1
|
Fabyanic EB, Hu P, Qiu Q, Berríos KN, Connolly DR, Wang T, Flournoy J, Zhou Z, Kohli RM, Wu H. Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects. Nat Biotechnol 2024; 42:960-974. [PMID: 37640946 DOI: 10.1038/s41587-023-01909-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/19/2023] [Indexed: 08/31/2023]
Abstract
Oxidative modification of 5-methylcytosine (5mC) by ten-eleven translocation (TET) DNA dioxygenases generates 5-hydroxymethylcytosine (5hmC), the most abundant form of oxidized 5mC. Existing single-cell bisulfite sequencing methods cannot resolve 5mC and 5hmC, leaving the cell-type-specific regulatory mechanisms of TET and 5hmC largely unknown. Here, we present joint single-nucleus (hydroxy)methylcytosine sequencing (Joint-snhmC-seq), a scalable and quantitative approach that simultaneously profiles 5hmC and true 5mC in single cells by harnessing differential deaminase activity of APOBEC3A toward 5mC and chemically protected 5hmC. Joint-snhmC-seq profiling of single nuclei from mouse brains reveals an unprecedented level of epigenetic heterogeneity of both 5hmC and true 5mC at single-cell resolution. We show that cell-type-specific profiles of 5hmC or true 5mC improve multimodal single-cell data integration, enable accurate identification of neuronal subtypes and uncover context-specific regulatory effects on cell-type-specific genes by TET enzymes.
Collapse
Affiliation(s)
- Emily B Fabyanic
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Peng Hu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Qi Qiu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Kiara N Berríos
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel R Connolly
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Tong Wang
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer Flournoy
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhaolan Zhou
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Rahul M Kohli
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
2
|
Moon S, Lee HH, Archer-Hartmann S, Nagai N, Mubasher Z, Parappurath M, Ahmed L, Ramos RL, Kimata K, Azadi P, Cai W, Zhao JY. Knockout of the intellectual disability-linked gene Hs6st2 in mice decreases heparan sulfate 6-O-sulfation, impairs dendritic spines of hippocampal neurons, and affects memory. Glycobiology 2024; 34:cwad095. [PMID: 38015989 PMCID: PMC10969535 DOI: 10.1093/glycob/cwad095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023] Open
Abstract
Heparan sulfate (HS) is a linear polysaccharide that plays a key role in cellular signaling networks. HS functions are regulated by its 6-O-sulfation, which is catalyzed by three HS 6-O-sulfotransferases (HS6STs). Notably, HS6ST2 is mainly expressed in the brain and HS6ST2 mutations are linked to brain disorders, but the underlying mechanisms remain poorly understood. To determine the role of Hs6st2 in the brain, we carried out a series of molecular and behavioral assessments on Hs6st2 knockout mice. We first carried out strong anion exchange-high performance liquid chromatography and found that knockout of Hs6st2 moderately decreases HS 6-O-sulfation levels in the brain. We then assessed body weights and found that Hs6st2 knockout mice exhibit increased body weight, which is associated with abnormal metabolic pathways. We also performed behavioral tests and found that Hs6st2 knockout mice showed memory deficits, which recapitulate patient clinical symptoms. To determine the molecular mechanisms underlying the memory deficits, we used RNA sequencing to examine transcriptomes in two memory-related brain regions, the hippocampus and cerebral cortex. We found that knockout of Hs6st2 impairs transcriptome in the hippocampus, but only mildly in the cerebral cortex. Furthermore, the transcriptome changes in the hippocampus are enriched in dendrite and synapse pathways. We also found that knockout of Hs6st2 decreases HS levels and impairs dendritic spines in hippocampal CA1 pyramidal neurons. Taken together, our study provides novel molecular and behavioral insights into the role of Hs6st2 in the brain, which facilitates a better understanding of HS6ST2 and HS-linked brain disorders.
Collapse
Affiliation(s)
- Sohyun Moon
- Department of Biomedical Sciences, New York Institute of Technology College of Osteopathic Medicine, Northern Boulevard, P.O. Box 8000, Old Westbury, New York 11568, United States
| | - Hiu Ham Lee
- Department of Biomedical Sciences, New York Institute of Technology College of Osteopathic Medicine, Northern Boulevard, P.O. Box 8000, Old Westbury, New York 11568, United States
| | - Stephanie Archer-Hartmann
- Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30602, United States
| | - Naoko Nagai
- Institute for Molecular Science of Medicine, Aichi Medical University, 1-1 Yazakokarimata, Nagakute, Aichi 480-1195, Japan
| | - Zainab Mubasher
- Department of Biomedical Sciences, New York Institute of Technology College of Osteopathic Medicine, Northern Boulevard, P.O. Box 8000, Old Westbury, New York 11568, United States
| | - Mahima Parappurath
- Department of Biomedical Sciences, New York Institute of Technology College of Osteopathic Medicine, Northern Boulevard, P.O. Box 8000, Old Westbury, New York 11568, United States
| | - Laiba Ahmed
- Department of Biomedical Sciences, New York Institute of Technology College of Osteopathic Medicine, Northern Boulevard, P.O. Box 8000, Old Westbury, New York 11568, United States
| | - Raddy L Ramos
- Department of Biomedical Sciences, New York Institute of Technology College of Osteopathic Medicine, Northern Boulevard, P.O. Box 8000, Old Westbury, New York 11568, United States
| | - Koji Kimata
- Multidisciplinary Pain Center, Aichi Medical University, 1-1 Yazakokarimata, Nagakute, Aichi 480-1195, Japan
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30602, United States
| | - Weikang Cai
- Department of Biomedical Sciences, New York Institute of Technology College of Osteopathic Medicine, Northern Boulevard, P.O. Box 8000, Old Westbury, New York 11568, United States
| | - Jerry Yingtao Zhao
- Department of Biomedical Sciences, New York Institute of Technology College of Osteopathic Medicine, Northern Boulevard, P.O. Box 8000, Old Westbury, New York 11568, United States
| |
Collapse
|
3
|
Takei Y, Yang Y, White J, Yun J, Prasad M, Ombelets LJ, Schindler S, Cai L. High-resolution spatial multi-omics reveals cell-type specific nuclear compartments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.07.539762. [PMID: 37214923 PMCID: PMC10197539 DOI: 10.1101/2023.05.07.539762] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The mammalian nucleus is compartmentalized by diverse subnuclear structures. These subnuclear structures, marked by nuclear bodies and histone modifications, are often cell-type specific and affect gene regulation and 3D genome organization1-3. Understanding nuclear organization requires identifying the molecular constituents of subnuclear structures and mapping their associations with specific genomic loci in individual cells, within complex tissues. Here, we introduce two-layer DNA seqFISH+, which allows simultaneous mapping of 100,049 genomic loci, together with nascent transcriptome for 17,856 genes and a diverse set of immunofluorescently labeled subnuclear structures all in single cells in cell lines and adult mouse cerebellum. Using these multi-omics datasets, we showed that repressive chromatin compartments are more variable by cell type than active compartments. We also discovered a single exception to this rule: an RNA polymerase II (RNAPII)-enriched compartment was associated with long, cell-type specific genes (> 200kb), in a manner distinct from nuclear speckles. Further, our analysis revealed that cell-type specific facultative and constitutive heterochromatin compartments marked by H3K27me3 and H4K20me3 are enriched at specific genes and gene clusters, respectively, and shape radial chromosomal positioning and inter-chromosomal interactions in neurons and glial cells. Together, our results provide a single-cell high-resolution multi-omics view of subnuclear compartments, associated genomic loci, and their impacts on gene regulation, directly within complex tissues.
