1
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Lewin TD, Liao IJY, Luo YJ. Annelid Comparative Genomics and the Evolution of Massive Lineage-Specific Genome Rearrangement in Bilaterians. Mol Biol Evol 2024; 41:msae172. [PMID: 39141777 PMCID: PMC11371463 DOI: 10.1093/molbev/msae172] [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: 05/15/2024] [Revised: 08/05/2024] [Accepted: 08/08/2024] [Indexed: 08/16/2024] Open
Abstract
The organization of genomes into chromosomes is critical for processes such as genetic recombination, environmental adaptation, and speciation. All animals with bilateral symmetry inherited a genome structure from their last common ancestor that has been highly conserved in some taxa but seemingly unconstrained in others. However, the evolutionary forces driving these differences and the processes by which they emerge have remained largely uncharacterized. Here, we analyze genome organization across the phylum Annelida using 23 chromosome-level annelid genomes. We find that while many annelid lineages have maintained the conserved bilaterian genome structure, the Clitellata, a group containing leeches and earthworms, possesses completely scrambled genomes. We develop a rearrangement index to quantify the extent of genome structure evolution and show that, compared to the last common ancestor of bilaterians, leeches and earthworms have among the most highly rearranged genomes of any currently sampled species. We further show that bilaterian genomes can be classified into two distinct categories-high and low rearrangement-largely influenced by the presence or absence, respectively, of chromosome fission events. Our findings demonstrate that animal genome structure can be highly variable within a phylum and reveal that genome rearrangement can occur both in a gradual, stepwise fashion, or rapid, all-encompassing changes over short evolutionary timescales.
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Affiliation(s)
- Thomas D Lewin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Yi-Jyun Luo
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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2
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Peraldi R, Kmita M. 40 years of the homeobox: mechanisms of Hox spatial-temporal collinearity in vertebrates. Development 2024; 151:dev202508. [PMID: 39167089 DOI: 10.1242/dev.202508] [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] [Indexed: 08/23/2024]
Abstract
Animal body plans are established during embryonic development by the Hox genes. This patterning process relies on the differential expression of Hox genes along the head-to-tail axis. Hox spatial collinearity refers to the relationship between the organization of Hox genes in clusters and the differential Hox expression, whereby the relative order of the Hox genes within a cluster mirrors the spatial sequence of expression in the developing embryo. In vertebrates, the cluster organization is also associated with the timing of Hox activation, which harmonizes Hox expression with the progressive emergence of axial tissues. Thereby, in vertebrates, Hox temporal collinearity is intimately linked to Hox spatial collinearity. Understanding the mechanisms contributing to Hox temporal and spatial collinearity is thus key to the comprehension of vertebrate patterning. Here, we provide an overview of the main discoveries pertaining to the mechanisms of Hox spatial-temporal collinearity.
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Affiliation(s)
- Rodrigue Peraldi
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec H2W 1R7, Canada
- Programme de Biologie Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Marie Kmita
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec H2W 1R7, Canada
- Programme de Biologie Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
- Département de Médecine, Université de Montréal, Montréal, Québec H3C 3J7, Canada
- Department of Experimental Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
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3
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David OG, Arce AV, Costa-da-Silva AL, Bellantuono AJ, DeGennaro M. Fertility decline in Aedes aegypti (Diptera: Culicidae) mosquitoes is associated with reduced maternal transcript deposition and does not depend on female age. JOURNAL OF MEDICAL ENTOMOLOGY 2024; 61:1064-1070. [PMID: 38757780 PMCID: PMC11239790 DOI: 10.1093/jme/tjae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/02/2024] [Accepted: 04/25/2024] [Indexed: 05/18/2024]
Abstract
Female mosquitoes undergo multiple rounds of reproduction known as gonotrophic cycles (GC). A gonotrophic cycle spans the period from blood meal intake to egg laying. Nutrients from vertebrate host blood are necessary for completing egg development. During oogenesis, a female prepackages mRNA into her oocytes, and these maternal transcripts drive the first 2 h of embryonic development prior to zygotic genome activation. In this study, we profiled transcriptional changes in 1-2 h of Aedes aegypti (Diptera: Culicidae) embryos across 2 GC. We found that homeotic genes which are regulators of embryogenesis are downregulated in embryos from the second gonotrophic cycle. Interestingly, embryos produced by Ae. aegypti females progressively reduced their ability to hatch as the number of GC increased. We show that this fertility decline is due to increased reproductive output and not the mosquitoes' age. Moreover, we found a similar decline in fertility and fecundity across 3 GC in Aedes albopictus. Our results are useful for predicting mosquito population dynamics to inform vector control efforts.
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Affiliation(s)
- Olayinka G David
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Andrea V Arce
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Andre Luis Costa-da-Silva
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Anthony J Bellantuono
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Matthew DeGennaro
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
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4
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Adachi U, Koita R, Seto A, Maeno A, Ishizu A, Oikawa S, Tani T, Ishizaka M, Yamada K, Satoh K, Nakazawa H, Furudate H, Kawakami K, Iwanami N, Matsuda M, Kawamura A. Teleost Hox code defines regional identities competent for the formation of dorsal and anal fins. Proc Natl Acad Sci U S A 2024; 121:e2403809121. [PMID: 38861596 PMCID: PMC11194558 DOI: 10.1073/pnas.2403809121] [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: 02/24/2024] [Accepted: 05/07/2024] [Indexed: 06/13/2024] Open
Abstract
The dorsal and anal fins can vary widely in position and length along the anterior-posterior axis in teleost fishes. However, the molecular mechanisms underlying the diversification of these fins remain unknown. Here, we used genetic approaches in zebrafish and medaka, in which the relative positions of the dorsal and anal fins are opposite, to demonstrate the crucial role of hox genes in the patterning of the teleost posterior body, including the dorsal and anal fins. By the CRISPR-Cas9-induced frameshift mutations and positional cloning of spontaneous dorsalfinless medaka, we show that various hox mutants exhibit the absence of dorsal or anal fins, or a stepwise posterior extension of these fins, with vertebral abnormalities. Our results indicate that multiple hox genes, primarily from hoxc-related clusters, encompass the regions responsible for the dorsal and anal fin formation along the anterior-posterior axis. These results further suggest that shifts in the anterior boundaries of hox expression which vary among fish species, lead to diversification in the position and size of the dorsal and anal fins, similar to how modulations in Hox expression can alter the number of anatomically distinct vertebrae in tetrapods. Furthermore, we show that hox genes responsible for dorsal fin formation are different between zebrafish and medaka. Our results suggest that a novel mechanism has occurred during teleost evolution, in which the gene network responsible for fin formation might have switched to the regulation downstream of other hox genes, leading to the remarkable diversity in the dorsal fin position.
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Affiliation(s)
- Urara Adachi
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama338-8570, Japan
| | - Rina Koita
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama338-8570, Japan
| | - Akira Seto
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya321-8505, Japan
| | - Akiteru Maeno
- Cell Architecture Laboratory, National Institute of Genetics, Mishima, Shizuoka411-8540, Japan
| | - Atsuki Ishizu
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama338-8570, Japan
| | - Sae Oikawa
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama338-8570, Japan
| | - Taisei Tani
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama338-8570, Japan
| | - Mizuki Ishizaka
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama338-8570, Japan
| | - Kazuya Yamada
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama338-8570, Japan
| | - Koumi Satoh
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama338-8570, Japan
| | - Hidemichi Nakazawa
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama338-8570, Japan
| | - Hiroyuki Furudate
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama338-8570, Japan
| | - Koichi Kawakami
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics, and Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka411-8540, Japan
| | - Norimasa Iwanami
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya321-8505, Japan
| | - Masaru Matsuda
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya321-8505, Japan
| | - Akinori Kawamura
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama338-8570, Japan
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5
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Kulakova MA, Maslakov GP, Poliushkevich LO. Irreducible Complexity of Hox Gene: Path to the Canonical Function of the Hox Cluster. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:987-1001. [PMID: 38981695 DOI: 10.1134/s0006297924060014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 07/11/2024]
Abstract
The evolution of major taxa is often associated with the emergence of new gene families. In all multicellular animals except sponges and comb jellies, the genomes contain Hox genes, which are crucial regulators of development. The canonical function of Hox genes involves colinear patterning of body parts in bilateral animals. This general function is implemented through complex, precisely coordinated mechanisms, not all of which are evolutionarily conserved and fully understood. We suggest that the emergence of this regulatory complexity was preceded by a stage of cooperation between more ancient morphogenetic programs or their individual elements. Footprints of these programs may be present in modern animals to execute non-canonical Hox functions. Non-canonical functions of Hox genes are involved in maintaining terminal nerve cell specificity, autophagy, oogenesis, pre-gastrulation embryogenesis, vertical signaling, and a number of general biological processes. These functions are realized by the basic properties of homeodomain protein and could have triggered the evolution of ParaHoxozoa and Nephrozoa subsequently. Some of these non-canonical Hox functions are discussed in our review.
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Affiliation(s)
- Milana A Kulakova
- Department of Embryology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia.
| | - Georgy P Maslakov
- Department of Embryology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Liudmila O Poliushkevich
- Department of Embryology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
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6
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Zhu Q, Liu P, Zhang M, Kang Y, Lv L, Xu H, Zhang Q, Li R, Pan C, Lan X. The Detection of a Functional 168 bp Deletion of the HOXB13 Gene Determining Short Tail and Its Association with Senior Growth Traits in Sheep Breeds Worldwide. Animals (Basel) 2024; 14:1617. [PMID: 38891664 PMCID: PMC11171003 DOI: 10.3390/ani14111617] [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: 03/11/2024] [Revised: 05/09/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024] Open
Abstract
In recent years, genome-wide association studies (GWAS) have uncovered that the HOXB13 gene is a key regulatory factor for the tail length trait of sheep. Further research has found that there is a functional 168 bp SINE element insertion upstream of the HOXB13 gene, which leads to the occurrence of long tails in sheep. However, the frequency of mutations in the 168 bp SINE element of the HOXB13 gene among different sheep breeds around the world and its relationship with growth traits are still unclear. This study used whole-genome sequencing (WGS) data, including 588 samples from 33 different sheep breeds around the world, to evaluate the frequency of HOXB13 gene mutations in different sheep breeds globally. At the same time, this study also selected 3392 sheep samples from six breeds. The genetic variation in the 168 bp InDel locus in the HOXB13 gene was determined through genotyping, and its association with the growth traits of Luxi black-headed sheep was analyzed. The research results indicate that the polymorphism of the 168 bp InDel locus is significantly correlated with the hip width of adult ewes in the Luxi black-headed sheep breed (p < 0.05) and that the hip width of adult ewes with the DD genotype is significantly larger than that of adult ewes with the ID genotype (p < 0.05). This study indicates that there is consistency between the research results on the sheep tail length trait and growth traits, which may contribute to the promotion of sheep breed improvement.
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Affiliation(s)
- Qihui Zhu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (Q.Z.); (P.L.); (Y.K.); (L.L.); (R.L.); (C.P.)
| | - Peiyao Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (Q.Z.); (P.L.); (Y.K.); (L.L.); (R.L.); (C.P.)
| | - Mingshi Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China;
| | - Yuxin Kang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (Q.Z.); (P.L.); (Y.K.); (L.L.); (R.L.); (C.P.)
| | - Linmi Lv
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (Q.Z.); (P.L.); (Y.K.); (L.L.); (R.L.); (C.P.)
| | - Hongwei Xu
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China;
| | - Qingfeng Zhang
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin 300000, China;
| | - Ran Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (Q.Z.); (P.L.); (Y.K.); (L.L.); (R.L.); (C.P.)
