{"id":"https://openalex.org/W2950319209","doi":"https://doi.org/10.1101/670463","title":"Reprogramming of 24nt siRNAs in rice gametes","display_name":"Reprogramming of 24nt siRNAs in rice gametes","publication_year":2019,"publication_date":"2019-06-13","ids":{"openalex":"https://openalex.org/W2950319209","doi":"https://doi.org/10.1101/670463","mag":"2950319209"},"language":"en","primary_location":{"id":"doi:10.1101/670463","doi":"https://doi.org/10.1101/670463","is_oa":true,"landing_page_url":"https://doi.org/10.1101/670463","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2019/06/13/670463.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2019/06/13/670463.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047137615","display_name":"Chenxin Li","orcid":"https://orcid.org/0000-0002-6276-7712","observed_orcids":["https://orcid.org/0000-0002-6276-7712","https://orcid.org/0009-0000-3624-5067","https://orcid.org/0009-0007-3216-6565"]},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chenxin Li","raw_affiliation_strings":["Department of Plant Biology, University of California, Davis, California 95616, USA","Department of Plant Biology, University of California, Davis, California 9566, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Plant Biology, University of California, Davis, California 95616, USA","institution_ids":["https://openalex.org/I84218800"]},{"raw_affiliation_string":"Department of Plant Biology, University of California, Davis, California 9566, USA","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011465655","display_name":"Hengping Xu","orcid":"https://orcid.org/0000-0001-6933-551X","observed_orcids":["https://orcid.org/0000-0001-6933-551X"]},"institutions":[{"id":"https://openalex.org/I8692664","display_name":"University of Oklahoma","ror":"https://ror.org/02aqsxs83","country_code":"US","type":"education","lineage":["https://openalex.org/I8692664"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hengping Xu","raw_affiliation_strings":["Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA","institution_ids":["https://openalex.org/I8692664"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024735253","display_name":"Fangfang Fu","orcid":"https://orcid.org/0000-0002-3187-9308","observed_orcids":["https://orcid.org/0000-0002-3187-9308"]},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fang-Fang Fu","raw_affiliation_strings":["Department of Plant Biology, University of Georgia, Athens, GA 30602, USA","Department of Plant Biology, University of Georgia, Athens, GA 0602, USA"],"raw_orcid":"https://orcid.org/0000-0002-3187-9308","affiliations":[{"raw_affiliation_string":"Department of Plant Biology, University of Georgia, Athens, GA 30602, USA","institution_ids":["https://openalex.org/I165733156"]},{"raw_affiliation_string":"Department of Plant Biology, University of Georgia, Athens, GA 0602, USA","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033771518","display_name":"Scott D. Russell","orcid":"https://orcid.org/0000-0001-8302-4160","observed_orcids":["https://orcid.org/0000-0001-8302-4160"]},"institutions":[{"id":"https://openalex.org/I8692664","display_name":"University of Oklahoma","ror":"https://ror.org/02aqsxs83","country_code":"US","type":"education","lineage":["https://openalex.org/I8692664"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Scott D. Russell","raw_affiliation_strings":["Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA"],"raw_orcid":"https://orcid.org/0000-0001-8302-4160","affiliations":[{"raw_affiliation_string":"Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA","institution_ids":["https://openalex.org/I8692664"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039726955","display_name":"Venkatesan Sundaresan","orcid":"https://orcid.org/0000-0002-4670-0630","observed_orcids":["https://orcid.org/0000-0002-4670-0630"]},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Venkatesan Sundaresan","raw_affiliation_strings":["Department of Plant Sciences, University of California, Davis, California 95616, USA"],"raw_orcid":"https://orcid.org/0000-0002-4670-0630","affiliations":[{"raw_affiliation_string":"Department of Plant Sciences, University of California, Davis, California 95616, USA","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032237809","display_name":"Jonathan Isaiah Gent","orcid":"https://orcid.org/0000-0002-3584-7717","observed_orcids":["https://orcid.org/0000-0002-3584-7717"]},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jonathan I. Gent","raw_affiliation_strings":["Department of Plant Biology, University of Georgia, Athens, GA 30602, USA","Department of Plant Biology, University of Georgia, Athens, GA 0602, USA"],"raw_orcid":"https://orcid.org/0000-0002-3584-7717","affiliations":[{"raw_affiliation_string":"Department of Plant Biology, University of Georgia, Athens, GA 30602, USA","institution_ids":["https://openalex.org/I165733156"]},{"raw_affiliation_string":"Department of Plant Biology, University of Georgia, Athens, GA 