1
|
Centofanti A, Vermiglio G, Cutroneo G, Favaloro A, Picciolo G, Festa F, Anastasi GP. Dystrophin-Glycoprotein Complex Behavior in Sternocleidomastoid Muscle of High- and Low-Ranking Baboons: A Possible Phylogenetic Arrangement. J Funct Morphol Kinesiol 2022; 7:jfmk7030062. [PMID: 36135420 PMCID: PMC9502455 DOI: 10.3390/jfmk7030062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
The dystrophin-glycoprotein complex is a multimeric system made up of the sarcoglycan sub-complex, the sarcomplasmatic complex and the dystroglycans complex. The sarcoglycan sub-complex stabilizes the sarcolemma during muscle activity and plays a role in force transduction. This protein system is also expressed in the muscle of non-human primates such as chimpanzees and baboons, and its expression changes depending on social ranking. In fact, previous data have shown that all muscle fibers of masseter and sternocleidomastoid muscles of chimpanzees and high- ranking baboons always express sarcoglycans, while middle- and low-ranking baboons are characterized by fibers that are negative for the sarcoglycan sub-complex. Given this information, the aim of the present work was to evaluate the expression of other proteins such as laminin, beta dystroglycan and dystrophin in the sternocleidomastoid muscle of high- and low-ranking baboons. The samples were processed by immunohistochemistry; results show that in high-ranking baboons, all tested proteins were always expressed while in low-ranking baboons, fibers that were negative for sarcoglycans and beta dystroglycan have been observed. No negative fibers for laminin and dystrophin have been found in low-ranking baboons suggesting that only the transmembrane proteins of the dystrophin glycoprotein complex change in their expression and that could be correlated to a phylogenetic arrangement.
Collapse
Affiliation(s)
- Antonio Centofanti
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98124 Messina, Italy
| | - Giovanna Vermiglio
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98124 Messina, Italy
- Correspondence:
| | - Giuseppina Cutroneo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98124 Messina, Italy
| | - Angelo Favaloro
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98124 Messina, Italy
| | - Giacomo Picciolo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98124 Messina, Italy
| | - Felice Festa
- Department of Innovative Technologies in Medicine and Dentistry, University “G. D’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
| | - Giuseppe Pio Anastasi
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98124 Messina, Italy
| |
Collapse
|
2
|
Marnetto D, Molineris I, Grassi E, Provero P. Genome-wide identification and characterization of fixed human-specific regulatory regions. Am J Hum Genet 2014; 95:39-48. [PMID: 24995867 DOI: 10.1016/j.ajhg.2014.05.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 05/29/2014] [Indexed: 01/01/2023] Open
Abstract
Changes in gene regulatory networks are believed to have played an important role in the development of human-specific anatomy and behavior. We identified the human genome regions that show the typical chromatin marks of regulatory regions but cannot be aligned to other mammalian genomes. Most of these regions have become fixed in the human genome. Their regulatory targets are enriched in genes involved in neural processes, CNS development, and diseases such as autism, depression, and schizophrenia. Specific transposable elements contributing to the rewiring of the human regulatory network can be identified by the creation of human-specific regulatory regions. Our results confirm the relevance of regulatory evolution in the emergence of human traits and cognitive abilities and the importance of newly acquired genomic elements for such evolution.
Collapse
Affiliation(s)
- Davide Marnetto
- Department of Molecular Biotechnology and Health Sciences, University of Turin, 10126 Turin, Italy
| | - Ivan Molineris
- Department of Molecular Biotechnology and Health Sciences, University of Turin, 10126 Turin, Italy
| | - Elena Grassi
- Department of Molecular Biotechnology and Health Sciences, University of Turin, 10126 Turin, Italy
| | - Paolo Provero
- Department of Molecular Biotechnology and Health Sciences, University of Turin, 10126 Turin, Italy; Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, 20132 Milan, Italy.
