Abstract：
:C2H2 zinc finger proteins represent the largest and most enigmatic class of human transcription factors. Their C2H2-ZF arrays are highly variable, indicating that most will have unique DNA binding motifs. However, most of the binding motifs have not been directly determined. In addition, little is known about whether or how these proteins regulate transcription. Most of the ∼700 human C2H2-ZF proteins also contain at least one KRAB, SCAN, BTB, or SET domain, suggesting that they may have common interacting partners and/or effector functions. Here, we report a multifaceted functional analysis of 131 human C2H2-ZF proteins, encompassing DNA binding sites, interacting proteins, and transcriptional response to genetic perturbation. We confirm the expected diversity in DNA binding motifs and genomic binding sites, and provide motif models for 78 previously uncharacterized C2H2-ZF proteins, most of which are unique. Surprisingly, the diversity in protein-protein interactions is nearly as high as diversity in DNA binding motifs: Most C2H2-ZF proteins interact with a unique spectrum of co-activators and co-repressors. Thus, multiparameter diversification likely underlies the evolutionary success of this large class of human proteins.
journal_name
Genome Resjournal_title
Genome researchauthors
Schmitges FW,Radovani E,Najafabadi HS,Barazandeh M,Campitelli LF,Yin Y,Jolma A,Zhong G,Guo H,Kanagalingam T,Dai WF,Taipale J,Emili A,Greenblatt JF,Hughes TRdoi
10.1101/gr.209643.116subject
Has Abstractpub_date
2016-12-01 00:00:00pages
1742-1752issue
12eissn
1088-9051issn
1549-5469pii
gr.209643.116journal_volume
26pub_type
杂志文章相关文献
GENOME RESEARCH文献大全abstract：:A total of 202 genes were cytogenetically mapped to goat chromosomes, multiplying by five the total number of regional gene localizations in domestic ruminants (255). This map encompasses 249 and 173 common anchor loci regularly spaced along human and murine chromosomes, respectively, which makes it possible to perfor...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.8.9.901
更新日期：1998-09-01 00:00:00
abstract：:We report on the development of a methylation analysis workflow for optical detection of fluorescent methylation profiles along chromosomal DNA molecules. In combination with Bionano Genomics genome mapping technology, these profiles provide a hybrid genetic/epigenetic genome-wide map composed of DNA molecules spannin...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.240739.118
更新日期：2019-04-01 00:00:00
abstract：:The genetics of aging in the yeast Saccharomyces cerevisiae has involved the manipulation of individual genes in laboratory strains. We have instituted a quantitative genetic analysis of the yeast replicative lifespan by sampling the natural genetic variation in a wild yeast isolate. Haploid segregants from a cross be...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.136549.111
更新日期：2012-10-01 00:00:00
abstract：:A large database of copy number profiles from cancer genomes can facilitate the identification of recurrent chromosomal alterations that often contain key cancer-related genes. It can also be used to explore low-prevalence genomic events such as chromothripsis. In this study, we report an analysis of 8227 human cancer...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.140301.112
更新日期：2013-02-01 00:00:00
abstract：:Cross-talk between DNA methylation and histone modifications drives the establishment of composite epigenetic signatures and is traditionally studied using correlative rather than direct approaches. Here, we present sequential ChIP-bisulfite-sequencing (ChIP-BS-seq) as an approach to quantitatively assess DNA methylat...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.133728.111
更新日期：2012-06-01 00:00:00
abstract：:Paternal X chromosome inactivation occurs in rodent extraembryonic membranes and in all tissues of marsupials. Methylation of CpG islands occurs on the inactive X in eutherians and is considered to be a stabilizing mechanism. The only previous study of a marsupial X-linked CpG island was of the G6PD gene of the Virgin...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.6.2.114
更新日期：1996-02-01 00:00:00
abstract：:The acquisition of new genes, via horizontal transfer or gene duplication/diversification, has been the dominant mechanism thus far implicated in the evolution of microbial pathogenicity. In contrast, the role of many other modes of evolution--such as changes in gene expression regulation-remains unknown. A transition...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.134080.111
更新日期：2012-10-01 00:00:00
