1
|
Doronin SA, Ilyin AA, Kononkova AD, Solovyev MA, Olenkina OM, Nenasheva VV, Mikhaleva EA, Lavrov SA, Ivannikova AY, Simonov RA, Fedotova AA, Khrameeva EE, Ulianov SV, Razin SV, Shevelyov YY. Nucleoporin Elys attaches peripheral chromatin to the nuclear pores in interphase nuclei. Commun Biol 2024; 7:783. [PMID: 38951619 PMCID: PMC11217421 DOI: 10.1038/s42003-024-06495-w] [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: 09/14/2023] [Accepted: 06/23/2024] [Indexed: 07/03/2024] Open
Abstract
Transport of macromolecules through the nuclear envelope (NE) is mediated by nuclear pore complexes (NPCs) consisting of nucleoporins (Nups). Elys/Mel-28 is the Nup that binds and connects the decondensing chromatin with the reassembled NPCs at the end of mitosis. Whether Elys links chromatin with the NE during interphase is unknown. Here, using DamID-seq, we identified Elys binding sites in Drosophila late embryos and divided them into those associated with nucleoplasmic or with NPC-linked Elys. These Elys binding sites are located within active or inactive chromatin, respectively. Strikingly, Elys knockdown in S2 cells results in peripheral chromatin displacement from the NE, in decondensation of NE-attached chromatin, and in derepression of genes within. It also leads to slightly more compact active chromatin regions. Our findings indicate that NPC-linked Elys, together with the nuclear lamina, anchors peripheral chromatin to the NE, whereas nucleoplasmic Elys decompacts active chromatin.
Collapse
Affiliation(s)
- Semen A Doronin
- Laboratory of Analysis of Gene Regulation, Institute of Molecular Genetics of NRC "Kurchatov Institute", 123182, Moscow, Russia
| | - Artem A Ilyin
- Laboratory of Analysis of Gene Regulation, Institute of Molecular Genetics of NRC "Kurchatov Institute", 123182, Moscow, Russia
- Department of Molecular Biosciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Anna D Kononkova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 143026, Skolkovo, Russia
| | - Mikhail A Solovyev
- Department of Cellular Genomics, Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Oxana M Olenkina
- Laboratory of Analysis of Gene Regulation, Institute of Molecular Genetics of NRC "Kurchatov Institute", 123182, Moscow, Russia
| | - Valentina V Nenasheva
- Laboratory of Molecular Neurogenetics and Innate Immunity, Institute of Molecular Genetics of NRC "Kurchatov Institute", 123182, Moscow, Russia
| | - Elena A Mikhaleva
- Laboratory of Biochemical Genetics of Animals, Institute of Molecular Genetics of NRC "Kurchatov Institute", 123182, Moscow, Russia
| | - Sergey A Lavrov
- Laboratory of Biochemical Genetics of Animals, Institute of Molecular Genetics of NRC "Kurchatov Institute", 123182, Moscow, Russia
| | - Anna Y Ivannikova
- Laboratory of Analysis of Gene Regulation, Institute of Molecular Genetics of NRC "Kurchatov Institute", 123182, Moscow, Russia
| | - Ruslan A Simonov
- Laboratory of Analysis of Gene Regulation, Institute of Molecular Genetics of NRC "Kurchatov Institute", 123182, Moscow, Russia
| | - Anna A Fedotova
- Laboratory of Analysis of Gene Regulation, Institute of Molecular Genetics of NRC "Kurchatov Institute", 123182, Moscow, Russia
- Department of Regulation of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
| | - Ekaterina E Khrameeva
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 143026, Skolkovo, Russia.
| | - Sergey V Ulianov
- Department of Cellular Genomics, Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Sergey V Razin
- Department of Cellular Genomics, Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Yuri Y Shevelyov
- Laboratory of Analysis of Gene Regulation, Institute of Molecular Genetics of NRC "Kurchatov Institute", 123182, Moscow, Russia.
