[ { "id": "authors:mx2mm-j1651", "collection": "authors", "collection_id": "mx2mm-j1651", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200310-130644860", "type": "article", "title": "A protein assembly mediates Xist localization and gene silencing", "author": [ { "family_name": "Pandya-Jones", "given_name": "Amy", "orcid": "0000-0001-5519-4613", "clpid": "Pandya-Jones-Amy" }, { "family_name": "Markaki", "given_name": "Yolanda", "orcid": "0000-0001-6013-2417", "clpid": "Markaki-Yolanda" }, { "family_name": "Serizay", "given_name": "Jacques", "orcid": "0000-0002-4295-0624", "clpid": "Serizay-Jacques" }, { "family_name": "Chitiashvili", "given_name": "Tsotne", "orcid": "0000-0002-4887-1097", "clpid": "Chitiashvili-Tsotne" }, { "family_name": "Mancia-Leon", "given_name": "Walter R.", "orcid": "0000-0002-1920-6514", "clpid": "Mancia-Leon-Walter-R" }, { "family_name": "Damianov", "given_name": "Andrey", "clpid": "Damianov-Andrey" }, { "family_name": "Chronis", "given_name": "Konstantinos", "orcid": "0000-0002-7783-8202", "clpid": "Chronis-Konstantinos" }, { "family_name": "Papp", "given_name": "Bernadett", "orcid": "0000-0001-5352-3946", "clpid": "Papp-Bernadett" }, { "family_name": "Chen", "given_name": "Chun-Kan", "orcid": "0000-0002-1194-9137", "clpid": "Chen-Chun-Kan" }, { "family_name": "McKee", "given_name": "Robin", "orcid": "0009-0002-2926-1856", "clpid": "McKee-Robin" }, { "family_name": "Wang", "given_name": "Xiao-Jun", "clpid": "Wang-Xiao-Jun" }, { "family_name": "Chau", "given_name": "Anthony", "clpid": "Chau-Anthony" }, { "family_name": "Sabri", "given_name": "Shan", "orcid": "0000-0002-0885-6159", "clpid": "Sabri-Shan" }, { "family_name": "Leonhardt", "given_name": "Heinrich", "orcid": "0000-0002-5086-6449", "clpid": "Leonhardt-Heinrich" }, { "family_name": "Zheng", "given_name": "Sika", "orcid": "0000-0002-0573-4981", "clpid": "Zheng-Sika" }, { "family_name": "Guttman", "given_name": "Mitchell", "orcid": "0000-0003-4748-9352", "clpid": "Guttman-M" }, { "family_name": "Black", "given_name": "Douglas L.", "orcid": "0000-0002-2705-8187", "clpid": "Black-Douglas-L" }, { "family_name": "Plath", "given_name": "Kathrin", "orcid": "0000-0001-7796-3372", "clpid": "Palth-Kathrin" } ], "abstract": "Nuclear compartments have diverse roles in regulating gene expression, yet the molecular forces and components that drive compartment formation remain largely unclear. The long non-coding RNA Xist establishes an intra-chromosomal compartment by localizing at a high concentration in a territory spatially close to its transcription locus and binding diverse proteins to achieve X-chromosome inactivation (XCI). The XCI process therefore serves as a paradigm for understanding how RNA-mediated recruitment of various proteins induces a functional compartment. The properties of the inactive X (Xi)-compartment are known to change over time, because after initial Xist spreading and transcriptional shutoff a state is reached in which gene silencing remains stable even if Xist is turned off. Here we show that the Xist RNA-binding proteins PTBP1, MATR3, TDP-43 and CELF1 assemble on the multivalent E-repeat element of Xist and, via self-aggregation and heterotypic protein\u2013protein interactions, form a condensate in the Xi. This condensate is required for gene silencing and for the anchoring of Xist to the Xi territory, and can be sustained in the absence of Xist. Notably, these E-repeat-binding proteins become essential coincident with transition to the Xist-independent XCI phase, indicating that the condensate seeded by the E-repeat underlies the developmental switch from Xist-dependence to Xist-independence. Taken together, our data show that Xist forms the Xi compartment by seeding a heteromeric condensate that consists of ubiquitous RNA-binding proteins, revealing an unanticipated mechanism for