abstract：:Legionella pneumophila is an environmental bacterium and the leading cause of Legionnaires' disease. Just five sequence types (ST), from more than 2000 currently described, cause nearly half of disease cases in northwest Europe. Here, we report the sequence and analyses of 364 L. pneumophila genomes, including 337 fro...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.209536.116
更新日期：2016-11-01 00:00:00
abstract：:A region-specific ENU mutagenesis screen was conducted to elucidate the functional content of proximal mouse Chr 5. We used the visibly marked, recessive, lethal inversion Rump White (Rw) as a balancer in a three-generation breeding scheme to identify recessive mutations within the approximately 50 megabases spanned b...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.3826505
更新日期：2005-08-01 00:00:00
abstract：:Cellular senescence is a mechanism that virtually irreversibly suppresses the proliferative capacity of cells in response to various stress signals. This includes the expression of activated oncogenes, which causes Oncogene-Induced Senescence (OIS). A body of evidence points to the involvement in OIS of chromatin reor...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.225763.117
更新日期：2017-10-01 00:00:00
abstract：:Quantification of mRNA levels in human cortical brain biopsies and autopsies was performed using a fluorogenic 5' nuclease assay. The reproducibility of the assay using replica plates was 97%-99%. Relative quantities of mRNA from 16 different genes were evaluated using a statistical approach based on ANCOVA analysis. ...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.10.8.1219
更新日期：2000-08-01 00:00:00
abstract：:Despite the importance of duplicate genes for evolutionary adaptation, accurate gene annotation is often incomplete, incorrect, or lacking in regions of segmental duplication. We developed an approach combining long-read sequencing and hybridization capture to yield full-length transcript information and confidently d...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.237610.118
更新日期：2018-10-01 00:00:00
abstract：:When transcription is to the right of the promoter, the "top," mRNA-synonymous strand of DNA tends to be purine-rich. When transcription is to the left of the promoter, the top, mRNA-template strand tends to be pyrimidine-rich. This transcription-direction rule suggests that there has been an evolutionary selection pr...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.10.2.228
更新日期：2000-02-01 00:00:00
abstract：:Large copy number variants (CNVs) have been recently found as structural polymorphisms of the human genome of still unknown biological significance. CNVs are significantly enriched in regions with segmental duplications or low-copy repeats (LCRs). Williams-Beuren syndrome (WBS) is a neurodevelopmental disorder caused ...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.073197.107
更新日期：2008-05-01 00:00:00
abstract：:Cot-based cloning and sequencing (CBCS) is a powerful tool for isolating and characterizing the various repetitive components of any genome, combining the established principles of DNA reassociation kinetics with high-throughput sequencing. CBCS was used to generate sequence libraries representing the high, middle, an...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.2438004
更新日期：2005-01-01 00:00:00
abstract：:Long sequencing reads generated by single-molecule sequencing technology offer the possibility of dramatically improving the contiguity of genome assemblies. The biggest challenge today is that long reads have relatively high error rates, currently around 15%. The high error rates make it difficult to use this data al...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.213405.116
更新日期：2017-05-01 00:00:00
abstract：:Dual channel imaging and warping of two-dimensional (2D) protein gels were used to visualize global changes of the gene expression patterns in growing Bacillus subtilis cells during entry into the stationary phase as triggered by glucose exhaustion. The 2D gels only depict single moments during the cells' growth cycle...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.905003
更新日期：2003-02-01 00:00:00
abstract：:Although more than thirty mammalian genomes have been sequenced to draft quality, very few of these include the Y chromosome. This has limited our understanding of the evolutionary dynamics of gene persistence and loss, our ability to identify conserved regulatory elements, as well our knowledge of the extent to which...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.154286.112
更新日期：2013-09-01 00:00:00