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (Q.Z.); (P.L.); (Y.K.); (L.L.); (R.L.); (C.P.)
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (Q.Z.); (P.L.); (Y.K.); (L.L.); (R.L.); (C.P.)
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7
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Rekaik H, Duboule D. A CTCF-dependent mechanism underlies the Hox timer: relation to a segmented body plan. Curr Opin Genet Dev 2024; 85:102160. [PMID: 38377879 DOI: 10.1016/j.gde.2024.102160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 01/27/2024] [Accepted: 01/28/2024] [Indexed: 02/22/2024]
Abstract
During gastrulation, Hox genes are activated in a time-sequence that follows the order of the genes along their clusters. This property, which is observed in all animals that develop following a progressive rostral-to-caudal morphogenesis, is associated with changes in the chromatin structure and epigenetic profiles of Hox clusters, suggesting a process at least partly based on sequential gene accessibility. Here, we discuss recent work on this issue, as well as a possible mechanism based on the surprising conservation in both the distribution and orientation of CTCF sites inside vertebrate Hox clusters.
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Affiliation(s)
- Hocine Rekaik
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France. https://twitter.com/@hocine_Rekaik
| | - Denis Duboule
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France.
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8
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Mulhair PO, Holland PWH. Evolution of the insect Hox gene cluster: Comparative analysis across 243 species. Semin Cell Dev Biol 2024; 152-153:4-15. [PMID: 36526530 PMCID: PMC10914929 DOI: 10.1016/j.semcdb.2022.11.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022]
Abstract
The Hox gene cluster is an iconic example of evolutionary conservation between divergent animal lineages, providing evidence for ancient similarities in the genetic control of embryonic development. However, there are differences between taxa in gene order, gene number and genomic organisation implying conservation is not absolute. There are also examples of radical functional change of Hox genes; for example, the ftz, zen and bcd genes in insects play roles in segmentation, extraembryonic membrane formation and body polarity, rather than specification of anteroposterior position. There have been detailed descriptions of Hox genes and Hox gene clusters in several insect species, including important model systems, but a large-scale overview has been lacking. Here we extend these studies using the publicly-available complete genome sequences of 243 insect species from 13 orders. We show that the insect Hox cluster is characterised by large intergenic distances, consistently extreme in Odonata, Orthoptera, Hemiptera and Trichoptera, and always larger between the 'posterior' Hox genes. We find duplications of ftz and zen in many species and multiple independent cluster breaks, although certain modules of neighbouring genes are rarely broken apart suggesting some organisational constraints. As more high-quality genomes are obtained, a challenge will be to relate structural genomic changes to phenotypic change across insect phylogeny.
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Affiliation(s)
- Peter O Mulhair
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK.
| | - Peter W H Holland
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK.
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9
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Aase-Remedios ME, Janssen R, Leite DJ, Sumner-Rooney L, McGregor AP. Evolution of the Spider Homeobox Gene Repertoire by Tandem and Whole Genome Duplication. Mol Biol Evol 2023; 40:msad239. [PMID: 37935059 PMCID: PMC10726417 DOI: 10.1093/molbev/msad239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 10/02/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
Gene duplication generates new genetic material that can contribute to the evolution of gene regulatory networks and phenotypes. Duplicated genes can undergo subfunctionalization to partition ancestral functions and/or neofunctionalization to assume a new function. We previously found there had been a whole genome duplication (WGD) in an ancestor of arachnopulmonates, the lineage including spiders and scorpions but excluding other arachnids like mites, ticks, and harvestmen. This WGD was evidenced by many duplicated homeobox genes, including two Hox clusters, in spiders. However, it was unclear which homeobox paralogues originated by WGD versus smaller-scale events such as tandem duplications. Understanding this is a key to determining the contribution of the WGD to arachnopulmonate genome evolution. Here we characterized the distribution of duplicated homeobox genes across eight chromosome-level spider genomes. We found that most duplicated homeobox genes in spiders are consistent with an origin by WGD. We also found two copies of conserved homeobox gene clusters, including the Hox, NK, HRO, Irx, and SINE clusters, in all eight species. Consistently, we observed one copy of each cluster was degenerated in terms of gene content and organization while the other remained more intact. Focussing on the NK cluster, we found evidence for regulatory subfunctionalization between the duplicated NK genes in the spider Parasteatoda tepidariorum compared to their single-copy orthologues in the harvestman Phalangium opilio. Our study provides new insights into the relative contributions of multiple modes of duplication to the homeobox gene repertoire during the evolution of spiders and the function of NK genes.
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Affiliation(s)
| | - Ralf Janssen
- Department of Earth Sciences, Uppsala University, Uppsala, 752 36, Sweden
| | - Daniel J Leite
- Department of Biosciences, Durham University, Durham, DH1 3LE, United Kingdom
| | - Lauren Sumner-Rooney
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, 10115, Germany
| | - Alistair P McGregor
- Department of Biosciences, Durham University, Durham, DH1 3LE, United Kingdom
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10
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Nuss AB, Lomas JS, Reyes JB, Garcia-Cruz O, Lei W, Sharma A, Pham MN, Beniwal S, Swain ML, McVicar M, Hinne IA, Zhang X, Yim WC, Gulia-Nuss M. The highly improved genome of Ixodes scapularis with X and Y pseudochromosomes. Life Sci Alliance 2023; 6:e202302109. [PMID: 37813487 PMCID: PMC10561763 DOI: 10.26508/lsa.202302109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/12/2023] Open
Abstract
Ixodes scapularis, the black-legged tick, is the principal vector of the Lyme disease spirochete, Borrelia burgdorferi, and is responsible for most of the ∼470,000 estimated Lyme disease cases annually in the USA. Ixodes scapularis can transmit six additional pathogens of human health significance. Because of its medical importance, I. scapularis was the first tick genome to be sequenced and annotated. However, the first assembly, I. scapularis Wikel (IscaW), was highly fragmented because of the technical challenges posed by the long, repetitive genome sequences characteristic of arthropod genomes and the lack of long-read sequencing techniques. Although I. scapularis has emerged as a model for tick research because of the availability of new tools such as embryo injection and CRISPR-Cas9-mediated gene editing yet the lack of chromosome-scale scaffolds has slowed progress in tick biology and the development of tools for their control. Here we combine diverse technologies to produce the I. scapularis Gulia-Nuss (IscGN) genome assembly and gene set. We used DNA from eggs and male and female adult ticks and took advantage of Hi-C, PacBio HiFi sequencing, and Illumina short-read sequencing technologies to produce a chromosome-level assembly. In this work, we present the predicted pseudochromosomes consisting of 13 autosomes and the sex pseudochromosomes: X and Y, and a markedly improved genome annotation compared with the existing assemblies and annotations.
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Affiliation(s)
- Andrew B Nuss
- https://ror.org/01keh0577 Department of Biochemistry and Molecular Biology, The University of Nevada, Reno, NV, USA
- https://ror.org/01keh0577 Department of Agriculture, Veterinary, and Rangeland Sciences, The University of Nevada, Reno, NV, USA
| | - Johnathan S Lomas
- https://ror.org/01keh0577 Department of Biochemistry and Molecular Biology, The University of Nevada, Reno, NV, USA
| | - Jeremiah B Reyes
- https://ror.org/01keh0577 Department of Biochemistry and Molecular Biology, The University of Nevada, Reno, NV, USA
- https://ror.org/01keh0577 Nevada Bioinformatics Center, University of Nevada, Reno, NV, USA
| | - Omar Garcia-Cruz
- https://ror.org/01keh0577 Department of Biochemistry and Molecular Biology, The University of Nevada, Reno, NV, USA
| | - Wenlong Lei
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Arvind Sharma
- https://ror.org/01keh0577 Department of Biochemistry and Molecular Biology, The University of Nevada, Reno, NV, USA
| | - Michael N Pham
- https://ror.org/01keh0577 Department of Biochemistry and Molecular Biology, The University of Nevada, Reno, NV, USA
| | - Saransh Beniwal
- https://ror.org/01keh0577 Department of Biochemistry and Molecular Biology, The University of Nevada, Reno, NV, USA
- https://ror.org/01keh0577 Department of Computer Science and Engineering, The University of Nevada, Reno, NV, USA
| | - Mia L Swain
- https://ror.org/01keh0577 Department of Biochemistry and Molecular Biology, The University of Nevada, Reno, NV, USA
| | - Molly McVicar
- https://ror.org/01keh0577 Department of Biochemistry and Molecular Biology, The University of Nevada, Reno, NV, USA
| | - Isaac Amankona Hinne
- https://ror.org/01keh0577 Department of Biochemistry and Molecular Biology, The University of Nevada, Reno, NV, USA
| | - Xingtan Zhang
- https://ror.org/01keh0577 Nevada Bioinformatics Center, University of Nevada, Reno, NV, USA
| | - Won C Yim
- https://ror.org/01keh0577 Department of Biochemistry and Molecular Biology, The University of Nevada, Reno, NV, USA
| | - Monika Gulia-Nuss
- https://ror.org/01keh0577 Department of Biochemistry and Molecular Biology, The University of Nevada, Reno, NV, USA
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11
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Rogers TF, Simakov O. Emerging questions on the mechanisms and dynamics of 3D genome evolution in spiralians. Brief Funct Genomics 2023; 22:533-542. [PMID: 37815133 PMCID: PMC10658181 DOI: 10.1093/bfgp/elad043] [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: 04/29/2023] [Revised: 08/17/2023] [Accepted: 09/12/2023] [Indexed: 10/11/2023] Open
Abstract
Information on how 3D genome topology emerged in animal evolution, how stable it is during development, its role in the evolution of phenotypic novelties and how exactly it affects gene expression is highly debated. So far, data to address these questions are lacking with the exception of a few key model species. Several gene regulatory mechanisms have been proposed, including scenarios where genome topology has little to no impact on gene expression, and vice versa. The ancient and diverse clade of spiralians may provide a crucial testing ground for such mechanisms. Sprialians have followed distinct evolutionary trajectories, with some clades experiencing genome expansions and/or large-scale genome rearrangements, and others undergoing genome contraction, substantially impacting their size and organisation. These changes have been associated with many phenotypic innovations in this clade. In this review, we describe how emerging genome topology data, along with functional tools, allow for testing these scenarios and discuss their predicted outcomes.