Collapse
Affiliation(s)
- Yodai Takei
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yujing Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jonathan White
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jina Yun
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Meera Prasad
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | | | - Long Cai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| |
Collapse
|
4
|
Dominguez-Alonso S, Carracedo A, Rodriguez-Fontenla C. The non-coding genome in Autism Spectrum Disorders. Eur J Med Genet 2023; 66:104752. [PMID: 37023975 DOI: 10.1016/j.ejmg.2023.104752] [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: 10/24/2022] [Revised: 03/10/2023] [Accepted: 03/19/2023] [Indexed: 04/08/2023]
Abstract
Autism Spectrum Disorders (ASD) are a group of neurodevelopmental disorders (NDDs) characterized by difficulties in social interaction and communication, repetitive behavior, and restricted interests. While ASD have been proven to have a strong genetic component, current research largely focuses on coding regions of the genome. However, non-coding DNA, which makes up for ∼99% of the human genome, has recently been recognized as an important contributor to the high heritability of ASD, and novel sequencing technologies have been a milestone in opening up new directions for the study of the gene regulatory networks embedded within the non-coding regions. Here, we summarize current progress on the contribution of non-coding alterations to the pathogenesis of ASD and provide an overview of existing methods allowing for the study of their functional relevance, discussing potential ways of unraveling ASD's "missing heritability".
Collapse
Affiliation(s)
- S Dominguez-Alonso
- Grupo de Medicina Xenómica, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - A Carracedo
- Grupo de Medicina Xenómica, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain; Grupo de Medicina Xenómica, Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - C Rodriguez-Fontenla
- Grupo de Medicina Xenómica, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain.
| |
Collapse
|
5
|
Nussinov R, Yavuz BR, Arici MK, Demirel HC, Zhang M, Liu Y, Tsai CJ, Jang H, Tuncbag N. Neurodevelopmental disorders, like cancer, are connected to impaired chromatin remodelers, PI3K/mTOR, and PAK1-regulated MAPK. Biophys Rev 2023; 15:163-181. [PMID: 37124926 PMCID: PMC10133437 DOI: 10.1007/s12551-023-01054-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 03/21/2023] [Indexed: 04/05/2023] Open
Abstract
Neurodevelopmental disorders (NDDs) and cancer share proteins, pathways, and mutations. Their clinical symptoms are different. However, individuals with NDDs have higher probabilities of eventually developing cancer. Here, we review the literature and ask how the shared features can lead to different medical conditions and why having an NDD first can increase the chances of malignancy. To explore these vital questions, we focus on dysregulated PI3K/mTOR, a major brain cell growth pathway in differentiation, and MAPK, a critical pathway in proliferation, a hallmark of cancer. Differentiation is governed by chromatin organization, making aberrant chromatin remodelers highly likely agents in NDDs. Dysregulated chromatin organization and accessibility influence the lineage of specific cell brain types at specific embryonic development stages. PAK1, with pivotal roles in brain development and in cancer, also regulates MAPK. We review, clarify, and connect dysregulated pathways with dysregulated proliferation and differentiation in cancer and NDDs and highlight PAK1 role in brain development and MAPK regulation. Exactly how PAK1 activation controls brain development, and why specific chromatin remodeler components, e.g., BAF170 encoded by SMARCC2 in autism, await clarification.
Collapse
Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702 USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Bengi Ruken Yavuz
- Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - M Kaan Arici
- Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Habibe Cansu Demirel
- Department of Chemical and Biological Engineering, College of Engineering, Koc University, 34450 Istanbul, Turkey
| | - Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702 USA
| | - Yonglan Liu
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702 USA
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702 USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702 USA
| | - Nurcan Tuncbag
- Department of Chemical and Biological Engineering, College of Engineering, Koc University, 34450 Istanbul, Turkey
- School of Medicine, Koc University, 34450 Istanbul, Turkey
| |
Collapse
|
6
|
Xu B, Ho Y, Fasolino M, Medina J, O’Brien WT, Lamonica JM, Nugent E, Brodkin ES, Fuccillo MV, Bucan M, Zhou Z. Allelic contribution of Nrxn1α to autism-relevant behavioral phenotypes in mice. PLoS Genet 2023; 19:e1010659. [PMID: 36848371 PMCID: PMC9997995 DOI: 10.1371/journal.pgen.1010659] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/09/2023] [Accepted: 02/08/2023] [Indexed: 03/01/2023] Open
Abstract
Copy number variations (CNVs) in the Neurexin 1 (NRXN1) gene, which encodes a presynaptic protein involved in neurotransmitter release, are some of the most frequently observed single-gene variants associated with autism spectrum disorder (ASD). To address the functional contribution of NRXN1 CNVs to behavioral phenotypes relevant to ASD, we carried out systematic behavioral phenotyping of an allelic series of Nrxn1 mouse models: one carrying promoter and exon 1 deletion abolishing Nrxn1α transcription, one carrying exon 9 deletion disrupting Nrxn1α protein translation, and one carrying an intronic deletion with no observable effect on Nrxn1α expression. We found that homozygous loss of Nrxn1α resulted in enhanced aggression in males, reduced affiliative social behaviors in females, and significantly altered circadian activities in both sexes. Heterozygous or homozygous loss of Nrxn1α affected the preference for social novelty in male mice, and notably, enhanced repetitive motor skills and motor coordination in both sexes. In contrast, mice bearing an intronic deletion of Nrxn1 did not display alterations in any of the behaviors assessed. These findings demonstrate the importance of Nrxn1α gene dosage in regulating social, circadian, and motor functions, and the variables of sex and genomic positioning of CNVs in the expression of autism-related phenotypes. Importantly, mice with heterozygous loss of Nrxn1, as found in numerous autistic individuals, show an elevated propensity to manifest autism-related phenotypes, supporting the use of models with this genomic architecture to study ASD etiology and assess additional genetic variants associated with autism.