heritable gene silencing.", "doi": "10.1038/s41586-020-2703-0", "pmcid": "PMC7644664", "issn": "0028-0836", "publisher": "Nature Publishing Group", "publication": "Nature", "publication_date": "2020-11-05", "series_number": "7832", "volume": "587", "issue": "7832", "pages": "145-151" }, { "id": "authors:d117s-7vb33", "collection": "authors", "collection_id": "d117s-7vb33", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170616-092953242", "type": "article", "title": "Response to Comment on \"Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing\"", "author": [ { "family_name": "Chen", "given_name": "Chun-Kan", "clpid": "Chen-Chun-Kan" }, { "family_name": "Chow", "given_name": "Amy", "clpid": "Chow-Amy" }, { "family_name": "Lai", "given_name": "Mason", "clpid": "Lai-Mason" }, { "family_name": "Guttman", "given_name": "Mitchell", "orcid": "0000-0003-4748-9352", "clpid": "Guttman-M" } ], "abstract": "Wang et al. question whether Lamin B receptor is required for Xist-mediated silencing because they claim that our cells contain an inversion rather than a deletion. We present evidence that these cells contain a proper deletion and that the confusion is caused by DNA probes used in the experiment. Accordingly, the points raised have no effect on the conclusions in our paper.", "doi": "10.1126/science.aam5439", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2017-06-16", "series_number": "6343", "volume": "356", "issue": "6343", "pages": "Art. No. eaam5439" }, { "id": "authors:wtmex-7yc03", "collection": "authors", "collection_id": "wtmex-7yc03", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160418-091128052", "type": "article", "title": "Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing", "author": [ { "family_name": "Chen", "given_name": "Chun-Kan", "clpid": "Chen-Chun-Kan" }, { "family_name": "Blanco", "given_name": "Mario", "clpid": "Blanco-Mario-R" }, { "family_name": "Jackson", "given_name": "Costanza", "clpid": "Jackson-C" }, { "family_name": "Aznauryan", "given_name": "Erik", "clpid": "Aznauryan-E" }, { "family_name": "Ollikainen", "given_name": "Noah", "clpid": "Ollikainen-N" }, { "family_name": "Surka", "given_name": "Christine", "clpid": "Surka-C-F" }, { "family_name": "Chow", "given_name": "Amy", "clpid": "Chow-Amy-Y" }, { "family_name": "Cerase", "given_name": "Andrea", "clpid": "Cerase-A" }, { "family_name": "McDonel", "given_name": "Patrick", "clpid": "McDonel-P" }, { "family_name": "Guttman", "given_name": "Mitchell", "orcid": "0000-0003-4748-9352", "clpid": "Guttman-M" } ], "abstract": "The Xist long noncoding RNA orchestrates X chromosome inactivation, a process that entails chromosome-wide silencing and remodeling of the three-dimensional (3D) structure of the X chromosome. Yet, it remains unclear whether these changes in nuclear structure are mediated by Xist and whether they are required for silencing. Here, we show that Xist directly interacts with the Lamin B receptor, an integral component of the nuclear lamina, and that this interaction is required for Xist-mediated silencing by recruiting the inactive X to the nuclear lamina and by doing so enables Xist to spread to actively transcribed genes across the X. Our results demonstrate that lamina recruitment changes the 3D structure of DNA, enabling Xist and its silencing proteins to spread across the X to silence transcription.", "doi": "10.1126/science.aae0047", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2016-10-28", "series_number": "6311", "volume": "354", "issue": "6311", "pages": "468-472" }, { "id": "authors:kw01x-0bx07", "collection": "authors", "collection_id": "kw01x-0bx07", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160912-092146480", "type": "article", "title": "m\u2076A RNA methylation promotes XIST-mediated transcriptional repression", "author": [ { "family_name": "Patil", "given_name": "Deepak