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Wilson CA, Postlethwait JH. A maternal-to-zygotic-transition gene block on the zebrafish sex chromosome. G3 (BETHESDA, MD.) 2024; 14:jkae050. [PMID: 38466753 PMCID: PMC11075544 DOI: 10.1093/g3journal/jkae050] [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: 12/05/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 03/13/2024]
Abstract
Wild zebrafish (Danio rerio) have a ZZ/ZW chromosomal sex-determination system with the major sex locus on the right arm of chromosome-4 (Chr4R) near the largest heterochromatic block in the genome, suggesting that Chr4R transcriptomics might differ from the rest of the genome. To test this hypothesis, we conducted an RNA-seq analysis of adult ZW ovaries and ZZ testes in the Nadia strain and identified 4 regions of Chr4 with different gene expression profiles. Unique in the genome, protein-coding genes in a 41.7 Mb section (Region-2) were expressed in testis but silent in ovary. The AB lab strain, which lacks sex chromosomes, verified this result, showing that testis-biased gene expression in Region-2 depends on gonad biology, not on sex-determining mechanism. RNA-seq analyses in female and male brains and livers validated reduced transcripts from Region-2 in somatic cells, but without sex specificity. Region-2 corresponds to the heterochromatic portion of Chr4R and its content of genes and repetitive elements distinguishes it from the rest of the genome. Region-2 lacks protein-coding genes with human orthologs; has zinc finger genes expressed early in zygotic genome activation; has maternal 5S rRNA genes, maternal spliceosome genes, a concentration of tRNA genes, and a distinct set of repetitive elements. The colocalization of (1) genes silenced in ovaries but not in testes that are (2) expressed in embryos briefly at the onset of zygotic genome activation; (3) maternal-specific genes for translation machinery; (4) maternal-specific spliceosome components; and (5) adjacent genes encoding miR-430, which mediates maternal transcript degradation, suggest that this is a maternal-to-zygotic-transition gene regulatory block.
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2
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Hong Y, Bie L, Zhang T, Yan X, Jin G, Chen Z, Wang Y, Li X, Pei G, Zhang Y, Hong Y, Gong L, Li P, Xie W, Zhu Y, Shen X, Liu N. SAFB restricts contact domain boundaries associated with L1 chimeric transcription. Mol Cell 2024; 84:1637-1650.e10. [PMID: 38604171 DOI: 10.1016/j.molcel.2024.03.021] [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: 10/31/2023] [Revised: 02/05/2024] [Accepted: 03/19/2024] [Indexed: 04/13/2024]
Abstract
Long interspersed element-1 (LINE-1 or L1) comprises 17% of the human genome, continuously generates genetic variations, and causes disease in certain cases. However, the regulation and function of L1 remain poorly understood. Here, we uncover that L1 can enrich RNA polymerase IIs (RNA Pol IIs), express L1 chimeric transcripts, and create contact domain boundaries in human cells. This impact of L1 is restricted by a nuclear matrix protein scaffold attachment factor B (SAFB) that recognizes transcriptionally active L1s by binding L1 transcripts to inhibit RNA Pol II enrichment. Acute inhibition of RNA Pol II transcription abolishes the domain boundaries associated with L1 chimeric transcripts, indicating a transcription-dependent mechanism. Deleting L1 impairs domain boundary formation, and L1 insertions during evolution have introduced species-specific domain boundaries. Our data show that L1 can create RNA Pol II-enriched regions that alter genome organization and that SAFB regulates L1 and RNA Pol II activity to preserve gene regulation.
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Affiliation(s)
- Yaqiang Hong
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Luyao Bie
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Tao Zhang
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaohan Yan
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guangpu Jin
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhuo Chen
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yang Wang
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiufeng Li
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Gaofeng Pei
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yongyan Zhang
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yantao Hong
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Liang Gong
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China
| | - Pilong Li
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wei Xie
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yanfen Zhu
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu 322000, China
| | - Xiaohua Shen
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Nian Liu
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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3
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Vukic M, Chouaref J, Della Chiara V, Dogan S, Ratner F, Hogenboom JZM, Epp TA, Chawengsaksophak K, Vonk KKD, Breukel C, Ariyurek Y, San Leon Granado D, Kloet SL, Daxinger L. CDCA7-associated global aberrant DNA hypomethylation translates to localized, tissue-specific transcriptional responses. SCIENCE ADVANCES 2024; 10:eadk3384. [PMID: 38335290 PMCID: PMC10857554 DOI: 10.1126/sciadv.adk3384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/09/2024] [Indexed: 02/12/2024]
Abstract
Disruption of cell division cycle associated 7 (CDCA7) has been linked to aberrant DNA hypomethylation, but the impact of DNA methylation loss on transcription has not been investigated. Here, we show that CDCA7 is critical for maintaining global DNA methylation levels across multiple tissues in vivo. A pathogenic Cdca7 missense variant leads to the formation of large, aberrantly hypomethylated domains overlapping with the B genomic compartment but without affecting the deposition of H3K9 trimethylation (H3K9me3). CDCA7-associated aberrant DNA hypomethylation translated to localized, tissue-specific transcriptional dysregulation that affected large gene clusters. In the brain, we identify CDCA7 as a transcriptional repressor and epigenetic regulator of clustered protocadherin isoform choice. Increased protocadherin isoform expression frequency is accompanied by DNA methylation loss, gain of H3K4 trimethylation (H3K4me3), and increased binding of the transcriptional regulator CCCTC-binding factor (CTCF). Overall, our in vivo work identifies a key role for CDCA7 in safeguarding tissue-specific expression of gene clusters via the DNA methylation pathway.
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Affiliation(s)
- Maja Vukic
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Jihed Chouaref
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Serkan Dogan
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Fallon Ratner
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Trevor A. Epp
- Laboratory of Cell Differentiation, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- CZ-OPENSCREEN, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Kallayanee Chawengsaksophak
- Laboratory of Cell Differentiation, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Kelly K. D. Vonk
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Cor Breukel
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Yavuz Ariyurek
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
- Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Susan L. Kloet
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
- Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
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4
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Kumari A, Vertii A. Perspective: "Current understanding of NADs dynamics and mechanisms of Disease". Gene 2024; 894:147960. [PMID: 37923094 DOI: 10.1016/j.gene.2023.147960] [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: 07/27/2023] [Revised: 10/09/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
Chromatin architecture is essential for gene regulation, and multiple levels of the 3D chromatin organization exhibit dynamic changes during organismal development and cell differentiation. Heterochromatin, termed compartment B in Hi-C datasets, is a phase-separating gene-silencing form of chromatin, preferentially located at the two nuclear sites, nuclear (lamina-associate chromatin domains, LADs) and nucleoli (nucleoli-associated chromatin domains, NADs) peripheries. LADs and NADs contain both interchangeable and location-specific chromatin domains. Recent studies suggest striking dynamics in LADs and NADs during the differentiation of embryonic stem cells into neural progenitors and neurons. Here we discuss recent advances in understanding NADs changes during neuronal differentiation and future questions on how NADs integrity can contribute to healthy neurodevelopment and neurodevelopment diseases.
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Affiliation(s)
- Amrita Kumari
- Department of Molecular, Cellular and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 1605, US
| | - Anastassiia Vertii
- Department of Molecular, Cellular and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 1605, US.
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5
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Braz CU, Passamonti MM, Khatib H. Characterization of genomic regions escaping epigenetic reprogramming in sheep. ENVIRONMENTAL EPIGENETICS 2023; 10:dvad010. [PMID: 38496251 PMCID: PMC10944287 DOI: 10.1093/eep/dvad010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 12/04/2023] [Accepted: 12/15/2023] [Indexed: 03/19/2024]
Abstract
The mammalian genome undergoes two global epigenetic reprogramming events during the establishment of primordial germ cells and in the pre-implantation embryo after fertilization. These events involve the erasure and re-establishment of DNA methylation marks. However, imprinted genes and transposable elements (TEs) maintain their DNA methylation signatures to ensure normal embryonic development and genome stability. Despite extensive research in mice and humans, there is limited knowledge regarding environmentally induced epigenetic marks that escape epigenetic reprogramming in other species. Therefore, the objective of this study was to examine the characteristics and locations of genomic regions that evade epigenetic reprogramming in sheep, as well as to explore the biological functions of the genes within these regions. In a previous study, we identified 107 transgenerationally inherited differentially methylated cytosines (DMCs) in the F1 and F2 generations in response to a paternal methionine-supplemented diet. These DMCs were found in TEs, non-repetitive regions, and imprinted and non-imprinted genes. Our findings suggest that genomic regions, rather than TEs and imprinted genes, have the propensity to escape reprogramming and serve as potential candidates for transgenerational epigenetic inheritance. Notably, 34 transgenerational methylated genes influenced by paternal nutrition escaped reprogramming, impacting growth, development, male fertility, cardiac disorders, and neurodevelopment. Intriguingly, among these genes, 21 have been associated with neural development and brain disorders, such as autism, schizophrenia, bipolar disease, and intellectual disability. This suggests a potential genetic overlap between brain and infertility disorders. Overall, our study supports the concept of transgenerational epigenetic inheritance of environmentally induced marks in mammals.
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Affiliation(s)
- Camila U Braz
- Department of Animal Sciences, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Matilde Maria Passamonti
- Department of Animal Science, Food and Nutrition, Universit’a Cattolica del Sacro Cuore, Piacenza, 29122, Italy
| | - Hasan Khatib
- Department of Animal and Dairy Sciences, University of Wisconsin–Madison, Madison, WI 53706, USA
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Piwczyński M, Granjon L, Trzeciak P, Carlos Brito J, Oana Popa M, Daba Dinka M, Johnston NP, Boratyński Z. Unraveling phylogenetic relationships and species boundaries in the arid adapted Gerbillus rodents (Muridae: Gerbillinae) by RAD-seq data. Mol Phylogenet Evol 2023; 189:107913. [PMID: 37659480 DOI: 10.1016/j.ympev.2023.107913] [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: 02/20/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/04/2023]
Abstract
Gerbillus is one of the most speciose genera among rodents, with ca. 51 recognized species. Previous attempts to reconstruct the evolutionary history of Gerbillus mainly relied on the mitochondrial cyt-b marker as a source of phylogenetic information. In this study, we utilize RAD-seq genomic data from 37 specimens representing 11 species to reconstruct the phylogenetic tree for Gerbillus, applying concatenation and coalescence methods. We identified four highly supported clades corresponding to the traditionally recognized subgenera: Dipodillus, Gerbillus, Hendecapleura and Monodia. Only two uncertain branches were detected in the resulting trees, with one leading to diversification of the main lineages in the genus, recognized by quartet sampling analysis as uncertain due to possible introgression. We also examined species boundaries for four pairs of sister taxa, including potentially new species from Morocco, using SNAPP. The results strongly supported a speciation model in which all taxa are treated as separate species. The dating analyses confirmed the Plio-Pleistocene diversification of the genus, with the uncertain branch coinciding with the beginning of aridification of the Sahara at the the Plio-Pleistocene boundary. This study aligns well with the earlier analyses based on the cyt-b marker, reaffirming its suitability as an adequate marker for estimating genetic diversity in Gerbillus.
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Affiliation(s)
- Marcin Piwczyński
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Lwowska 1, PL-87-100 Toruń, Poland.
| | - Laurent Granjon
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Université de Montpellier, Montpellier, France
| | - Paulina Trzeciak
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Lwowska 1, PL-87-100 Toruń, Poland
| | - José Carlos Brito
- CIBIO-InBio, Research Center in Biodiversity and Genetic Resources, University of Porto, Campus de Vairão, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Madalina Oana Popa
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Lwowska 1, PL-87-100 Toruń, Poland; "Stejarul" Research Centre for Biological Sciences, National Institute of Research and Development for Biological Sciences, Alexandru cel Bun 6, RO-610004, Piatra Neamţ, Romania
| | - Mergi Daba Dinka
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Lwowska 1, PL-87-100 Toruń, Poland
| | - Nikolas P Johnston
- School of Life Sciences, University of Technology Sydney, 15 Broadway, Ultimo, NSW 2007, Australia; Centre for Sustainable Ecosystem Solutions, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Northfields Ave, Wollongong, NSW 2500, Australia
| | - Zbyszek Boratyński
- CIBIO-InBio, Research Center in Biodiversity and Genetic Resources, University of Porto, Campus de Vairão, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
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7
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Lai F, Li L, Hu X, Liu B, Zhu Z, Liu L, Fan Q, Tian H, Xu K, Lu X, Li Q, Feng K, Wang L, Lin Z, Deng H, Li J, Xie W. NR5A2 connects zygotic genome activation to the first lineage segregation in totipotent embryos. Cell Res 2023; 33:952-966. [PMID: 37935903 PMCID: PMC10709309 DOI: 10.1038/s41422-023-00887-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 10/08/2023] [Indexed: 11/09/2023] Open
Abstract
Zygotic genome activation (ZGA) marks the beginning of the embryonic program for a totipotent embryo, which gives rise to the inner cell mass (ICM) where pluripotent epiblast arises, and extraembryonic trophectoderm. However, how ZGA is connected to the first lineage segregation in mammalian embryos remains elusive. Here, we investigated the role of nuclear receptor (NR) transcription factors (TFs), whose motifs are highly enriched and accessible from the 2-cell (2C) to 8-cell (8C) stages in mouse embryos. We found that NR5A2, an NR TF strongly induced upon ZGA, was required for this connection. Upon Nr5a2 knockdown or knockout, embryos developed beyond 2C normally with the zygotic genome largely activated. However, 4-8C-specific gene activation was substantially impaired and Nr5a2-deficient embryos subsequently arrested at the morula stage. Genome-wide chromatin binding analysis showed that NR5A2-bound cis-regulatory elements in both 2C and 8C embryos are strongly enriched for B1 elements where its binding motif is embedded. NR5A2 was not required for the global opening of its binding sites in 2C embryos but was essential to the opening of its 8C-specific binding sites. These 8C-specific, but not 2C-specific, binding sites are enriched near genes involved in blastocyst and stem cell regulation, and are often bound by master pluripotency TFs in blastocysts and embryonic stem cells (ESCs). Importantly, NR5A2 regulated key pluripotency genes Nanog and Pou5f1/Oct4, and primitive endoderm regulatory genes including Gata6 among many early ICM genes, as well as key trophectoderm regulatory genes including Tead4 and Gata3 at the 8C stage. By contrast, master pluripotency TFs NANOG, SOX2, and OCT4 targeted both early and late ICM genes in mouse ESCs. Taken together, these data identify NR5A2 as a key regulator in totipotent embryos that bridges ZGA to the first lineage segregation during mouse early development.