0602, USA","institution_ids":["https://openalex.org/I165733156"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5032237809","https://openalex.org/A5033771518","https://openalex.org/A5039726955"],"corresponding_institution_ids":["https://openalex.org/I165733156","https://openalex.org/I84218800","https://openalex.org/I8692664"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"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/T10184","display_name":"Plant Molecular Biology Research","score":0.67330002784729,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10184","display_name":"Plant Molecular Biology Research","score":0.67330002784729,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.22120000422000885,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.07209999859333038,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/24-nt-sirnas","display_name":"24-nt siRNAs","score":0.871999979019165},{"id":"https://openalex.org/keywords/oocytes","display_name":"oocytes","score":0.8029999732971191},{"id":"https://openalex.org/keywords/spermatozoa","display_name":"spermatozoa","score":0.9769999980926514},{"id":"https://openalex.org/keywords/genome-reprogramming","display_name":"genome reprogramming","score":0.6949999928474426},{"id":"https://openalex.org/keywords/rna-directed-dna-methylation","display_name":"RNA-directed DNA methylation","score":0.9570000171661377},{"id":"https://openalex.org/keywords/heterochromatin-boundaries","display_name":"heterochromatin boundaries","score":0.8650000095367432},{"id":"https://openalex.org/keywords/chh-methylation","display_name":"CHH methylation","score":0.9110000133514404},{"id":"https://openalex.org/keywords/small-rna-transcriptome","display_name":"small RNA transcriptome","score":0.8849999904632568},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.7200000286102295},{"id":"https://openalex.org/keywords/fertilisation-biology","display_name":"fertilisation (biology)","score":0.5600000023841858}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8216996192932129},{"id":"https://openalex.org/C103435993","wikidata":"https://www.wikidata.org/wiki/Q837783","display_name":"Heterochromatin","level":4,"score":0.7533004283905029},{"id":"https://openalex.org/C77255625","wikidata":"https://www.wikidata.org/wiki/Q402093","display_name":"Reprogramming","level":3,"score":0.7025298476219177},{"id":"https://openalex.org/C22615655","wikidata":"https://www.wikidata.org/wiki/Q203221","display_name":"Small interfering RNA","level":4,"score":0.6276010870933533},{"id":"https://openalex.org/C2779341050","wikidata":"https://www.wikidata.org/wiki/Q24287527","display_name":"Small RNA","level":4,"score":0.5872419476509094},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.545522153377533},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5035457015037537},{"id":"https://openalex.org/C2777095108","wikidata":"https://www.wikidata.org/wiki/Q1321695","display_name":"Egg cell","level":3,"score":0.4894465506076813},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.4859544038772583},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.45236605405807495},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4251667559146881},{"id":"https://openalex.org/C2776803348","wikidata":"https://www.wikidata.org/wiki/Q211050","display_name":"Gamete","level":3,"score":0.42426547408103943},{"id":"https://openalex.org/C2781087480","wikidata":"https://www.wikidata.org/wiki/Q17145","display_name":"Sperm","level":2,"score":0.41444793343544006},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.41147828102111816},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.30322161316871643},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.2880842089653015},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.21687859296798706},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.11533308029174805}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1101/670463","doi":"https://doi.org/10.1101/670463","is_oa":true,"landing_page_url":"https://doi.org/10.1101/670463","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2019/06/13/670463.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.1101/670463","doi":"https://doi.org/10.1101/670463","is_oa":true,"landing_page_url":"https://doi.org/10.1101/670463","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2019/06/13/670463.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G671283121","display_name":null,"funder_award_id":"CA-D-XXX-6973-H","funder_id":"https://openalex.org/F4320306114","funder_display_name":"U.S. Department of Agriculture"},{"id":"https://openalex.org/G782854594","display_name":"RESEARCH-PGR: Zygotic Genome Activation in Rice","funder_award_id":"1547760","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306114","display_name":"U.S. Department of Agriculture","ror":"https://ror.org/01na82s61"},{"id":"https://openalex.org/F4320332564","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69"},{"id":"https://openalex.org/F4320337813","display_name":"Genome Center, University of