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Affiliation(s)
- Thea F Rogers
- Department of Neuroscience and Developmental Biology, Division of Molecular Evolution and Development, University of Vienna, Vienna, Austria
| | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, Division of Molecular Evolution and Development, University of Vienna, Vienna, Austria
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12
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Schnitzler CE, Chang ES, Waletich J, Quiroga-Artigas G, Wong WY, Nguyen AD, Barreira SN, Doonan L, Gonzalez P, Koren S, Gahan JM, Sanders SM, Bradshaw B, DuBuc TQ, Febrimarsa, de Jong D, Nawrocki EP, Larson A, Klasfeld S, Gornik SG, Moreland RT, Wolfsberg TG, Phillippy AM, Mullikin JC, Simakov O, Cartwright P, Nicotra M, Frank U, Baxevanis AD. The genome of the colonial hydroid Hydractinia reveals their stem cells utilize a toolkit of evolutionarily shared genes with all animals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.25.554815. [PMID: 37786714 PMCID: PMC10541594 DOI: 10.1101/2023.08.25.554815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Hydractinia is a colonial marine hydroid that exhibits remarkable biological properties, including the capacity to regenerate its entire body throughout its lifetime, a process made possible by its adult migratory stem cells, known as i-cells. Here, we provide an in-depth characterization of the genomic structure and gene content of two Hydractinia species, H. symbiolongicarpus and H. echinata, placing them in a comparative evolutionary framework with other cnidarian genomes. We also generated and annotated a single-cell transcriptomic atlas for adult male H. symbiolongicarpus and identified cell type markers for all major cell types, including key i-cell markers. Orthology analyses based on the markers revealed that Hydractinia's i-cells are highly enriched in genes that are widely shared amongst animals, a striking finding given that Hydractinia has a higher proportion of phylum-specific genes than any of the other 41 animals in our orthology analysis. These results indicate that Hydractinia's stem cells and early progenitor cells may use a toolkit shared with all animals, making it a promising model organism for future exploration of stem cell biology and regenerative medicine. The genomic and transcriptomic resources for Hydractinia presented here will enable further studies of their regenerative capacity, colonial morphology, and ability to distinguish self from non-self.
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Affiliation(s)
- Christine E Schnitzler
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - E Sally Chang
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Justin Waletich
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Gonzalo Quiroga-Artigas
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, Centre National de la Recherche Scientifique, 34293 Montpellier CEDEX 05, France
| | - Wai Yee Wong
- Department of Molecular Evolution and Development, Faculty of Life Science, University of Vienna, A-1090 Vienna, Austria
| | - Anh-Dao Nguyen
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sofia N Barreira
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Liam Doonan
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
| | - Paul Gonzalez
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sergey Koren
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James M Gahan
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Steven M Sanders
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Brian Bradshaw
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
| | - Timothy Q DuBuc
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
- Swarthmore College, Swarthmore, PA 19081, USA
| | - Febrimarsa
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
| | - Danielle de Jong
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Eric P Nawrocki
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexandra Larson
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
| | - Samantha Klasfeld
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sebastian G Gornik
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
- Centre for Organismal Studies, University of Heidelberg, Germany
| | - R Travis Moreland
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tyra G Wolfsberg
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam M Phillippy
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James C Mullikin
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
- NIH Intramural Sequencing Center, Rockville, MD 20852, USA
| | - Oleg Simakov
- Department of Molecular Evolution and Development, Faculty of Life Science, University of Vienna, A-1090 Vienna, Austria
| | - Paulyn Cartwright
- Department of Evolution and Ecology, University of Kansas, Lawrence, KS 66045, USA
| | - Matthew Nicotra
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Uri Frank
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
| | - Andreas D Baxevanis
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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13
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Kessler S, Minoux M, Joshi O, Ben Zouari Y, Ducret S, Ross F, Vilain N, Salvi A, Wolff J, Kohler H, Stadler MB, Rijli FM. A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest. Nat Commun 2023; 14:3242. [PMID: 37277355 DOI: 10.1038/s41467-023-38953-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 05/19/2023] [Indexed: 06/07/2023] Open
Abstract
Enhancer-promoter interactions preferentially occur within boundary-insulated topologically associating domains (TADs), limiting inter-TAD interactions. Enhancer clusters in linear proximity, termed super-enhancers (SEs), ensure high target gene expression levels. Little is known about SE topological regulatory impact during craniofacial development. Here, we identify 2232 genome-wide putative SEs in mouse cranial neural crest cells (CNCCs), 147 of which target genes establishing CNCC positional identity during face formation. In second pharyngeal arch (PA2) CNCCs, a multiple SE-containing region, partitioned into Hoxa Inter-TAD Regulatory Element 1 and 2 (HIRE1 and HIRE2), establishes long-range inter-TAD interactions selectively with Hoxa2, that is required for external and middle ear structures. HIRE2 deletion in a Hoxa2 haploinsufficient background results in microtia. HIRE1 deletion phenocopies the full homeotic Hoxa2 knockout phenotype and induces PA3 and PA4 CNCC abnormalities correlating with Hoxa2 and Hoxa3 transcriptional downregulation. Thus, SEs can overcome TAD insulation and regulate anterior Hoxa gene collinear expression in a CNCC subpopulation-specific manner during craniofacial development.
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Affiliation(s)
- Sandra Kessler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Maryline Minoux
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
- INSERM UMR 1121, Université de Strasbourg, Faculté de Chirurgie Dentaire, 8, rue Sainte Elisabeth, 67 000, Strasbourg, France
| | - Onkar Joshi
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Yousra Ben Zouari
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Sebastien Ducret
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Fiona Ross
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Nathalie Vilain
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Adwait Salvi
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Joachim Wolff
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Hubertus Kohler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Michael B Stadler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Filippo M Rijli
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
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14
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Li MH, Kuetemeyer JM, Yallowitz AR, Wellik DM. Characterization of a novel Hoxa5eGFP mouse line. Dev Dyn 2023; 252:536-546. [PMID: 36577717 PMCID: PMC10066829 DOI: 10.1002/dvdy.563] [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: 11/02/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Hox genes encode transcription factors that are important for establishing the body plan. Hoxa5 is a member of the mammalian Hox5 paralogous group that regulates the patterning and morphology of the cervical-thoracic region of the axial skeleton. Hoxa5 also plays crucial functions in lung morphogenesis. RESULTS We generated a Hoxa5eGFP reporter mouse line using CRISPR technology, allowing real-time visualization of Hoxa5 expression. Hoxa5eGFP recapitulates reported embryonic Hoxa5 mRNA expression patterns. Specifically, Hoxa5eGFP can be visualized in the developing mouse neural tube, somites, lung, diaphragm, foregut, and midgut, among other organs. In the stomach, posteriorly biased Hoxa5eGFP expression correlates with a drastic morphological reduction of the corpus in Hox5 paralogous mutants. Expression of Hoxa5eGFP in the lung continues in all lung fibroblast populations through postnatal and adult stages. CONCLUSIONS We identified cell types that express Hoxa5 in postnatal and adult mouse lungs, including various fibroblasts and vascular endothelial cells. This reporter line will be a powerful tool for studies of the function of Hoxa5 during mouse development, homeostasis, and disease processes.
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Affiliation(s)
- Mu-Hang Li
- Genetics Training Program, University of Wisconsin-Madison, Madison, WI, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, United States
| | - Julia M. Kuetemeyer
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, United States
| | - Alisha R. Yallowitz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Deneen M. Wellik
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, United States
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15
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Clarence T, Robert NS, Sarigol F, Fu X, Bates PA, Simakov O. Robust 3D modeling reveals spatiosyntenic properties of animal genomes. iScience 2023; 26:106136. [PMID: 36876129 PMCID: PMC9976460 DOI: 10.1016/j.isci.2023.106136] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/18/2022] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Animal genomes are organized into chromosomes that are remarkably conserved in their gene content, forming distinct evolutionary units (synteny). Using versatile chromosomal modeling, we infer three-dimensional topology of genomes from representative clades spanning the earliest animal diversification. We apply a partitioning approach using interaction spheres to compensate for varying quality of topological data. Using comparative genomics approaches, we test whether syntenic signal at gene pair, local, and whole chromosomal scale is reflected in the reconstructed spatial organization. We identify evolutionarily conserved three-dimensional networks at all syntenic scales revealing novel evolutionarily maintained interactors associated with known conserved local gene linkages (such as hox). We thus present evidence for evolutionary constraints that are associated with three-, rather than just two-, dimensional animal genome organization, which we term spatiosynteny. As more accurate topological data become available, together with validation approaches, spatiosynteny may become relevant in understanding the functionality behind the observed conservation of animal chromosomes.
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Affiliation(s)
- Tereza Clarence
- Biomolecular Modelling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Roussos Lab/Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Corresponding author
| | - Nicolas S.M. Robert
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Fatih Sarigol
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Xiao Fu
- Biomolecular Modelling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Paul A. Bates
- Biomolecular Modelling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Corresponding author
| | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
- Corresponding author
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16
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Gopinathan G, Zhang X, Luan X, Diekwisch TGH. Changes in Hox Gene Chromatin Organization during Odontogenic Lineage Specification. Genes (Basel) 2023; 14:198. [PMID: 36672939 PMCID: PMC9859321 DOI: 10.3390/genes14010198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Craniofacial tissues comprise highly evolved organs characterized by a relative lack of expression in the HOX family transcription factors. In the present study, we sought to define the epigenetic events that limit HOX gene expression from undifferentiated neural crest cells to semi-differentiated odontogenic progenitors and to explore the effects of elevated levels of HOX. The ChIP-chip data demonstrated high levels of repressive H3K27me3 marks on the HOX gene promoters in ES and cranial neural crest cells when compared to the H3K4me3 marks, while the K4/K27 ratio was less repressive in the odontogenic progenitors, dental follicle, dental pulp, periodontal ligament fibroblasts, alveolar bone osteoblasts, and cementoblasts. The gene expression of multiple HOX genes, especially those from the HOXA and HOXB clusters, was significantly elevated and many times higher in alveolar bone cells than in the dental follicle cells. In addition, the HOX levels in the skeletal osteoblasts were many times higher in the trunk osteoblasts compared to the alveolar bone osteoblasts, and the repressive mark H3K27me3 promoter occupancy was substantially and significantly elevated in the alveolar bone osteoblasts when compared to the trunk osteoblasts. To explore the effect of elevated HOX levels in craniofacial neural crest cells, HOX expression was induced by transfecting cells with the Cdx4 transcription factor, resulting in a significant decrease in the mineralization markers, RUNX2, OSX, and OCN upon HOX elevation. Promoting HOX gene expression in developing teeth using the small molecule EZH2 inhibitor GSK126 resulted in an increased number of patterning events, supernumerary cusp formation, and increased Hoxa4 and Hoxb6 gene expression when compared to the controls. Together, these studies illustrate the profound effects of epigenetic regulatory events at all stages of the differentiation of craniofacial peripheral tissues from the neural crest, including lineage specification, tissue differentiation, and patterning.
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Affiliation(s)
- Gokul Gopinathan
- Center for Craniofacial Research and Diagnosis, Texas A&M University, Dallas, TX 75246, USA
| | - Xinmin Zhang
- Bioinforx Inc., 510 Charmany Dr#275a, Madison, WI 53719, USA
| | - Xianghong Luan
- Center for Craniofacial Research and Diagnosis, Texas A&M University, Dallas, TX 75246, USA
| | - Thomas G. H. Diekwisch
- Center for Craniofacial Research and Diagnosis, Texas A&M University, Dallas, TX 75246, USA
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17
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Aryal S, Zhang Y, Wren S, Li C, Lu R. Molecular regulators of HOXA9 in acute myeloid leukemia. FEBS J 2023; 290:321-339. [PMID: 34743404 DOI: 10.1111/febs.16268] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/30/2021] [Accepted: 11/05/2021] [Indexed: 02/05/2023]
Abstract
Dysregulation of the oncogenic transcription factor HOXA9 is a prominent feature for most aggressive acute myeloid leukemia cases and a strong indicator of poor prognosis in patients. Leukemia subtypes with hallmark overexpression of HOXA9 include those carrying MLL gene rearrangements, NPM1c mutations, and other genetic alternations. A growing body of evidence indicates that HOXA9 dysregulation is both sufficient and necessary for leukemic transformation. The HOXA9 mRNA and protein regulation includes multilayered controls by transcription factors (such as CDX2/4 and USF2/1), epigenetic factors (such as MLL-menin-LEDGF, DOT1L, ENL, HBO1, NPM1c-XPO1, and polycomb proteins), microRNAs (such as miR-126 and miR-196b), long noncoding RNAs (such as HOTTIP), three-dimensional chromatin interactions, and post-translational protein modifications. Recently, insights into the dynamic regulation of HOXA9 have led to an advanced understanding of the HOXA9 regulome and provided new cancer therapeutic opportunities, including developing inhibitors targeting DOT1L, menin, and ENL proteins. This review summarizes recent advances in understanding the molecular mechanisms controlling HOXA9 regulation and the pharmacological approaches that target HOXA9 regulators to treat HOXA9-driven acute myeloid leukemia.