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Affiliation(s)
- Fangnong Lai
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Lijia Li
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Xiaoyu Hu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Bofeng Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Ziqi Zhu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Ling Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Qiang Fan
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Huabin Tian
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Kai Xu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Xukun Lu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Qing Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Kong Feng
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Lijuan Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Zili Lin
- College of Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Hongyu Deng
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
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Khan M, Shah S, Lv B, Lv Z, Ji N, Song Z, Wu P, Wang X, Mehmood A. Molecular Mechanisms of Alu and LINE-1 Interspersed Repetitive Sequences Reveal Diseases of Visual System Dysfunction. Ocul Immunol Inflamm 2023; 31:1848-1858. [PMID: 36040959 DOI: 10.1080/09273948.2022.2112238] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/05/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND Short interspersed nuclear elements (SINEs) and long interspersed nuclear elements (LINE-1s) are the abundant and well-characterized repetitive elements in the human genome. METHODS For this review, all relevant original research studies were assessed by searching electronic databases, including PubMed, Google Scholar, and Web of Science, by using relevant keywords. Accumulating evidence indicates that the disorder of gene expression regulated by these repetitive sequences is one of the causes of the diseases of visual system dysfunction, including retinal degenerations, glaucoma, retinitis punctata albescens, retinitis pigmentosa, geographic atrophy, and age-related macular degeneration, suggesting that SINEs and LINE-1s may have great potential implications in ophthalmology. RESULTS Alu elements belonging to the SINEs are present in more than one million copies, comprising 10% of the human genome. CONCLUSION This study offers recent advances in Alu and LINE-1 mechanisms in the development of eye diseases. The current study could advance our knowledge of the roles of SINEs and LINE-1s in the developing process of eye diseases, suggesting new diagnostic biomarkers, therapeutic strategies, and significant points for future studies.
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Affiliation(s)
- Murad Khan
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Suleman Shah
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Baixue Lv
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
- Hubei Province Key Laboratory of Molecular Imaging, Wuhan, Hubei Province, China
| | - Zhanjun Lv
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Ning Ji
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Zhixue Song
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Peiyuan Wu
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Xiufang Wang
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Arshad Mehmood
- Department of Neurology, the Second Hospital of Hebei Medical University, City Shijiazhuang, P.R. China
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9
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Kuang S, Pollard KS. Exploring the Roles of RNAs in Chromatin Architecture Using Deep Learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.22.563498. [PMID: 37961712 PMCID: PMC10634726 DOI: 10.1101/2023.10.22.563498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Recent studies have highlighted the impact of both transcription and transcripts on 3D genome organization, particularly its dynamics. Here, we propose a deep learning framework, called AkitaR, that leverages both genome sequences and genome-wide RNA-DNA interactions to investigate the roles of chromatin-associated RNAs (caRNAs) on genome folding in HFFc6 cells. In order to disentangle the cis- and trans-regulatory roles of caRNAs, we compared models with nascent transcripts, trans-located caRNAs, open chromatin data, or DNA sequence alone. Both nascent transcripts and trans-located caRNAs improved the models' predictions, especially at cell-type-specific genomic regions. Analyses of feature importance scores revealed the contribution of caRNAs at TAD boundaries, chromatin loops and nuclear sub-structures such as nuclear speckles and nucleoli to the models' predictions. Furthermore, we identified non-coding RNAs (ncRNAs) known to regulate chromatin structures, such as MALAT1 and NEAT1, as well as several novel RNAs, RNY5, RPPH1, POLG-DT and THBS1-IT, that might modulate chromatin architecture through trans-interactions in HFFc6. Our modeling also suggests that transcripts from Alus and other repetitive elements may facilitate chromatin interactions through trans R-loop formation. Our findings provide new insights and generate testable hypotheses about the roles of caRNAs in shaping chromatin organization.
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Affiliation(s)
- Shuzhen Kuang
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA
| | - Katherine S. Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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10
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Liu H, Caliz AD, Learnard H, Koupenova M, Keaney JF, Kant S, Zhu LJ, Vertii A. Inflammatory stress-mediated chromatin changes underlie dysfunction in endothelial cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.11.561959. [PMID: 37905100 PMCID: PMC10614786 DOI: 10.1101/2023.10.11.561959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Inflammatory stresses underlie endothelial dysfunction and contribute to the development of chronic cardiovascular disorders such as atherosclerosis and vascular fibrosis. The initial transcriptional response of endothelial cells to pro-inflammatory cytokines such as TNF-alpha is well established. However, very few studies uncover the effects of inflammatory stresses on chromatin architecture. We used integrative analysis of ATAC-seq and RNA-seq data to investigate chromatin alterations in human endothelial cells in response to TNF-alpha and febrile-range heat stress exposure. Multi-omics data analysis suggests a correlation between the transcription of stress-related genes and endothelial dysfunction drivers with chromatin regions exhibiting differential accessibility. Moreover, microscopy identified the dynamics in the nuclear organization, specifically, the changes in a subset of heterochromatic nucleoli-associated chromatin domains, the centromeres. Upon inflammatory stress exposure, the centromeres decreased association with nucleoli in a p38-dependent manner and increased the number of transcripts from pericentromeric regions. Overall, we provide two lines of evidence that suggest chromatin alterations in vascular endothelial cells during inflammatory stresses.
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Affiliation(s)
- Haibo Liu
- Molecular, Cell and Cancer Biology Department, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Amada D. Caliz
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Heather Learnard
- Cardiovascular Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Milka Koupenova
- Cardiovascular Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - John F. Keaney
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Shashi Kant
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Lihua Julie Zhu
- Molecular, Cell and Cancer Biology Department, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Program in Molecular Medicine, Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Anastassiia Vertii
- Molecular, Cell and Cancer Biology Department, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Program in Innate Immunity, University of Massachusetts Chan Medical School, Worcester, MA, USA
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11
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Yin Y, Shen X. Noncoding RNA-chromatin association: Functions and mechanisms. FUNDAMENTAL RESEARCH 2023; 3:665-675. [PMID: 38933302 PMCID: PMC11197541 DOI: 10.1016/j.fmre.2023.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/12/2023] [Accepted: 03/23/2023] [Indexed: 06/28/2024] Open
Abstract
Pervasive transcription of the mammalian genome produces hundreds of thousands of noncoding RNAs (ncRNAs). Numerous studies have suggested that some of these ncRNAs regulate multiple cellular processes and play important roles in physiological and pathological processes. Notably, a large subset of ncRNAs is enriched on chromatin and participates in regulating gene expression and the dynamics of chromatin structure and status. In this review, we summarize recent advances in the functional study of chromatin-associated ncRNAs and mechanistic insights into how these ncRNAs associate with chromatin. We also discuss the potential future challenges which still need to be overcome in this field.
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Affiliation(s)
- Yafei Yin
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Yuhangtang Road, Hangzhou, Zhejiang 310058, China
| | - Xiaohua Shen
- Tsinghua-Peking Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China
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12
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Han JDJ. LncRNAs: the missing link to senescence nuclear architecture. Trends Biochem Sci 2023; 48:618-628. [PMID: 37069045 DOI: 10.1016/j.tibs.2023.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 04/19/2023]
Abstract
During cellular senescence and organismal aging, cells display various molecular and morphological changes. Although many aging-related long noncoding RNAs (lncRNAs) are highly associated with senescence-associated secretory phenotype, the roles of lncRNAs in senescence-associated nuclear architecture and morphological changes are just starting to emerge. Here I review lncRNAs associated with nuclear structure establishment and maintenance, their aging-related changes, and then focus on the pervasive, yet underappreciated, role of RNA double-strand DNA triplexes for lncRNAs to recognize targeted genomic regions, making lncRNAs the nexus between DNA and proteins to regulate nuclear structural changes. Finally, I discuss the future of deciphering direct links of lncRNA changes to various nuclear morphology changes assisted by artificial intelligence and genetic perturbations.
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Affiliation(s)
- Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China; International Center for Aging and Cancer (ICAC), The First Affiliated Hospital, Hainan Medical University, Haikou, China.
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13
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Spirito G, Filosi M, Domenici E, Mangoni D, Gustincich S, Sanges R. Exploratory analysis of L1 retrotransposons expression in autism. Mol Autism 2023; 14:22. [PMID: 37381037 DOI: 10.1186/s13229-023-00554-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 06/15/2023] [Indexed: 06/30/2023] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a set of highly heterogeneous neurodevelopmental diseases whose genetic etiology is not completely understood. Several investigations have relied on transcriptome analysis from peripheral tissues to dissect ASD into homogenous molecular phenotypes. Recently, analysis of changes in gene expression from postmortem brain tissues has identified sets of genes that are involved in pathways previously associated with ASD etiology. In addition to protein-coding transcripts, the human transcriptome is composed by a large set of non-coding RNAs and transposable elements (TEs). Advancements in sequencing technologies have proven that TEs can be transcribed in a regulated fashion, and their dysregulation might have a role in brain diseases. METHODS We exploited published datasets comprising RNA-seq data from (1) postmortem brain of ASD subjects, (2) in vitro cell cultures where ten different ASD-relevant genes were knocked out and (3) blood of discordant siblings. We measured the expression levels of evolutionarily young full-length transposable L1 elements and characterized the genomic location of deregulated L1s assessing their potential impact on the transcription of ASD-relevant genes. We analyzed every sample independently, avoiding to pool together the disease subjects to unmask the heterogeneity of the molecular phenotypes. RESULTS We detected a strong upregulation of intronic full-length L1s in a subset of postmortem brain samples and in in vitro differentiated neurons from iPSC knocked out for ATRX. L1 upregulation correlated with an high number of deregulated genes and retained introns. In the anterior cingulate cortex of one subject, a small number of significantly upregulated L1s overlapped with ASD-relevant genes that were significantly downregulated, suggesting the possible existence of a negative effect of L1 transcription on host transcripts. LIMITATIONS Our analyses must be considered exploratory and will need to be validated in bigger cohorts. The main limitation is given by the small sample size and by the lack of replicates for postmortem brain samples. Measuring the transcription of locus-specific TEs is complicated by the repetitive nature of their sequence, which reduces the accuracy in mapping sequencing reads to the correct genomic locus. CONCLUSIONS L1 upregulation in ASD appears to be limited to a subset of subjects that are also characterized by a general deregulation of the expression of canonical genes and an increase in intron retention. In some samples from the anterior cingulate cortex, L1s upregulation seems to directly impair the expression of some ASD-relevant genes by a still unknown mechanism. L1s upregulation may therefore identify a group of ASD subjects with common molecular features and helps stratifying individuals for novel strategies of therapeutic intervention.
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Affiliation(s)
- Giovanni Spirito
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Area of Neuroscience, Via Bonomea 265, 34136, Trieste, Italy
- Central RNA Laboratory, Istituto Italiano di Tecnologia - IIT, Via Enrico Melen 83, Building B, 16152, Genoa, Italy
- CMP3vda, Via Lavoratori Vittime del Col Du Mont 28, Aosta, Italy
| | - Michele Filosi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, TN, Italy
- Eurac Research, Institute for Biomedicine, Bolzano, BZ, Italy
| | - Enrico Domenici
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, TN, Italy
- Fondazione The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, TN, Italy
| | - Damiano Mangoni
- Central RNA Laboratory, Istituto Italiano di Tecnologia - IIT, Via Enrico Melen 83, Building B, 16152, Genoa, Italy
| | - Stefano Gustincich
- Central RNA Laboratory, Istituto Italiano di Tecnologia - IIT, Via Enrico Melen 83, Building B, 16152, Genoa, Italy.
- CMP3vda, Via Lavoratori Vittime del Col Du Mont 28, Aosta, Italy.
| | - Remo Sanges
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Area of Neuroscience, Via Bonomea 265, 34136, Trieste, Italy.