P.", "clpid": "Patil-Deepak-P" }, { "family_name": "Chen", "given_name": "Chun-Kan", "orcid": "0000-0002-1194-9137", "clpid": "Chen-Chun-Kan" }, { "family_name": "Pickering", "given_name": "Brian F.", "clpid": "Pickering-Brian-F" }, { "family_name": "Chow", "given_name": "Amy", "clpid": "Chow-Amy-Y" }, { "family_name": "Jackson", "given_name": "Constanza", "clpid": "Jackson-Constanza" }, { "family_name": "Guttman", "given_name": "Mitchell", "orcid": "0000-0003-4748-9352", "clpid": "Guttman-M" }, { "family_name": "Jaffrey", "given_name": "Samie R.", "clpid": "Jaffrey-Samie-R" } ], "abstract": "The long non-coding RNA X-inactive specific transcript (XIST) mediates the transcriptional silencing of genes on the X chromosome. Here we show that, in human cells, XIST is highly methylated with at least 78 N\u2076-methyladenosine (m\u2076A) residues\u2014a reversible base modification of unknown function in long non-coding RNAs. We show that m^6A formation in XIST, as well as in cellular mRNAs, is mediated by RNA-binding motif protein 15 (RBM15) and its paralogue RBM15B, which bind the m\u2076A-methylation complex and recruit it to specific sites in RNA. This results in the methylation of adenosine nucleotides in adjacent m\u2076A consensus motifs. Furthermore, we show that knockdown of RBM15 and RBM15B, or knockdown of methyltransferase like 3 (METTL3), an m\u2076A methyltransferase, impairs XIST-mediated gene silencing. A systematic comparison of m\u2076A-binding proteins shows that YTH domain containing 1 (YTHDC1) preferentially recognizes m^6A residues on XIST and is required for XIST function. Additionally, artificial tethering of YTHDC1 to XIST rescues XIST-mediated silencing upon loss of m\u2076A. These data reveal a pathway of m\u2076A formation and recognition required for XIST-mediated transcriptional repression.", "doi": "10.1038/nature19342", "pmcid": "PMC5509218", "issn": "0028-0836", "publisher": "Nature Publishing Group", "publication": "Nature", "publication_date": "2016-09-15", "series_number": "7620", "volume": "537", "issue": "7620", "pages": "369-373" }, { "id": "authors:sk95x-xrq97", "collection": "authors", "collection_id": "sk95x-xrq97", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161013-150940217", "type": "article", "title": "Phosphorylation of Synaptojanin Differentially Regulates Endocytosis of Functionally Distinct Synaptic Vesicle Pools", "author": [ { "family_name": "Geng", "given_name": "Junhua", "clpid": "Geng-Junhua" }, { "family_name": "Wang", "given_name": "Liping", "clpid": "Wang-Liping" }, { "family_name": "Lee", "given_name": "Joo Yeun", "clpid": "Lee-Joo-Yeun" }, { "family_name": "Chen", "given_name": "Chun-Kan", "clpid": "Chen-Chun-Kan" }, { "family_name": "Chang", "given_name": "Karen T.", "clpid": "Chang-Karen-T" } ], "abstract": "The rapid replenishment of synaptic vesicles through endocytosis is crucial for sustaining synaptic transmission during intense neuronal activity. Synaptojanin (Synj), a phosphoinositide phosphatase, is known to play an important role in vesicle recycling by promoting the uncoating of clathrin following synaptic vesicle uptake. Synj has been shown to be a substrate of the minibrain (Mnb) kinase, a fly homolog of the dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A); however, the functional impacts of Synj phosphorylation by Mnb are not well understood. Here we identify that Mnb phosphorylates Synj at S1029 in Drosophila. We find that phosphorylation of Synj at S1029 enhances Synj phosphatase activity, alters interaction between Synj and endophilin, and promotes efficient endocytosis of the active cycling vesicle pool (also referred to as exo-endo cycling pool) at the expense of reserve pool vesicle endocytosis. Dephosphorylated Synj, on the other hand, is deficient in the endocytosis of the