California, Davis","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2950319209.pdf","grobid_xml":"https://content.openalex.org/works/W2950319209.grobid-xml"},"referenced_works_count":75,"referenced_works":["https://openalex.org/W1616463662","https://openalex.org/W1900961661","https://openalex.org/W1958388479","https://openalex.org/W1964388814","https://openalex.org/W1983671446","https://openalex.org/W1984380891","https://openalex.org/W1987293097","https://openalex.org/W1998929945","https://openalex.org/W2004955906","https://openalex.org/W2008138798","https://openalex.org/W2009790316","https://openalex.org/W2016813268","https://openalex.org/W2018249152","https://openalex.org/W2020173141","https://openalex.org/W2033514566","https://openalex.org/W2036897871","https://openalex.org/W2051465150","https://openalex.org/W2057748410","https://openalex.org/W2072022791","https://openalex.org/W2082276197","https://openalex.org/W2087268291","https://openalex.org/W2088044011","https://openalex.org/W2096955838","https://openalex.org/W2097470338","https://openalex.org/W2101184565","https://openalex.org/W2102619694","https://openalex.org/W2103441770","https://openalex.org/W2107018762","https://openalex.org/W2117131162","https://openalex.org/W2119663816","https://openalex.org/W2120847972","https://openalex.org/W2126038413","https://openalex.org/W2126310951","https://openalex.org/W2130116522","https://openalex.org/W2130535352","https://openalex.org/W2133289818","https://openalex.org/W2138098955","https://openalex.org/W2141507532","https://openalex.org/W2143375483","https://openalex.org/W2151753597","https://openalex.org/W2156247618","https://openalex.org/W2159225362","https://openalex.org/W2162691890","https://openalex.org/W2170551349","https://openalex.org/W2223836536","https://openalex.org/W2460353198","https://openalex.org/W2547090345","https://openalex.org/W2561680509","https://openalex.org/W2566954290","https://openalex.org/W2568435111","https://openalex.org/W2581180469","https://openalex.org/W2754256904","https://openalex.org/W2763192805","https://openalex.org/W2763573503","https://openalex.org/W2767292246","https://openalex.org/W2769936082","https://openalex.org/W2776592421","https://openalex.org/W2783502736","https://openalex.org/W2790779827","https://openalex.org/W2793412152","https://openalex.org/W2804369390","https://openalex.org/W2806742579","https://openalex.org/W2807420818","https://openalex.org/W2884411614","https://openalex.org/W2898440040","https://openalex.org/W2898730423","https://openalex.org/W2901009864","https://openalex.org/W2905059551","https://openalex.org/W2913635973","https://openalex.org/W2914389452","https://openalex.org/W2935979075","https://openalex.org/W2936335334","https://openalex.org/W2939954111","https://openalex.org/W2944440052","https://openalex.org/W2950103832"],"related_works":["https://openalex.org/W2997003254","https://openalex.org/W7056749393","https://openalex.org/W4206815652","https://openalex.org/W4317360442","https://openalex.org/W4283799384","https://openalex.org/W6966548539","https://openalex.org/W2799415276","https://openalex.org/W2937261132","https://openalex.org/W4393433025","https://openalex.org/W6920721600"],"abstract_inverted_index":{"ABSTRACT":[0],"Gametes":[1],"constitute":[2],"a":[3,45,102,127],"critical":[4],"stage":[5],"of":[6,28,40,47,60,76,105,123,130,164,171,175],"the":[7,13,24,109,145],"plant":[8],"life":[9],"cycle,":[10],"during":[11],"which":[12,43,111,158],"genome":[14],"undergoes":[15,149],"reprogramming":[16],"in":[17,52,72,79,95,139,152,167,179],"preparation":[18],"for":[19],"embryogenesis.":[20],"Here":[21],"we":[22],"characterized":[23],"small":[25,146,177],"RNA":[26,147],"transcriptomes":[27],"egg":[29],"cells":[30,33],"and":[31,54,117,155,169],"sperm":[32],"from":[34,69],"rice":[35],"to":[36,134],"elucidate":[37],"genome-wide":[38],"distributions":[39],"24nt":[41,65,86,97],"siRNAs,":[42],"are":[44,55],"hallmark":[46],"RNA-directed":[48],"DNA":[49,165],"methylation":[50],"(RdDM)":[51],"plants":[53],"typically":[56,126],"concentrated":[57,100],"at":[58,101],"boundaries":[59,71],"heterochromatin.":[61],"We":[62],"found":[63],"that":[64,144],"siRNAs":[66,87,98],"were":[67,88,99,112,132],"depleted":[68],"heterochromatin":[70],"both":[73,120,153],"gametes,":[74,121,157],"reminiscent":[75],"siRNA":[77],"patterns":[78,122],"DDM1-type":[80],"nucleosome":[81],"remodeler":[82],"mutants.":[83],"In":[84,119],"sperm,":[85],"spread":[89],"across":[90],"broad":[91],"heterochromatic":[92,106],"regions,":[93],"while":[94],"eggs,":[96],"smaller":[103],"number":[104],"loci":[107],"throughout":[108],"genome,":[110],"shared":[113],"with":[114,162],"vegetative":[115,135],"tissues":[116],"sperm.":[118],"CHH":[124],"methylation,":[125],"strong":[128],"indicator":[129],"RdDM,":[131],"similar":[133],"tissues,":[136],"although":[137],"lower":[138],"magnitude.":[140],"These":[141],"findings":[142],"indicate":[143],"transcriptome":[148],"large-scale":[150],"re-programming":[151],"male":[154],"female":[156],"is":[159],"not":[160],"correlated":[161],"recruitment":[163],"methyltransferases":[166],"gametes":[168],"suggestive":[170],"unexplored":[172],"regulatory":[173],"activities":[174],"gamete":[176],"RNAs":[178],"seeds":[180],"after":[181],"fertilization.":[182]},"counts_by_year":[{"year":2019,"cited_by_count":1}],"updated_date":"2026-10-16T09:59:22.235173","created_date":"2019-06-27T00:00:00"}