Collapse
Affiliation(s)
- Bing Xu
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Autism Spectrum Program of Excellence (ASPE), University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Urology, The First Affiliated Hospital of Shandong First Medical University & Shandong Province Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Organ Transplantation and Nephrosis, Shandong Institute of Nephrology, Jinan, Shandong, China
| | - Yugong Ho
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Autism Spectrum Program of Excellence (ASPE), University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Maria Fasolino
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Autism Spectrum Program of Excellence (ASPE), University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Joanna Medina
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Autism Spectrum Program of Excellence (ASPE), University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - William Timothy O’Brien
- Preclinical Models Core, Intellectual and Developmental Disability Research Center (IDDRC) Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Janine M. Lamonica
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Autism Spectrum Program of Excellence (ASPE), University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Erin Nugent
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Autism Spectrum Program of Excellence (ASPE), University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Edward S. Brodkin
- Autism Spectrum Program of Excellence (ASPE), University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Marc V. Fuccillo
- Autism Spectrum Program of Excellence (ASPE), University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Maja Bucan
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Autism Spectrum Program of Excellence (ASPE), University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Zhaolan Zhou
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Autism Spectrum Program of Excellence (ASPE), University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Preclinical Models Core, Intellectual and Developmental Disability Research Center (IDDRC) Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| |
Collapse
|
7
|
Davis O. Abnormal Chromatin Folding in the Molecular Pathogenesis of Epilepsy and Autism Spectrum Disorder: a Meta-synthesis with Systematic Searching. Mol Neurobiol 2023; 60:768-779. [PMID: 36367658 PMCID: PMC9849311 DOI: 10.1007/s12035-022-03106-9] [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: 07/25/2022] [Accepted: 10/25/2022] [Indexed: 11/13/2022]
Abstract
How DNA is folded and packaged in nucleosomes is an essential regulator of gene expression. Abnormal patterns of chromatin folding are implicated in a wide range of diseases and disorders, including epilepsy and autism spectrum disorder (ASD). These disorders are thought to have a shared pathogenesis involving an imbalance in the number of excitatory-inhibitory neurons formed during neurodevelopment; however, the underlying pathological mechanism behind this imbalance is poorly understood. Studies are increasingly implicating abnormal chromatin folding in neural stem cells as one of the candidate pathological mechanisms, but no review has yet attempted to summarise the knowledge in this field. This meta-synthesis is a systematic search of all the articles on epilepsy, ASD, and chromatin folding. Its two main objectives were to determine to what extent abnormal chromatin folding is implicated in the pathogenesis of epilepsy and ASD, and secondly how abnormal chromatin folding leads to pathological disease processes. This search produced 22 relevant articles, which together strongly implicate abnormal chromatin folding in the pathogenesis of epilepsy and ASD. A range of mutations and chromosomal structural abnormalities lead to this effect, including single nucleotide polymorphisms, copy number variants, translocations and mutations in chromatin modifying. However, knowledge is much more limited into how abnormal chromatin organisation subsequently causes pathological disease processes, not yet showing, for example, whether it leads to abnormal excitation-inhibitory neuron imbalance in human brain organoids.
Collapse
Affiliation(s)
- Oliver Davis
- grid.5335.00000000121885934Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
| |
Collapse
|
8
|
Thudium S, Palozola K, L'Her É, Korb E. Identification of a transcriptional signature found in multiple models of ASD and related disorders. Genome Res 2022; 32:1642-1654. [PMID: 36104286 PMCID: PMC9528985 DOI: 10.1101/gr.276591.122] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 07/22/2022] [Indexed: 11/25/2022]
Abstract
Epigenetic regulation plays a critical role in many neurodevelopmental disorders (NDDs), including autism spectrum disorder (ASD). In particular, many such disorders are the result of mutations in genes that encode chromatin-modifying proteins. However, although these disorders share many features, it is unclear whether they also share gene expression disruptions resulting from the aberrant regulation of chromatin. We examined five chromatin modifiers that are all linked to ASD despite their different roles in regulating chromatin. Specifically, we depleted ASH1L, CHD8, CREBBP, EHMT1, and NSD1 in parallel in a highly controlled neuronal culture system. We then identified sets of shared genes, or transcriptional signatures, that are differentially expressed following loss of multiple ASD-linked chromatin modifiers. We examined the functions of genes within the transcriptional signatures and found an enrichment in many neurotransmitter transport genes and activity-dependent genes. In addition, these genes are enriched for specific chromatin features such as bivalent domains that allow for highly dynamic regulation of gene expression. The down-regulated transcriptional signature is also observed within multiple mouse models of NDDs that result in ASD, but not those only associated with intellectual disability. Finally, the down-regulated transcriptional signature can distinguish between control and idiopathic ASD patient iPSC-derived neurons as well as postmortem tissue, demonstrating that this gene set is relevant to the human disorder. This work identifies a transcriptional signature that is found within many neurodevelopmental syndromes, helping to elucidate the link between epigenetic regulation and the underlying cellular mechanisms that result in ASD.
