{"data":{"id":"10.6084/m9.figshare.1405686","type":"dois","attributes":{"doi":"10.6084/m9.figshare.1405686","prefix":"10.6084","suffix":"m9.figshare.1405686","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"Garcia, Marlene","nameType":"Personal","givenName":"Marlene","familyName":"Garcia","affiliation":[],"nameIdentifiers":[]},{"name":"Mauro, James A","nameType":"Personal","givenName":"James A","familyName":"Mauro","affiliation":[],"nameIdentifiers":[]},{"name":"Ramsamooj, Michael","nameType":"Personal","givenName":"Michael","familyName":"Ramsamooj","affiliation":[],"nameIdentifiers":[]},{"name":"Blanck, George","nameType":"Personal","givenName":"George","familyName":"Blanck","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"Tumor suppressor genes are larger than apoptosis-effector genes and have more regions of active chromatin: Connection to a stochastic paradigm for sequential gene expression programs"}],"publisher":"Taylor \u0026 Francis","container":{},"publicationYear":2015,"subjects":[{"subject":"Cell Biology"},{"subject":"Genetics"},{"subject":"FOS: Biological sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Biological sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Molecular Biology"},{"subject":"Pharmacology"},{"subject":"69999 Biological Sciences not elsewhere classified","subjectScheme":"FOR"},{"subject":"Developmental Biology"},{"subject":"Cancer"},{"subject":"111714 Mental Health","subjectScheme":"FOR"},{"subject":"FOS: Health sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Health sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"110309 Infectious Diseases","subjectScheme":"FOR"},{"subject":"Plant Biology"},{"subject":"Computational Biology"}],"contributors":[],"dates":[{"date":"2015-05-06","dateType":"Created"},{"date":"2019-06-03","dateType":"Updated"},{"date":"2015","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[{"relationType":"IsSupplementTo","relatedIdentifier":"10.1080/15384101.2015.1044179","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":["841684 Bytes"],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"Apoptosis- and proliferation-effector genes are substantially regulated by the same transactivators, with E2F-1 and Oct-1 being notable examples. The larger proliferation-effector genes have more binding sites for the transactivators that regulate both sets of genes, and proliferation-effector genes have more regions of active chromatin, i.e, DNase I hypersensitive and histone 3, lysine-4 trimethylation sites. Thus, the size differences between the 2 classes of genes suggest a transcriptional regulation paradigm whereby the accumulation of transcription factors that regulate both sets of genes, merely as an aspect of stochastic behavior, accumulate first on the larger proliferation-effector gene “traps,” and then accumulate on the apoptosis effector genes, thereby effecting sequential activation of the 2 different gene sets. As IRF-1 and p53 levels increase, tumor suppressor proteins are first activated, followed by the activation of apoptosis-effector genes, for example during S-phase pausing for DNA repair. Tumor suppressor genes are larger than apoptosis-effector genes and have more IRF-1 and p53 binding sites, thereby likewise suggesting a paradigm for transcription sequencing based on stochastic interactions of transcription factors with different gene classes. In this report, using the ENCODE database, we determined that tumor suppressor genes have a greater number of open chromatin regions and histone 3 lysine-4 trimethylation sites, consistent with the idea that a larger gene size can facilitate earlier transcriptional activation via the inclusion of more transactivator binding sites.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"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