1
|
Popadin K, Gunbin K, Peshkin L, Annis S, Fleischmann Z, Franco M, Kraytsberg Y, Markuzon N, Ackermann RR, Khrapko K. Mitochondrial Pseudogenes Suggest Repeated Inter-Species Hybridization among Direct Human Ancestors. Genes (Basel) 2022; 13:810. [PMID: 35627195 PMCID: PMC9140377 DOI: 10.3390/genes13050810] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/12/2022] [Accepted: 04/16/2022] [Indexed: 12/02/2022] Open
Abstract
The hypothesis that the evolution of humans involves hybridization between diverged species has been actively debated in recent years. We present the following novel evidence in support of this hypothesis: the analysis of nuclear pseudogenes of mtDNA ("NUMTs"). NUMTs are considered "mtDNA fossils" as they preserve sequences of ancient mtDNA and thus carry unique information about ancestral populations. Our comparison of a NUMT sequence shared by humans, chimpanzees, and gorillas with their mtDNAs implies that, around the time of divergence between humans and chimpanzees, our evolutionary history involved the interbreeding of individuals whose mtDNA had diverged as much as ~4.5 Myr prior. This large divergence suggests a distant interspecies hybridization. Additionally, analysis of two other NUMTs suggests that such events occur repeatedly. Our findings suggest a complex pattern of speciation in primate/human ancestors and provide one potential explanation for the mosaic nature of fossil morphology found at the emergence of the hominin lineage. A preliminary version of this manuscript was uploaded to the preprint server BioRxiv in 2017 (10.1101/134502).
Collapse
Affiliation(s)
- Konstantin Popadin
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland;
- Center for Mitochondrial Functional Genomics, Institute of Living Systems, Immanuel Kant Baltic Federal University, 236040 Kaliningrad, Russia
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | | | - Leonid Peshkin
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA;
| | - Sofia Annis
- Department of Biology, Northeastern University, Boston, MA 02115, USA; (S.A.); (Z.F.); (M.F.)
| | - Zoe Fleischmann
- Department of Biology, Northeastern University, Boston, MA 02115, USA; (S.A.); (Z.F.); (M.F.)
| | - Melissa Franco
- Department of Biology, Northeastern University, Boston, MA 02115, USA; (S.A.); (Z.F.); (M.F.)
| | | | | | - Rebecca R. Ackermann
- Human Evolution Research Institute, Department of Archaeology, University of Cape Town, Cape Town 7700, South Africa;
| | - Konstantin Khrapko
- Department of Biology, Northeastern University, Boston, MA 02115, USA; (S.A.); (Z.F.); (M.F.)
| |
Collapse
|
2
|
Altered Gene Expression in the Testis of Infertile Patients with Nonobstructive Azoospermia. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:5533483. [PMID: 34221106 PMCID: PMC8211532 DOI: 10.1155/2021/5533483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 05/14/2021] [Accepted: 05/28/2021] [Indexed: 11/18/2022]
Abstract
Background The molecular mechanism of nonobstructive azoospermia (NOA) remains unclear. The aim of this study was to identify gene expression changes in NOA patients and to explore potential biomarkers and therapeutic targets. Methods The gene expression profiles of GSE45885 and GSE145467 were collected from the Gene Expression Omnibus (GEO) database, and the differences between NOA and normal spermatogenesis were analyzed. Enrichment analysis was performed to explore biological functions for common differentially expressed genes (DEGs) in GSE45885 and GSE145467. Coexpression analysis of DEGs in GSE45885 was performed, and two modules with the highest correlation with NOA were screened. Key genes were then screened from the intersection genes of the two modules and common DEGs and PPI network. The expression of key genes was validated by quantitative real-time polymerase chain reaction (qRT-PCR) experiments. Finally, through miRTarBase, miRDB, and RAID, the miRNAs were predicted to regulate key genes, respectively. Results A total of 345 common DEGs were identified and they were mainly related to spermatogenesis, insulin signaling pathway. Coexpression analysis of DEGs in GSE45885 yielded eight modules; MEblack and MEturquoise had the highest correlation with NOA. Six genes in MEturquoise and RNF141 in MEblack were identified as key genes. qRT-PCR experiments validated the differential expression of key genes between NOA and control. Furthermore, RNF141 was regulated by the largest number of miRNAs. Conclusion Our findings suggest that the significant change expression of key genes may be potential markers and therapeutic targets of NOA and may have some impact on the development of NOA.