Collapse
Affiliation(s)
- Samuel Thudium
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Epigenetics Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Katherine Palozola
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Epigenetics Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Éloïse L'Her
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Epigenetics Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Erica Korb
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Epigenetics Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| |
Collapse
|
9
|
Moon S, Zhao YT. Convergent biological pathways underlying the Kallmann syndrome-linked genes Hs6st1 and Fgfr1. Hum Mol Genet 2022; 31:4207-4216. [PMID: 35899427 PMCID: PMC9759331 DOI: 10.1093/hmg/ddac172] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/05/2022] [Accepted: 07/24/2022] [Indexed: 01/21/2023] Open
Abstract
Kallmann syndrome (KS) is a congenital disorder characterized by idiopathic hypogonadotropic hypogonadism and olfactory dysfunction. KS is linked to variants in >34 genes, which are scattered across the human genome and show disparate biological functions. Although the genetic basis of KS is well studied, the mechanisms by which disruptions of these diverse genes cause the same outcome of KS are not fully understood. Here we show that disruptions of KS-linked genes affect the same biological processes, indicating convergent molecular mechanisms underlying KS. We carried out machine learning-based predictions and found that KS-linked mutations in heparan sulfate 6-O-sulfotransferase 1 (HS6ST1) are likely loss-of-function mutations. We next disrupted Hs6st1 and another KS-linked gene, fibroblast growth factor receptor 1 (Fgfr1), in mouse neuronal cells and measured transcriptome changes using RNA sequencing. We found that disruptions of Hs6st1 and Fgfr1 altered genes in the same biological processes, including the upregulation of genes in extracellular pathways and the downregulation of genes in chromatin pathways. Moreover, we performed genomics and bioinformatics analyses and found that Hs6st1 and Fgfr1 regulate gene transcription likely via the transcription factor Sox9/Sox10 and the chromatin regulator Chd7, which are also associated with KS. Together, our results demonstrate how different KS-linked genes work coordinately in a convergent signaling pathway to regulate the same biological processes, thus providing new insights into KS.
Collapse
Affiliation(s)
- Sohyun Moon
- Department of Biomedical Sciences, New York Institute of Technology College of Osteopathic Medicine, Old Westbury, NY 11568, USA
| | - Ying-Tao Zhao
- To whom correspondence should be addressed: Tel: 516-686-3764; Fax: 516-686-3832;
| |
Collapse
|
10
|
Flanagan K, Baradaran-Heravi A, Yin Q, Dao Duc K, Spradling AC, Greenblatt EJ. FMRP-dependent production of large dosage-sensitive proteins is highly conserved. Genetics 2022; 221:6613139. [PMID: 35731217 PMCID: PMC9339308 DOI: 10.1093/genetics/iyac094] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/07/2022] [Indexed: 12/01/2022] Open
Abstract
Mutations in FMR1 are the most common heritable cause of autism spectrum disorder. FMR1 encodes an RNA-binding protein, FMRP, which binds to long, autism-relevant transcripts and is essential for normal neuronal and ovarian development. In contrast to the prevailing model that FMRP acts to block translation elongation, we previously found that FMRP activates the translation initiation of large proteins in Drosophila oocytes. We now provide evidence that FMRP-dependent translation is conserved and occurs in the mammalian brain. Our comparisons of the mammalian cortex and Drosophila oocyte ribosome profiling data show that translation of FMRP-bound mRNAs decreases to a similar magnitude in FMRP-deficient tissues from both species. The steady-state levels of several FMRP targets were reduced in the Fmr1 KO mouse cortex, including a ∼50% reduction of Auts2, a gene implicated in an autosomal dominant autism spectrum disorder. To distinguish between effects on elongation and initiation, we used a novel metric to detect the rate-limiting ribosome stalling. We found no evidence that FMRP target protein production is governed by translation elongation rates. FMRP translational activation of large proteins may be critical for normal human development, as more than 20 FMRP targets including Auts2 are dosage sensitive and are associated with neurodevelopmental disorders caused by haploinsufficiency.
Collapse
Affiliation(s)
- Keegan Flanagan
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, V6T 1Z3 Canada.,Department of Mathematics, University of British Columbia, 1984 Mathematics Road, Vancouver, British Columbia, BC V6T 1Z2
| | - Alireza Baradaran-Heravi
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, V6T 1Z3 Canada
| | - Qi Yin
- Howard Hughes Medical Institute Research Laboratories, Department of Embryology, Carnegie Institution for Science, 3520 San Martin Dr., Baltimore, Maryland 21218 USA
| | - Khanh Dao Duc
- Department of Mathematics, University of British Columbia, 1984 Mathematics Road, Vancouver, British Columbia, BC V6T 1Z2
| | - Allan C Spradling
- Howard Hughes Medical Institute Research Laboratories, Department of Embryology, Carnegie Institution for Science, 3520 San Martin Dr., Baltimore, Maryland 21218 USA
| | - Ethan J Greenblatt
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, V6T 1Z3 Canada.,Howard Hughes Medical Institute Research Laboratories, Department of Embryology, Carnegie Institution for Science, 3520 San Martin Dr., Baltimore, Maryland 21218 USA
| |
Collapse
|
11
|
Moon S, Zhao YT. Recursive splicing is a rare event in the mouse brain. PLoS One 2022; 17:e0263082. [PMID: 35089962 PMCID: PMC8797253 DOI: 10.1371/journal.pone.0263082] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/11/2022] [Indexed: 11/18/2022] Open
Abstract
Recursive splicing (RS) is a splicing mechanism to remove long introns from messenger RNA precursors of long genes. Compared to the hundreds of RS events identified in humans and drosophila, only ten RS events have been reported in mice. To further investigate RS in mice, we analyzed RS in the mouse brain, a tissue that is enriched in the expression of long genes. We found that nuclear total RNA sequencing is an efficient approach to investigate RS events. We analyzed 1.15 billion uniquely mapped reads from the nuclear total RNA sequencing data in the mouse cerebral cortex. Unexpectedly, we only identified 20 RS sites, suggesting that RS is a rare event in the mouse brain. We also identified that RS is constitutive between excitatory and inhibitory neurons and between sexes in the mouse cerebral cortex. In addition, we found that the primary sequence context is associated with RS splicing intermediates and distinguishes RS AGGT site from non-RS AGGT sites, indicating the importance of the primary sequence context in RS sites. Moreover, we discovered that cryptic exons may use an RS-like mechanism for splicing. Overall, we provide novel findings about RS in long genes in the mouse brain.
