{"id":"https://openalex.org/W2601034779","doi":null,"title":"Deciphering the tetrad of epigenetic cytosine modifications","display_name":"Deciphering the tetrad of epigenetic cytosine modifications","publication_year":2016,"publication_date":"2016-01-01","ids":{"openalex":"https://openalex.org/W2601034779","mag":"2601034779"},"language":"en","primary_location":{"id":"pmh:oai:repository.upenn.edu:20.500.14332/29348","doi":null,"is_oa":false,"landing_page_url":"https://repository.upenn.edu/handle/20.500.14332/29348","pdf_url":null,"source":{"id":"https://openalex.org/S4306402083","display_name":"ScholarlyCommons (University of Pennsylvania)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I79576946","host_organization_name":"University of Pennsylvania","host_organization_lineage":["https://openalex.org/I79576946"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"published","raw_type":"Dissertation/Thesis"},"volume":null,"type":"dissertation","indexed_in":[],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100414737","display_name":"Monica Yun Liu","orcid":"https://orcid.org/0000-0003-3936-9377","observed_orcids":["https://orcid.org/0000-0003-3936-9377"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Monica Yun Liu","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0003-3936-9377","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5100414737"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9945999979972839,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9945999979972839,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.0006000000284984708,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.00039999998989515007,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.6800000071525574},{"id":"https://openalex.org/keywords/tet-enzymes","display_name":"TET enzymes","score":0.7919999957084656},{"id":"https://openalex.org/keywords/5-hydroxymethylcytosine","display_name":"5-hydroxymethylcytosine","score":0.9490000009536743},{"id":"https://openalex.org/keywords/5-formylcytosine","display_name":"5-formylcytosine","score":0.996999979019165},{"id":"https://openalex.org/keywords/5-carboxylcytosine","display_name":"5-carboxylcytosine","score":0.9940000176429749},{"id":"https://openalex.org/keywords/tet2","display_name":"TET2","score":0.7350000143051147},{"id":"https://openalex.org/keywords/dna-demethylation","display_name":"DNA demethylation","score":0.7440000176429749},{"id":"https://openalex.org/keywords/epigenetic-modifications","display_name":"epigenetic modifications","score":0.6209999918937683}],"concepts":[{"id":"https://openalex.org/C117717151","wikidata":"https://www.wikidata.org/wiki/Q3589155","display_name":"Epigenome","level":5,"score":0.7557283639907837},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.7346294522285461},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.714780867099762},{"id":"https://openalex.org/C2778901553","wikidata":"https://www.wikidata.org/wiki/Q238535","display_name":"5-Hydroxymethylcytosine","level":5,"score":0.6984370946884155},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5605394840240479},{"id":"https://openalex.org/C2776023528","wikidata":"https://www.wikidata.org/wiki/Q178425","display_name":"Cytosine","level":3,"score":0.5343930125236511},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5184340476989746},{"id":"https://openalex.org/C91965660","wikidata":"https://www.wikidata.org/wiki/Q415875","display_name":"Methyltransferase","level":4,"score":0.5168067216873169},{"id":"https://openalex.org/C77255625","wikidata":"https://www.wikidata.org/wiki/Q402093","display_name":"Reprogramming","level":3,"score":0.4931292235851288},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4648617208003998},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.45944392681121826},{"id":"https://openalex.org/C2779979206","wikidata":"https://www.wikidata.org/wiki/Q1154602","display_name":"DNA methyltransferase","level":5,"score":0.42092639207839966},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3617574870586395},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.3329707384109497},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.3218343257904053},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.26657557487487793},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08742731809616089}],"mesh":[],"locations_count":4,"locations":[{"id":"pmh:oai:repository.upenn.edu:20.500.14332/29348","doi":null,"is_oa":false,"landing_page_url":"https://repository.upenn.edu/handle/20.500.14332/29348","pdf_url":null,"source":{"id":"https://openalex.org/S4306402083","display_name":"ScholarlyCommons (University of Pennsylvania)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I79576946","host_organization_name":"University of Pennsylvania","host_organization_lineage":["https://openalex.org/I79576946"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"published","raw_type":"Dissertation/Thesis"},{"id":"pmh:oai:repository.upenn.edu:dissertations-13803","doi":null,"is_oa":false,"landing_page_url":"https://repository.upenn.edu/dissertations/AAI10241556","pdf_url":null,"source":{"id":"https://openalex.org/S4377196331","display_name":"Scholarly Commons (University of Pennsylvania)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I79576946","host_organization_name":"University