- Central RNA Laboratory, Istituto Italiano di Tecnologia - IIT, Via Enrico Melen 83, Building B, 16152, Genoa, Italy.
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14
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Arratia F, Fierro C, Blanco A, Fuentes S, Nahuelquen D, Montecino M, Rojas A, Aguilar R. Selective Concurrence of the Long Non-Coding RNA MALAT1 and the Polycomb Repressive Complex 2 to Promoter Regions of Active Genes in MCF7 Breast Cancer Cells. Curr Issues Mol Biol 2023; 45:4735-4748. [PMID: 37367050 DOI: 10.3390/cimb45060301] [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: 03/17/2023] [Revised: 05/23/2023] [Accepted: 05/28/2023] [Indexed: 06/28/2023] Open
Abstract
In cancer cells, the long non-coding RNA (lncRNA) MALAT1 has arisen as a key partner for the Polycomb Repressive Complex 2 (PRC2), an epigenetic modifier. However, it is unknown whether this partnership occurs genome-wide at the chromatin level, as most of the studies focus on single genes that are usually repressed. Due to the genomic binding properties of both macromolecules, we wondered whether there are binding sites shared by PRC2 and MALAT1. Using public genome-binding datasets for PRC2 and MALAT1 derived from independent ChIP- and CHART-seq experiments performed with the breast cancer cell line MCF7, we searched for regions containing PRC2 and MALAT1 overlapping peaks. Peak calls for each molecule were performed using MACS2 and then overlapping peaks were identified by bedtools intersect. Using this approach, we identified 1293 genomic sites where PRC2 and MALAT1 concur. Interestingly, 54.75% of those sites are within gene promoter regions (<3000 bases from the TSS). These analyses were also linked with the transcription profiles of MCF7 cells, obtained from public RNA-seq data. Hence, it is suggested that MALAT1 and PRC2 can concomitantly bind to promoters of actively-transcribed genes in MCF7 cells. Gene ontology analyses revealed an enrichment of genes related to categories including cancer malignancy and epigenetic regulation. Thus, by re-visiting occupancy and transcriptomic data, we identified a key gene subset controlled by the collaboration of MALAT1 and PRC2.
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Affiliation(s)
- Felipe Arratia
- Institute of Biomedical Sciences (ICB), Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370071, Chile
| | - Cristopher Fierro
- Institute of Biomedical Sciences (ICB), Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370071, Chile
| | - Alejandro Blanco
- Institute of Biomedical Sciences (ICB), Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370071, Chile
| | - Sebastian Fuentes
- Institute of Biomedical Sciences (ICB), Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370071, Chile
| | - Daniela Nahuelquen
- Institute of Biomedical Sciences (ICB), Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370071, Chile
| | - Martin Montecino
- Institute of Biomedical Sciences (ICB), Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370071, Chile
| | - Adriana Rojas
- Institute of Human Genetics, Faculty of Medicine, Pontificia Universidad Javeriana, Bogotá 110211, Colombia
| | - Rodrigo Aguilar
- Institute of Biomedical Sciences (ICB), Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370071, Chile
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15
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Lu F, Ruan S, Li Y, Wang Y, Xie P, Zhao X, Chao J, Ma H. Assessment of DNA mutagenicity induced by He-Ne laser using Salmonella typhimurium strains. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12566-5. [PMID: 37231160 DOI: 10.1007/s00253-023-12566-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 04/23/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023]
Abstract
Helium-neon (He-Ne) laser mutagenesis is widely used in microbiology and plant breeding. In this study, two frameshift mutant representative strains of Salmonella typhimurium TA97a and TA98 and two base pair substitution types TA100 and TA102 were employed as model microorganisms to assess DNA mutagenicity induced by He-Ne laser (3 J·cm-2·s-1, 632.8 nm) for 10, 20, and 30 min. The results revealed that the optimal laser application was 6 h in the mid-logarithmic growth stage. Low-power He-Ne laser for short treatment inhibited cell growth, and continued treatment stimulated the metabolism. The effects of the laser on TA98 and TA100 were the most prominent. Sequencing results from 1500 TA98 revertants showed that there were 88 insertion and deletion (InDel) types in the hisD3052 gene, of which the InDels unique to laser were 21 more than that of the control. Sequencing results from 760 TA100 revertants indicated that laser treatment created Pro (CCC) in the product of the hisG46 gene more likely to be replaced by His (CAC) or Ser (TCC) than by Leu (CTC). Two unique non-classical base substitutions, CCC → TAC and CCC → CAA, also appeared in the laser group. These findings will provide a theoretical basis for further exploration of laser mutagenesis breeding. KEY POINTS: • Salmonella typhimurium served as model organism for laser mutagenesis study. • Laser promoted the occurrence of InDels in the hisD3052 gene of TA98. • Laser promoted the occurrence of base substitution in the hisG46 gene of TA100.
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Affiliation(s)
- Feng Lu
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang City, 212013, Jiangsu, China
| | - Siyu Ruan
- College of Tea and Food Science Technology, Jiangsu Polytechnic College of Agriculture and Forestry, 19 Wenchangdong Road, Jurong City, 212400, Jiangsu, China
| | - Yunliang Li
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang City, 212013, Jiangsu, China
- Institute of Food Physical Processing, Jiangsu University, 301 Xuefu Road, Zhenjiang City, 212013, Jiangsu, China
| | - Yining Wang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang City, 212013, Jiangsu, China
| | - Pengfei Xie
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang City, 212013, Jiangsu, China
| | - Xiaoxue Zhao
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang City, 212013, Jiangsu, China
| | - Jiapin Chao
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang City, 212013, Jiangsu, China
| | - Haile Ma
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang City, 212013, Jiangsu, China.
- Institute of Food Physical Processing, Jiangsu University, 301 Xuefu Road, Zhenjiang City, 212013, Jiangsu, China.
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16
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Li S, Shen X. Long interspersed nuclear element 1 and B1/Alu repeats blueprint genome compartmentalization. Curr Opin Genet Dev 2023; 80:102049. [PMID: 37229928 DOI: 10.1016/j.gde.2023.102049] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/14/2023] [Accepted: 04/15/2023] [Indexed: 05/27/2023]
Abstract
The organization of the genome into euchromatin and heterochromatin has been known for almost 100 years [1]. More than 50% of mammalian genomes contain repetitive sequences [2,3]. Recently, a functional link between the genome and its folding has been identified [4,5]. Homotypic clustering of long interspersed nuclear element 1 (LINE1 or L1) and B1/Alu retrotransposons forms grossly exclusive nuclear domains that characterize and predict heterochromatin and euchromatin, respectively. The spatial segregation of L1 and B1/Alu-rich compartments is conserved in mammalian cells and can be rebuilt during the cell cycle and established de novo in early embryogenesis. Inhibition of L1 RNA drastically weakened homotypic repeat contacts and compartmental segregation, indicating that L1 plays a more significant role than just being a compartmental marker. This simple and inclusive genetic coding model of L1 and B1/Alu in shaping the macroscopic structure of the genome provides a plausible explanation for the remarkable conservation and robustness of its folding in mammalian cells. It also proposes a conserved core structure on which subsequent dynamic regulation takes place.
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Affiliation(s)
- Siyang Li
- Department of Basic Medical Sciences, School of Medicine, Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaohua Shen
- Department of Basic Medical Sciences, School of Medicine, Center for Life Sciences, Tsinghua University, Beijing 100084, China.
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17
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Ryabykh GK, Kuznetsov SV, Korostelev YD, Sigorskikh AI, Zharikova AA, Mironov AA. RNA-Chrom: a manually curated analytical database of RNA-chromatin interactome. Database (Oxford) 2023; 2023:baad025. [PMID: 37221043 PMCID: PMC10205464 DOI: 10.1093/database/baad025] [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: 12/22/2022] [Revised: 03/12/2023] [Accepted: 04/01/2023] [Indexed: 05/25/2023]
Abstract
Every year there is more and more evidence that non-coding RNAs play an important role in biological processes affecting various levels of organization of living systems: from the cellular (regulation of gene expression, remodeling and maintenance of chromatin structure, co-transcriptional suppression of transposons, splicing, post-transcriptional RNA modifications, etc.) to cell populations and even organismal ones (development, aging, cancer, cardiovascular and many other diseases). The development and creation of mutually complementary databases that will aggregate, unify and structure different types of data can help to reach the system level of studying non-coding RNAs. Here we present the RNA-Chrom manually curated analytical database, which contains the coordinates of billions of contacts of thousands of human and mouse RNAs with chromatin. Through the user-friendly web interface (https://rnachrom2.bioinf.fbb.msu.ru/), two approaches to the analysis of the RNA-chromatin interactome were implemented. Firstly, to find out whether the RNA of interest to a user contacts with chromatin, and if so, with which genes or DNA loci? Secondly, to find out which RNAs are in contact with the DNA locus of interest to a user (and probably participate in its regulation), and if there are such, what is the nature of their interaction? For a more detailed study of contact maps and their comparison with other data, the web interface allows a user to view them in the UCSC Genome Browser. Database URL https://genome.ucsc.edu/.
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Affiliation(s)
- G K Ryabykh
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye Gory, Moscow 119234, Russia
- Kharkevich Institute for Information Transmission Problems RAS, Bolshoy Karetny per., Moscow 127051, Russia
| | - S V Kuznetsov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye Gory, Moscow 119234, Russia
| | - Y D Korostelev
- Kharkevich Institute for Information Transmission Problems RAS, Bolshoy Karetny per., Moscow 127051, Russia
| | - A I Sigorskikh
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye Gory, Moscow 119234, Russia
| | - A A Zharikova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye Gory, Moscow 119234, Russia
- Kharkevich Institute for Information Transmission Problems RAS, Bolshoy Karetny per., Moscow 127051, Russia
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigsky per., Moscow, 101000, Russia
| | - A A Mironov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye Gory, Moscow 119234, Russia
- Kharkevich Institute for Information Transmission Problems RAS, Bolshoy Karetny per., Moscow 127051, Russia
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18
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Lismer A, Kimmins S. Emerging evidence that the mammalian sperm epigenome serves as a template for embryo development. Nat Commun 2023; 14:2142. [PMID: 37059740 PMCID: PMC10104880 DOI: 10.1038/s41467-023-37820-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 03/31/2023] [Indexed: 04/16/2023] Open
Abstract
Although more studies are demonstrating that a father's environment can influence child health and disease, the molecular mechanisms underlying non-genetic inheritance remain unclear. It was previously thought that sperm exclusively contributed its genome to the egg. More recently, association studies have shown that various environmental exposures including poor diet, toxicants, and stress, perturbed epigenetic marks in sperm at important reproductive and developmental loci that were associated with offspring phenotypes. The molecular and cellular routes that underlie how epigenetic marks are transmitted at fertilization, to resist epigenetic reprogramming in the embryo, and drive phenotypic changes are only now beginning to be unraveled. Here, we provide an overview of the state of the field of intergenerational paternal epigenetic inheritance in mammals and present new insights into the relationship between embryo development and the three pillars of epigenetic inheritance: chromatin, DNA methylation, and non-coding RNAs. We evaluate compelling evidence of sperm-mediated transmission and retention of paternal epigenetic marks in the embryo. Using landmark examples, we discuss how sperm-inherited regions may escape reprogramming to impact development via mechanisms that implicate transcription factors, chromatin organization, and transposable elements. Finally, we link paternally transmitted epigenetic marks to functional changes in the pre- and post-implantation embryo. Understanding how sperm-inherited epigenetic factors influence embryo development will permit a greater understanding related to the developmental origins of health and disease.
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Affiliation(s)
- Ariane Lismer
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Sarah Kimmins
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC, H3G 1Y6, Canada.
- Department of Pathology and Cell Biology, Faculty of Medicine, University of Montreal Hospital Research Centre, Montreal, QC, H2X 0A9, Canada.
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19
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Gaspa-Toneu L, Peters AH. Nucleosomes in mammalian sperm: conveying paternal epigenetic inheritance or subject to reprogramming between generations? Curr Opin Genet Dev 2023; 79:102034. [PMID: 36893482 PMCID: PMC10109108 DOI: 10.1016/j.gde.2023.102034] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/09/2023] [Accepted: 02/21/2023] [Indexed: 03/09/2023]
Abstract
The genome of mammalian sperm is largely packaged by sperm-specific proteins termed protamines. The presence of some residual nucleosomes has, however, emerged as a potential source of paternal epigenetic inheritance between generations. Sperm nucleosomes bear important regulatory histone marks and locate at gene-regulatory regions, functional elements, and intergenic regions. It is unclear whether sperm nucleosomes are retained at specific genomic locations in a deterministic manner or are randomly preserved due to inefficient exchange of histones by protamines. Recent studies indicate heterogeneity in chromatin packaging within sperm populations and an extensive reprogramming of paternal histone marks post fertilization. Obtaining single-sperm nucleosome distributions is fundamental to estimating the potential of sperm-borne nucleosomes in instructing mammalian embryonic development and in the transmission of acquired phenotypes.