Collapse
Affiliation(s)
- Sohyun Moon
- Department of Biomedical Sciences, New York Institute of Technology College of Osteopathic Medicine, Old Westbury, New York, United States of America
| | - Ying-Tao Zhao
- Department of Biomedical Sciences, New York Institute of Technology College of Osteopathic Medicine, Old Westbury, New York, United States of America
- * E-mail:
| |
Collapse
|
12
|
Neuronal Yin Yang1 in the prefrontal cortex regulates transcriptional and behavioral responses to chronic stress in mice. Nat Commun 2022; 13:55. [PMID: 35013139 PMCID: PMC8748737 DOI: 10.1038/s41467-021-27571-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/30/2021] [Indexed: 12/28/2022] Open
Abstract
Although the synaptic alterations associated with the stress-related mood disorder major depression has been well-documented, the underlying transcriptional mechanisms remain poorly understood. Here, we perform complementary bulk nuclei- and single-nucleus transcriptome profiling and map locus-specific chromatin interactions in mouse neocortex to identify the cell type-specific transcriptional changes associated with stress-induced behavioral maladaptation. We find that cortical excitatory neurons, layer 2/3 neurons in particular, are vulnerable to chronic stress and acquire signatures of gene transcription and chromatin structure associated with reduced neuronal activity and expression of Yin Yang 1 (YY1). Selective ablation of YY1 in cortical excitatory neurons enhances stress sensitivity in both male and female mice and alters the expression of stress-associated genes following an abbreviated stress exposure. These findings demonstrate how chronic stress impacts transcription in cortical excitatory neurons and identify YY1 as a regulator of stress-induced maladaptive behavior in mice. The mechanisms underlying the chronic stress-induced increased risk for major depressive disorder and anxiety are unclear. Here, the authors show the transcriptional changes occurring in neocortical neurons and identify YY1 as a regulator of chronic stress-induced maladaptive behavior in mice.
Collapse
|
13
|
Winick-Ng W, Kukalev A, Harabula I, Zea-Redondo L, Szabó D, Meijer M, Serebreni L, Zhang Y, Bianco S, Chiariello AM, Irastorza-Azcarate I, Thieme CJ, Sparks TM, Carvalho S, Fiorillo L, Musella F, Irani E, Torlai Triglia E, Kolodziejczyk AA, Abentung A, Apostolova G, Paul EJ, Franke V, Kempfer R, Akalin A, Teichmann SA, Dechant G, Ungless MA, Nicodemi M, Welch L, Castelo-Branco G, Pombo A. Cell-type specialization is encoded by specific chromatin topologies. Nature 2021; 599:684-691. [PMID: 34789882 PMCID: PMC8612935 DOI: 10.1038/s41586-021-04081-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/30/2021] [Indexed: 11/09/2022]
Abstract
The three-dimensional (3D) structure of chromatin is intrinsically associated with gene regulation and cell function1-3. Methods based on chromatin conformation capture have mapped chromatin structures in neuronal systems such as in vitro differentiated neurons, neurons isolated through fluorescence-activated cell sorting from cortical tissues pooled from different animals and from dissociated whole hippocampi4-6. However, changes in chromatin organization captured by imaging, such as the relocation of Bdnf away from the nuclear periphery after activation7, are invisible with such approaches8. Here we developed immunoGAM, an extension of genome architecture mapping (GAM)2,9, to map 3D chromatin topology genome-wide in specific brain cell types, without tissue disruption, from single animals. GAM is a ligation-free technology that maps genome topology by sequencing the DNA content from thin (about 220 nm) nuclear cryosections. Chromatin interactions are identified from the increased probability of co-segregation of contacting loci across a collection of nuclear slices. ImmunoGAM expands the scope of GAM to enable the selection of specific cell types using low cell numbers (approximately 1,000 cells) within a complex tissue and avoids tissue dissociation2,10. We report cell-type specialized 3D chromatin structures at multiple genomic scales that relate to patterns of gene expression. We discover extensive 'melting' of long genes when they are highly expressed and/or have high chromatin accessibility. The contacts most specific of neuron subtypes contain genes associated with specialized processes, such as addiction and synaptic plasticity, which harbour putative binding sites for neuronal transcription factors within accessible chromatin regions. Moreover, sensory receptor genes are preferentially found in heterochromatic compartments in brain cells, which establish strong contacts across tens of megabases. Our results demonstrate that highly specific chromatin conformations in brain cells are tightly related to gene regulation mechanisms and specialized functions.
Collapse
Affiliation(s)
- Warren Winick-Ng
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany.
| | - Alexander Kukalev
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
| | - Izabela Harabula
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Luna Zea-Redondo
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dominik Szabó
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Mandy Meijer
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Leonid Serebreni
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Yingnan Zhang
- School of Electrical Engineering and Computer Science, Ohio University, Athens, OH, USA
| | - Simona Bianco
- Dipartimentio di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Andrea M Chiariello
- Dipartimentio di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Ibai Irastorza-Azcarate
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
| | - Christoph J Thieme
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
| | - Thomas M Sparks
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
| | - Sílvia Carvalho
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
- Graduate Program in Areas of Basic and Applied Biology, Universidade do Porto, Porto, Portugal
| | - Luca Fiorillo
- Dipartimentio di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Francesco Musella
- Dipartimentio di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Ehsan Irani
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Elena Torlai Triglia
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aleksandra A Kolodziejczyk
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Andreas Abentung
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck, Austria
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Galina Apostolova
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck, Austria
| | - Eleanor J Paul
- Institute of Clinical Sciences, Imperial College London, London, UK
- Center for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MRC Center for Neurodevelopmental Disorders, King's College London, London, UK
| | - Vedran Franke
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Bioinformatics and Omics Data Science Platform, Berlin, Germany
| | - Rieke Kempfer
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Altuna Akalin
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Bioinformatics and Omics Data Science Platform, Berlin, Germany
| | - Sarah A Teichmann
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Georg Dechant
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck, Austria
| | - Mark A Ungless
- Institute of Clinical Sciences, Imperial College London, London, UK
| | - Mario Nicodemi
- Dipartimentio di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
- Berlin Institute of Health, Berlin, Germany
| | - Lonnie Welch
- School of Electrical Engineering and Computer Science, Ohio University, Athens, OH, USA
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Ana Pombo
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany.
- Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
- Berlin Institute of Health, Berlin, Germany.
| |
Collapse
|
14
|
Liu N, Low WY, Alinejad-Rokny H, Pederson S, Sadlon T, Barry S, Breen J. Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C. Epigenetics Chromatin 2021; 14:41. [PMID: 34454581 PMCID: PMC8399707 DOI: 10.1186/s13072-021-00417-4] [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: 04/29/2021] [Accepted: 08/19/2021] [Indexed: 11/30/2022] Open
Abstract
Eukaryotic genomes are highly organised within the nucleus of a cell, allowing widely dispersed regulatory elements such as enhancers to interact with gene promoters through physical contacts in three-dimensional space. Recent chromosome conformation capture methodologies such as Hi-C have enabled the analysis of interacting regions of the genome providing a valuable insight into the three-dimensional organisation of the chromatin in the nucleus, including chromosome compartmentalisation and gene expression. Complicating the analysis of Hi-C data, however, is the massive amount of identified interactions, many of which do not directly drive gene function, thus hindering the identification of potentially biologically functional 3D interactions. In this review, we collate and examine the downstream analysis of Hi-C data with particular focus on methods that prioritise potentially functional interactions. We classify three groups of approaches: structural-based discovery methods, e.g. A/B compartments and topologically associated domains, detection of statistically significant chromatin interactions, and the use of epigenomic data integration to narrow down useful interaction information. Careful use of these three approaches is crucial to successfully identifying potentially functional interactions within the genome.
Collapse
Affiliation(s)
- Ning Liu
- Computational & Systems Biology, Precision Medicine Theme, South Australian Health & Medical Research Institute, SA, 5000, Adelaide, Australia
- Robinson Research Institute, University of Adelaide, SA, 5005, Adelaide, Australia
- Adelaide Medical School, University of Adelaide, SA, 5005, Adelaide, Australia
| | - Wai Yee Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
| | - Hamid Alinejad-Rokny
- BioMedical Machine Learning Lab, The Graduate School of Biomedical Engineering, The University of New South Wales, NSW, 2052, Sydney, Australia
- Core Member of UNSW Data Science Hub, The University of New South Wales, 2052, Sydney, Australia
| | - Stephen Pederson
- Adelaide Medical School, University of Adelaide, SA, 5005, Adelaide, Australia
- Dame Roma Mitchell Cancer Research Laboratories (DRMCRL), Adelaide Medical School, University of Adelaide, SA, 5005, Adelaide, Australia
| | - Timothy Sadlon
- Robinson Research Institute, University of Adelaide, SA, 5005, Adelaide, Australia
- Women's & Children's Health Network, SA, 5006, North Adelaide, Australia
| | - Simon Barry
- Robinson Research Institute, University of Adelaide, SA, 5005, Adelaide, Australia
- Core Member of UNSW Data Science Hub, The University of New South Wales, 2052, Sydney, Australia
- Women's & Children's Health Network, SA, 5006, North Adelaide, Australia
| | - James Breen
- Computational & Systems Biology, Precision Medicine Theme, South Australian Health & Medical Research Institute, SA, 5000, Adelaide, Australia.
- Robinson Research Institute, University of Adelaide, SA, 5005, Adelaide, Australia.
- Adelaide Medical School, University of Adelaide, SA, 5005, Adelaide, Australia.
- South Australian Genomics Centre (SAGC), South Australian Health & Medical Research Institute (SAHMRI), SA, 5000, Adelaide, Australia.
| |
Collapse
|
15
|
Moon S, Zhao YT. Spatial, temporal, and cell-type-specific expression profiles of genes encoding heparan sulfate biosynthesis enzymes and proteoglycan core proteins. Glycobiology 2021; 31:1308-1318. [PMID: 34132783 DOI: 10.1093/glycob/cwab054] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/28/2021] [Accepted: 06/09/2021] [Indexed: 12/22/2022] Open
Abstract
Heparan sulfate (HS) is a linear polysaccharide found in almost all animal cells and plays an important role in various biological processes. HS functions mainly via covalently binding to core proteins to form HS proteoglycans (HSPGs), which are heterogeneous in the lengths of the HS chain, the modifications on HS, and the core proteins. The molecular mechanisms underlying HSPG heterogeneity, although widely studied, are not yet fully defined. The expression profiles of HS biosynthesis enzymes and HSPG core proteins likely contribute to the HSPG heterogeneity, but these expression profiles remain poorly characterized. To investigate the expression profiles of genes encoding HS biosynthesis enzymes and HSPG core proteins, we systematically integrated the publicly available RNA sequencing data in mice. To reveal the spatial expression of these genes, we analyzed their expression in 21 mouse tissues. To reveal the temporal expression of these genes, we analyzed their expression at 17 time points during the mouse forebrain development. To determine the cell-type-specific expression of these genes, we obtained their expression profiles in 23 cell types in the mouse cerebral cortex by integrating single nucleus RNA sequencing data. Our findings demonstrate the spatial, temporal, and cell-type-specific expression of genes encoding HS biosynthesis enzymes and HSPG core proteins and represent a valuable resource to the HS research community.
Collapse
Affiliation(s)
- Sohyun Moon
- Department of Biomedical Sciences, New York Institute of Technology College of Osteopathic Medicine, Old Westbury, NY, 11568, USA
| | - Ying-Tao Zhao
- Department of Biomedical Sciences, New York Institute of Technology College of Osteopathic Medicine, Old Westbury, NY, 11568, USA
| |
Collapse
|
16
|
Tsang B, Pritišanac I, Scherer SW, Moses AM, Forman-Kay JD. Phase Separation as a Missing Mechanism for Interpretation of Disease Mutations. Cell 2020; 183:1742-1756. [DOI: 10.1016/j.cell.2020.11.050] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/04/2020] [Accepted: 11/25/2020] [Indexed: 02/08/2023]
|
17
|
Lobzhanidze G, Japaridze N, Lordkipanidze T, Rzayev F, MacFabe D, Zhvania M. Behavioural and brain ultrastructural changes following the systemic administration of propionic acid in adolescent male rats. Further development of a rodent model of autism. Int J Dev Neurosci 2020; 80:139-156. [PMID: 31997401 DOI: 10.1002/jdn.10011] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/08/2020] [Accepted: 01/19/2020] [Indexed: 12/18/2022] Open
Abstract
Short chain fatty acids, produced as gut microbiome metabolites but also present in the diet, exert broad effects in host physiology. Propionic acid (PPA), along with butyrate and acetate, plays a growing role in health, but also in neurological conditions. Increased PPA exposure in humans, animal models and cell lines elicit diverse behavioural and biochemical changes consistent with organic acidurias, mitochondrial disorders and autism spectrum disorders (ASD). ASD is considered a disorder of synaptic dysfunction and cell signalling, but also neuroinflammatory and neurometabolic components. We examined behaviour (Morris water and radial arm mazes) and the ultrastructure of the hippocampus and medial prefrontal cortex (electron microscopy) following a single intraperitoneal (i.p.) injection of PPA (175 mg/kg) in male adolescent rats. PPA treatment showed altered social and locomotor behaviour without changes in learning and memory. Both transient and enduring ultrastructural alterations in synapses, astro- and microglia were detected in the CA1 hippocampal area. Electron microscopic analysis showed the PPA treatment significantly decreased the total number of synaptic vesicles, presynaptic mitochondria and synapses with a symmetric active zone. Thus, brief systemic administration of this dietary and enteric short chain fatty acid produced behavioural and dynamic brain ultrastructural changes, providing further validation of the PPA model of ASD.
