2022
Building integrative functional maps of gene regulation
Xu J, Pratt HE, Moore JE, Gerstein MB, Weng Z. Building integrative functional maps of gene regulation. Human Molecular Genetics 2022, 31: r114-r122. PMID: 36083269, PMCID: PMC9585680, DOI: 10.1093/hmg/ddac195.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsGene regulationRegulatory mapSame genetic informationNon-coding genesSuch regulatory elementsEvolutionary analysisHuman genomeRegulatory elementsGenetic informationGene expressionType diversityRegulatory roleGenomeBase pairsIndividual cellsFunctional assaysSpecific functionsRegulationCellsFunctional mapsGenesDNADiversityCopiesSequence
2021
Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites
Pratt H, Andrews G, Phalke N, Huey J, Purcaro M, van der Velde A, Moore J, Weng Z. Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites. Nucleic Acids Research 2021, 50: d141-d149. PMID: 34755879, PMCID: PMC8728199, DOI: 10.1093/nar/gkab1039.Peer-Reviewed Original ResearchConceptsChIP-seqHT-SELEXTranscription factorsDNA-binding transcription factorsHT-SELEX experimentsChIP-seq dataChIP-seq experimentsAnnotation of variantsTF binding sitesCis-regulatory elementsTranscriptional regulatory proteinsDatabase of annotationsIntegrated analysisENCODE projectHuman genomeMotif modelsTrait heritabilityRegulatory proteinsBinding specificityGene expressionMotifBinding sitesCell typesRegulatory effectsComprehensive collectionInvestigating the Potential Roles of SINEs in the Human Genome
Zhang X, Pratt H, Weng Z. Investigating the Potential Roles of SINEs in the Human Genome. Annual Review Of Genomics And Human Genetics 2021, 22: 1-20. PMID: 33792357, DOI: 10.1146/annurev-genom-111620-100736.Peer-Reviewed Original ResearchConceptsShort interspersed nuclear elementsHuman genomePol II-transcribed genesFunctional regulatory elementsGene-rich regionsRNA polymerase IIIProximity to genesInterspersed nuclear elementsRegulate gene expressionPotential regulatory functionsSINE RNAsNonautonomous retrotransposonsPolymerase IIIGene regulationRegulatory elementsAutonomous retroelementsGenomeNuclear elementsGene expressionGenesRNARNA levelsPolPotential roleRetrotransposons