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Affiliation(s)
- Laura Gaspa-Toneu
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4056 Basel, Switzerland
| | - Antoine Hfm Peters
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4056 Basel, Switzerland.
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20
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Bersaglieri C, Santoro R. Methods for mapping 3D-chromosome architecture around nucleoli. Curr Opin Cell Biol 2023; 81:102171. [PMID: 37230037 DOI: 10.1016/j.ceb.2023.102171] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/03/2023] [Accepted: 04/23/2023] [Indexed: 05/27/2023]
Abstract
The nucleolus is the largest subcompartment of the nucleus, known to be the place of ribosome biogenesis. Emerging evidence has started to implicate the nucleolus in the organization of chromosomes in the nucleus. Genomic domains contacting the nucleolus are defined as nucleolar associated domains (NADs) and are generally characterized by repressive chromatin states. However, the role of the nucleolus in genome architecture remains still not fully understood mainly because the lack of a membrane has challenged the establishment of methods for accurate identification of NADs. Here, we will discuss recent advances on methods to identify and characterize NADs, discuss their improvements relative to old methods, and highlight future perspectives.
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Affiliation(s)
- Cristiana Bersaglieri
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland.
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21
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Pezone A, Olivieri F, Napoli MV, Procopio A, Avvedimento EV, Gabrielli A. Inflammation and DNA damage: cause, effect or both. Nat Rev Rheumatol 2023; 19:200-211. [PMID: 36750681 DOI: 10.1038/s41584-022-00905-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2022] [Indexed: 02/09/2023]
Abstract
Inflammation is a biological response involving immune cells, blood vessels and mediators induced by endogenous and exogenous stimuli, such as pathogens, damaged cells or chemicals. Unresolved (chronic) inflammation is characterized by the secretion of cytokines that maintain inflammation and redox stress. Mitochondrial or nuclear redox imbalance induces DNA damage, which triggers the DNA damage response (DDR) that is orchestrated by ATM and ATR kinases, which modify gene expression and metabolism and, eventually, establish the senescent phenotype. DDR-mediated senescence is induced by the signalling proteins p53, p16 and p21, which arrest the cell cycle in G1 or G2 and promote cytokine secretion, producing the senescence-associated secretory phenotype. Senescence and inflammation phenotypes are intimately associated, but highly heterogeneous because they vary according to the cell type that is involved. The vicious cycle of inflammation, DNA damage and DDR-mediated senescence, along with the constitutive activation of the immune system, is the core of an evolutionarily conserved circuitry, which arrests the cell cycle to reduce the accumulation of mutations generated by DNA replication during redox stress caused by infection or inflammation. Evidence suggests that specific organ dysfunctions in apparently unrelated diseases of autoimmune, rheumatic, degenerative and vascular origins are caused by inflammation resulting from DNA damage-induced senescence.
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Affiliation(s)
- Antonio Pezone
- Dipartimento di Biologia, Università Federico II, Napoli, Italy.
| | - Fabiola Olivieri
- Dipartimento di Scienze Cliniche e Molecolari, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
- Clinica di Medicina di Laboratorio e di Precisione, IRCCS INRCA, Ancona, Italy
| | - Maria Vittoria Napoli
- Dipartimento di Scienze Cliniche e Molecolari, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
| | - Antonio Procopio
- Dipartimento di Scienze Cliniche e Molecolari, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
- Clinica di Medicina di Laboratorio e di Precisione, IRCCS INRCA, Ancona, Italy
| | - Enrico Vittorio Avvedimento
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Istituto di Endocrinologia ed Oncologia Sperimentale del C.N.R., Università Federico II, Napoli, Italy.
| | - Armando Gabrielli
- Fondazione di Medicina Molecolare e Terapia Cellulare, Università Politecnica delle Marche, Ancona, Italy.
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22
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Yeo SJ, Ying C, Fullwood MJ, Tergaonkar V. Emerging regulatory mechanisms of noncoding RNAs in topologically associating domains. Trends Genet 2023; 39:217-232. [PMID: 36642680 DOI: 10.1016/j.tig.2022.12.003] [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: 08/15/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 01/15/2023]
Abstract
Topologically associating domains (TADs) are integral to spatial genome organization, instructing gene expression, and cell fate. Recently, several advances have uncovered roles for noncoding RNAs (ncRNAs) in the regulation of the form and function of mammalian TADs. Phase separation has also emerged as a potential arbiter of ncRNAs in the regulation of TADs. In this review we discuss the implications of these novel findings in relation to how ncRNAs might structurally and functionally regulate TADs from two perspectives: moderating loop extrusion through interactions with architectural proteins, and facilitating TAD phase separation. Additionally, we propose future studies and directions to investigate these phenomena.
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Affiliation(s)
- Samuel Jianjie Yeo
- Laboratory of NFκB Signaling, Institute of Molecular Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University (NTU), Singapore 308232, Singapore
| | - Chen Ying
- Laboratory of NFκB Signaling, Institute of Molecular Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Melissa Jane Fullwood
- Cancer Science Institute of Singapore, Centre for Translational Medicine, National University of Singapore, Singapore 117599, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
| | - Vinay Tergaonkar
- Laboratory of NFκB Signaling, Institute of Molecular Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore; Department of Pathology and the Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117597, Singapore.
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23
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Gasparotto E, Burattin FV, Di Gioia V, Panepuccia M, Ranzani V, Marasca F, Bodega B. Transposable Elements Co-Option in Genome Evolution and Gene Regulation. Int J Mol Sci 2023; 24:ijms24032610. [PMID: 36768929 PMCID: PMC9917352 DOI: 10.3390/ijms24032610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 01/31/2023] Open
Abstract
The genome is no longer deemed as a fixed and inert item but rather as a moldable matter that is continuously evolving and adapting. Within this frame, Transposable Elements (TEs), ubiquitous, mobile, repetitive elements, are considered an alive portion of the genomes to date, whose functions, although long considered "dark", are now coming to light. Here we will review that, besides the detrimental effects that TE mobilization can induce, TEs have shaped genomes in their current form, promoting genome sizing, genomic rearrangements and shuffling of DNA sequences. Although TEs are mostly represented in the genomes by evolutionarily old, short, degenerated, and sedentary fossils, they have been thoroughly co-opted by the hosts as a prolific and original source of regulatory instruments for the control of gene transcription and genome organization in the nuclear space. For these reasons, the deregulation of TE expression and/or activity is implicated in the onset and progression of several diseases. It is likely that we have just revealed the outermost layers of TE functions. Further studies on this portion of the genome are required to unlock novel regulatory functions that could also be exploited for diagnostic and therapeutic approaches.
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Affiliation(s)
- Erica Gasparotto
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- SEMM, European School of Molecular Medicine, 20139 Milan, Italy
| | - Filippo Vittorio Burattin
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Valeria Di Gioia
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- SEMM, European School of Molecular Medicine, 20139 Milan, Italy
| | - Michele Panepuccia
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
| | - Valeria Ranzani
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
| | - Federica Marasca
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
| | - Beatrice Bodega
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- Department of Biosciences, University of Milan, 20133 Milan, Italy
- Correspondence:
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24
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B1 SINE-binding ZFP266 impedes mouse iPSC generation through suppression of chromatin opening mediated by reprogramming factors. Nat Commun 2023; 14:488. [PMID: 36717582 PMCID: PMC9887000 DOI: 10.1038/s41467-023-36097-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 01/13/2023] [Indexed: 01/31/2023] Open
Abstract
Induced pluripotent stem cell (iPSC) reprogramming is inefficient and understanding the molecular mechanisms underlying this inefficiency holds the key to successfully control cellular identity. Here, we report 24 reprogramming roadblock genes identified by CRISPR/Cas9-mediated genome-wide knockout (KO) screening. Of these, depletion of the predicted KRAB zinc finger protein (KRAB-ZFP) Zfp266 strongly and consistently enhances murine iPSC generation in several reprogramming settings, emerging as the most robust roadblock. We show that ZFP266 binds Short Interspersed Nuclear Elements (SINEs) adjacent to binding sites of pioneering factors, OCT4 (POU5F1), SOX2, and KLF4, and impedes chromatin opening. Replacing the KRAB co-suppressor with co-activator domains converts ZFP266 from an inhibitor to a potent facilitator of iPSC reprogramming. We propose that the SINE-KRAB-ZFP interaction is a critical regulator of chromatin accessibility at regulatory elements required for efficient cellular identity changes. In addition, this work serves as a resource to further illuminate molecular mechanisms hindering reprogramming.
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25
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Li Y, Ruan S, Lu F, Xie P, Liu X, Ma H. Studies on ultrasound-mediated insertion-deletion polymorphisms of DNA and underlying mechanisms based on Ames tester strains. ULTRASONICS SONOCHEMISTRY 2023; 92:106270. [PMID: 36543046 PMCID: PMC9794972 DOI: 10.1016/j.ultsonch.2022.106270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/05/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
Low-lethality ultrasound technology has received more and more attention in regulating microorganisms of fermentation industry. Herein, two representative Ames tester strains TA97a and TA98 as model organisms were used to explore the effects of ultrasound on insertion-deletion (InDel) polymorphisms of microbial DNA and its underlying mechanisms. Results revealed that a promotion was observed in the reversion mutation of TA98 upon sonication. Sequencing results from 1752 TA98 revertants showed that there was a total of 127 InDels, of which the InDels unique to ultrasound were 36 more than that of the control. Compared with the control, ultrasound-mediated InDels of DNA displayed additional -29 bp deletion and +7 ∼ +43 bp insertions of direct repeat sequences. Combined with the analysis of transcriptomics and prediction of secondary structure of single-stranded DNA from InDels core region (No. 832 ∼ 915 bp) in hisD3052 gene of TA98 strain, ultrasound-mediated "thermal breathing" mechanism was proposed based on the formation of DNA hairpin structure with micro-homologous sequence. This finding implied that low-intensity ultrasound is expected to be developed a new low-lethal mutagenic technology for continuous mutagenesis.
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Affiliation(s)
- Yunliang Li
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, PR China; Institute of Food Physical Processing, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China
| | - Siyu Ruan
- College of Tea and Food Science Technology, Jiangsu Polytechnic College of Agriculture and Forestry, 19 Wenchangdong Road, Jurong, Jiangsu 212400, PR China.
| | - Feng Lu
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, PR China
| | - Pengfei Xie
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, PR China
| | - Xiaoshuang Liu
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, PR China
| | - Haile Ma
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, PR China; Institute of Food Physical Processing, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China.
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26
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Dumetier B, Sauter C, Hajmirza A, Pernon B, Aucagne R, Fournier C, Row C, Guidez F, Rossi C, Lepage C, Delva L, Callanan MB. Repeat Element Activation-Driven Inflammation: Role of NFκB and Implications in Normal Development and Cancer? Biomedicines 2022; 10:biomedicines10123101. [PMID: 36551854 PMCID: PMC9775655 DOI: 10.3390/biomedicines10123101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/14/2022] [Accepted: 11/23/2022] [Indexed: 12/04/2022] Open
Abstract
The human genome is composed of unique DNA sequences that encode proteins and unique sequence noncoding RNAs that are essential for normal development and cellular differentiation. The human genome also contains over 50% of genome sequences that are repeat in nature (tandem and interspersed repeats) that are now known to contribute dynamically to genetic diversity in populations, to be transcriptionally active under certain physiological conditions, and to be aberrantly active in disease states including cancer, where consequences are pleiotropic with impact on cancer cell phenotypes and on the tumor immune microenvironment. Repeat element-derived RNAs play unique roles in exogenous and endogenous cell signaling under normal and disease conditions. A key component of repeat element-derived transcript-dependent signaling occurs via triggering of innate immune receptor signaling that then feeds forward to inflammatory responses through interferon and NFκB signaling. It has recently been shown that cancer cells display abnormal transcriptional activity of repeat elements and that this is linked to either aggressive disease and treatment failure or to improved prognosis/treatment response, depending on cell context and the amplitude of the so-called 'viral mimicry' response that is engaged. 'Viral mimicry' refers to a cellular state of active antiviral response triggered by endogenous nucleic acids often derived from aberrantly transcribed endogenous retrotransposons and other repeat elements. In this paper, the literature regarding transcriptional activation of repeat elements and engagement of inflammatory signaling in normal (focusing on hematopoiesis) and cancer is reviewed with an emphasis on the role of innate immune receptor signaling, in particular by dsRNA receptors of the RIG-1 like receptor family and interferons/NFκB. How repeat element-derived RNA reprograms cell identity through RNA-guided chromatin state modulation is also discussed.