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Affiliation(s)
- Sajesan Aryal
- Division of Hematology and Oncology & O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, AL, USA
| | - Yang Zhang
- Department of Tumor Cell Biology & Cancer Biology Program/Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Spencer Wren
- Division of Hematology and Oncology & O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, AL, USA
| | - Chunliang Li
- Department of Tumor Cell Biology & Cancer Biology Program/Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Rui Lu
- Division of Hematology and Oncology & O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, AL, USA
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18
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Abstract
Hox genes encode evolutionarily conserved transcription factors that are essential for the proper development of bilaterian organisms. Hox genes are unique because they are spatially and temporally regulated during development in a manner that is dictated by their tightly linked genomic organization. Although their genetic function during embryonic development has been interrogated, less is known about how these transcription factors regulate downstream genes to direct morphogenetic events. Moreover, the continued expression and function of Hox genes at postnatal and adult stages highlights crucial roles for these genes throughout the life of an organism. Here, we provide an overview of Hox genes, highlighting their evolutionary history, their unique genomic organization and how this impacts the regulation of their expression, what is known about their protein structure, and their deployment in development and beyond.
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Affiliation(s)
- Katharine A. Hubert
- Program in Genetics, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Deneen M. Wellik
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
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19
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Mulhair PO, Crowley L, Boyes DH, Harper A, Lewis OT, Holland PWH. Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera. Genome Res 2023; 33:32-44. [PMID: 36617663 PMCID: PMC9977156 DOI: 10.1101/gr.277118.122] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022]
Abstract
Homeobox genes encode transcription factors with essential roles in patterning and cell fate in developing animal embryos. Many homeobox genes, including Hox and NK genes, are arranged in gene clusters, a feature likely related to transcriptional control. Sparse taxon sampling and fragmentary genome assemblies mean that little is known about the dynamics of homeobox gene evolution across Lepidoptera or about how changes in homeobox gene number and organization relate to diversity in this large order of insects. Here we analyze an extensive data set of high-quality genomes to characterize the number and organization of all homeobox genes in 123 species of Lepidoptera from 23 taxonomic families. We find most Lepidoptera have around 100 homeobox loci, including an unusual Hox gene cluster in which the lab gene is repositioned and the ro gene is next to pb A topologically associating domain spans much of the gene cluster, suggesting deep regulatory conservation of the Hox cluster arrangement in this insect order. Most Lepidoptera have four Shx genes, divergent zen-derived loci, but these loci underwent dramatic duplication in several lineages, with some moths having over 165 homeobox loci in the Hox gene cluster; this expansion is associated with local LINE element density. In contrast, the NK gene cluster content is more stable, although there are differences in organization compared with other insects, as well as major rearrangements within butterflies. Our analysis represents the first description of homeobox gene content across the order Lepidoptera, exemplifying the potential of newly generated genome assemblies for understanding genome and gene family evolution.
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Affiliation(s)
- Peter O Mulhair
- Department of Biology, University of Oxford, Oxford OX1 3SZ, United Kingdom
| | - Liam Crowley
- Department of Biology, University of Oxford, Oxford OX1 3SZ, United Kingdom
| | - Douglas H Boyes
- Department of Biology, University of Oxford, Oxford OX1 3SZ, United Kingdom
- UK Centre for Ecology and Hydrology, Wallingford OX10 8BB, United Kingdom
| | - Amber Harper
- Department of Biology, University of Oxford, Oxford OX1 3SZ, United Kingdom
| | - Owen T Lewis
- Department of Biology, University of Oxford, Oxford OX1 3SZ, United Kingdom
| | - Peter W H Holland
- Department of Biology, University of Oxford, Oxford OX1 3SZ, United Kingdom
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20
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High-Density Genetic Linkage Map of the Southern Blue-ringed Octopus (Octopodidae: Hapalochlaena maculosa). DIVERSITY 2022. [DOI: 10.3390/d14121068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genetic linkage maps provide a useful resource for non-model genomes and can aid in genome reassembly to form more contiguous pseudo-chromosomes. We present the first linkage map of any cephalopod, H. maculosa, composed of 47 linkage groups (LG). A total of 2166 single nucleotide polymorphisms and 2455 presence–absence variant loci were utilised by Lep-Map3 in linkage map construction. The map length spans 2016.62 cM with an average marker distance of 0.85 cM. Integration of the recent H. maculosa genome allowed 1151 scaffolds comprising 34% of the total genomic sequence to be orientated and/or placed using 1278 markers across all 47 LG. The linkage map generated provides a new perspective on HOX gene distribution in octopods. In the H. maculosa linkage map three (SCR, LOX4 and POST1) of six identified HOX genes (HOX1/LAB, SCR, LOX2, LOX4, LOX5, POST1) were located within the same LG (LG 9). The generation of a linkage map for H. maculosa has provided a valuable resource for understanding the evolution of cephalopod genomes and will provide a base for future work.
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21
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Gaunt SJ. Seeking Sense in the Hox Gene Cluster. J Dev Biol 2022; 10:48. [PMID: 36412642 PMCID: PMC9680502 DOI: 10.3390/jdb10040048] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/31/2022] [Accepted: 11/09/2022] [Indexed: 11/18/2022] Open
Abstract
The Hox gene cluster, responsible for patterning of the head-tail axis, is an ancestral feature of all bilaterally symmetrical animals (the Bilateria) that remains intact in a wide range of species. We can say that the Hox cluster evolved successfully only once since it is commonly the same in all groups, with labial-like genes at one end of the cluster expressed in the anterior embryo, and Abd-B-like genes at the other end of the cluster expressed posteriorly. This review attempts to make sense of the Hox gene cluster and to address the following questions. How did the Hox cluster form in the protostome-deuterostome last common ancestor, and why was this with a particular head-tail polarity? Why is gene clustering usually maintained? Why is there collinearity between the order of genes along the cluster and the positions of their expressions along the embryo? Why do the Hox gene expression domains overlap along the embryo? Why have vertebrates duplicated the Hox cluster? Why do Hox gene knockouts typically result in anterior homeotic transformations? How do animals adapt their Hox clusters to evolve new structural patterns along the head-tail axis?
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Affiliation(s)
- Stephen J Gaunt
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
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22
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Yoshida MA, Hirota K, Imoto J, Okuno M, Tanaka H, Kajitani R, Toyoda A, Itoh T, Ikeo K, Sasaki T, Setiamarga DHE. Gene Recruitments and Dismissals in the Argonaut Genome Provide Insights into Pelagic Lifestyle Adaptation and Shell-like Eggcase Reacquisition. Genome Biol Evol 2022; 14:evac140. [PMID: 36283693 PMCID: PMC9635652 DOI: 10.1093/gbe/evac140] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2022] [Indexed: 10/01/2023] Open
Abstract
The paper nautilus or greater argonaut, Argonauta argo, is a species of octopods which is characterized by its pelagic lifestyle and by the presence of a protective spiral-shaped shell-like eggcase in females. To reveal the genomic background of how the species adapted to the pelagic lifestyle and acquired its shell-like eggcase, we sequenced the draft genome of the species. The genome size was 1.1 Gb, which is the smallest among the cephalopods known to date, with the top 215 scaffolds (average length 5,064,479 bp) covering 81% (1.09 Gb) of the total assembly. A total of 26,433 protein-coding genes were predicted from 16,802 assembled scaffolds. From these, we identified nearly intact HOX, Parahox, Wnt clusters, and some gene clusters that could probably be related to the pelagic lifestyle, such as reflectin, tyrosinase, and opsin. The gene models also revealed several homologous genes related to calcified shell formation in Conchiferan mollusks, such as Pif-like, SOD, and TRX. Interestingly, comparative genomics analysis revealed that the homologous genes for such genes were also found in the genome of the shell-less octopus, as well as Nautilus, which has a true outer shell. Therefore, the draft genome sequence of Arg. argo presented here has helped us to gain further insights into the genetic background of the dynamic recruitment and dismissal of genes to form an important, converging extended phenotypic structure such as the shell and the shell-like eggcase. Additionally, it allows us to explore the evolution of from benthic to pelagic lifestyles in cephalopods and octopods.
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Affiliation(s)
- Masa-aki Yoshida
- Marine Biological Science Section, Education and Research Center for Biological Resources, Faculty of Life and Environmental Science, Shimane University, Okinoshima, Shimane 685-0024, Japan
| | - Kazuki Hirota
- Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
- Department of Applied Chemistry and Biochemistry, National Institute of Technology (KOSEN), Wakayama College, Gobo, Wakayama 644-0012, Japan
| | - Junichi Imoto
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Miki Okuno
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka 830-0011, Japan
| | - Hiroyuki Tanaka
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Rei Kajitani
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Kazuho Ikeo
- Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Takenori Sasaki
- Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
- The University Museum, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Davin H E Setiamarga
- Department of Applied Chemistry and Biochemistry, National Institute of Technology (KOSEN), Wakayama College, Gobo, Wakayama 644-0012, Japan
- The University Museum, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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23
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Wei M, Qin Z, Kong D, Liu D, Zheng Q, Bai S, Zhang Z, Ma Y. Echiuran Hox genes provide new insights into the correspondence between Hox subcluster organization and collinearity pattern. Proc Biol Sci 2022; 289:20220705. [PMID: 36264643 PMCID: PMC9449475 DOI: 10.1098/rspb.2022.0705] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 07/29/2022] [Indexed: 09/16/2023] Open
Abstract
In many bilaterians, Hox genes are generally clustered along the chromosomes and expressed in spatial and temporal order. In vertebrates, the expression of Hox genes follows a whole-cluster spatio-temporal collinearity (WSTC) pattern, whereas in some invertebrates the expression of Hox genes exhibits a subcluster-level spatio-temporal collinearity pattern. In bilaterians, the diversity of collinearity patterns and the cause of collinearity differences in Hox gene expression remain poorly understood. Here, we investigate genomic organization and expression pattern of Hox genes in the echiuran worm Urechis unicinctus (Annelida, Echiura). Urechis unicinctus has a split cluster with four subclusters divided by non-Hox genes: first subcluster (Hox1 and Hox2), second subcluster (Hox3), third subcluster (Hox4, Hox5, Lox5, Antp and Lox4), fourth subcluster (Lox2 and Post2). The expression of U. unicinctus Hox genes shows a subcluster-based whole-cluster spatio-temporal collinearity (S-WSTC) pattern: the anterior-most genes in each subcluster are activated in a spatially and temporally colinear manner (reminiscent of WSTC), with the subsequent genes in each subcluster then being very similar to their respective anterior-most subcluster gene. Combining genomic organization and expression profiles of Hox genes in different invertebrate lineages, we propose that the spatio-temporal collinearity of invertebrate Hox is subcluster-based.