abstract：:Genome-wide association studies (GWAS) have consistently implicated noncoding variation within the TCF7L2 locus with type 2 diabetes (T2D) risk. While this locus represents the strongest genetic determinant for T2D risk in humans, it remains unclear how these noncoding variants affect disease etiology. To test the hyp...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.123745.111
更新日期：2011-09-01 00:00:00
abstract：:Nucleosomes containing the CenH3 (CENPA or CENP-A) histone variant replace H3 nucleosomes at centromeres to provide a foundation for kinetochore assembly. CENPA nucleosomes are part of the constitutive centromere associated network (CCAN) that forms the inner kinetochore on which outer kinetochore proteins assemble. T...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.204784.116
更新日期：2016-09-01 00:00:00
abstract：:Transcript leaders (TLs) can have profound effects on mRNA translation and stability. To map TL boundaries genome-wide, we developed TL-sequencing (TL-seq), a technique combining enzymatic capture of m(7)G-capped mRNA 5' ends with high-throughput sequencing. TL-seq identified mRNA start sites for the majority of yeast...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.150342.112
更新日期：2013-06-01 00:00:00
abstract：:It is critical to avoid delays in detecting strain manipulations, such as the addition/deletion of a gene or modification of genes for increased virulence or antibiotic resistance, using genome analysis during an epidemic outbreak or a bioterrorist attack. Our objective was to evaluate the efficiency of genome analysi...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.071266.107
更新日期：2008-05-01 00:00:00
abstract：:The recent publication of the FANTOM mouse transcriptome has provided a unique opportunity to study the diversity of transcripts arising from a single gene locus. We have focused on the Gnas complex, as imprinting loci themselves provide unique insights into transcriptional regulation. Thirteen full-length cDNAs from ...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.955503
更新日期：2003-06-01 00:00:00
abstract：:We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which a...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.188839.114
更新日期：2016-01-01 00:00:00
abstract：:The world of noncoding RNAs (ncRNAs) is composed of an enormous and growing number of transcripts, ranging in length from tens of bases to tens of kilobases, involved in all biological processes and altered in expression and/or function in many types of human disorders. The premise of this review is the concept that n...
journal_title：Genome research
pub_type： 杂志文章,评审
doi：10.1101/gr.247239.118
更新日期：2019-09-01 00:00:00
abstract：:Advances in high-throughput technologies, such as ChIP-chip, and the completion of human and mouse genomic sequences now allow analysis of the mechanisms of gene regulation on a systems level. In this study, we have developed a computational genomics approach (termed ChIPModules), which begins with experimentally dete...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.5520206
更新日期：2006-12-01 00:00:00
abstract：:Tissue development and function are exquisitely dependent on proper regulation of gene expression, but it remains controversial whether the genomic signals controlling this process are subject to strong selective constraint. While some studies show that highly constrained noncoding regions act to enhance transcription...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.083089.108
更新日期：2008-12-01 00:00:00
abstract：:A DNA mutation detection protocol able to identify and characterize a previously unknown change in a given sequence in a rapid, efficient, sensitive, and inexpensive manner is required to take advantage of the resources now available to researchers through the genome sequencing projects. We have developed a method bas...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.gr-1578r
更新日期：2002-09-01 00:00:00
abstract：:Long and short interspersed elements (LINEs and SINEs) are retroelements that make up almost half of the human genome. L1 and Alu represent the most prolific human LINE and SINE families, respectively. Only a few Alu elements are able to retropose, and the factors determining their retroposition capacity are poorly un...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.384802
更新日期：2002-09-01 00:00:00
abstract：:We have assembled a first-generation anchor map of the mouse genome using a panel of 94 whole-genome-radiation hybrids (WG-RHs) and 271 sequence-tagged sites (STSs). This is the first genome-wide RH anchor map of a model organism. All of the STSs have been previously localized on the genetic map and are located 8.8 Mb...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.7.12.1153
更新日期：1997-12-01 00:00:00