Collapse
Affiliation(s)
- Giorgi Lobzhanidze
- School of Natural Sciences and Medicine, Ilia State University, Tbilisi, Georgia.,Department of Brain Ultrastructure and Nanoarchitecture, I. Beritashvili Center of Experimental Biomedicine, Tbilisi, Georgia
| | - Nadezhda Japaridze
- Department of Brain Ultrastructure and Nanoarchitecture, I. Beritashvili Center of Experimental Biomedicine, Tbilisi, Georgia.,Medical School, New Vision University, Tbilisi, Georgia
| | - Tamar Lordkipanidze
- School of Natural Sciences and Medicine, Ilia State University, Tbilisi, Georgia.,Department of Brain Ultrastructure and Nanoarchitecture, I. Beritashvili Center of Experimental Biomedicine, Tbilisi, Georgia
| | - Fuad Rzayev
- Laboratory of Electron Microscopy, Research Center of Azerbaijan Medical University, Baku, Azerbaijan
| | - Derrick MacFabe
- The Kilee Patchell-Evans Autism Research Group, London, ON, Canada.,Faculty of Medicine, Department of Microbiology, Center for Healthy Eating and Food Innovation, Maastricht University, Maastricht, the Netherlands
| | - Mzia Zhvania
- School of Natural Sciences and Medicine, Ilia State University, Tbilisi, Georgia.,Department of Brain Ultrastructure and Nanoarchitecture, I. Beritashvili Center of Experimental Biomedicine, Tbilisi, Georgia
| |
Collapse
|
18
|
|
19
|
Kinyamu HK, Bennett BD, Bushel PR, Archer TK. Proteasome inhibition creates a chromatin landscape favorable to RNA Pol II processivity. J Biol Chem 2019; 295:1271-1287. [PMID: 31806706 DOI: 10.1074/jbc.ra119.011174] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/02/2019] [Indexed: 11/06/2022] Open
Abstract
Proteasome activity is required for diverse cellular processes, including transcriptional and epigenetic regulation. However, inhibiting proteasome activity can lead to an increase in transcriptional output that is correlated with enriched levels of trimethyl H3K4 and phosphorylated forms of RNA polymerase (Pol) II at the promoter and gene body. Here, we perform gene expression analysis and ChIP followed by sequencing (ChIP-seq) in MCF-7 breast cancer cells treated with the proteasome inhibitor MG132, and we further explore genome-wide effects of proteasome inhibition on the chromatin state and RNA Pol II transcription. Analysis of gene expression programs and chromatin architecture reveals that chemically inhibiting proteasome activity creates a distinct chromatin state, defined by spreading of the H3K4me3 mark into the gene bodies of differentially-expressed genes. The distinct H3K4me3 chromatin profile and hyperacetylated nucleosomes at transcription start sites establish a chromatin landscape that facilitates recruitment of Ser-5- and Ser-2-phosphorylated RNA Pol II. Subsequent transcriptional events result in diverse gene expression changes. Alterations of H3K36me3 levels in the gene body reflect productive RNA Pol II elongation of transcripts of genes that are induced, underscoring the requirement for proteasome activity at multiple phases of the transcriptional cycle. Finally, by integrating genomics data and pathway analysis, we find that the differential effects of proteasome inhibition on the chromatin state modulate genes that are fundamental for cancer cell survival. Together, our results uncover underappreciated downstream effects of proteasome inhibitors that may underlie targeting of distinct chromatin states and key steps of RNA Pol II-mediated transcription in cancer cells.
Collapse
Affiliation(s)
- H Karimi Kinyamu
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709
| | - Brian D Bennett
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709.,Integrative Bioinformatics Support Group, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709
| | - Pierre R Bushel
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709
| | - Trevor K Archer
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709
| |
Collapse
|
20
|
Wnuk K, Sudol J, Givechian KB, Soon-Shiong P, Rabizadeh S, Szeto C, Vaske C. Deep Learning Implicitly Handles Tissue Specific Phenomena to Predict Tumor DNA Accessibility and Immune Activity. iScience 2019; 20:119-136. [PMID: 31563852 PMCID: PMC6823659 DOI: 10.1016/j.isci.2019.09.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 08/23/2019] [Accepted: 09/11/2019] [Indexed: 01/22/2023] Open
Abstract
DNA accessibility is a key dynamic feature of chromatin regulation that can potentiate transcriptional events and tumor progression. To gain insight into chromatin state across existing tumor data, we improved neural network models for predicting accessibility from DNA sequence and extended them to incorporate a global set of RNA sequencing gene expression inputs. Our expression-informed model expanded the application domain beyond specific tissue types to tissues not present in training and achieved consistently high accuracy in predicting DNA accessibility at promoter and promoter flank regions. We then leveraged our new tool by analyzing the DNA accessibility landscape of promoters across The Cancer Genome Atlas. We show that in lung adenocarcinoma the accessibility perspective uniquely highlights immune pathways inversely correlated with a more open chromatin state and that accessibility patterns learned from even a single tumor type can discriminate immune inflammation across many cancers, often with direct relation to patient prognosis.