active recycling pool vesicles but maintains reserve pool vesicle endocytosis to restore total vesicle pool size and sustain synaptic transmission. Together, our findings reveal a novel role for Synj in modulating reserve pool vesicle endocytosis and further indicate that dynamic phosphorylation and dephosphorylation of Synj differentially maintain endocytosis of distinct functional synaptic vesicle pools. \n\nSIGNIFICANCE STATEMENT Synaptic vesicle endocytosis sustains communication between neurons during a wide range of neuronal activities by recycling used vesicle membrane and protein components. Here we identify that Synaptojanin, a protein with a known role in synaptic vesicle endocytosis, is phosphorylated at S1029 in vivo by the Minibrain kinase. We further demonstrate that the phosphorylation status of Synaptojanin at S1029 differentially regulates its participation in the recycling of distinct synaptic vesicle pools. Our results reveal a new role for Synaptojanin in maintaining synaptic vesicle pool size and in reserve vesicle endocytosis. As Synaptojanin and Minibrain perturbations are associated with various neurological disorders, such as Parkinson's, autism, and Down syndrome, understanding mechanisms modulating Synaptojanin function provides valuable insights into processes affecting neuronal communication.", "doi": "10.1523/JNEUROSCI.1470-16.2016", "pmcid": "PMC4995302", "issn": "0270-6474", "publisher": "Society for Neuroscience", "publication": "Journal of Neuroscience", "publication_date": "2016-08-24", "series_number": "34", "volume": "36", "issue": "34", "pages": "8882-8894" }, { "id": "authors:rcqh4-c5m79", "collection": "authors", "collection_id": "rcqh4-c5m79", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150319-091012142", "type": "article", "title": "The Xist lncRNA interacts with SHARP to silence transcription through HDAC3", "author": [ { "family_name": "McHugh", "given_name": "Colleen A.", "clpid": "McHugh-C-A" }, { "family_name": "Chen", "given_name": "Chun-Kan", "clpid": "Chen-Chun-Kan" }, { "family_name": "Chow", "given_name": "Amy", "clpid": "Chow-Amy-Y" }, { "family_name": "Surka", "given_name": "Christine F.", "clpid": "Surka-C-F" }, { "family_name": "Tran", "given_name": "Christina", "clpid": "Tran-Christina" }, { "family_name": "McDonel", "given_name": "Patrick", "clpid": "McDonel-P" }, { "family_name": "Pandya-Jones", "given_name": "Amy", "clpid": "Pandya-Jones-A" }, { "family_name": "Blanco", "given_name": "Mario", "clpid": "Blanco-Mario-R" }, { "family_name": "Burghard", "given_name": "Christina", "clpid": "Burghard-C" }, { "family_name": "Moradian", "given_name": "Annie", "orcid": "0000-0002-0407-2031", "clpid": "Moradian-A" }, { "family_name": "Sweredoski", "given_name": "Michael J.", "orcid": "0000-0003-0878-3831", "clpid": "Sweredoski-M-J" }, { "family_name": "Shishkin", "given_name": "Alexander A.", "clpid": "Shishkin-A-A" }, { "family_name": "Su", "given_name": "Julia", "clpid": "Su-Julia" }, { "family_name": "Lander", "given_name": "Eric S.", "orcid": "0000-0003-2662-4631", "clpid": "Lander-E-S" }, { "family_name": "Hess", "given_name": "Sonja", "orcid": "0000-0002-5904-9816", "clpid": "Hess-S" }, { "family_name": "Plath", "given_name": "Kathrin", "clpid": "Palth-K" }, { "family_name": "Guttman", "given_name": "Mitchell", "orcid": "0000-0003-4748-9352", "clpid": "Guttman-M" } ], "abstract": "Many long non-coding RNAs (lncRNAs) affect gene expression, but the mechanisms by which they act are still largely unknown. One of the best-studied lncRNAs is Xist, which is required for transcriptional silencing of one X chromosome during development in female mammals. Despite extensive efforts to define the mechanism of Xist-mediated transcriptional silencing, we still do not know any proteins required for this role. The main challenge is that there