Collapse
|
3
|
RNF141 interacts with KRAS to promote colorectal cancer progression. Oncogene 2021; 40:5829-5842. [PMID: 34345014 PMCID: PMC8484013 DOI: 10.1038/s41388-021-01877-4] [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: 11/21/2020] [Revised: 05/22/2021] [Accepted: 05/28/2021] [Indexed: 02/07/2023]
Abstract
RING finger proteins (RNFs) play a critical role in cancer initiation and progression. RNF141 is a member of RNFs family; however, its clinical significance, roles, and mechanism in colorectal cancer (CRC) remain poorly understood. Here, we examined the expression of RNF141 in 64 pairs of CRC and adjacent normal tissues by real-time PCR, Western blot, and immunohistochemical analysis. We found that there was more expression of RNF141 in CRC tissue compared with its adjacent normal tissue and high RNF141 expression associated with T stage. In vivo and in vitro functional experiments were conducted and revealed the oncogenic role of RNF141 in CRC. RNF141 knockdown suppressed proliferation, arrested the cell cycle in the G1 phase, inhibited migration, invasion and HUVEC tube formation but promoted apoptosis, whereas RNF141 overexpression exerted the opposite effects in CRC cells. The subcutaneous xenograft models showed that RNF141 knockdown reduced tumor growth, but its overexpression promoted tumor growth. Mechanistically, liquid chromatography-tandem mass spectrometry indicated RNF141 interacted with KRAS, which was confirmed by Co-immunoprecipitation, Immunofluorescence assay. Further analysis with bimolecular fluorescence complementation (BiFC) and Glutathione-S-transferase (GST) pull-down assays showed that RNF141 could directly bind to KRAS. Importantly, the upregulation of RNF141 increased GTP-bound KRAS, but its knockdown resulted in a reduction accordingly. Next, we demonstrated that RNF141 induced KRAS activation via increasing its enrichment on the plasma membrane not altering total KRAS expression, which was facilitated by the interaction with LYPLA1. Moreover, KRAS silencing partially abolished the effect of RNF141 on cell proliferation and apoptosis. In addition, our findings presented that RNF141 functioned as an oncogene by upregulating KRAS activity in a manner of promoting KRAS enrichment on the plasma membrane in CRC.
Collapse
|
4
|
Replication analysis confirms the association of several variants with acute myeloid leukemia in Chinese population. J Cancer Res Clin Oncol 2015; 142:149-55. [DOI: 10.1007/s00432-015-2010-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 06/27/2015] [Indexed: 10/23/2022]
|
5
|
Liu Y, Tao D, Lu Y, Yang Y, Ma Y, Zhang S. Targeted disruption of the mouse testis-enriched gene Znf230 does not affect spermatogenesis or fertility. Genet Mol Biol 2014; 37:708-15. [PMID: 25505846 PMCID: PMC4261971 DOI: 10.1590/s1415-47572014005000013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 06/24/2014] [Indexed: 02/05/2023] Open
Abstract
The mouse testis-enriched Znf230 gene, which encodes a type of RING finger protein, is present primarily in the nuclei of spermatogonia, the acrosome and the tail of spermatozoa. To investigate the role of Znf230 in spermatogenesis, we generated Znf230-deficient mice by disrupting Znf230 exon-5 and exon-6 using homologous recombination. The homozygous Znf230-knockout (KO) mice did not exhibit Znf230 mRNA expression and Znf230 protein production. Znf230 KO mice exhibited no obvious impairment in body growth or fertility. Male Znf230 KO mice had integral reproductive systems and mature sperm that were regular in number and shape. The developmental stages of male germ cells of Znf230 KO mice were also normal. We further examined variations in the transcriptomes of testicular tissue between Znf230 KO and wild-type mice through microarray analysis. The results showed that the mRNA level of one unclassified transcript 4921513I08Rik was increased and that the mRNA levels of three other transcripts, i.e., 4930448A20Rik, 4931431B13Rik and potassium channel tetramerisation domain containing 14(Kctd14), were reduced more than two-fold in Znf230 KO mice compared with wild-type mice. Using our current examination techniques, these findings suggested that Znf230 deficiency in mice may not affect growth, fertility or spermatogenesis.
Collapse
Affiliation(s)
- Yunqiang Liu
- Department of Medical Genetics and Division of Human Morbid Genomics , State Key Laboratory of Biotherapy , West China Hospital , West China Medical School , Sichuan Universtiy , Chengdu, Sichuan Province , China
| | - Dachang Tao
- Department of Medical Genetics and Division of Human Morbid Genomics , State Key Laboratory of Biotherapy , West China Hospital , West China Medical School , Sichuan Universtiy , Chengdu, Sichuan Province , China
| | - Yongjie Lu
- Department of Medical Genetics and Division of Human Morbid Genomics , State Key Laboratory of Biotherapy , West China Hospital , West China Medical School , Sichuan Universtiy , Chengdu, Sichuan Province , China
| | - Yuan Yang
- Department of Medical Genetics and Division of Human Morbid Genomics , State Key Laboratory of Biotherapy , West China Hospital , West China Medical School , Sichuan Universtiy , Chengdu, Sichuan Province , China
| | - Yongxin Ma
- Department of Medical Genetics and Division of Human Morbid Genomics , State Key Laboratory of Biotherapy , West China Hospital , West China Medical School , Sichuan Universtiy , Chengdu, Sichuan Province , China
| | - Sizhong Zhang
- Department of Medical Genetics and Division of Human Morbid Genomics , State Key Laboratory of Biotherapy , West China Hospital , West China Medical School , Sichuan Universtiy , Chengdu, Sichuan Province , China
| |
Collapse
|
6
|
Unmethylated state of 5′ upstream CpG islands may be necessary but not sufficient for the testis-enriched expression of ZNF230/Znf230. Genes Genomics 2014. [DOI: 10.1007/s13258-013-0153-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