Collapse
Affiliation(s)
- Kamil Wnuk
- ImmunityBio Inc., Culver City, CA 90232, USA.
| | | | | | | | | | | | | |
Collapse
|
21
|
Lamonica JM, Zhou Z. Disentangling chromatin architecture to gain insights into the etiology of brain disorders. Curr Opin Genet Dev 2019; 55:76-81. [PMID: 31323465 DOI: 10.1016/j.gde.2019.06.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/09/2019] [Accepted: 06/15/2019] [Indexed: 11/25/2022]
Abstract
Chromatin organization, together with DNA and histone modifications, is directly linked to the spatiotemporal control of gene expression that specifies and maintains cell type-specific functions. This is particularly important in the brain where hundreds of cell types with distinct functions reside. Recent advances in molecular and computational technologies have enabled the query of chromatin architecture at unprecedented resolution and detail. Here, we review recent studies on the emerging importance of chromatin architecture in the pathogenesis of brain disorders, with emphasis on schizophrenia, autism spectrum disorders (ASD), and unstable repeat expansion disorders. These studies provide molecular insights into how these brain disorders arise at the level of chromatin architecture and implicate new therapeutic directions.
Collapse
Affiliation(s)
- Janine M Lamonica
- Department of Genetics and Epigenetics Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Zhaolan Zhou
- Department of Genetics and Epigenetics Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
| |
Collapse
|
22
|
Sullivan JM, De Rubeis S, Schaefer A. Convergence of spectrums: neuronal gene network states in autism spectrum disorder. Curr Opin Neurobiol 2019; 59:102-111. [PMID: 31220745 DOI: 10.1016/j.conb.2019.04.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/20/2019] [Accepted: 04/24/2019] [Indexed: 12/24/2022]
Abstract
Autism spectrum disorder (ASD) is a prevalent neurodevelopmental disorder characterized by social deficits and restrictive and/or repetitive behaviors. The breadth of ASD symptoms is paralleled by the multiplicity of genes that have been implicated in its etiology. Initial findings revealed numerous ASD risk genes that contribute to synaptic function. More recently, genomic and gene expression studies point to altered chromatin function and impaired transcriptional control as additional risk factors for ASD. The consequences of impaired transcriptional alterations in ASD involve consistent changes in synaptic gene expression and cortical neuron specification during brain development. The multiplicity of genetic and environmental factors associated with ASD risk and their convergence onto common molecular pathways in neurons point to ASD as a disorder of gene regulatory networks.
Collapse
Affiliation(s)
- Josefa M Sullivan
- Nash Family Department of Neuroscience, New York, NY, USA; Department of Psychiatry, New York, NY, USA; Friedman Brain Institute, New York, NY, USA; Seaver Autism Center for Research and Treatment, New York, NY, USA
| | - Silvia De Rubeis
- Department of Psychiatry, New York, NY, USA; Seaver Autism Center for Research and Treatment, New York, NY, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anne Schaefer
- Nash Family Department of Neuroscience, New York, NY, USA; Department of Psychiatry, New York, NY, USA; Friedman Brain Institute, New York, NY, USA; Seaver Autism Center for Research and Treatment, New York, NY, USA.
| |
Collapse
|
23
|
Dyer M, Phipps AJ, Mitew S, Taberlay PC, Woodhouse A. Age, but Not Amyloidosis, Induced Changes in Global Levels of Histone Modifications in Susceptible and Disease-Resistant Neurons in Alzheimer's Disease Model Mice. Front Aging Neurosci 2019; 11:68. [PMID: 31001106 PMCID: PMC6456813 DOI: 10.3389/fnagi.2019.00068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 03/11/2019] [Indexed: 12/23/2022] Open
Abstract
There is increasing interest in the role of epigenetic alterations in Alzheimer’s disease (AD). The epigenome of every cell type is distinct, yet data regarding epigenetic change in specific cell types in aging and AD is limited. We investigated histone tail modifications in neuronal subtypes in wild-type and APP/PS1 mice at 3 (pre-pathology), 6 (pathology-onset) and 12 (pathology-rich) months of age. In neurofilament (NF)-positive pyramidal neurons (vulnerable to AD pathology), and in calretinin-labeled interneurons (resistant to AD pathology) there were no global alterations in histone 3 lysine 4 trimethylation (H3K4me3), histone 3 lysine 27 acetylation (H3K27ac) or histone 3 lysine 27 trimethylation (H3K27me3) in APP/PS1 compared to wild-type mice at any age. Interestingly, age-related changes in the presence of H3K27ac and H3K27me3 were detected in NF-labeled pyramidal neurons and calretinin-positive interneurons, respectively. These data suggest that the global levels of histone modifications change with age, whilst amyloid plaque deposition and its sequelae do not result in global alterations of H3K4me3, H3K27ac and H3K27me3 in NF-positive pyramidal neurons or calretinin-labeled interneurons.
Collapse
Affiliation(s)
- Marcus Dyer
- Wicking Dementia Research and Education Centre, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia.,Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Andrew J Phipps
- Wicking Dementia Research and Education Centre, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Stanislaw Mitew
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Phillippa C Taberlay
- School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Adele Woodhouse
- Wicking Dementia Research and Education Centre, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia
| |
Collapse
|
24
|
Sugino K, Clark E, Schulmann A, Shima Y, Wang L, Hunt DL, Hooks BM, Tränkner D, Chandrashekar J, Picard S, Lemire AL, Spruston N, Hantman AW, Nelson SB. Mapping the transcriptional diversity of genetically and anatomically defined cell populations in the mouse brain. eLife 2019; 8:38619. [PMID: 30977723 PMCID: PMC6499542 DOI: 10.7554/elife.38619] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 04/11/2019] [Indexed: 01/27/2023] Open
Abstract
Understanding the principles governing neuronal diversity is a fundamental goal for neuroscience. Here, we provide an anatomical and transcriptomic database of nearly 200 genetically identified cell populations. By separately analyzing the robustness and pattern of expression differences across these cell populations, we identify two gene classes contributing distinctly to neuronal diversity. Short homeobox transcription factors distinguish neuronal populations combinatorially, and exhibit extremely low transcriptional noise, enabling highly robust expression differences. Long neuronal effector genes, such as channels and cell adhesion molecules, contribute disproportionately to neuronal diversity, based on their patterns rather than robustness of expression differences. By linking transcriptional identity to genetic strains and anatomical atlases, we provide an extensive resource for further investigation of mouse neuronal cell types.
Collapse
Affiliation(s)
- Ken Sugino
- Janelia Research CampusAshburnUnited States
| | | | | | | | - Lihua Wang
- Janelia Research CampusAshburnUnited States
| | | | | | | | | | | | | | | | | | | |
Collapse
|