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Affiliation(s)
- Maokai Wei
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Zhenkui Qin
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Dexu Kong
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Danwen Liu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Qiaojun Zheng
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Shumiao Bai
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Zhifeng Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, People's Republic of China
| | - Yubin Ma
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
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24
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Ozernyuk N, Schepetov D. HOX-Gene Cluster Organization and Genome Duplications in Fishes and Mammals: Transcript Variant Distribution along the Anterior–Posterior Axis. Int J Mol Sci 2022; 23:ijms23179990. [PMID: 36077385 PMCID: PMC9456325 DOI: 10.3390/ijms23179990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/16/2022] Open
Abstract
Hox genes play a crucial role in morphogenesis, especially in anterior–posterior body axis patterning. The organization of Hox clusters in vertebrates is a result of several genome duplications: two rounds of duplication in the ancestors of all vertebrates and a third round that was specific for teleost fishes. Teleostei cluster structure has been significantly modified in the evolutionary processes by Hox gene losses and co-options, while mammals show no such tendency. In mammals, the Hox gene number in a single cluster is stable and generally large, and the numbers are similar to those in the Chondrichthyes. Hox gene alternative splicing activity slightly differs between fishes and mammals. Fishes and mammals have differences in their known alternative splicing activity for Hox gene distribution along the anterior–posterior body axis. The analyzed fish groups—the Coelacanthiformes, Chondrichthyes, and Teleostei—all have higher known alternative mRNA numbers from the anterior and posterior regions, whereas mammals have a more uniform Hox transcript distribution along this axis. In fishes, most Hox transcripts produce functioning proteins, whereas mammals have significantly more known transcripts that do not produce functioning proteins.
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Affiliation(s)
- Nikolay Ozernyuk
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 26 Vavilov Street, 119334 Moscow, Russia
- Correspondence:
| | - Dimitry Schepetov
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119991 Moscow, Russia
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25
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Martynov AV, Korshunova TA. Renewed perspectives on the sedentary-pelagic last common bilaterian ancestor. CONTRIBUTIONS TO ZOOLOGY 2022. [DOI: 10.1163/18759866-bja10034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Various evaluations of the last common bilaterian ancestor (lcba) currently suggest that it resembled either a microscopic, non-segmented motile adult; or, on the contrary, a complex segmented adult motile urbilaterian. These fundamental inconsistencies remain largely unexplained. A majority of multidisciplinary data regarding sedentary adult ancestral bilaterian organization is overlooked. The sedentary-pelagic model is supported now by a number of novel developmental, paleontological and molecular phylogenetic data: (1) data in support of sedentary sponges, in the adult stage, as sister to all other Metazoa; (2) a similarity of molecular developmental pathways in both adults and larvae across sedentary sponges, cnidarians, and bilaterians; (3) a cnidarian-bilaterian relationship, including a unique sharing of a bona fide Hox-gene cluster, of which the evolutionary appearance does not connect directly to a bilaterian motile organization; (4) the presence of sedentary and tube-dwelling representatives of the main bilaterian clades in the early Cambrian; (5) an absence of definite taxonomic attribution of Ediacaran taxa reconstructed as motile to any true bilaterian phyla; (6) a similarity of tube morphology (and the clear presence of a protoconch-like apical structure of the Ediacaran sedentary Cloudinidae) among shells of the early Cambrian, and later true bilaterians, such as semi-sedentary hyoliths and motile molluscs; (7) recent data that provide growing evidence for a complex urbilaterian, despite a continuous molecular phylogenetic controversy. The present review compares the main existing models and reconciles the sedentary model of an urbilaterian and the model of a larva-like lcba with a unified sedentary(adult)-pelagic(larva) model of the lcba.
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Affiliation(s)
- Alexander V. Martynov
- Zoological Museum, Moscow State University, Bolshaya Nikitskaya Str. 6, 125009 Moscow, Russia,
| | - Tatiana A. Korshunova
- Koltzov Institute of Developmental Biology RAS, 26 Vavilova Str., 119334 Moscow, Russia
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26
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Pinglay S, Bulajić M, Rahe DP, Huang E, Brosh R, Mamrak NE, King BR, German S, Cadley JA, Rieber L, Easo N, Lionnet T, Mahony S, Maurano MT, Holt LJ, Mazzoni EO, Boeke JD. Synthetic regulatory reconstitution reveals principles of mammalian Hox cluster regulation. Science 2022; 377:eabk2820. [PMID: 35771912 PMCID: PMC9648154 DOI: 10.1126/science.abk2820] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Precise Hox gene expression is crucial for embryonic patterning. Intra-Hox transcription factor binding and distal enhancer elements have emerged as the major regulatory modules controlling Hox gene expression. However, quantifying their relative contributions has remained elusive. Here, we introduce "synthetic regulatory reconstitution," a conceptual framework for studying gene regulation, and apply it to the HoxA cluster. We synthesized and delivered variant rat HoxA clusters (130 to 170 kilobases) to an ectopic location in the mouse genome. We found that a minimal HoxA cluster recapitulated correct patterns of chromatin remodeling and transcription in response to patterning signals, whereas the addition of distal enhancers was needed for full transcriptional output. Synthetic regulatory reconstitution could provide a generalizable strategy for deciphering the regulatory logic of gene expression in complex genomes.
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Affiliation(s)
- Sudarshan Pinglay
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Milica Bulajić
- Department of Biology, New York University, New York, NY 10003, USA
| | - Dylan P. Rahe
- Department of Biology, New York University, New York, NY 10003, USA
| | - Emily Huang
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Ran Brosh
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Nicholas E. Mamrak
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Benjamin R. King
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Sergei German
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - John A. Cadley
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Lila Rieber
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Nicole Easo
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Timothée Lionnet
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Cell Biology, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Shaun Mahony
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Matthew T. Maurano
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Liam J. Holt
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | | | - Jef D. Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
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27
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Liu S, Tengstedt ANB, Jacobsen MW, Pujolar JM, Jónsson B, Lobón-Cervià J, Bernatchez L, Hansen MM. Genome-wide methylation in the panmictic European eel (Anguilla anguilla). Mol Ecol 2022; 31:4286-4306. [PMID: 35767387 DOI: 10.1111/mec.16586] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 11/30/2022]
Abstract
The role of methylation in adaptive, developmental and speciation processes has attracted considerable interest, but interpretation of results is complicated by diffuse boundaries between genetic and non-genetic variation. We studied whole genome genetic and methylation variation in the European eel, distributed from subarctic to subtropical environments, but with panmixia precluding genetically based local adaptation beyond single-generation responses. Overall methylation was 70.9%, with hypomethylation predominantly found in promoters and first exons. Redundancy analyses involving juvenile glass eels showed 0.06% and 0.03% of the variance at SNPs to be explained by localities and environmental variables, respectively, with GO terms of genes associated with outliers primarily involving neural system functioning. For CpGs 2.98% and 1.36% of variance was explained by localities and environmental variables. Differentially methylated regions particularly included genes involved in developmental processes, with hox clusters featuring prominently. Life stage (adult versus glass eels) was the most important source of inter-individual variation in methylation, likely reflecting both ageing and developmental processes. Demethylation of transposable elements relative to pure European eel was observed in European X American eel hybrids, possibly representing postzygotic barriers in this system characterized by prolonged speciation and ongoing gene flow. Whereas the genetic data are consistent with a role of single-generation selective responses, the methylation results underpin the importance of epigenetics in the life cycle of eels and suggests interactions between local environments, development and phenotypic variation mediated by methylation variation. Eels are remarkable by having retained eight hox clusters, and the results suggest important roles of methylation at hox genes for adaptive processes.
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Affiliation(s)
- Shenglin Liu
- Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Magnus W Jacobsen
- Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Jose Martin Pujolar
- Centre for Gelatinous Plankton Ecology and Evolution, National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Bjarni Jónsson
- North West Iceland Nature Center, Iceland.,The Icelandic Parliament, Reykjavík, Iceland
| | | | - Louis Bernatchez
- IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Québec, Canada
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28
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Ke C, Feng X, Li J, Chen S, Hu X. Association between long non‑coding RNA HOTAIR polymorphism and lung cancer risk: A systematic review and meta‑analysis. Exp Ther Med 2022; 24:540. [PMID: 35837044 PMCID: PMC9257968 DOI: 10.3892/etm.2022.11477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/07/2022] [Indexed: 12/24/2022] Open
Abstract
Single nucleotide polymorphism (SNP) of long noncoding RNA (lnc)RNA has been reported to be an important factor in cancer development. Recently, lncRNA homeobox transcript antisense intergenic RNA (HOTAIR) was indicated to induce tumorigenesis of several cancer types, but the association between the SNP of lncRNA HOTAIR and lung cancer susceptibility has remained undetermined. The present meta-analysis aimed to investigate the effect of HOTAIR polymorphism on susceptibility to lung cancer. The PubMed, Ovid Medline, Embase and Cochrane Library databases were thoroughly searched. Studies containing data on the incidence of lung cancer in patients with different HOTAIR SNPs were included. The Hardy-Weinberg equilibrium was analyzed to determine genotype distribution and allele frequencies. The odds ratio (OR) was pooled to evaluate the association of different SNPs with the susceptibility to lung cancer. A total of six studies comprising 1,715 patients with lung cancer and 2,745 healthy controls were finally included. A total of 4 SNPs (rs12826786, rs1899663, rs920778 and rs4759314) were reported. Analyses for all of these SNPs individually indicated that the lncRNA HOTAIR rs1899663 C>A polymorphism was a risk factor for lung cancer (dominant mode, AA+CA vs. CC: OR=0.816, 95% CI=0.707-0.942, P=0.005). The present study was the first meta-analysis investigating the association between lncRNA HOTAIR and lung cancer susceptibility. The results indicated that the lncRNA HOTAIR rs1899663 C>A polymorphism is a risk factor for lung cancer. LncRNA HOTAIR may be of value in lung cancer screening, particularly for populations with high-risk factors, as well as prognosis prediction. Future investigations are required to further clarify the intrinsic mechanism of the role of HOTAIR in the oncogenesis of lung cancer.