| |
Collapse
|
3
|
He Z, Bammann H, Han D, Xie G, Khaitovich P. Conserved expression of lincRNA during human and macaque prefrontal cortex development and maturation. RNA (NEW YORK, N.Y.) 2014; 20:1103-11. [PMID: 24847104 PMCID: PMC4074677 DOI: 10.1261/rna.043075.113] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 04/09/2014] [Indexed: 05/20/2023]
Abstract
The current annotation of the human genome includes more than 12,000 long intergenic noncoding RNAs (lincRNA). While a handful of lincRNA have been shown to play important regulatory roles, the functionality of most remains unclear. Here, we examined the expression conservation and putative functionality of lincRNA in human and macaque prefrontal cortex (PFC) development and maturation. We analyzed transcriptome sequence (RNA-seq) data from 38 human and 40 macaque individuals covering the entire postnatal development interval. Using the human data set, we detected the expression of 5835 lincRNA annotated in GENCODE and further identified 1888 novel lincRNA. Most of these lincRNA show low DNA sequence conservation, as well as low expression levels. Remarkably, developmental expression patterns of these lincRNA were as conserved between humans and macaques as those of protein-coding genes. Transfection of development-associated lincRNA into human SH-SY5Y cells affected gene expression, indicating their regulatory potential. In brain, expression of these putative target genes correlated with the expression of the corresponding lincRNA during human and macaque PFC development. These results support the potential functionality of lincRNA in primate PFC development.
Collapse
Affiliation(s)
- Zhisong He
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai 200031, China
- Graduate School of Chinese Academy of Sciences, 100039 Beijing, China
| | - Hindrike Bammann
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai 200031, China
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Dingding Han
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai 200031, China
| | - Gangcai Xie
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai 200031, China
- Graduate School of Chinese Academy of Sciences, 100039 Beijing, China
| | - Philipp Khaitovich
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai 200031, China
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Corresponding authorE-mail
| |
Collapse
|
4
|
Weiss ML, Tackney J. An Introduction to Genetics. Hum Biol 2012. [DOI: 10.1002/9781118108062.ch3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
5
|
Molineris I, Grassi E, Ala U, Di Cunto F, Provero P. Evolution of promoter affinity for transcription factors in the human lineage. Mol Biol Evol 2011; 28:2173-83. [PMID: 21335606 DOI: 10.1093/molbev/msr027] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Changes in gene regulation are believed to play an important role in the evolution of animals. It has been suggested that changes in cis-regulatory regions are responsible for many or most of the anatomical and behavioral differences between humans and apes. However, the study of the evolution of cis-regulatory regions is made problematic by the degeneracy of transcription factor (TF) binding sites and the shuffling of their positions. In this work, we use the predicted total affinity of a promoter for a large collection of TFs as the basis for studying the evolution of cis-regulatory regions in mammals. We introduce the human specificity of a promoter, measuring the divergence between the affinity profile of a human promoter and its orthologous promoters in other mammals. The promoters of genes involved in functional categories such as neural processes and signal transduction, among others, have higher human specificity compared with the rest of the genome. Clustering of the human-specific affinities (HSAs) of neural genes reveals patterns of promoter evolution associated with functional categories such as synaptic transmission and brain development and to diseases such as bipolar disorder and autism.
Collapse
Affiliation(s)
- Ivan Molineris
- Department of Genetics, Biology and Biochemistry, Molecular Biotechnology Center, University of Turin, Turin, Italy
| | | | | | | | | |
Collapse
|
6
|
Muscle-specific integrins in masseter muscle fibers of chimpanzees: an immunohistochemical study. Folia Histochem Cytobiol 2010; 47:551-8. [DOI: 10.2478/v10042-009-0095-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
7
|
Bradley BJ. Reconstructing phylogenies and phenotypes: a molecular view of human evolution. J Anat 2008; 212:337-53. [PMID: 18380860 PMCID: PMC2409108 DOI: 10.1111/j.1469-7580.2007.00840.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2007] [Indexed: 12/19/2022] Open
Abstract
This review broadly summarizes how molecular biology has contributed to our understanding of human evolution. Molecular anthropology began in the 1960s with immunological comparisons indicating that African apes and humans were closely related and, indeed, shared a common ancestor as recently as 5 million years ago. Although initially dismissed, this finding has proven robust and numerous lines of molecular evidence now firmly place the human-ape divergence at 4-8 Ma. Resolving the trichotomy among humans, chimpanzees and gorillas took a few more decades. Despite the readily apparent physical similarities shared by African apes to the exclusion of modern humans (body hair, knuckle-walking, thin tooth enamel), the molecular support for a human-chimpanzee clade is now overwhelming. More recently, whole genome sequencing and gene mapping have shifted the focus of molecular anthropology from phylogenetic analyses to phenotypic reconstruction and functional genomics. We are starting to identify the genetic basis of the morphological, physiological and behavioural traits that distinguish modern humans from apes and apes from other primates. Most notably, recent comparative genomic analyses strongly indicate that the marked differences between modern humans and chimpanzees are likely due more to changes in gene regulation than to modifications of the genes themselves, an idea first proposed over 30 years ago. Almost weekly, press releases describe newly identified genes and regulatory elements that seem to have undergone strong positive selection along the human lineage. Loci involved in speech (e.g. FOXP2), brain development (e.g. ASPM), and skull musculature (e.g. MYH16) have been of particular interest, but some surprising candidate loci (e.g. those involved in auditory capabilities) have emerged as well. Exciting new research avenues, such as the Neanderthal Genome Project, promise that molecular analyses will continue to provide novel insights about our evolution. Ultimately, however, these molecular findings can only be understood in light of data from field sites, morphology labs, and museum collections. Indeed, molecular anthropology depends on these sources for calibrating molecular clocks and placing genetic data within the context of key morphological and ecological transitions in human evolution.
