Sciences Rawalpindi, Pakistan
| | - Hizran Khatoon
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, 45320, Islamabad Pakistan
| | - Matteo Zoia
- Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Axel Visel
- Environmental Genomics and System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, USA
- School of Natural Sciences, University of California, Merced, Merced, CA 95343, USA
| | - Neil H. Shubin
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL 60637, USA
| | - Marco Osterwalder
- Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
- Department of Cardiology, Bern University Hospital, Bern, Switzerland
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, 45320, Islamabad Pakistan
| |
Collapse
|
2
|
Romero VI, Arias-Almeida B, Aguiar SA. NSD1 gene evolves under episodic selection within primates and mutations of specific exons in humans cause Sotos syndrome. BMC Genomics 2022; 23:849. [PMID: 36550402 PMCID: PMC9783842 DOI: 10.1186/s12864-022-09071-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Modern human brains and skull shapes differ from other hominids. Brain growth disorders as micro- (ASPM, MCPH1) and macrocephaly (NFIX, GLI3) have been highlighted as relevant for the evolution in humans due to the impact in early brain development. Genes associated with macrocephaly have been reported to cause this change, for example NSD1 which causes Sotos syndrome. RESULTS In this study we performed a systematic literature review, located the reported variants associated to Sotos syndrome along the gene domains, compared the sequences with close primates, calculated their similarity, Ka/Ks ratios, nucleotide diversity and selection, and analyzed the sequence and structural conservation with distant primates. We aimed to understand if NSD1 in humans differs from other primates since the evolution of NSD1 has not been analyzed in primates, nor if the localization of the mutations is limited to humans. Our study found that most variations causing Sotos syndrome are in exon 19, 22 and 10. In the primate comparison we did not detect Ka/Ks ratios > 1, but a high nucleotide diversity with non-synonymous variations in exons 10, 5, 9, 11 and 23, and sites under episodic selection in exon 5 and 23, and human, macaque/colobus/tarsier/galago and tarsier/lemur/colobus. Most of the domains are conserved in distant primates with a particular progressive development from a simple PWWP1 in O. garnetti to a complex structure in Human. CONCLUSION NSD1 is a chromatin modifier that suggests that the selection could influence brain development during modern human evolution and is not present in other primates; however, nowadays the nucleotide diversity is associated with Sotos syndrome.
Collapse
Affiliation(s)
- Vanessa I. Romero
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| | | | | |
Collapse
|
3
|
Zug R, Uller T. Evolution and dysfunction of human cognitive and social traits: A transcriptional regulation perspective. EVOLUTIONARY HUMAN SCIENCES 2022; 4:e43. [PMID: 37588924 PMCID: PMC10426018 DOI: 10.1017/ehs.2022.42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/11/2022] [Accepted: 09/11/2022] [Indexed: 11/07/2022] Open
Abstract
Evolutionary changes in brain and craniofacial development have endowed humans with unique cognitive and social skills, but also predisposed us to debilitating disorders in which these traits are disrupted. What are the developmental genetic underpinnings that connect the adaptive evolution of our cognition and sociality with the persistence of mental disorders with severe negative fitness effects? We argue that loss of function of genes involved in transcriptional regulation represents a crucial link between the evolution and dysfunction of human cognitive and social traits. The argument is based on the haploinsufficiency of many transcriptional regulator genes, which makes them particularly sensitive to loss-of-function mutations. We discuss how human brain and craniofacial traits evolved through partial loss of function (i.e. reduced expression) of these genes, a perspective compatible with the idea of human self-domestication. Moreover, we explain why selection against loss-of-function variants supports the view that mutation-selection-drift, rather than balancing selection, underlies the persistence of psychiatric disorders. Finally, we discuss testable predictions.
Collapse
Affiliation(s)
- Roman Zug
- Department of Biology, Lund University, Lund, Sweden
| | - Tobias Uller
- Department of Biology, Lund University, Lund, Sweden
| |
Collapse
|