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Affiliation(s)
- Chunlin Ke
- Department of Radiotherapy, Cancer Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
| | - Xuegang Feng
- Department of Cardio‑Thoracic Surgery, 900 Hospital of The Joint Logistics Team, Fuzhou, Fujian 350025, P.R. China
| | - Jie Li
- Department of Oncology, 900 Hospital of The Joint Logistics Team, Fuzhou, Fujian 350025, P.R. China
| | - Siyu Chen
- Department of Oncology, 900 Hospital of The Joint Logistics Team, Fuzhou, Fujian 350025, P.R. China
| | - Xinyu Hu
- Department of Oncology, 900 Hospital of The Joint Logistics Team, Fuzhou, Fujian 350025, P.R. China
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29
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Xue S, Ly TTN, Vijayakar RS, Chen J, Ng J, Mathuru AS, Magdinier F, Reversade B. HOX epimutations driven by maternal SMCHD1/LRIF1 haploinsufficiency trigger homeotic transformations in genetically wildtype offspring. Nat Commun 2022; 13:3583. [PMID: 35739109 PMCID: PMC9226161 DOI: 10.1038/s41467-022-31185-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 06/07/2022] [Indexed: 11/09/2022] Open
Abstract
The body plan of animals is laid out by an evolutionary-conserved HOX code which is colinearly transcribed after zygotic genome activation (ZGA). Here we report that SMCHD1, a chromatin-modifying enzyme needed for X-inactivation in mammals, is maternally required for timely HOX expression. Using zebrafish and mouse Smchd1 knockout animals, we demonstrate that Smchd1 haplo-insufficiency brings about precocious and ectopic HOX transcription during oogenesis and embryogenesis. Unexpectedly, wild-type offspring born to heterozygous knockout zebrafish smchd1 mothers exhibited patent vertebrate patterning defects. The loss of maternal Smchd1 was accompanied by HOX epi-mutations driven by aberrant DNA methylation. We further show that this regulation is mediated by Lrif1, a direct interacting partner of Smchd1, whose knockout in zebrafish phenocopies that of Smchd1. Rather than being a short-lived maternal effect, HOX mis-regulation is stably inherited through cell divisions and persists in cultured fibroblasts derived from FSHD2 patients haploinsufficient for SMCHD1. We conclude that maternal SMCHD1/LRIF1 sets up an epigenetic state in the HOX loci that can only be reset in the germline. Such an unusual inter-generational inheritance, whereby a phenotype can be one generation removed from its genotype, casts a new light on how unresolved Mendelian diseases may be interpreted.
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Affiliation(s)
- Shifeng Xue
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore.
| | - Thanh Thao Nguyen Ly
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | | | - Jingyi Chen
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Joel Ng
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Ajay S Mathuru
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
- Yale-NUS College, Singapore, Singapore
- Department of Physiology, School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - Bruno Reversade
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore.
- Genome Institute of Singapore, A*STAR, Singapore, Singapore.
- Department of Paediatrics, School of Medicine, National University of Singapore, Singapore, Singapore.
- Department of Medical Genetics, KOÇ University, Istanbul, Turkey.
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30
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Retallack GJ. Damaged Dickinsonia specimens provide clues to Ediacaran vendobiont biology. PLoS One 2022; 17:e0269638. [PMID: 35709144 PMCID: PMC9202952 DOI: 10.1371/journal.pone.0269638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/19/2022] [Indexed: 12/14/2022] Open
Abstract
Recently reported specimens of the enigmatic Ediacaran fossil Dickinsonia from Russia show damage and repair that provides evidence of how they grew, and of their biological affinities. Marginal and terminal areas of wilting deformation are necrotic zones separating regenerated growth, sometimes on two divergent axes, rather than a single axis. Necrotic zones of damage to Dickinsonia are not a thick scar or callus, like a wound or amputation. Nor are they smooth transitions to a regenerated tail or arm. The wilted necrotic zone is most like damage by freezing, salt, or sunburn of leaves and lichens, compatible with evidence of terrestrial habitat from associated frigid and gypsic paleosols. Dickinsonia did not regrow by postembryonic addition of modules from a subterminal or patterned growth zone as in earthworms, myriapods, trilobites, crustaceans, and lizards. Rather Dickinsonia postembryonic regrowth from sublethal damage was from microscopic apical and lateral meristems, as in plants and lichens. Considered as fungal, Dickinsonia, and perhaps others of Class Vendobionta, were more likely Glomeromycota or Mucoromycotina, rather than Ascomycota or Basidiomycota.
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Affiliation(s)
- Gregory J. Retallack
- Department of Earth Sciences, University of Oregon, Eugene, Oregon, United States of America
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31
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Minelli A, Valero-Gracia A. Spatially and Temporally Distributed Complexity-A Refreshed Framework for the Study of GRN Evolution. Cells 2022; 11:cells11111790. [PMID: 35681485 PMCID: PMC9179533 DOI: 10.3390/cells11111790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/24/2022] [Accepted: 05/28/2022] [Indexed: 11/16/2022] Open
Abstract
Irrespective of the heuristic value of interpretations of developmental processes in terms of gene regulatory networks (GRNs), larger-angle views often suffer from: (i) an inadequate understanding of the relationship between genotype and phenotype; (ii) a predominantly zoocentric vision; and (iii) overconfidence in a putatively hierarchical organization of animal body plans. Here, we constructively criticize these assumptions. First, developmental biology is pervaded by adultocentrism, but development is not necessarily egg to adult. Second, during development, many unicells undergo transcriptomic profile transitions that are comparable to those recorded in pluricellular organisms; thus, their study should not be neglected from the GRN perspective. Third, the putatively hierarchical nature of the animal body is mirrored in the GRN logic, but in relating genotype to phenotype, independent assessments of the dynamics of the regulatory machinery and the animal’s architecture are required, better served by a combinatorial than by a hierarchical approach. The trade-offs between spatial and temporal aspects of regulation, as well as their evolutionary consequences, are also discussed. Multicellularity may derive from a unicell’s sequential phenotypes turned into different but coexisting, spatially arranged cell types. In turn, polyphenism may have been a crucial mechanism involved in the origin of complex life cycles.
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Affiliation(s)
- Alessandro Minelli
- Department of Biology, University of Padova, Via U. Bassi 58B, 35132 Padova, Italy
- Correspondence:
| | - Alberto Valero-Gracia
- Natural History Museum, University of Oslo, Blindern, P.O. Box 1172, 0318 Oslo, Norway;
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32
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Singh NP, Krumlauf R. Diversification and Functional Evolution of HOX Proteins. Front Cell Dev Biol 2022; 10:798812. [PMID: 35646905 PMCID: PMC9136108 DOI: 10.3389/fcell.2022.798812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/08/2022] [Indexed: 01/07/2023] Open
Abstract
Gene duplication and divergence is a major contributor to the generation of morphological diversity and the emergence of novel features in vertebrates during evolution. The availability of sequenced genomes has facilitated our understanding of the evolution of genes and regulatory elements. However, progress in understanding conservation and divergence in the function of proteins has been slow and mainly assessed by comparing protein sequences in combination with in vitro analyses. These approaches help to classify proteins into different families and sub-families, such as distinct types of transcription factors, but how protein function varies within a gene family is less well understood. Some studies have explored the functional evolution of closely related proteins and important insights have begun to emerge. In this review, we will provide a general overview of gene duplication and functional divergence and then focus on the functional evolution of HOX proteins to illustrate evolutionary changes underlying diversification and their role in animal evolution.
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Affiliation(s)
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, United States
- Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS, United States
- *Correspondence: Robb Krumlauf,
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Allievi A, Canavesi M, Ferrario C, Sugni M, Bonasoro F. An evo-devo perspective on the regeneration patterns of continuous arm structures in stellate echinoderms. THE EUROPEAN ZOOLOGICAL JOURNAL 2022. [DOI: 10.1080/24750263.2022.2039309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- A. Allievi
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - M. Canavesi
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - C. Ferrario
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
- Center for Complexity and Biosystems, Department of Physics, University of Milan, Milan, Italy
| | - M. Sugni
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
- Center for Complexity and Biosystems, Department of Physics, University of Milan, Milan, Italy
- GAIA 2050 Center, Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - F. Bonasoro
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
- GAIA 2050 Center, Department of Environmental Science and Policy, University of Milan, Milan, Italy
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Buffry AD, McGregor AP. Micromanagement of Drosophila Post-Embryonic Development by Hox Genes. J Dev Biol 2022; 10:13. [PMID: 35225966 PMCID: PMC8883937 DOI: 10.3390/jdb10010013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 02/06/2022] [Accepted: 02/11/2022] [Indexed: 01/27/2023] Open
Abstract
Hox genes function early in development to determine regional identity in animals. Consequently, the loss or gain of Hox gene expression can change this identity and cause homeotic transformations. Over 20 years ago, it was observed that the role of Hox genes in patterning animal body plans involves the fine-scale regulation of cell fate and identity during development, playing the role of 'micromanagers' as proposed by Michael Akam in key perspective papers. Therefore, as well as specifying where structures develop on animal bodies, Hox genes can help to precisely sculpt their morphology. Here, we review work that has provided important insights about the roles of Hox genes in influencing cell fate during post-embryonic development in Drosophila to regulate fine-scale patterning and morphology. We also explore how this is achieved through the regulation of Hox genes, specific co-factors and their complex regulation of hundreds of target genes. We argue that further investigating the regulation and roles of Hox genes in Drosophila post-embryonic development has great potential for understanding gene regulation, cell fate and phenotypic differentiation more generally.
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Robert NSM, Sarigol F, Zimmermann B, Meyer A, Voolstra CR, Simakov O. Emergence of distinct syntenic density regimes is associated with early metazoan genomic transitions. BMC Genomics 2022; 23:143. [PMID: 35177000 PMCID: PMC8851819 DOI: 10.1186/s12864-022-08304-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/10/2022] [Indexed: 12/03/2022] Open
Abstract
Background Animal genomes are strikingly conserved in terms of local gene order (microsynteny). While some of these microsyntenies have been shown to be coregulated or to form gene regulatory blocks, the diversity of their genomic and regulatory properties across the metazoan tree of life remains largely unknown. Results Our comparative analyses of 49 animal genomes reveal that the largest gains of synteny occurred in the last common ancestor of bilaterians and cnidarians and in that of bilaterians. Depending on their node of emergence, we further show that novel syntenic blocks are characterized by distinct functional compositions (Gene Ontology terms enrichment) and gene density properties, such as high, average and low gene density regimes. This is particularly pronounced among bilaterian novel microsyntenies, most of which fall into high gene density regime associated with higher gene coexpression levels. Conversely, a majority of vertebrate novel microsyntenies display a low gene density regime associated with lower gene coexpression levels. Conclusions Our study provides first evidence for evolutionary transitions between different modes of microsyntenic block regulation that coincide with key events of metazoan evolution. Moreover, the microsyntenic profiling strategy and interactive online application (Syntenic Density Browser, available at: http://synteny.csb.univie.ac.at/) we present here can be used to explore regulatory properties of microsyntenic blocks and predict their coexpression in a wide-range of animal genomes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08304-2.
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Affiliation(s)
- Nicolas S M Robert
- Department of Neurosciences and Developmental Biology, University of Vienna, Althanstrasse 14, 1090, Wien, Austria.
| | - Fatih Sarigol
- Department of Neurosciences and Developmental Biology, University of Vienna, Althanstrasse 14, 1090, Wien, Austria
| | - Bob Zimmermann
- Department of Neurosciences and Developmental Biology, University of Vienna, Althanstrasse 14, 1090, Wien, Austria
| | - Axel Meyer
- Department of Biology, University of Konstanz, 78457, Constance, Germany
| | | | - Oleg Simakov
- Department of Neurosciences and Developmental Biology, University of Vienna, Althanstrasse 14, 1090, Wien, Austria.