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Affiliation(s)
- Baptiste Dumetier
- Faculty of Medicine, INSERM1231, University of Burgundy, 21000 Dijon, France
- Correspondence: (B.D.); (M.B.C.)
| | - Camille Sauter
- Faculty of Medicine, INSERM1231, University of Burgundy, 21000 Dijon, France
| | - Azadeh Hajmirza
- Institute for Research in Immunology and Cancer, Montreal, QC H3C 3J7, Canada
| | - Baptiste Pernon
- Faculty of Medicine, INSERM1231, University of Burgundy, 21000 Dijon, France
| | - Romain Aucagne
- Faculty of Medicine, INSERM1231, University of Burgundy, 21000 Dijon, France
- Unit for Innovation in Genetics and Epigenetics in Oncology, Dijon University Hospital, 21000 Dijon, France
- CRIGEN, Crispr-Functional Genomics, Dijon University Hospital and University of Burgundy, 21000 Dijon, France
| | - Cyril Fournier
- Faculty of Medicine, INSERM1231, University of Burgundy, 21000 Dijon, France
- Unit for Innovation in Genetics and Epigenetics in Oncology, Dijon University Hospital, 21000 Dijon, France
| | - Céline Row
- Faculty of Medicine, INSERM1231, University of Burgundy, 21000 Dijon, France
- Unit for Innovation in Genetics and Epigenetics in Oncology, Dijon University Hospital, 21000 Dijon, France
| | - Fabien Guidez
- Faculty of Medicine, INSERM1231, University of Burgundy, 21000 Dijon, France
| | - Cédric Rossi
- School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Côme Lepage
- Faculty of Medicine, INSERM1231, University of Burgundy, 21000 Dijon, France
| | - Laurent Delva
- Faculty of Medicine, INSERM1231, University of Burgundy, 21000 Dijon, France
| | - Mary B. Callanan
- Faculty of Medicine, INSERM1231, University of Burgundy, 21000 Dijon, France
- Unit for Innovation in Genetics and Epigenetics in Oncology, Dijon University Hospital, 21000 Dijon, France
- CRIGEN, Crispr-Functional Genomics, Dijon University Hospital and University of Burgundy, 21000 Dijon, France
- Correspondence: (B.D.); (M.B.C.)
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27
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Bhadsavle SS, Golding MC. Paternal epigenetic influences on placental health and their impacts on offspring development and disease. Front Genet 2022; 13:1068408. [PMID: 36468017 PMCID: PMC9716072 DOI: 10.3389/fgene.2022.1068408] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/04/2022] [Indexed: 07/25/2023] Open
Abstract
Our efforts to understand the developmental origins of birth defects and disease have primarily focused on maternal exposures and intrauterine stressors. Recently, research into non-genomic mechanisms of inheritance has led to the recognition that epigenetic factors carried in sperm also significantly impact the health of future generations. However, although researchers have described a range of potential epigenetic signals transmitted through sperm, we have yet to obtain a mechanistic understanding of how these paternally-inherited factors influence offspring development and modify life-long health. In this endeavor, the emerging influence of the paternal epigenetic program on placental development, patterning, and function may help explain how a diverse range of male exposures induce comparable intergenerational effects on offspring health. During pregnancy, the placenta serves as the dynamic interface between mother and fetus, regulating nutrient, oxygen, and waste exchange and coordinating fetal growth and maturation. Studies examining intrauterine maternal stressors routinely describe alterations in placental growth, histological organization, and glycogen content, which correlate with well-described influences on infant health and adult onset of disease. Significantly, the emergence of similar phenotypes in models examining preconception male exposures indicates that paternal stressors transmit an epigenetic memory to their offspring that also negatively impacts placental function. Like maternal models, paternally programmed placental dysfunction exerts life-long consequences on offspring health, particularly metabolic function. Here, focusing primarily on rodent models, we review the literature and discuss the influences of preconception male health and exposure history on placental growth and patterning. We emphasize the emergence of common placental phenotypes shared between models examining preconception male and intrauterine stressors but note that the direction of change frequently differs between maternal and paternal exposures. We posit that alterations in placental growth, histological organization, and glycogen content broadly serve as reliable markers of altered paternal developmental programming, predicting the emergence of structural and metabolic defects in the offspring. Finally, we suggest the existence of an unrecognized developmental axis between the male germline and the extraembryonic lineages that may have evolved to enhance fetal adaptation.
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Affiliation(s)
| | - Michael C. Golding
- Department of Veterinary Physiology and Pharmacology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
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28
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Malik V, Zang R, Fuentes-Iglesias A, Huang X, Li D, Fidalgo M, Zhou H, Wang J. Comparative functional genomics identifies unique molecular features of EPSCs. Life Sci Alliance 2022; 5:5/11/e202201608. [PMID: 35961778 PMCID: PMC9378845 DOI: 10.26508/lsa.202201608] [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: 07/15/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 12/03/2022] Open
Abstract
The authors provide a comprehensive resource on proteomics, transcriptomic, and epigenetic level details of EPSCs to shed light on possible molecular pathways regulating their expanded pluripotency potential. Extended pluripotent or expanded potential stem cells (EPSCs) possess superior developmental potential to embryonic stem cells (ESCs). However, the molecular underpinning of EPSC maintenance in vitro is not well defined. We comparatively studied transcriptome, chromatin accessibility, active histone modification marks, and relative proteomes of ESCs and the two well-established EPSC lines to probe the molecular foundation underlying EPSC developmental potential. Despite some overlapping transcriptomic and chromatin accessibility features, we defined sets of molecular signatures that distinguish EPSCs from ESCs in transcriptional and translational regulation as well as metabolic control. Interestingly, EPSCs show similar reliance on pluripotency factors Oct4, Sox2, and Nanog for self-renewal as ESCs. Our study provides a rich resource for dissecting the regulatory network that governs the developmental potency of EPSCs and exploring alternative strategies to capture totipotent stem cells in culture.
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Affiliation(s)
- Vikas Malik
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Ruge Zang
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Alejandro Fuentes-Iglesias
- Department of Physiology, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela (USC)-Health Research Institute (IDIS), Santiago de Compostela, Spain
| | - Xin Huang
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Dan Li
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Miguel Fidalgo
- Department of Physiology, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela (USC)-Health Research Institute (IDIS), Santiago de Compostela, Spain
| | - Hongwei Zhou
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Jianlong Wang
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
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29
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Fu B, Ma H, Liu D. 2-Cell-like Cells: An Avenue for Improving SCNT Efficiency. Biomolecules 2022; 12:1611. [PMID: 36358959 PMCID: PMC9687756 DOI: 10.3390/biom12111611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/23/2022] [Accepted: 10/26/2022] [Indexed: 03/25/2024] Open
Abstract
After fertilization, the zygote genome undergoes dramatic structural reorganization to ensure the establishment of totipotency, and then the totipotent potential of the zygote or 2-cell-stage embryo progressively declines. However, cellular potency is not always a one-way street. Specifically, a small number of embryonic stem cells (ESCs) occasionally overcome epigenetic barriers and transiently convert to a totipotent status. Despite the significant potential of the somatic cell nuclear transfer (SCNT) technique, the establishment of totipotency is often deficient in cloned embryos. Because of this phenomenon, the question arises as to whether strategies attempting to induce 2-cell-like cells (2CLCs) can provide practical applications, such as reprogramming of somatic cell nuclei. Inspired by strategies that convert ESCs into 2CLCs, we hypothesized that there will be a similar pathway by which cloned embryos can establish totipotent status after SCNT. In this review, we provide a snapshot of the practical strategies utilized to induce 2CLCs during investigations of the development of cloned embryos. The 2CLCs have similar transcriptome and chromatin features to that of 2-cell-stage embryos, and we propose that 2CLCs, already a valuable in vitro model for dissecting totipotency, will provide new opportunities to improve SCNT efficiency.
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Affiliation(s)
- Bo Fu
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
| | - Hong Ma
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
| | - Di Liu
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
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30
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Wei J, Yu X, Yang L, Liu X, Gao B, Huang B, Dou X, Liu J, Zou Z, Cui XL, Zhang LS, Zhao X, Liu Q, He PC, Sepich-Poore C, Zhong N, Liu W, Li Y, Kou X, Zhao Y, Wu Y, Cheng X, Chen C, An Y, Dong X, Wang H, Shu Q, Hao Z, Duan T, He YY, Li X, Gao S, Gao Y, He C. FTO mediates LINE1 m 6A demethylation and chromatin regulation in mESCs and mouse development. Science 2022; 376:968-973. [PMID: 35511947 PMCID: PMC9746489 DOI: 10.1126/science.abe9582] [Citation(s) in RCA: 93] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
N6-methyladenosine (m6A) is the most abundant internal modification on mammalian messenger RNA. It is installed by a writer complex and can be reversed by erasers such as the fat mass and obesity-associated protein FTO. Despite extensive research, the primary physiological substrates of FTO in mammalian tissues and development remain elusive. Here, we show that FTO mediates m6A demethylation of long-interspersed element-1 (LINE1) RNA in mouse embryonic stem cells (mESCs), regulating LINE1 RNA abundance and the local chromatin state, which in turn modulates the transcription of LINE1-containing genes. FTO-mediated LINE1 RNA m6A demethylation also plays regulatory roles in shaping chromatin state and gene expression during mouse oocyte and embryonic development. Our results suggest broad effects of LINE1 RNA m6A demethylation by FTO in mammals.
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Affiliation(s)
- Jiangbo Wei
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Xianbin Yu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Lei Yang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xuelian Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Boyang Gao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Boxian Huang
- State Key Laboratory of Reproductive Medicine, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou 215002, China
| | - Xiaoyang Dou
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Jun Liu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Zhongyu Zou
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Xiao-Long Cui
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Li-Sheng Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Xingsen Zhao
- The Children's Hospital, School of Medicine, Zhejiang University, National Clinical Research Center for Child Health, Hangzhou 310052, China
- The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310029, China
| | - Qinzhe Liu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - P. Cody He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Caraline Sepich-Poore
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Nicole Zhong
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Wenqiang Liu
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yanhe Li
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiaochen Kou
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Yanhong Zhao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - You Wu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Xuejun Cheng
- The Children's Hospital, School of Medicine, Zhejiang University, National Clinical Research Center for Child Health, Hangzhou 310052, China
- The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310029, China
| | - Chuan Chen
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Yiming An
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Xueyang Dong
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Huanyu Wang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Qiang Shu
- The Children's Hospital, School of Medicine, Zhejiang University, National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Ziyang Hao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Tao Duan
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yu-Ying He
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL 60637, USA
| | - Xuekun Li
- The Children's Hospital, School of Medicine, Zhejiang University, National Clinical Research Center for Child Health, Hangzhou 310052, China
- The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310029, China
| | - Shaorong Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yawei Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
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31
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Li D, He M, Tang Q, Tian S, Zhang J, Li Y, Wang D, Jin L, Ning C, Zhu W, Hu S, Long K, Ma J, Liu J, Zhang Z, Li M. Comparative 3D genome architecture in vertebrates. BMC Biol 2022; 20:99. [PMID: 35524220 PMCID: PMC9077971 DOI: 10.1186/s12915-022-01301-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 04/20/2022] [Indexed: 12/14/2022] Open
Abstract
Background The three-dimensional (3D) architecture of the genome has a highly ordered and hierarchical nature, which influences the regulation of essential nuclear processes at the basis of gene expression, such as gene transcription. While the hierarchical organization of heterochromatin and euchromatin can underlie differences in gene expression that determine evolutionary differences among species, the way 3D genome architecture is affected by evolutionary forces within major lineages remains unclear. Here, we report a comprehensive comparison of 3D genomes, using high resolution Hi-C data in fibroblast cells of fish, chickens, and 10 mammalian species. Results This analysis shows a correlation between genome size and chromosome length that affects chromosome territory (CT) organization in the upper hierarchy of genome architecture, whereas lower hierarchical features, including local transcriptional availability of DNA, are selected through the evolution of vertebrates. Furthermore, conservation of topologically associating domains (TADs) appears strongly associated with the modularity of expression profiles across species. Additionally, LINE and SINE transposable elements likely contribute to heterochromatin and euchromatin organization, respectively, during the evolution of genome architecture. Conclusions Our analysis uncovers organizational features that appear to determine the conservation and transcriptional regulation of functional genes across species. These findings can guide ongoing investigations of genome evolution by extending our understanding of the mechanisms shaping genome architecture. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01301-7.
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Affiliation(s)
- Diyan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mengnan He
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shilin Tian
- Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China.,Novogene Bioinformatics Institute, Beijing, 100000, China
| | - Jiaman Zhang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Danyang Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chunyou Ning
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Zhu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Silu Hu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Keren Long
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jideng Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jing Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhihua Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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32
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Razin SV, Ulianov SV. Genome-Directed Cell Nucleus Assembly. BIOLOGY 2022; 11:biology11050708. [PMID: 35625436 PMCID: PMC9138775 DOI: 10.3390/biology11050708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/02/2022] [Accepted: 05/02/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Speckles and other nuclear bodies, the nucleolus and perinucleolar zone, transcription/replication factories and the lamina-associated compartment, serve as a structural basis for various genomic functions. In turn, genome activity and specific chromatin 3D organization directly impact the integrity of intranuclear assemblies, initiating/facilitating their formation and dictating their composition. Thus, the large-scale nucleus structure and genome activity mutually influence each other. The cell nucleus is frequently considered a compartment in which the genome is placed to protect it from external forces. Here, we discuss the evidence demonstrating that the cell nucleus should be considered, rather, as structure built around the folded genome. Decondensing chromosomes provide a scaffold for the assembly of the nuclear envelope after mitosis, whereas genome activity directs the assembly of various nuclear compartments, including nucleolus, speckles and transcription factories. Abstract The cell nucleus is frequently considered a cage in which the genome is placed to protect it from various external factors. Inside the nucleus, many functional compartments have been identified that are directly or indirectly involved in implementing genomic DNA’s genetic functions. For many years, it was assumed that these compartments are assembled on a proteinaceous scaffold (nuclear matrix), which provides a structural milieu for nuclear compartmentalization and genome folding while simultaneously offering some rigidity to the cell nucleus. The results of research in recent years have made it possible to consider the cell nucleus from a different angle. From the “box” in which the genome is placed, the nucleus has become a kind of mobile exoskeleton, which is formed around the packaged genome, under the influence of transcription and other processes directly related to the genome activity. In this review, we summarize the main arguments in favor of this point of view by analyzing the mechanisms that mediate cell nucleus assembly and support its resistance to mechanical stresses.