Collapse
Affiliation(s)
- Brenda J Bradley
- Department of Zoology and Christ's College, University of Cambridge, UK.
| |
Collapse
|
8
|
On the relation between promoter divergence and gene expression evolution. Mol Syst Biol 2008; 4:159. [PMID: 18197176 PMCID: PMC2238714 DOI: 10.1038/msb4100198] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2007] [Accepted: 11/06/2007] [Indexed: 01/05/2023] Open
Abstract
Recent studies have characterized significant differences in the cis-regulatory sequences of related organisms, but the impact of these differences on gene expression remains largely unexplored. Here, we show that most previously identified differences in transcription factor (TF)-binding sequences of yeasts and mammals have no detectable effect on gene expression, suggesting that compensatory mechanisms allow promoters to rapidly evolve while maintaining a stabilized expression pattern. To examine the impact of changes in cis-regulatory elements in a more controlled setting, we compared the genes induced during mating of three yeast species. This response is governed by a single TF (STE12), and variations in its predicted binding sites can indeed account for about half of the observed expression differences. The remaining unexplained differences are correlated with the increased divergence of the sequences that flank the binding sites and an apparent modulation of chromatin structure. Our analysis emphasizes the flexibility of promoter structure, and highlights the interplay between specific binding sites and general chromatin structure in the control of gene expression.
Collapse
|
9
|
Mahony S, Corcoran DL, Feingold E, Benos PV. Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome. Genome Biol 2007; 8:R84. [PMID: 17506886 PMCID: PMC1929153 DOI: 10.1186/gb-2007-8-5-r84] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Revised: 01/29/2007] [Accepted: 05/16/2007] [Indexed: 02/07/2023] Open
Abstract
A study of conservation of non-coding sequences, cis-regulatory elements and biological functions of regulated genes in opossum and other vertebrates enables better estimation of promoter conservation and transcription factor binding site turnover among mammals Background Being the first noneutherian mammal sequenced, Monodelphis domestica (opossum) offers great potential for enhancing our understanding of the evolutionary processes that take place in mammals. This study focuses on the evolutionary relationships between conservation of noncoding sequences, cis-regulatory elements, and biologic functions of regulated genes in opossum and eight vertebrate species. Results Analysis of 145 intergenic microRNA and all protein coding genes revealed that the upstream sequences of the former are up to twice as conserved as the latter among mammals, except in the first 500 base pairs, where the conservation is similar. Comparison of promoter conservation in 513 protein coding genes and related transcription factor binding sites (TFBSs) showed that 41% of the known human TFBSs are located in the 6.7% of promoter regions that are conserved between human and opossum. Some core biologic processes exhibited significantly fewer conserved TFBSs in human-opossum comparisons, suggesting greater functional divergence. A new measure of efficiency in multigenome phylogenetic footprinting (base regulatory potential rate [BRPR]) shows that including human-opossum conservation increases specificity in finding human TFBSs. Conclusion Opossum facilitates better estimation of promoter conservation and TFBS turnover among mammals. The fact that substantial TFBS numbers are located in a small proportion of the human-opossum conserved sequences emphasizes the importance of marsupial genomes for phylogenetic footprinting-based motif discovery strategies. The BRPR measure is expected to help select genome combinations for optimal performance of these algorithms. Finally, although the etiology of the microRNA upstream increased conservation remains unknown, it is expected to have strong implications for our understanding of regulation of their expression.