7
|
Liu Y, Tao D, Ma S, Kuang Y, Su D, Zhang H, Yang Y, Ma Y, Zhang S. A new mutant transcript generated in Znf230 exon 2 knockout mice reveals a potential exon structure in the targeting vector sequence. Acta Biochim Biophys Sin (Shanghai) 2013. [PMID: 23196134 DOI: 10.1093/abbs/gms101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Testis gene Znf230 may play a role in mammalian spermatogenesis according to previous reports. Deleting 5' important exons to block the formation of protein was a routine way in gene-knockout experiments. To investigate the physiological function of Znf230 gene, the mutant mice with disrupted exon 2 of Znf230 were generated in this study. Results showed that, mutant Znf230 mice were fertile and showed normal body, genitourinary organs, testes weights, and spermatid number but the litter size of the offspring reduced with unclear reasons. Hematoxylin and eosin staining showed that the testicular tissue of mutant mice was intact. Reverse transcriptase polymerase chain reaction analysis showed that two novel mutant transcripts appeared in the mutant mice: the short one including exon-1 and exon-3 to -6, the long one unexpectedly containing a partial sequence from the pPNT vector acting as a new exon 2. Bioinformatic analysis of the long transcript revealed that it might code a 24-kDa N-terminal mutant protein with the same 182 amino acids as that of the wild-type Znf230 in the C-terminus, indicating that the potential functional region of C3HC4-type RING finger was intact in mutant protein. Western blot and immunohistochemistry analyses also implied that this N-terminal mutation of Znf230 might not disrupt the possible role that wild-type Znf230 played in spermatogenesis. In summary, a potential exon structure in the targeting vector sequence involved in the expression of targeting Znf230 gene and disturbed the strategy of this gene-targeting experiment.
Collapse
Affiliation(s)
- Yunqiang Liu
- Department of Medical Genetics & Division of Human Morbid Genomics, State Key Laboratory of Biotherapy , West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Human RING finger protein ZNF645 is a novel testis-specific E3 ubiquitin ligase. Asian J Androl 2010; 12:658-66. [PMID: 20657603 DOI: 10.1038/aja.2010.54] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A large number of testis-specific genes are involved in the complex process of mammalian spermatogenesis. Identification of these genes and their roles is important for understanding the mechanisms underlying spermatogenesis. Here we report on a novel human RING finger protein, ZNF645, which contains a C3HC4 RING finger domain, a C2H2 zinc-finger domain, and a proline-rich region, indicating that it has a structure similar to that of the c-Cbl-like protein Hakai. ZNF645 was exclusively expressed in normal human testicular tissue. Immunohistochemical analysis confirmed that ZNF645 protein was present in spermatocytes, round and elongated spermatids, and Leydig cells. Immunofluorescence staining of mature sperms further showed that the ZNF645 protein was localized over the postacrosomal perinuclear theca region and the entire length of sperm tail. An in vitro ubiquitination assay indicated that the RING finger domain of the ZNF645 protein had E3 ubiquitin ligase activity. Therefore, we suggest that ZNF645 might act as an E3 ubiquitin-protein ligase and play a role in human sperm production and quality control.
Collapse
|
9
|
Hermo L, Pelletier RM, Cyr DG, Smith CE. Surfing the wave, cycle, life history, and genes/proteins expressed by testicular germ cells. Part 4: intercellular bridges, mitochondria, nuclear envelope, apoptosis, ubiquitination, membrane/voltage-gated channels, methylation/acetylation, and transcription factors. Microsc Res Tech 2010; 73:364-408. [PMID: 19941288 DOI: 10.1002/jemt.20785] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
As germ cells divide and differentiate from spermatogonia to spermatozoa, they share a number of structural and functional features that are common to all generations of germ cells and these features are discussed herein. Germ cells are linked to one another by large intercellular bridges which serve to move molecules and even large organelles from the cytoplasm of one cell to another. Mitochondria take on different shapes and features and topographical arrangements to accommodate their specific needs during spermatogenesis. The nuclear envelope and pore complex also undergo extensive modifications concomitant with the development of germ cell generations. Apoptosis is an event that is normally triggered by germ cells and involves many proteins. It occurs to limit the germ cell pool and acts as a quality control mechanism. The ubiquitin pathway comprises enzymes that ubiquitinate as well as deubiquitinate target proteins and this pathway is present and functional in germ cells. Germ cells express many proteins involved in water balance and pH control as well as voltage-gated ion channel movement. In the nucleus, proteins undergo epigenetic modifications which include methylation, acetylation, and phosphorylation, with each of these modifications signaling changes in chromatin structure. Germ cells contain specialized transcription complexes that coordinate the differentiation program of spermatogenesis, and there are many male germ cell-specific differences in the components of this machinery. All of the above features of germ cells will be discussed along with the specific proteins/genes and abnormalities to fertility related to each topic.
Collapse
Affiliation(s)
- Louis Hermo
- Department of Anatomy and Cell Biology, Faculty of Medicine, McGill University, 3640 University Street, Montreal, QC Canada H3A 2B2.
| | | | | | | |
Collapse
|