of Pennsylvania","host_organization_lineage":["https://openalex.org/I79576946"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Dissertations available from ProQuest","raw_type":"text"},{"id":"pmh:oai:repository.upenn.edu:edissertations-4216","doi":null,"is_oa":false,"landing_page_url":"https://repository.upenn.edu/bitstreams/6cd0a5a1-1335-4c1e-916b-db73269da71d/download","pdf_url":null,"source":{"id":"https://openalex.org/S4306402083","display_name":"ScholarlyCommons (University of Pennsylvania)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I79576946","host_organization_name":"University of Pennsylvania","host_organization_lineage":["https://openalex.org/I79576946"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Publicly Accessible Penn Dissertations","raw_type":"text"},{"id":"mag:2601034779","doi":null,"is_oa":false,"landing_page_url":"https://repository.upenn.edu/cgi/viewcontent.cgi?article=13803&context=dissertations","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2477025491","https://openalex.org/W2225448323","https://openalex.org/W2560742044","https://openalex.org/W4391636729","https://openalex.org/W4224229332","https://openalex.org/W3044653739","https://openalex.org/W2062552240","https://openalex.org/W2775667910","https://openalex.org/W2062252774","https://openalex.org/W2976684485"],"abstract_inverted_index":{"A":[0],"tetrad":[1],"of":[2,23,59,98,146,179,194,206,213,233,252,276,296,299,335],"epigenetic":[3,79,319],"cytosine":[4,162],"modifications":[5,163],"imbues":[6],"the":[7,21,45,95,99,111,147,154,231,250,262,268,285,294,310,336],"DNA":[8,14,200],"code":[9],"with":[10,164,331],"complex,":[11],"dynamic":[12,337],"meaning.":[13],"methyltransferase":[15],"enzymes":[16,43,132],"deposit":[17],"methyl":[18,46],"marks":[19],"on":[20,198],"5-carbon":[22],"cytosine,":[24],"forming":[25,51],"5-methylcytosine":[26],"(mC),":[27],"which":[28,303],"generally":[29],"mediates":[30],"long-term,":[31],"locus-specific":[32],"transcriptional":[33],"repression":[34],"during":[35],"development":[36],"and":[37,62,91,117,129,136,184,208,215,235,301],"reprogramming.":[38],"Ten-eleven":[39],"translocation":[40],"(TET)":[41],"family":[42],"oxidize":[44],"group":[47],"in":[48,81,151,244,289,327],"three":[49,254],"steps,":[50],"predominantly":[52],"5-hydroxymethylcytosine":[53],"(hmC)":[54],"but":[55,74],"also":[56,77],"low":[57],"levels":[58],"5-formylcytosine":[60],"(fC)":[61],"5-carboxylcytosine":[63],"(caC).":[64],"These":[65,280],"additional":[66],"bases":[67,138,314],"likely":[68],"provide":[69],"pathways":[70],"for":[71,230,287,318],"erasing":[72],"methylation,":[73],"they":[75],"may":[76],"harbor":[78],"functions":[80,92],"their":[82],"own":[83],"right.":[84],"Questions":[85],"regarding":[86],"how":[87,128,180],"each":[88],"base":[89],"forms":[90],"drive":[93],"at":[94,113,278],"fundamental":[96],"biology":[97],"epigenome.":[100,338],"In":[101,122,167,220],"this":[102],"thesis,":[103],"I":[104,149,321],"chronicle":[105],"our":[106,323],"lab\u2019s":[107],"efforts":[108],"to":[109,126,159,174,202,273,292,307,325],"probe":[110],"epigenome":[112],"its":[114],"source\u2014by":[115],"deciphering":[116],"manipulating":[118],"TET":[119,131],"enzyme":[120],"mechanisms.":[121],"particular,":[123],"we":[124,157,170,223,265],"aim":[125],"understand":[127],"why":[130],"generate":[133],"rare":[134,161],"fC":[135,214,234,300],"caC":[137,216],"rather":[139],"than":[140],"hmC":[141,297],"alone.":[142],"Following":[143],"a":[144,175,199,239],"review":[145],"field,":[148],"describe":[150,322],"Chapter":[152,168,221,328],"2":[153],"methods":[155],"that":[156,190,247],"developed":[158],"study":[160,178],"high":[165],"sensitivity.":[166],"3,":[169],"applied":[171],"these":[172],"techniques":[173],"rigorous":[176],"kinetic":[177],"mouse":[181],"Tet2":[182,191],"establishes":[183],"maintains":[185],"oxidized":[186,255,313],"cytosines.":[187],"We":[188,237],"found":[189],"is":[192],"capable":[193],"iterative":[195],"oxidation,":[196],"staying":[197],"strand":[201],"catalyze":[203],"multiple":[204],"rounds":[205],"oxidation":[207,277],"thereby":[209],"enabling":[210],"efficient":[211],"generation":[212,232],"under":[217],"certain":[218],"circumstances.":[219],"4,":[222],"asked":[224],"what":[225],"structure-function":[226],"determinants":[227],"could":[228,266],"allow":[229,305],"caC.":[236],"discovered":[238],"conserved":[240],"active":[241,263],"site":[242],"scaffold":[243],"human":[245],"TET2":[246],"specifically":[248],"supports":[249],"formation":[251],"all":[253],"bases,":[256],"not":[257],"just":[258],"hmC.":[259,279],"By":[260],"mutating":[261],"site,":[264],"alter":[267],"interactions":[269],"between":[270],"key":[271],"residues":[272],"achieve":[274],"stalling":[275],"mutants":[281],"have":[282],"now":[283],"paved":[284],"way":[286],"applications":[288],"model":[290],"systems":[291],"examine":[293],"function":[295],"independently":[298],"caC,":[302],"will":[304],"us":[306],"dissect":[308],"whether":[309],"rare,":[311],"highly":[312],"are":[315],"truly":[316],"critical":[317],"processes.":[320],"progress":[324],"date":[326],"5,":[329],"along":[330],"further":[332],"mechanistic":[333],"explorations":[334]},"counts_by_year":[{"year":2023,"cited_by_count":1}],"updated_date":"2026-09-11T09:22:31.653822","created_date":"2017-04-07T00:00:00"}