Collapse
Affiliation(s)
- Shaun Mahony
- Department of Computational Biology, School of Medicine, University of Pittsburgh, Fifth Avenue, Pittsburgh, PA 15260, USA
| | - David L Corcoran
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, DeSoto Street, Pittsburgh, PA 15261, USA
| | - Eleanor Feingold
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, DeSoto Street, Pittsburgh, PA 15261, USA
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, DeSoto Street, Pittsburgh, PA 15261, USA
| | - Panayiotis V Benos
- Department of Computational Biology, School of Medicine, University of Pittsburgh, Fifth Avenue, Pittsburgh, PA 15260, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, DeSoto Street, Pittsburgh, PA 15261, USA
- University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Centre Avenue, Pittsburgh, PA 15232, USA
| |
Collapse
|
10
|
Kehrer-Sawatzki H, Cooper DN. Understanding the recent evolution of the human genome: insights from human-chimpanzee genome comparisons. Hum Mutat 2007; 28:99-130. [PMID: 17024666 DOI: 10.1002/humu.20420] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The sequencing of the chimpanzee genome and the comparison with its human counterpart have begun to reveal the spectrum of genetic changes that has accompanied human evolution. In addition to gross karyotypic rearrangements such as the fusion that formed human chromosome 2 and the human-specific pericentric inversions of chromosomes 1 and 18, there is considerable submicroscopic structural variation involving deletions, duplications, and inversions. Lineage-specific segmental duplications, detected by array comparative genomic hybridization and direct sequence comparison, have made a very significant contribution to this structural divergence, which is at least three-fold greater than that due to nucleotide substitutions. Since structural genomic changes may have given rise to irreversible functional differences between the diverging species, their detailed analysis could help to identify the biological processes that have accompanied speciation. To this end, interspecies comparisons have revealed numerous human-specific gains and losses of genes as well as changes in gene expression. The very considerable structural diversity (polymorphism) evident within both lineages has, however, hampered the analysis of the structural divergence between the human and chimpanzee genomes. The concomitant evaluation of genetic divergence and diversity at the nucleotide level has nevertheless served to identify many genes that have evolved under positive selection and may thus have been involved in the development of human lineage-specific traits. Genes that display signs of weak negative selection have also been identified and could represent candidate loci for complex genomic disorders. Here, we review recent progress in comparing the human and chimpanzee genomes and discuss how the differences detected have improved our understanding of the evolution of the human genome.
Collapse
|
11
|
Mekel-Bobrov N, Lahn BT. What makes us human: revisiting an age-old question in the genomic era. JOURNAL OF BIOMEDICAL DISCOVERY AND COLLABORATION 2006; 1:18. [PMID: 17134487 PMCID: PMC1716182 DOI: 10.1186/1747-5333-1-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/30/2006] [Accepted: 11/29/2006] [Indexed: 12/25/2022]
Abstract
In 1970, Karl Pribram took on the immense challenge of asking the question, what makes us human? Nearly four decades later, the most significant finding has been the undeniable realization of how incredibly subtle and fine-scaled the unique biological features of our species must be. The recent explosion in the availability of large-scale sequence data, however, and the consequent emergence of comparative genomics, are rapidly transforming the study of human evolution. The field of comparative genomics is allowing us to reach unparalleled resolution, reframing our questions in reference to DNA sequence--the very unit that evolution operates on. But like any reductionist approach, it comes at a price. Comparative genomics may provide the necessary resolution for identifying rare DNA sequence differences in a vast sea of conservation, but ultimately we will have to face the challenge of figuring out how DNA sequence divergence translates into phenotypic divergence. Our goal here is to provide a brief outline of the major findings made in the study of human brain evolution since the Pribram lecture, focusing specifically on the field of comparative genomics. We then discuss the broader implications of these findings and the future challenges that are in store.
Collapse
Affiliation(s)
- Nitzan Mekel-Bobrov
- Howard Hughes Medical Institute, Department of Human Genetics and Committee on Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Bruce T Lahn
- Howard Hughes Medical Institute, Department of Human Genetics and Committee on Genetics, University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|