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Essay the (unusual) heuristic value of Hox gene clusters; a matter of time? Dev Biol 2022; 484:75-87. [PMID: 35182536 DOI: 10.1016/j.ydbio.2022.02.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 12/22/2022]
Abstract
Ever since their first report in 1984, Antennapedia-type homeobox (Hox) genes have been involved in such a series of interesting observations, in particular due to their conserved clustered organization between vertebrates and arthropods, that one may legitimately wonder about the origin of this heuristic value. In this essay, I first consider different examples where Hox gene clusters have been instrumental in providing conceptual advances, taken from various fields of research and mostly involving vertebrate embryos. These examples touch upon our understanding of genomic evolution, the revisiting of 19th century views on the relationships between development and evolution and the building of a new framework to understand long-range and pleiotropic gene regulation during development. I then discuss whether the high value of the Hox gene family, when considered as an epistemic object, is related to its clustered structure (and the absence thereof in some animal species) and, if so, what is it in such particular genetic oddities that made them so generous in providing the scientific community with interesting information.
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Pourquié O. A brief history of the segmentation clock. Dev Biol 2022; 485:24-36. [DOI: 10.1016/j.ydbio.2022.02.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 11/16/2022]
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Ranz JM, González PM, Su RN, Bedford SJ, Abreu-Goodger C, Markow T. Multiscale analysis of the randomization limits of the chromosomal gene organization between Lepidoptera and Diptera. Proc Biol Sci 2022; 289:20212183. [PMID: 35042416 PMCID: PMC8767184 DOI: 10.1098/rspb.2021.2183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/13/2021] [Indexed: 11/12/2022] Open
Abstract
How chromosome gene organization and gene content evolve among distantly related and structurally malleable genomes remains unresolved. This is particularly the case when considering different insect orders. We have compared the highly contiguous genome assemblies of the lepidopteran Danaus plexippus and the dipteran Drosophila melanogaster, which shared a common ancestor around 290 Ma. The gene content of 23 out of 30 D. plexippus chromosomes was significantly associated with one or two of the six chromosomal elements of the Drosophila genome, denoting common ancestry. Despite the phylogenetic distance, 9.6% of the 1-to-1 orthologues still reside within the same ancestral genome neighbourhood. Furthermore, the comparison D. plexippus-Bombyx mori indicated that the rates of chromosome repatterning are lower in Lepidoptera than in Diptera, although still within the same order of magnitude. Concordantly, 14 developmental gene clusters showed a higher tendency to retain full or partial clustering in D. plexippus, further supporting that the physical association between the SuperHox and NK clusters existed in the ancestral bilaterian. Our results illuminate the scope and limits of the evolution of the gene organization and content of the ancestral chromosomes to the Lepidoptera and Diptera while helping reconstruct portions of the genome in their most recent common ancestor.
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Affiliation(s)
- José M. Ranz
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine CA 92647, USA
| | - Pablo M. González
- Unidad de Genómica Avanzada (Langebio), CINVESTAV, Irapuato GTO 36824, México
| | - Ryan N. Su
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine CA 92647, USA
| | - Sarah J. Bedford
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine CA 92647, USA
| | - Cei Abreu-Goodger
- Unidad de Genómica Avanzada (Langebio), CINVESTAV, Irapuato GTO 36824, México
| | - Therese Markow
- Unidad de Genómica Avanzada (Langebio), CINVESTAV, Irapuato GTO 36824, México
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
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Chakraborty P. Gene cluster from plant to microbes: Their role in genome architecture, organism's development, specialized metabolism and drug discovery. Biochimie 2021; 193:1-15. [PMID: 34890733 DOI: 10.1016/j.biochi.2021.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 12/01/2021] [Accepted: 12/04/2021] [Indexed: 02/07/2023]
Abstract
Plants and microbes fulfil our daily requirements through different high-value chemicals, e.g., nutraceuticals, pharmaceuticals, cosmetics, and through varieties of fruits, crops, vegetables, and many more. Utmost care would therefore be taken for growth, development and sustainability of these important crops and medicinal plants and microbes. Homeobox genes and HOX clusters and their recently characterized expanded family members, including newly discovered homeobox, WOX gene from medicinal herb, Panax ginseng, significantly contributes in the growth and development of these organisms. On the other hand, secondary metabolites produced through secondary metabolism of plants and microbes are used as organisms defense as well as drugs/drug-like molecules for humans. Both the developmental HOX cluster and the biosynthetic gene-cluster (BGC) for secondary metabolites are organised in organisms genome. Genome mining and genomewide analysis of these clusters will definitely identify and characterize many more important molecules from unexplored plants and microbes and underexplored human microbiota and the evolution studies of these clusters will indicate their source of origin. Although genomics revolution now continues at a pace, till date only few hundred plant genome sequences are available. However, next-generation sequencing (NGS) technology now in market and may be applied even for plants with recalcitrant genomes, eventually may discover genomic potential towards production of secondary metabolites of diverse plants and micro-organisms present in the environment and microbiota. Additionally, the development of tools for genome mining e.g., antiSMASH, plantiSMASH, and more and more computational approaches that predicts hundreds of secondary metabolite BGCs will be discussed.
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Affiliation(s)
- Prasanta Chakraborty
- Kalpana Chawla Center for Space and Nanoscience, Kolkata, Indian Institute of Chemical Biology (retd.), Kolkata, 700032, India.
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40
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de Oliveira AL, Mitchell J, Girguis P, Bright M. Novel insights on obligate symbiont lifestyle and adaptation to chemosynthetic environment as revealed by the giant tubeworm genome. Mol Biol Evol 2021; 39:6454105. [PMID: 34893862 PMCID: PMC8789280 DOI: 10.1093/molbev/msab347] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The mutualism between the giant tubeworm Riftia pachyptila and its endosymbiont Candidatus Endoriftia persephone has been extensively researched over the past 40 years. However, the lack of the host whole genome information has impeded the full comprehension of the genotype/phenotype interface in Riftia. Here we described the high-quality draft genome of Riftia, its complete mitogenome, and tissue-specific transcriptomic data. The Riftia genome presents signs of reductive evolution, with gene family contractions exceeding expansions. Expanded gene families are related to sulphur metabolism, detoxification, anti-oxidative stress, oxygen transport, immune system, and lysosomal digestion, reflecting evolutionary adaptations to the vent environment and endosymbiosis. Despite the derived body plan, the developmental gene repertoire in the gutless tubeworm is extremely conserved with the presence of a near intact and complete Hox cluster. Gene expression analyses establishes that the trophosome is a multi-functional organ marked by intracellular digestion of endosymbionts, storage of excretory products and haematopoietic functions. Overall, the plume and gonad tissues both in contact to the environment harbour highly expressed genes involved with cell cycle, programmed cell death, and immunity indicating a high cell turnover and defence mechanisms against pathogens. We posit that the innate immune system plays a more prominent role into the establishment of the symbiosis during the infection in the larval stage, rather than maintaining the symbiostasis in the trophosome. This genome bridges four decades of physiological research in Riftia, whilst simultaneously provides new insights into the development, whole organism functions and evolution in the giant tubeworm.
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Affiliation(s)
| | - Jessica Mitchell
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Peter Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Monika Bright
- Department of Functional and Evolutionary Ecology, University of Vienna, Austria
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Zhao B, Pan Y, Qiao L, Liu J, Yang K, Liang Y, Liu W. miR-301a inhibits adipogenic differentiation of adipose-derived stromal vascular fractions by targeting HOXC8 in sheep. Anim Sci J 2021; 92:e13661. [PMID: 34856652 DOI: 10.1111/asj.13661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/09/2021] [Accepted: 10/21/2021] [Indexed: 01/13/2023]
Abstract
MicroRNAs (miRNAs) regulate adipogenic differentiation in stromal vascular fractions (SVFs) through post-transcriptional regulation of transcription factors and other functional genes. miR-301 and the homeobox C8 (HOXC8) gene are involved in lipid homeostasis; however, their roles in the adipogenic differentiation of ovine SVFs are unknown. Here, we explored the effects of miR-301 and HOXC8 on adipogenic differentiation in ovine SVFs and the regulatory role of miR-301a in HOXC8 expression. Additionally, we evaluated the effect of miR-301a and HOXC8 on the mRNA abundance of adipogenic markers and the ability of ovine SVFs to accumulate lipids. We found that miR-301a regulates adipogenic differentiation in ovine SVFs by directly targeting the 3'-untranslated region of HOXC8, resulting in significant downregulation of the HOXC8 mRNA and protein. Moreover, miR-301a overexpression suppressed adipogenic differentiation in ovine SVFs and significantly inhibited the expression of adipogenesis-related genes-including adiponectin, C/EBPα, PPARγ, and FABP4. Conversely, HOXC8 overexpression in ovine SVFs increased the accumulation of lipid droplets and remarkably promoted the expression of adipogenic markers. Taken together, our results indicate that miR-301a attenuates the adipogenic differentiation of ovine SVFs by targeting HOXC8. These findings improve our understanding of the mechanism of lipid accumulation and metabolism in sheep.
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Affiliation(s)
- Bishi Zhao
- College of Animal Science, Shanxi Agricultural University, Taigu, China
| | - Yangyang Pan
- College of Animal Science, Shanxi Agricultural University, Taigu, China
| | - Liying Qiao
- College of Animal Science, Shanxi Agricultural University, Taigu, China
| | - Jianhua Liu
- College of Animal Science, Shanxi Agricultural University, Taigu, China
| | - Kaijie Yang
- College of Animal Science, Shanxi Agricultural University, Taigu, China
| | - Yu Liang
- College of Animal Science, Shanxi Agricultural University, Taigu, China
| | - Wenzhong Liu
- College of Animal Science, Shanxi Agricultural University, Taigu, China
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42
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Mallen J, Kalsan M, Zarrineh P, Bridoux L, Ahmad S, Bobola N. Molecular Characterization of HOXA2 and HOXA3 Binding Properties. J Dev Biol 2021; 9:jdb9040055. [PMID: 34940502 PMCID: PMC8707757 DOI: 10.3390/jdb9040055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/17/2021] [Accepted: 11/30/2021] [Indexed: 01/06/2023] Open
Abstract
The highly conserved HOX homeodomain (HD) transcription factors (TFs) establish the identity of different body parts along the antero–posterior axis of bilaterian animals. Segment diversification and the morphogenesis of different structures is achieved by generating precise patterns of HOX expression along the antero–posterior axis and by the ability of different HOX TFs to instruct unique and specific transcriptional programs. However, HOX binding properties in vitro, characterised by the recognition of similar AT-rich binding sequences, do not account for the ability of different HOX to instruct segment-specific transcriptional programs. To address this problem, we previously compared HOXA2 and HOXA3 binding in vivo. Here, we explore if sequence motif enrichments observed in vivo are explained by binding affinities in vitro. Unexpectedly, we found that the highest enriched motif in HOXA2 peaks was not recognised by HOXA2 in vitro, highlighting the importance of investigating HOX binding in its physiological context. We also report the ability of HOXA2 and HOXA3 to heterodimerise, which may have functional consequences for the HOX patterning function in vivo.
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Affiliation(s)
- Joshua Mallen
- School of Medical Sciences, University of Manchester, Manchester M13 9PT, UK; (J.M.); (P.Z.)
| | - Manisha Kalsan
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (M.K.); (S.A.)
| | - Peyman Zarrineh
- School of Medical Sciences, University of Manchester, Manchester M13 9PT, UK; (J.M.); (P.Z.)
| | - Laure Bridoux
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 5 (L7.07.10) Place Croix du Sud, 1348 Louvain-la-Neuve, Belgium;
| | - Shandar Ahmad
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (M.K.); (S.A.)
| | - Nicoletta Bobola
- School of Medical Sciences, University of Manchester, Manchester M13 9PT, UK; (J.M.); (P.Z.)