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Affiliation(s)
- Sergey V. Razin
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
- Correspondence: or
| | - Sergey V. Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
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33
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Li C, Shi X, Yang J, Li K, Dai L, Zhang Y, Zhou M, Su J. Genome-wide characterization of RNA editing highlights roles of high editing events of glutamatergic synapse during mouse retinal development. Comput Struct Biotechnol J 2022; 20:2648-2656. [PMID: 35685368 PMCID: PMC9162912 DOI: 10.1016/j.csbj.2022.05.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/14/2022] [Accepted: 05/14/2022] [Indexed: 11/30/2022] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing leads to functional change of neurotransmitter receptor which is essential for neurotransmission and normal neuronal development. As a highly accessible part of central nervous system, retina has been extensively studied, however, it remains largely unknown how RNA editing regulates its development. Here, a genome-wide screening of high-confidence RNA editing events were performed to decipher the dynamic transcriptome regulation by RNA editing during mouse retinal development. 2000 high-confidence editing sites across eight developmental stages of retina were called. Three unique patterns (RNA-editinghigh pattern, RNA-editingmedium pattern and RNA-editinglow pattern) were identified by clustering these editing sites based on their editing level during retinal development. Editing events from RNA-editinghigh pattern were significantly associated with glutamate receptors and regulated synaptic transmission. Interestingly, most non-synonymous high-editing sites were mapped to ion channel genes of glutamatergic synapse which were associated with neurotransmission by controlling ion channel permeability and affecting exocytosis. Meanwhile, these non-synonymous editing sites were evolutionarily conserved and exhibited a consistently increasing editing levels between mouse and human retinal development. Single-cell RNA-seq data analysis revealed that RNA editing events prefer to occur in two main cell types including bipolar and amacrine cells. Genes with non-synonymous high-editing sites were enriched in both bipolar cells and retina ganglion cells, which may mediate retina ganglion cell differentiation by altering channel ion permeability. Together, our results provide novel insights into mechanism of post-transcriptional regulation during retinal development and help to develop novel RNA editing-guided therapeutic strategies for retinal disorders.
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Affiliation(s)
- Chenghao Li
- School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang 325001, China
| | - Xinrui Shi
- School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Jiaying Yang
- School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Ke Li
- School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Lijun Dai
- School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Yan Zhang
- School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Meng Zhou
- School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Corresponding authorsat: School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China (J. Su).
| | - Jianzhong Su
- School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang 325001, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325011, China
- Corresponding authorsat: School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China (J. Su).
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Vrooman LA, Rhon-Calderon EA, Suri KV, Dahiya AK, Lan Y, Schultz RM, Bartolomei MS. Placental Abnormalities are Associated With Specific Windows of Embryo Culture in a Mouse Model. Front Cell Dev Biol 2022; 10:884088. [PMID: 35547813 PMCID: PMC9081528 DOI: 10.3389/fcell.2022.884088] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/07/2022] [Indexed: 11/20/2022] Open
Abstract
Assisted Reproductive Technologies (ART) employ gamete/embryo handling and culture in vitro to produce offspring. ART pregnancies have an increased risk of low birth weight, abnormal placentation, pregnancy complications, and imprinting disorders. Embryo culture induces low birth weight, abnormal placental morphology, and lower levels of DNA methylation in placentas in a mouse model of ART. Whether preimplantation embryos at specific stages of development are more susceptible to these perturbations remains unresolved. Accordingly, we performed embryo culture for several discrete periods of preimplantation development and following embryo transfer, assessed fetal and placental outcomes at term. We observed a reduction in fetal:placental ratio associated with two distinct windows of preimplantation embryo development, one prior to the morula stage and the other from the morula to blastocyst stage, whereas placental morphological abnormalities and reduced imprinting control region methylation were only associated with culture prior to the morula stage. Extended culture to the blastocyst stage also induces additional placental DNA methylation changes compared to embryos transferred at the morula stage, and female concepti exhibited a higher loss of DNA methylation than males. By identifying specific developmental windows of susceptibility, this study provides a framework to optimize further culture conditions to minimize risks associated with ART pregnancies.
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Affiliation(s)
- Lisa A. Vrooman
- Department of Cell and Developmental Biology, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, United States
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Eric A. Rhon-Calderon
- Department of Cell and Developmental Biology, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, United States
| | - Kashviya V. Suri
- Department of Cell and Developmental Biology, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, United States
| | - Asha K. Dahiya
- Department of Cell and Developmental Biology, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, United States
| | - Yemin Lan
- Department of Cell and Developmental Biology, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, United States
| | - Richard M. Schultz
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, United States
| | - Marisa S. Bartolomei
- Department of Cell and Developmental Biology, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, United States
- *Correspondence: Marisa S. Bartolomei,
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35
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Dynamics of nuclear matrix attachment regions during 5 th instar posterior silk gland development in Bombyx mori. BMC Genomics 2022; 23:247. [PMID: 35361117 PMCID: PMC8973518 DOI: 10.1186/s12864-022-08446-3] [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: 07/29/2021] [Accepted: 03/06/2022] [Indexed: 12/02/2022] Open
Abstract
Background Chromatin architecture is critical for gene expression during development. Matrix attachment regions (MARs) control and regulate chromatin dynamics. The position of MARs in the genome determines the expression of genes in the organism. In this study, we set out to elucidate how MARs temporally regulate the expression of the fibroin heavy chain (FIBH) gene during development. We addressed this by identifying MARs and studying their distribution and differentiation, in the posterior silk glands of Bombyx mori during 5th instar development. Results Of the MARs identified on three different days, 7.15% MARs were common to all 3 days, whereas, 1.41, 19.27 and 52.47% MARs were unique to day 1, day 5, and day 7, respectively highlighting the dynamic nature of the matrix associated DNA. The average chromatin loop length based on the chromosome wise distribution of MARs and the distances between these MAR regions decreased from day 1 (253.91 kb) to day 5 (73.54 kb) to day 7 (39.19 kb). Further significant changes in the MARs in the vicinity of the FIBH gene were found during different days of 5th instar development which implied their role in the regulation and expression of the FIBH gene. Conclusions The presence of MARs in the flanking regions of genes found to exhibit differential expression during 5th instar development indicates their possible role in the regulation of their expression. This reiterates the importance of MARs in the genomic functioning as regulators of the molecular mechanisms in the nucleus. This is the first study that takes into account the tissue specific genome-wide MAR association and the potential role of these MARs in developmentally regulated gene expression. The current study lays a foundation to understand the genome wide regulation of chromatin during development. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08446-3.
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36
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Genome-wide maps of nucleolus interactions reveal distinct layers of repressive chromatin domains. Nat Commun 2022; 13:1483. [PMID: 35304483 PMCID: PMC8933459 DOI: 10.1038/s41467-022-29146-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 02/28/2022] [Indexed: 12/22/2022] Open
Abstract
Eukaryotic chromosomes are folded into hierarchical domains, forming functional compartments. Nuclear periphery and nucleolus are two nuclear landmarks contributing to repressive chromosome architecture. However, while the role of nuclear lamina (NL) in genome organization has been well documented, the function of the nucleolus remains under-investigated due to the lack of methods for the identification of nucleolar associated domains (NADs). Here we have established DamID- and HiC-based methodologies to generate accurate genome-wide maps of NADs in embryonic stem cells (ESCs) and neural progenitor cells (NPCs), revealing layers of genome compartmentalization with distinct, repressive chromatin states based on the interaction with the nucleolus, NL, or both. NADs show higher H3K9me2 and lower H3K27me3 content than regions exclusively interacting with NL. Upon ESC differentiation into NPCs, chromosomes around the nucleolus acquire a more compact, rigid architecture with neural genes moving away from nucleoli and becoming unlocked for later activation. Further, histone modifications and the interaction strength within A and B compartments of NADs and LADs in ESCs set the choice to associate with NL or nucleoli upon dissociation from their respective compartments during differentiation. The methodologies here developed will make possible to include the nucleolar contribution in nuclear space and genome function in diverse biological systems.
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37
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Xie SQ, Leeke BJ, Whilding C, Wagner RT, Garcia-Llagostera F, Low Y, Chammas P, Cheung NTF, Dormann D, McManus MT, Percharde M. Nucleolar-based Dux repression is essential for embryonic two-cell stage exit. Genes Dev 2022; 36:331-347. [PMID: 35273077 PMCID: PMC8973846 DOI: 10.1101/gad.349172.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 02/17/2022] [Indexed: 12/14/2022]
Abstract
Upon fertilization, the mammalian embryo must switch from dependence on maternal transcripts to transcribing its own genome, and in mice this involves the transient up-regulation of MERVL transposons and MERVL-driven genes at the two-cell stage. The mechanisms and requirement for MERVL and two-cell (2C) gene up-regulation are poorly understood. Moreover, this MERVL-driven transcriptional program must be rapidly shut off to allow two-cell exit and developmental progression. Here, we report that robust ribosomal RNA (rRNA) synthesis and nucleolar maturation are essential for exit from the 2C state. 2C-like cells and two-cell embryos show similar immature nucleoli with altered structure and reduced rRNA output. We reveal that nucleolar disruption via blocking RNA polymerase I activity or preventing nucleolar phase separation enhances conversion to a 2C-like state in embryonic stem cells (ESCs) by detachment of the MERVL activator Dux from the nucleolar surface. In embryos, nucleolar disruption prevents proper nucleolar maturation and Dux silencing and leads to two- to four-cell arrest. Our findings reveal an intriguing link between rRNA synthesis, nucleolar maturation, and gene repression during early development.
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Affiliation(s)
- Sheila Q Xie
- MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom.,Institute of Clinical Sciences, Imperial College London, London W12 0NN, United Kingdom
| | - Bryony J Leeke
- MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom.,Institute of Clinical Sciences, Imperial College London, London W12 0NN, United Kingdom
| | - Chad Whilding
- MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom.,Institute of Clinical Sciences, Imperial College London, London W12 0NN, United Kingdom
| | - Ryan T Wagner
- University of California at San Francisco, San Francisco, California 91413, USA
| | - Ferran Garcia-Llagostera
- MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom.,Institute of Clinical Sciences, Imperial College London, London W12 0NN, United Kingdom
| | - YiXuan Low
- MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom.,Institute of Clinical Sciences, Imperial College London, London W12 0NN, United Kingdom
| | - Paul Chammas
- MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom.,Institute of Clinical Sciences, Imperial College London, London W12 0NN, United Kingdom
| | - Nathan T-F Cheung
- MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom.,Institute of Clinical Sciences, Imperial College London, London W12 0NN, United Kingdom
| | - Dirk Dormann
- MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom.,Institute of Clinical Sciences, Imperial College London, London W12 0NN, United Kingdom
| | - Michael T McManus
- University of California at San Francisco, San Francisco, California 91413, USA
| | - Michelle Percharde
- MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom.,Institute of Clinical Sciences, Imperial College London, London W12 0NN, United Kingdom
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38
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Bennett C, Thornton M, Park C, Henry G, Zhang Y, Malladi V, Kim D. SeqWho: reliable, rapid determination of sequence file identity using k-mer frequencies in Random Forest classifiers. Bioinformatics 2022; 38:1830-1837. [PMID: 35134110 PMCID: PMC8963323 DOI: 10.1093/bioinformatics/btac050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 01/12/2022] [Accepted: 01/26/2022] [Indexed: 02/05/2023] Open
Abstract
MOTIVATION With the vast improvements in sequencing technologies and increased number of protocols, sequencing is being used to answer complex biological problems. Subsequently, analysis pipelines have become more time consuming and complicated, usually requiring highly extensive prevalidation steps. Here, we present SeqWho, a program designed to assess heuristically the quality of sequencing files and reliably classify the organism and protocol type by using Random Forest classifiers trained on biases native in k-mer frequencies and repeat sequence identities. RESULTS Using one of our primary models, we show that our method accurately and rapidly classifies human and mouse sequences from nine different sequencing libraries by species, library and both together, 98.32%, 97.86% and 96.38% of the time, respectively. Ultimately, we demonstrate that SeqWho is a powerful method for reliably validating the quality and identity of the sequencing files used in any pipeline. AVAILABILITY AND IMPLEMENTATION https://github.com/DaehwanKimLab/seqwho. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Chanhee Park
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern, Dallas, TX 75390, USA
| | - Gervaise Henry
- Department of Urology, University of Texas Southwestern, Dallas, TX 75390, USA
| | - Yun Zhang
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern, Dallas, TX 75390, USA
| | - Venkat Malladi
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern, Dallas, TX 75390, USA
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39
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Marasca F, Sinha S, Vadalà R, Polimeni B, Ranzani V, Paraboschi EM, Burattin FV, Ghilotti M, Crosti M, Negri ML, Campagnoli S, Notarbartolo S, Sartore-Bianchi A, Siena S, Prati D, Montini G, Viale G, Torre O, Harari S, Grifantini R, Soldà G, Biffo S, Abrignani S, Bodega B. LINE1 are spliced in non-canonical transcript variants to regulate T cell quiescence and exhaustion. Nat Genet 2022; 54:180-193. [PMID: 35039641 DOI: 10.1038/s41588-021-00989-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 11/18/2021] [Indexed: 12/12/2022]
Abstract
How gene expression is controlled to preserve human T cell quiescence is poorly understood. Here we show that non-canonical splicing variants containing long interspersed nuclear element 1 (LINE1) enforce naive CD4+ T cell quiescence. LINE1-containing transcripts are derived from CD4+ T cell-specific genes upregulated during T cell activation. In naive CD4+ T cells, LINE1-containing transcripts are regulated by the transcription factor IRF4 and kept at chromatin by nucleolin; these transcripts act in cis, hampering levels of histone 3 (H3) lysine 36 trimethyl (H3K36me3) and stalling gene expression. T cell activation induces LINE1-containing transcript downregulation by the splicing suppressor PTBP1 and promotes expression of the corresponding protein-coding genes by the elongating factor GTF2F1 through mTORC1. Dysfunctional T cells, exhausted in vitro or tumor-infiltrating lymphocytes (TILs), accumulate LINE1-containing transcripts at chromatin. Remarkably, depletion of LINE1-containing transcripts restores TIL effector function. Our study identifies a role for LINE1 elements in maintaining T cell quiescence and suggests that an abundance of LINE1-containing transcripts is critical for T cell effector function and exhaustion.
