A comprehensive catalog of human KRAB-associated zinc finger genes: Insights into the evolutionary history of a large family of transcriptional repressors Export

@article{citeulike:804192, abstract = {10.1101/gr.4842106 Kr\"{u}ppel-type zinc finger (ZNF) motifs are prevalent components of transcription factor proteins in all eukaryotes. KRAB-ZNF proteins, in which a potent repressor domain is attached to a tandem array of DNA-binding zinc-finger motifs, are specific to tetrapod vertebrates and represent the largest class of ZNF proteins in mammals. To define the full repertoire of human KRAB-ZNF proteins, we searched the genome sequence for key motifs and then constructed and manually curated gene models incorporating those sequences. The resulting gene catalog contains 423 KRAB-ZNF protein-coding loci, yielding alternative transcripts that altogether predict at least 742 structurally distinct proteins. Active rounds of segmental duplication, involving single genes or larger regions and including both tandem and distributed duplication events, have driven the expansion of this mammalian gene family. Comparisons between the human genes and ZNF loci mined from the draft mouse, dog, and chimpanzee genomes not only identified 103 KRAB-ZNF genes that are conserved in mammals but also highlighted a substantial level of lineage-specific change; at least 136 KRAB-ZNF coding genes are primate specific, including many recent duplicates. KRAB-ZNF genes are widely expressed and clustered genes are typically not coregulated, indicating that paralogs have evolved to fill roles in many different biological processes. To facilitate further study, we have developed a Web-based public resource with access to gene models, sequences, and other data, including visualization tools to provide genomic context and interaction with other public data sets.}, address = {Genome Biology, Lawrence Livermore National Laboratory, CA 94550, USA.}, author = {Huntley, Stuart and Baggott, Daniel M. and Hamilton, Aaron T. and Tran-Gyamfi, Mary and Yang, Shan and Kim, Joomyeong and Gordon, Laurie and Branscomb, Elbert and Stubbs, Lisa}, citeulike-article-id = {804192}, citeulike-linkout-0 = {http://dx.doi.org/10.1101/gr.4842106}, citeulike-linkout-1 = {http://genome.cshlp.org/content/16/5/669.abstract}, citeulike-linkout-2 = {http://genome.cshlp.org/content/16/5/669.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/16606702}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=16606702}, doi = {10.1101/gr.4842106}, issn = {1088-9051}, journal = {Genome Research}, keywords = {human, tf}, month = {May}, number = {5}, pages = {669--677}, posted-at = {2006-08-17 14:44:57}, priority = {2}, title = {A comprehensive catalog of human KRAB-associated zinc finger genes: Insights into the evolutionary history of a large family of transcriptional repressors}, url = {http://dx.doi.org/10.1101/gr.4842106}, volume = {16}, year = {2006} }

TY - JOUR ID - citeulike:804192 L3 - citeulike-article-id:804192 N2 - 10.1101/gr.4842106 Krüppel-type zinc finger (ZNF) motifs are prevalent components of transcription factor proteins in all eukaryotes. KRAB-ZNF proteins, in which a potent repressor domain is attached to a tandem array of DNA-binding zinc-finger motifs, are specific to tetrapod vertebrates and represent the largest class of ZNF proteins in mammals. To define the full repertoire of human KRAB-ZNF proteins, we searched the genome sequence for key motifs and then constructed and manually curated gene models incorporating those sequences. The resulting gene catalog contains 423 KRAB-ZNF protein-coding loci, yielding alternative transcripts that altogether predict at least 742 structurally distinct proteins. Active rounds of segmental duplication, involving single genes or larger regions and including both tandem and distributed duplication events, have driven the expansion of this mammalian gene family. Comparisons between the human genes and ZNF loci mined from the draft mouse, dog, and chimpanzee genomes not only identified 103 KRAB-ZNF genes that are conserved in mammals but also highlighted a substantial level of lineage-specific change; at least 136 KRAB-ZNF coding genes are primate specific, including many recent duplicates. KRAB-ZNF genes are widely expressed and clustered genes are typically not coregulated, indicating that paralogs have evolved to fill roles in many different biological processes. To facilitate further study, we have developed a Web-based public resource with access to gene models, sequences, and other data, including visualization tools to provide genomic context and interaction with other public data sets. IS - 5 JF - Genome Research SN - 1088-9051 AD - Genome Biology, Lawrence Livermore National Laboratory, CA 94550, USA. EP - 677 TI - A comprehensive catalog of human KRAB-associated zinc finger genes: Insights into the evolutionary history of a large family of transcriptional repressors VL - 16 SP - 669 KW - human KW - tf AU - Huntley, Stuart AU - Baggott, Daniel AU - Hamilton, Aaron AU - Tran-Gyamfi, Mary AU - Yang, Shan AU - Kim, Joomyeong AU - Gordon, Laurie AU - Branscomb, Elbert AU - Stubbs, Lisa PY - 2006/05// UR - http://dx.doi.org/10.1101/gr.4842106 ER -