- Correspondence:
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Hajirnis N, Mishra RK. Homeotic Genes: Clustering, Modularity, and Diversity. Front Cell Dev Biol 2021; 9:718308. [PMID: 34458272 PMCID: PMC8386295 DOI: 10.3389/fcell.2021.718308] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/22/2021] [Indexed: 11/13/2022] Open
Abstract
Hox genes code for transcription factors and are evolutionarily conserved. They regulate a plethora of downstream targets to define the anterior-posterior (AP) body axis of a developing bilaterian embryo. Early work suggested a possible role of clustering and ordering of Hox to regulate their expression in a spatially restricted manner along the AP axis. However, the recent availability of many genome assemblies for different organisms uncovered several examples that defy this constraint. With recent advancements in genomics, the current review discusses the arrangement of Hox in various organisms. Further, we revisit their discovery and regulation in Drosophila melanogaster. We also review their regulation in different arthropods and vertebrates, with a significant focus on Hox expression in the crustacean Parahyale hawaiensis. It is noteworthy that subtle changes in the levels of Hox gene expression can contribute to the development of novel features in an organism. We, therefore, delve into the distinct regulation of these genes during primary axis formation, segment identity, and extra-embryonic roles such as in the formation of hair follicles or misregulation leading to cancer. Toward the end of each section, we emphasize the possibilities of several experiments involving various organisms, owing to the advancements in the field of genomics and CRISPR-based genome engineering. Overall, we present a holistic view of the functioning of Hox in the animal world.
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Affiliation(s)
- Nikhil Hajirnis
- CSIR – Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - Rakesh K. Mishra
- CSIR – Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
- AcSIR – Academy of Scientific and Innovative Research, Ghaziabad, India
- Tata Institute for Genetics and Society (TIGS), Bangalore, India
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Xu Z, Gao T, Xu Y, Li X, Li J, Lin H, Yan W, Pan J, Tang J. A chromosome-level reference genome of red swamp crayfish Procambarus clarkii provides insights into the gene families regarding growth or development in crustaceans. Genomics 2021; 113:3274-3284. [PMID: 34303807 DOI: 10.1016/j.ygeno.2021.07.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/28/2021] [Accepted: 07/14/2021] [Indexed: 11/27/2022]
Abstract
Red swamp crayfish Procambarus clarkii is an ecologically and economically important crustacean species. Here, based on a de novo assembly strategy combining PacBio with Hi-C sequencing, we presented a high quality chromosome-level P. clarkii genome. The assembled genome is 2.75 Gb in size with a contig N50 of 216.75 kb. Transposable elements (TEs) make up the largest fraction of the genome (~79.61%), and LINEs comprise the majority of the TEs. Frequent molting and rapid growth of the red swamp crayfish may be explained by the expansion of multiple gene families regarding growth or development. Phylogenetic analysis revealed that P. clarkii diverged from Portunus trituberculatus at 278-407 million years ago (Mya). PSMC analysis identified multiple bottleneck events of the P. clarkii population between 2 kaBP to 14 kaBP. The obtained P. clarkii genome should not only facilitate us understanding the development and evolution of the crayfish species, but also contribute to the genetic improvement in future breeding selections.
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Affiliation(s)
- Zhiqiang Xu
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China; Institute of Marine Biology, College of Oceanography, Hohai University, Nanjing 210098, China; Jiangsu Key laboratory for Conservation and Utilization of freshwater Fisheries Germplasm Resources, Nanjing 210017, China.
| | - Tianheng Gao
- Institute of Marine Biology, College of Oceanography, Hohai University, Nanjing 210098, China; Jiangsu Key laboratory for Conservation and Utilization of freshwater Fisheries Germplasm Resources, Nanjing 210017, China
| | - Yu Xu
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China; Jiangsu Key laboratory for Conservation and Utilization of freshwater Fisheries Germplasm Resources, Nanjing 210017, China
| | - Xuguang Li
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China; Jiangsu Key laboratory for Conservation and Utilization of freshwater Fisheries Germplasm Resources, Nanjing 210017, China
| | - Jiajia Li
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
| | - Hai Lin
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
| | - Weihui Yan
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
| | - Jianlin Pan
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China; Institute of Marine Biology, College of Oceanography, Hohai University, Nanjing 210098, China; Jiangsu Key laboratory for Conservation and Utilization of freshwater Fisheries Germplasm Resources, Nanjing 210017, China
| | - Jianqing Tang
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China; Jiangsu Key laboratory for Conservation and Utilization of freshwater Fisheries Germplasm Resources, Nanjing 210017, China.
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Novikova EL, Kulakova MA. There and Back Again: Hox Clusters Use Both DNA Strands. J Dev Biol 2021; 9:28. [PMID: 34287306 PMCID: PMC8293171 DOI: 10.3390/jdb9030028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 12/25/2022] Open
Abstract
Bilaterian animals operate the clusters of Hox genes through a rich repertoire of diverse mechanisms. In this review, we will summarize and analyze the accumulated data concerning long non-coding RNAs (lncRNAs) that are transcribed from sense (coding) DNA strands of Hox clusters. It was shown that antisense regulatory RNAs control the work of Hox genes in cis and trans, participate in the establishment and maintenance of the epigenetic code of Hox loci, and can even serve as a source of regulatory peptides that switch cellular energetic metabolism. Moreover, these molecules can be considered as a force that consolidates the cluster into a single whole. We will discuss the examples of antisense transcription of Hox genes in well-studied systems (cell cultures, morphogenesis of vertebrates) and bear upon some interesting examples of antisense Hox RNAs in non-model Protostomia.
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Affiliation(s)
- Elena L. Novikova
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7–9, 199034 Saint Petersburg, Russia;
- Laboratory of Evolutionary Morphology, Zoological Institute RAS, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia
| | - Milana A. Kulakova
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7–9, 199034 Saint Petersburg, Russia;
- Laboratory of Evolutionary Morphology, Zoological Institute RAS, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia
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Lewin TD, Royall AH, Holland PWH. Dynamic Molecular Evolution of Mammalian Homeobox Genes: Duplication, Loss, Divergence and Gene Conversion Sculpt PRD Class Repertoires. J Mol Evol 2021; 89:396-414. [PMID: 34097121 PMCID: PMC8208926 DOI: 10.1007/s00239-021-10012-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/11/2021] [Indexed: 11/21/2022]
Abstract
The majority of homeobox genes are highly conserved across animals, but the eutherian-specific ETCHbox genes, embryonically expressed and highly divergent duplicates of CRX, are a notable exception. Here we compare the ETCHbox genes of 34 mammalian species, uncovering dynamic patterns of gene loss and tandem duplication, including the presence of a large tandem array of LEUTX loci in the genome of the European rabbit (Oryctolagus cuniculus). Despite extensive gene gain and loss, all sampled species possess at least two ETCHbox genes, suggesting their collective role is indispensable. We find evidence for positive selection and show that TPRX1 and TPRX2 have been the subject of repeated gene conversion across the Boreoeutheria, homogenising their sequences and preventing divergence, especially in the homeobox region. Together, these results are consistent with a model where mammalian ETCHbox genes are dynamic in evolution due to functional overlap, yet have collective indispensable roles.
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Affiliation(s)
- Thomas D Lewin
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Amy H Royall
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Peter W H Holland
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
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Aase-Remedios ME, Ferrier DEK. Improved Understanding of the Role of Gene and Genome Duplications in Chordate Evolution With New Genome and Transcriptome Sequences. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.703163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Comparative approaches to understanding chordate genomes have uncovered a significant role for gene duplications, including whole genome duplications (WGDs), giving rise to and expanding gene families. In developmental biology, gene families created and expanded by both tandem and WGDs are paramount. These genes, often involved in transcription and signalling, are candidates for underpinning major evolutionary transitions because they are particularly prone to retention and subfunctionalisation, neofunctionalisation, or specialisation following duplication. Under the subfunctionalisation model, duplication lays the foundation for the diversification of paralogues, especially in the context of gene regulation. Tandemly duplicated paralogues reside in the same regulatory environment, which may constrain them and result in a gene cluster with closely linked but subtly different expression patterns and functions. Ohnologues (WGD paralogues) often diversify by partitioning their expression domains between retained paralogues, amidst the many changes in the genome during rediploidisation, including chromosomal rearrangements and extensive gene losses. The patterns of these retentions and losses are still not fully understood, nor is the full extent of the impact of gene duplication on chordate evolution. The growing number of sequencing projects, genomic resources, transcriptomics, and improvements to genome assemblies for diverse chordates from non-model and under-sampled lineages like the coelacanth, as well as key lineages, such as amphioxus and lamprey, has allowed more informative comparisons within developmental gene families as well as revealing the extent of conserved synteny across whole genomes. This influx of data provides the tools necessary for phylogenetically informed comparative genomics, which will bring us closer to understanding the evolution of chordate body plan diversity and the changes underpinning the origin and diversification of vertebrates.
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Bayramov AV, Ermakova GV, Kuchryavyy AV, Zaraisky AG. Genome Duplications as the Basis of Vertebrates’ Evolutionary Success. Russ J Dev Biol 2021. [DOI: 10.1134/s1062360421030024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Razin SV, Ioudinkova ES, Kantidze OL, Iarovaia OV. Co-Regulated Genes and Gene Clusters. Genes (Basel) 2021; 12:907. [PMID: 34208174 PMCID: PMC8230824 DOI: 10.3390/genes12060907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/27/2022] Open
Abstract
There are many co-regulated genes in eukaryotic cells. The coordinated activation or repression of such genes occurs at specific stages of differentiation, or under the influence of external stimuli. As a rule, co-regulated genes are dispersed in the genome. However, there are also gene clusters, which contain paralogous genes that encode proteins with similar functions. In this aspect, they differ significantly from bacterial operons containing functionally linked genes that are not paralogs. In this review, we discuss the reasons for the existence of gene clusters in vertebrate cells and propose that clustering is necessary to ensure the possibility of selective activation of one of several similar genes.
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Affiliation(s)
- Sergey V. Razin
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Elena S. Ioudinkova
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
| | - Omar L. Kantidze
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
| | - Olga V. Iarovaia
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
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The Hox protein conundrum: The "specifics" of DNA binding for Hox proteins and their partners. Dev Biol 2021; 477:284-292. [PMID: 34102167 PMCID: PMC8846413 DOI: 10.1016/j.ydbio.2021.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 11/25/2022]
Abstract
Homeotic genes (Hox genes) are homeodomain-transcription factors involved in conferring segmental identity along the anterior-posterior body axis. Molecular characterization of HOX protein function raises some interesting questions regarding the source of the binding specificity of the HOX proteins. How do HOX proteins regulate common and unique target specificity across space and time? This review attempts to summarize and interpret findings in this area, largely focused on results from in vitro and in vivo studies in Drosophila and mouse systems. Recent studies related to HOX protein binding specificity compel us to reconsider some of our current models for transcription factor-DNA interactions. It is crucial to study transcription factor binding by incorporating components of more complex, multi-protein interactions in concert with small changes in binding motifs that can significantly impact DNA binding specificity and subsequent alterations in gene expression. To incorporate the multiple elements that can determine HOX protein binding specificity, we propose a more integrative Cooperative Binding model.
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