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Affiliation(s)
- Federica Marasca
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Shruti Sinha
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Rebecca Vadalà
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
- Ph.D. Program in Translational and Molecular Medicine, DIMET, University of Milan-Bicocca, Monza, Italy
| | - Benedetto Polimeni
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
- Ph.D. Program in Translational and Molecular Medicine, DIMET, University of Milan-Bicocca, Monza, Italy
| | - Valeria Ranzani
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Elvezia Maria Paraboschi
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | | | - Marco Ghilotti
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Mariacristina Crosti
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Maria Luce Negri
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | | | - Samuele Notarbartolo
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Andrea Sartore-Bianchi
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
- Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Salvatore Siena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
- Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Daniele Prati
- Department of Transfusion Medicine and Hematology, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Giovanni Montini
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- Pediatric Nephrology and Dialysis Unit, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Giuseppe Viale
- University of Milan, European Institute of Oncology IRCCS, Milan, Italy
| | - Olga Torre
- Department of Medical Sciences, San Giuseppe Hospital MultiMedica IRCCS, Milan, Italy
| | - Sergio Harari
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- Department of Medical Sciences, San Giuseppe Hospital MultiMedica IRCCS, Milan, Italy
| | - Renata Grifantini
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
- CheckmAb Srl, Milan, Italy
| | - Giulia Soldà
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | - Stefano Biffo
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
| | - Sergio Abrignani
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy.
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy.
| | - Beatrice Bodega
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy.
- Department of Biosciences, University of Milan, Milan, Italy.
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40
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Lusic M, Mhlanga MM. Walking the LINEs hidden in the dark matter of the genome. Nat Genet 2022; 54:98-99. [DOI: 10.1038/s41588-021-01003-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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41
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Floreani L, Ansaloni F, Mangoni D, Agostoni E, Sanges R, Persichetti F, Gustincich S. Analysis of LINE1 Retrotransposons in Huntington’s Disease. Front Cell Neurosci 2022; 15:743797. [PMID: 35095420 PMCID: PMC8795916 DOI: 10.3389/fncel.2021.743797] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/27/2021] [Indexed: 12/27/2022] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that made up about half the human genome. Among them, the autonomous non-LTR retrotransposon long interspersed nuclear element-1 (L1) is the only currently active TE in mammals and covers about 17% of the mammalian genome. L1s exert their function as structural elements in the genome, as transcribed RNAs to influence chromatin structure and as retrotransposed elements to shape genomic variation in somatic cells. L1s activity has been shown altered in several diseases of the nervous system. Huntington disease (HD) is a dominantly inherited neurodegenerative disorder caused by an expansion of a CAG repeat in the HTT gene which leads to a gradual loss of neurons most prominently in the striatum and, to a lesser extent, in cortical brain regions. The length of the expanded CAG tract is related to age at disease onset, with longer repeats leading to earlier onset. Here we carried out bioinformatic analysis of public RNA-seq data of a panel of HD mouse models showing that a decrease of L1 RNA expression recapitulates two hallmarks of the disease: it correlates to CAG repeat length and it occurs in the striatum, the site of neurodegeneration. Results were then experimentally validated in HttQ111 knock-in mice. The expression of L1-encoded proteins was independent from L1 RNA levels and differentially regulated in time and tissues. The pattern of expression L1 RNAs in human HD post-mortem brains showed similarity to mouse models of the disease. This work suggests the need for further study of L1s in HD and adds support to the current hypothesis that dysregulation of TEs may be involved in neurodegenerative diseases.
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Affiliation(s)
- Lavinia Floreani
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Federico Ansaloni
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
- Central RNA Laboratory, Istituto Italiano di Tecnologia—IIT, Genova, Italy
| | - Damiano Mangoni
- Central RNA Laboratory, Istituto Italiano di Tecnologia—IIT, Genova, Italy
| | - Elena Agostoni
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Remo Sanges
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
- Central RNA Laboratory, Istituto Italiano di Tecnologia—IIT, Genova, Italy
- *Correspondence: Remo Sanges,
| | - Francesca Persichetti
- Department of Health Sciences, University of Piemonte Orientale “ A. Avogadro,”Novara, Italy
- Francesca Persichetti,
| | - Stefano Gustincich
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
- Central RNA Laboratory, Istituto Italiano di Tecnologia—IIT, Genova, Italy
- Stefano Gustincich,
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42
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RNA gradients: Shapers of 3D genome architecture. Curr Opin Cell Biol 2022; 74:7-12. [PMID: 34998095 DOI: 10.1016/j.ceb.2021.12.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 01/13/2023]
Abstract
A growing body of evidence points to a role of nuclear RNAs (nucRNAs) in shaping the three-dimensional (3D) architecture of the genome within the nucleus of a eukaryotic cell. nucRNAs are non-homogeneously distributed within the nucleus where they can form global and local gradients that might contribute to instructing the formation and coordinating the function of different types of 3D genome structures. In this article, we highlight the available literature supporting a role of nucRNAs as 3D genome shapers and propose that nucRNA gradients are key mediators of genome structure and function.
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43
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Zhu Z, Ge S, Cai Z, Wu Y, Lu C, Zhang Z, Fu P, Mao L, Wu X, Peng Y. Systematic identification and characterization of repeat sequences in African swine fever virus genomes. Vet Res 2022; 53:101. [PMID: 36461107 PMCID: PMC9717548 DOI: 10.1186/s13567-022-01119-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/19/2022] [Indexed: 12/03/2022] Open
Abstract
African swine fever virus (ASFV) is a large DNA virus that infects domestic pigs with high morbidity and mortality rates. Repeat sequences, which are DNA sequence elements that are repeated more than twice in the genome, play an important role in the ASFV genome. The majority of repeat sequences, however, have not been identified and characterized in a systematic manner. In this study, three types of repeat sequences, including microsatellites, minisatellites and short interspersed nuclear elements (SINEs), were identified in the ASFV genome, and their distribution, structure, function, and evolutionary history were investigated. Most repeat sequences were observed in noncoding regions and at the 5' end of the genome. Noncoding repeat sequences tended to form enhancers, whereas coding repeat sequences had a lower ratio of alpha-helix and beta-sheet and a higher ratio of loop structure and surface amino acids than nonrepeat sequences. In addition, the repeat sequences tended to encode penetrating and antimicrobial peptides. Further analysis of the evolution of repeat sequences revealed that the pan-repeat sequences presented an open state, showing the diversity of repeat sequences. Finally, CpG islands were observed to be negatively correlated with repeat sequence occurrences, suggesting that they may affect the generation of repeat sequences. Overall, this study emphasizes the importance of repeat sequences in ASFVs, and these results can aid in understanding the virus's function and evolution.
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Affiliation(s)
- Zhaozhong Zhu
- grid.67293.39Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082 China
| | - Shengqiang Ge
- grid.414245.20000 0004 6063 681XChina Animal Health and Epidemiology Center, Qingdao, 266032 China ,grid.418524.e0000 0004 0369 6250Key Laboratory of Animal Biosafety Risk Prevention and Control (South), Ministry of Agriculture and Rural Affairs, Qingdao, China
| | - Zena Cai
- grid.67293.39Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082 China
| | - Yifan Wu
- grid.67293.39Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082 China
| | - Congyu Lu
- grid.67293.39Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082 China
| | - Zheng Zhang
- grid.67293.39Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082 China
| | - Ping Fu
- grid.67293.39Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082 China
| | - Longfei Mao
- grid.67293.39Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082 China
| | - Xiaodong Wu
- grid.414245.20000 0004 6063 681XChina Animal Health and Epidemiology Center, Qingdao, 266032 China ,grid.418524.e0000 0004 0369 6250Key Laboratory of Animal Biosafety Risk Prevention and Control (South), Ministry of Agriculture and Rural Affairs, Qingdao, China
| | - Yousong Peng
- grid.67293.39Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082 China
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44
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Shao W, Bi X, Pan Y, Gao B, Wu J, Yin Y, Liu Z, Peng M, Zhang W, Jiang X, Ren W, Xu Y, Wu Z, Wang K, Zhan G, Lu JY, Han X, Li T, Wang J, Li G, Deng H, Li B, Shen X. Phase separation of RNA-binding protein promotes polymerase binding and transcription. Nat Chem Biol 2022; 18:70-80. [PMID: 34916619 DOI: 10.1038/s41589-021-00904-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/22/2021] [Indexed: 01/27/2023]
Abstract
An RNA-involved phase-separation model has been proposed for transcription control. However, the molecular links that connect RNA to the transcription machinery remain missing. Here we find that RNA-binding proteins (RBPs) constitute half of the chromatin proteome in embryonic stem cells (ESCs), some being colocalized with RNA polymerase (Pol) II at promoters and enhancers. Biochemical analyses of representative RBPs show that the paraspeckle protein PSPC1 inhibits the RNA-induced premature release of Pol II, and makes use of RNA as multivalent molecules to enhance the formation of transcription condensates and subsequent phosphorylation and release of Pol II. This synergistic interplay enhances polymerase engagement and activity via the RNA-binding and phase-separation activities of PSPC1. In ESCs, auxin-induced acute degradation of PSPC1 leads to genome-wide defects in Pol II binding and nascent transcription. We propose that promoter-associated RNAs and their binding proteins synergize the phase separation of polymerase condensates to promote active transcription.
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Affiliation(s)
- Wen Shao
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Xianju Bi
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Yixuan Pan
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Boyang Gao
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Jun Wu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yafei Yin
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Zhimin Liu
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Mengyuan Peng
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenhao Zhang
- Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xu Jiang
- Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Wenlin Ren
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Yanhui Xu
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Zhongyang Wu
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Kaili Wang
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Ge Zhan
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - J Yuyang Lu
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Xue Han
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Tong Li
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Jianlong Wang
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Guohong Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Haiteng Deng
- Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Bing Li
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Xiaohua Shen
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China.
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45
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Liao X, Hu K, Salhi A, Zou Y, Wang J, Gao X. msRepDB: a comprehensive repetitive sequence database of over 80 000 species. Nucleic Acids Res 2021; 50:D236-D245. [PMID: 34850956 PMCID: PMC8728181 DOI: 10.1093/nar/gkab1089] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 10/18/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
Repeats are prevalent in the genomes of all bacteria, plants and animals, and they cover nearly half of the Human genome, which play indispensable roles in the evolution, inheritance, variation and genomic instability, and serve as substrates for chromosomal rearrangements that include disease-causing deletions, inversions, and translocations. Comprehensive identification, classification and annotation of repeats in genomes can provide accurate and targeted solutions towards understanding and diagnosis of complex diseases, optimization of plant properties and development of new drugs. RepBase and Dfam are two most frequently used repeat databases, but they are not sufficiently complete. Due to the lack of a comprehensive repeat database of multiple species, the current research in this field is far from being satisfactory. LongRepMarker is a new framework developed recently by our group for comprehensive identification of genomic repeats. We here propose msRepDB based on LongRepMarker, which is currently the most comprehensive multi-species repeat database, covering >80 000 species. Comprehensive evaluations show that msRepDB contains more species, and more complete repeats and families than RepBase and Dfam databases. (https://msrepdb.cbrc.kaust.edu.sa/pages/msRepDB/index.html).