are currently no methods to comprehensively define the proteins that directly interact with a lncRNA in the cell. Here we develop a method to purify a lncRNA from cells and identify proteins interacting with it directly using quantitative mass spectrometry. We identify ten proteins that specifically associate with Xist, three of these proteins\u2014SHARP, SAF-A and LBR\u2014are required for Xist-mediated transcriptional silencing. We show that SHARP, which interacts with the SMRT co-repressor that activates HDAC3, is not only essential for silencing, but is also required for the exclusion of RNA polymerase II (Pol II) from the inactive X. Both SMRT and HDAC3 are also required for silencing and Pol II exclusion. In addition to silencing transcription, SHARP and HDAC3 are required for Xist-mediated recruitment of the polycomb repressive complex 2 (PRC2) across the X chromosome. Our results suggest that Xist silences transcription by directly interacting with SHARP, recruiting SMRT, activating HDAC3, and deacetylating histones to exclude Pol II across the X chromosome.", "doi": "10.1038/nature14443", "pmcid": "PMC4516396", "issn": "0028-0836", "publisher": "Nature Publishing Group", "publication": "Nature", "publication_date": "2015-05-14", "series_number": "7551", "volume": "521", "issue": "7551", "pages": "232-236" }, { "id": "authors:k57mg-mbq97", "collection": "authors", "collection_id": "k57mg-mbq97", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140801-121634734", "type": "article", "title": "Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing", "author": [ { "family_name": "Yang", "given_name": "Bin", "clpid": "Yang-Bin" }, { "family_name": "Treweek", "given_name": "Jennifer B.", "clpid": "Treweek-J-B" }, { "family_name": "Kulkarni", "given_name": "Rajan P.", "clpid": "Kulkarni-R-P" }, { "family_name": "Deverman", "given_name": "Benjamin E.", "orcid": "0000-0002-6223-9303", "clpid": "Deverman-B-E" }, { "family_name": "Chen", "given_name": "Chun-Kan", "clpid": "Chen-Chun-Kan" }, { "family_name": "Lubeck", "given_name": "Eric", "orcid": "0000-0002-5457-0258", "clpid": "Lubeck-E" }, { "family_name": "Shah", "given_name": "Sheel", "clpid": "Shah-Sheel" }, { "family_name": "Cai", "given_name": "Long", "orcid": "0000-0002-7154-5361", "clpid": "Cai-Long" }, { "family_name": "Gradinaru", "given_name": "Viviana", "orcid": "0000-0001-5868-348X", "clpid": "Gradinaru-V" } ], "abstract": "Understanding the structure-function relationships at cellular, circuit, and organ-wide scale requires 3D anatomical and phenotypical maps, currently unavailable for many organs across species. At the root of this knowledge gap is the absence of a method that enables whole-organ imaging. Herein, we present techniques for tissue clearing in which whole organs and bodies are rendered macromolecule-permeable and optically transparent, thereby exposing their cellular structure with intact connectivity. We describe PACT (passive clarity technique), a protocol for passive tissue clearing and immunostaining of intact organs; RIMS (refractive index matching solution), a mounting media for imaging thick tissue; and PARS (perfusion-assisted agent release in situ), a method for whole-body clearing and immunolabeling. We show that in rodents PACT, RIMS, and PARS are compatible with endogenous-fluorescence, immunohistochemistry, RNA single-molecule FISH, long-term storage, and microscopy with cellular and subcellular resolution. These methods are applicable for high-resolution, high-content mapping and phenotyping of normal and pathological elements within intact organs and bodies.", "doi": "10.1016/j.cell.2014.07.017", "pmcid": "PMC4153367", "issn": "0092-8674", "publisher": "Elsevier", "publication": "Cell", "publication_date": "2014-08-14", "series_number": "4", "volume": "158", "issue": "4", "pages": "945-958" } ]