| |
Collapse
|
2
|
Wei KHC, Chatla K, Bachtrog D. Single-cell RNA-seq of Drosophila miranda testis reveals the evolution and trajectory of germline sex chromosome regulation. PLoS Biol 2024; 22:e3002605. [PMID: 38687805 PMCID: PMC11135767 DOI: 10.1371/journal.pbio.3002605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 05/29/2024] [Accepted: 03/27/2024] [Indexed: 05/02/2024] Open
Abstract
Although sex chromosomes have evolved from autosomes, they often have unusual regulatory regimes that are sex- and cell-type-specific such as dosage compensation (DC) and meiotic sex chromosome inactivation (MSCI). The molecular mechanisms and evolutionary forces driving these unique transcriptional programs are critical for genome evolution but have been, in the case of MSCI in Drosophila, subject to continuous debate. Here, we take advantage of the younger sex chromosomes in D. miranda (XR and the neo-X) to infer how former autosomes acquire sex-chromosome-specific regulatory programs using single-cell and bulk RNA sequencing and ribosome profiling, in a comparative evolutionary context. We show that contrary to mammals and worms, the X down-regulation through germline progression is most consistent with the shutdown of DC instead of MSCI, resulting in half gene dosage at the end of meiosis for all 3 X's. Moreover, lowly expressed germline and meiotic genes on the neo-X are ancestrally lowly expressed, instead of acquired suppression after sex linkage. For the young neo-X, DC is incomplete across all tissue and cell types and this dosage imbalance is rescued by contributions from Y-linked gametologs which produce transcripts that are translated to compensate both gene and protein dosage. We find an excess of previously autosomal testis genes becoming Y-specific, showing that the neo-Y and its masculinization likely resolve sexual antagonism. Multicopy neo-sex genes are predominantly expressed during meiotic stages of spermatogenesis, consistent with their amplification being driven to interfere with mendelian segregation. Altogether, this study reveals germline regulation of evolving sex chromosomes and elucidates the consequences these unique regulatory mechanisms have on the evolution of sex chromosome architecture.
Collapse
Affiliation(s)
- Kevin H-C. Wei
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kamalakar Chatla
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Doris Bachtrog
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| |
Collapse
|
3
|
Shevelyov YY. Interactions of Chromatin with the Nuclear Lamina and Nuclear Pore Complexes. Int J Mol Sci 2023; 24:15771. [PMID: 37958755 PMCID: PMC10649103 DOI: 10.3390/ijms242115771] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/26/2023] [Accepted: 10/29/2023] [Indexed: 11/15/2023] Open
Abstract
Heterochromatin and euchromatin form different spatial compartments in the interphase nucleus, with heterochromatin being localized mainly at the nuclear periphery. The mechanisms responsible for peripheral localization of heterochromatin are still not fully understood. The nuclear lamina and nuclear pore complexes were obvious candidates for the role of heterochromatin binders. This review is focused on recent studies showing that heterochromatin interactions with the nuclear lamina and nuclear pore complexes maintain its peripheral localization. Differences in chromatin interactions with the nuclear envelope in cell populations and in individual cells are also discussed.
Collapse
Affiliation(s)
- Yuri Y Shevelyov
- Laboratory of Analysis of Gene Regulation, National Research Centre "Kurchatov Institute", Kurchatov Sq. 2, 123182 Moscow, Russia
| |
Collapse
|
4
|
Romanov SE, Shloma VV, Koryakov DE, Belyakin SN, Laktionov PP. Insulator Protein CP190 Regulates Expression оf Spermatocyte Differentiation Genes in Drosophila melanogaster Male Germline. Mol Biol 2022. [DOI: 10.1134/s0026893323010120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
5
|
Dosage Compensation in Drosophila: Its Canonical and Non-Canonical Mechanisms. Int J Mol Sci 2022; 23:ijms231810976. [PMID: 36142884 PMCID: PMC9506574 DOI: 10.3390/ijms231810976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/16/2022] [Accepted: 09/17/2022] [Indexed: 11/17/2022] Open
Abstract
Dosage compensation equalizes gene expression in a single male X chromosome with that in the pairs of autosomes and female X chromosomes. In the fruit fly Drosophila, canonical dosage compensation is implemented by the male-specific lethal (MSL) complex functioning in all male somatic cells. This complex contains acetyl transferase males absent on the first (MOF), which performs H4K16 hyperacetylation specifically in the male X chromosome, thus facilitating transcription of the X-linked genes. However, accumulating evidence points to an existence of additional, non-canonical dosage compensation mechanisms operating in somatic and germline cells. In this review, we discuss current advances in the understanding of both canonical and non-canonical mechanisms of dosage compensation in Drosophila.
Collapse
|