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Affiliation(s)
- Xingyu Liao
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia.,Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China
| | - Kang Hu
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China
| | - Adil Salhi
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - You Zou
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China
| | - Jianxin Wang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
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46
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Young Chae G, Hong WJ, Jeong Jang M, Jung KH, Kim S. Recurrent mutations promote widespread structural and functional divergence of MULE-derived genes in plants. Nucleic Acids Res 2021; 49:11765-11777. [PMID: 34725701 PMCID: PMC8599713 DOI: 10.1093/nar/gkab932] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/08/2021] [Accepted: 09/29/2021] [Indexed: 11/23/2022] Open
Abstract
Transposable element (TE)-derived genes are increasingly recognized as major sources conferring essential traits in agriculturally important crops but underlying evolutionary mechanisms remain obscure. We updated previous annotations and constructed 18,744 FAR-RED IMPAIRED RESPONSE1 (FAR1) genes, a transcription factor family derived from Mutator-like elements (MULEs), from 80 plant species, including 15,546 genes omitted in previous annotations. In-depth sequence comparison of the updated gene repertoire revealed that FAR1 genes underwent continuous structural divergence via frameshift and nonsense mutations that caused premature translation termination or specific domain truncations. CRISPR/Cas9-based genome editing and transcriptome analysis determined a novel gene involved in fertility-regulating transcription of rice pollen, denoting the functional capacity of our re-annotated gene models especially in monocots which had the highest copy numbers. Genomic evidence showed that the functional gene adapted by obtaining a shortened form through a frameshift mutation caused by a tandem duplication of a 79-bp sequence resulting in premature translation termination. Our findings provide improved resources for comprehensive studies of FAR1 genes with beneficial agricultural traits and unveil novel evolutionary mechanisms generating structural divergence and subsequent adaptation of TE-derived genes in plants.
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Affiliation(s)
- Geun Young Chae
- Department of Environmental Horticulture, University of Seoul, Seoul 02504, Republic of Korea
| | - Woo-Jong Hong
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Min Jeong Jang
- Department of Environmental Horticulture, University of Seoul, Seoul 02504, Republic of Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Seungill Kim
- Department of Environmental Horticulture, University of Seoul, Seoul 02504, Republic of Korea
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47
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Wakim JG, Sandholtz SH, Spakowitz AJ. Impact of chromosomal organization on epigenetic drift and domain stability revealed by physics-based simulations. Biophys J 2021; 120:4932-4943. [PMID: 34687722 DOI: 10.1016/j.bpj.2021.10.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/07/2021] [Accepted: 10/18/2021] [Indexed: 12/21/2022] Open
Abstract
We examine the relationship between the size of domains of epigenetic marks and the stability of those domains using our theoretical model that captures the physical mechanisms governing the maintenance of epigenetic modifications. We focus our study on histone H3 lysine-9 trimethylation, one of the most common and consequential epigenetic marks with roles in chromatin compaction and gene repression. Our model combines the effects of methyl spreading by methyltransferases and chromatin segregation into heterochromatin and euchromatin because of preferential heterochromatin protein 1 (HP1) binding. Our model indicates that, although large methylated domains are passed successfully from one chromatin generation to the next, small alterations to the methylation sequence are not maintained during chromatin replication. Using our predictive model, we investigate the size required for an epigenetic domain to persist over chromatin generations while surrounded by a much larger domain of opposite methylation and compaction state. We find that there is a critical size threshold in the hundreds-of-nucleosomes scale above which an epigenetic domain will be reliably maintained over generations. The precise size of the threshold differs for heterochromatic and euchromatic domains. Our results are consistent with natural alterations to the epigenetic sequence occurring during embryonic development and due to age-related epigenetic drift.
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Affiliation(s)
- Joseph G Wakim
- Department of Chemical Engineering, Stanford University, Stanford, California
| | | | - Andrew J Spakowitz
- Department of Chemical Engineering, Stanford University, Stanford, California; Department of Materials Science and Engineering, Stanford University, Stanford, California; Biophysics Program, Stanford University, Stanford, California; Department of Applied Physics, Stanford University, Stanford, California.
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48
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Yu H, Sun Z, Tan T, Pan H, Zhao J, Zhang L, Chen J, Lei A, Zhu Y, Chen L, Xu Y, Liu Y, Chen M, Sheng J, Xu Z, Qian P, Li C, Gao S, Daley GQ, Zhang J. rRNA biogenesis regulates mouse 2C-like state by 3D structure reorganization of peri-nucleolar heterochromatin. Nat Commun 2021; 12:6365. [PMID: 34753899 PMCID: PMC8578659 DOI: 10.1038/s41467-021-26576-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 10/06/2021] [Indexed: 11/09/2022] Open
Abstract
The nucleolus is the organelle for ribosome biogenesis and sensing various types of stress. However, its role in regulating stem cell fate remains unclear. Here, we present evidence that nucleolar stress induced by interfering rRNA biogenesis can drive the 2-cell stage embryo-like (2C-like) program and induce an expanded 2C-like cell population in mouse embryonic stem (mES) cells. Mechanistically, nucleolar integrity maintains normal liquid-liquid phase separation (LLPS) of the nucleolus and the formation of peri-nucleolar heterochromatin (PNH). Upon defects in rRNA biogenesis, the natural state of nucleolus LLPS is disrupted, causing dissociation of the NCL/TRIM28 complex from PNH and changes in epigenetic state and reorganization of the 3D structure of PNH, which leads to release of Dux, a 2C program transcription factor, from PNH to activate a 2C-like program. Correspondingly, embryos with rRNA biogenesis defect are unable to develop from 2-cell (2C) to 4-cell embryos, with delayed repression of 2C/ERV genes and a transcriptome skewed toward earlier cleavage embryo signatures. Our results highlight that rRNA-mediated nucleolar integrity and 3D structure reshaping of the PNH compartment regulates the fate transition of mES cells to 2C-like cells, and that rRNA biogenesis is a critical regulator during the 2-cell to 4-cell transition of murine pre-implantation embryo development.
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Affiliation(s)
- Hua Yu
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, 1369 West Wenyi Road, 311121, Hangzhou, China
- Institute of Hematology, Zhejiang University, 310058, Hangzhou, China
- Center of Gene/Cell Engineering and Genome Medicine, 310058, Hangzhou, Zhejiang, China
| | - Zhen Sun
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, 1369 West Wenyi Road, 311121, Hangzhou, China
- Institute of Hematology, Zhejiang University, 310058, Hangzhou, China
- Center of Gene/Cell Engineering and Genome Medicine, 310058, Hangzhou, Zhejiang, China
| | - Tianyu Tan
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, 1369 West Wenyi Road, 311121, Hangzhou, China
- Institute of Hematology, Zhejiang University, 310058, Hangzhou, China
- Center of Gene/Cell Engineering and Genome Medicine, 310058, Hangzhou, Zhejiang, China
| | - Hongru Pan
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, 1369 West Wenyi Road, 311121, Hangzhou, China
- Institute of Hematology, Zhejiang University, 310058, Hangzhou, China
- Center of Gene/Cell Engineering and Genome Medicine, 310058, Hangzhou, Zhejiang, China
| | - Jing Zhao
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, 1369 West Wenyi Road, 311121, Hangzhou, China
- Institute of Hematology, Zhejiang University, 310058, Hangzhou, China
- Center of Gene/Cell Engineering and Genome Medicine, 310058, Hangzhou, Zhejiang, China
| | - Ling Zhang
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, 1369 West Wenyi Road, 311121, Hangzhou, China
- Institute of Hematology, Zhejiang University, 310058, Hangzhou, China
- Center of Gene/Cell Engineering and Genome Medicine, 310058, Hangzhou, Zhejiang, China
| | - Jiayu Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Anhua Lei
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, 1369 West Wenyi Road, 311121, Hangzhou, China
- Institute of Hematology, Zhejiang University, 310058, Hangzhou, China
- Center of Gene/Cell Engineering and Genome Medicine, 310058, Hangzhou, Zhejiang, China
| | - Yuqing Zhu
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, 1369 West Wenyi Road, 311121, Hangzhou, China
- Institute of Hematology, Zhejiang University, 310058, Hangzhou, China
- Center of Gene/Cell Engineering and Genome Medicine, 310058, Hangzhou, Zhejiang, China
| | - Lang Chen
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, 1369 West Wenyi Road, 311121, Hangzhou, China
- Institute of Hematology, Zhejiang University, 310058, Hangzhou, China
- Center of Gene/Cell Engineering and Genome Medicine, 310058, Hangzhou, Zhejiang, China
| | - Yuyan Xu
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, 1369 West Wenyi Road, 311121, Hangzhou, China
- Institute of Hematology, Zhejiang University, 310058, Hangzhou, China
- Center of Gene/Cell Engineering and Genome Medicine, 310058, Hangzhou, Zhejiang, China
| | - Yaxin Liu
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China
| | - Ming Chen
- College of Life Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Jinghao Sheng
- Institute of Environmental Medicine, and Cancer Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Zhengping Xu
- Institute of Environmental Medicine, and Cancer Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Pengxu Qian
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, 1369 West Wenyi Road, 311121, Hangzhou, China
- Institute of Hematology, Zhejiang University, 310058, Hangzhou, China
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, 100871, Beijing, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - George Q Daley
- Stem Cell Transplantation Program, Division of Pediatric Hematology Oncology, Boston Children's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jin Zhang
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China.
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, 1369 West Wenyi Road, 311121, Hangzhou, China.
- Institute of Hematology, Zhejiang University, 310058, Hangzhou, China.
- Center of Gene/Cell Engineering and Genome Medicine, 310058, Hangzhou, Zhejiang, China.
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49
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Vojvoda Zeljko T, Ugarković Đ, Pezer Ž. Differential enrichment of H3K9me3 at annotated satellite DNA repeats in human cell lines and during fetal development in mouse. Epigenetics Chromatin 2021; 14:47. [PMID: 34663449 PMCID: PMC8524813 DOI: 10.1186/s13072-021-00423-6] [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: 07/14/2021] [Accepted: 10/05/2021] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Trimethylation of histone H3 on lysine 9 (H3K9me3) at satellite DNA sequences has been primarily studied at (peri)centromeric regions, where its level shows differences associated with various processes such as development and malignant transformation. However, the dynamics of H3K9me3 at distal satellite DNA repeats has not been thoroughly investigated. RESULTS We exploit the sets of publicly available data derived from chromatin immunoprecipitation combined with massively parallel DNA sequencing (ChIP-Seq), produced by the The Encyclopedia of DNA Elements (ENCODE) project, to analyze H3K9me3 at assembled satellite DNA repeats in genomes of human cell lines and during mouse fetal development. We show that annotated satellite elements are generally enriched for H3K9me3, but its level in cancer cell lines is on average lower than in normal cell lines. We find 407 satellite DNA instances with differential H3K9me3 enrichment between cancer and normal cells including a large 115-kb cluster of GSATII elements on chromosome 12. Differentially enriched regions are not limited to satellite DNA instances, but instead encompass a wider region of flanking sequences. We found no correlation between the levels of H3K9me3 and noncoding RNA at corresponding satellite DNA loci. The analysis of data derived from multiple tissues identified 864 instances of satellite DNA sequences in the mouse reference genome that are differentially enriched between fetal developmental stages. CONCLUSIONS Our study reveals significant differences in H3K9me3 level at a subset of satellite repeats between biological states and as such contributes to understanding of the role of satellite DNA repeats in epigenetic regulation during development and carcinogenesis.
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Affiliation(s)
| | | | - Željka Pezer
- Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia.
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50
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Chen R, Ishak CA, De Carvalho DD. Endogenous Retroelements and the Viral Mimicry Response in Cancer Therapy and Cellular Homeostasis. Cancer Discov 2021; 11:2707-2725. [PMID: 34649957 DOI: 10.1158/2159-8290.cd-21-0506] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/14/2021] [Accepted: 07/08/2021] [Indexed: 11/16/2022]
Abstract
Features of the cancer epigenome distinguish cancers from their respective cell of origin and establish therapeutic vulnerabilities that can be exploited through pharmacologic inhibition of DNA- or histone-modifying enzymes. Epigenetic therapies converge with cancer immunotherapies through "viral mimicry," a cellular state of active antiviral response triggered by endogenous nucleic acids often derived from aberrantly transcribed endogenous retrotransposons. This review describes the initial characterization and expansion of viral mimicry-inducing approaches as well as features that "prime" cancers for viral mimicry induction. Increased understanding of viral mimicry in therapeutic contexts suggests potential physiologic roles in cellular homeostasis. SIGNIFICANCE: Recent literature establishes elevated cytosolic double strand RNA (dsRNA) levels as a cancer-specific therapeutic vulnerability that can be elevated by viral mimicry-inducing therapies beyond tolerable thresholds to induce antiviral signaling and increase dependence on dsRNA stress responses mediated by ADAR1. Improved understanding of viral mimicry signaling and tolerance mechanisms reveals synergistic treatment combinations with epigenetic therapies that include inhibition of BCL2, ADAR1, and immune checkpoint blockade. Further characterization of viral mimicry tolerance may identify contexts that maximize efficacy of conventional cancer therapies.
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Affiliation(s)
- Raymond Chen
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Charles A Ishak
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Daniel D De Carvalho
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. .,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
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