Abstract:
:Most mutations in cancer genomes occur in the non-coding regions with unknown impact on tumor development. Although the increase in the number of cancer whole-genome sequences has revealed numerous putative non-coding cancer drivers, their information is dispersed across multiple studies making it difficult to understand their roles in tumorigenesis of different cancer types. We have developed CNCDatabase, Cornell Non-coding Cancer driver Database (https://cncdatabase.med.cornell.edu/) that contains detailed information about predicted non-coding drivers at gene promoters, 5' and 3' UTRs (untranslated regions), enhancers, CTCF insulators and non-coding RNAs. CNCDatabase documents 1111 protein-coding genes and 90 non-coding RNAs with reported drivers in their non-coding regions from 32 cancer types by computational predictions of positive selection using whole-genome sequences; differential gene expression in samples with and without mutations; or another set of experimental validations including luciferase reporter assays and genome editing. The database can be easily modified and scaled as lists of non-coding drivers are revised in the community with larger whole-genome sequencing studies, CRISPR screens and further experimental validations. Overall, CNCDatabase provides a helpful resource for researchers to explore the pathological role of non-coding alterations in human cancers.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Liu EM,Martinez-Fundichely A,Bollapragada R,Spiewack M,Khurana Edoi
10.1093/nar/gkaa915subject
Has Abstractpub_date
2021-01-08 00:00:00pages
D1094-D1101issue
D1eissn
0305-1048issn
1362-4962pii
5937084journal_volume
49pub_type
杂志文章abstract::Escherichia coli cells lacking the ribosomal RNA processing enzyme RNase III do no excise the normal RNA precursors p16a (17S) and p23a from nascent rRNA transcripts. These cells produce, instead, slightly larger p16b and p23b precursors. Digestion of p16b or p23b rRNA with RNases A plus T1 yields double-stranded frag...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.8.1873
更新日期:1980-04-25 00:00:00
abstract::DEAD-box helicases catalyze the non-processive unwinding of double-stranded RNA (dsRNA) at the expense of adenosine triphosphate (ATP) hydrolysis. Nucleotide and RNA binding and unwinding are mediated by the RecA domains of the helicase core, but their cooperation in these processes remains poorly understood. We there...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku747
更新日期:2014-01-01 00:00:00
abstract::Proteins engage in highly selective interactions with their macromolecular partners. Sequence variants that alter protein binding affinity may cause significant perturbations or complete abolishment of function, potentially leading to diseases. There exists a persistent need to develop a mechanistic understanding of i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw374
更新日期:2016-07-08 00:00:00
abstract::RNA editing by adensosine deaminases is a widespread mechanism to alter genetic information in metazoa. In addition to modifications in non-coding regions, editing contributes to diversification of protein function, in analogy to alternative splicing. However, although splicing programs respond to external signals, fa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1045
更新日期:2013-01-01 00:00:00
abstract::The specific recognition of homopurine-homo pyrimidine regions in duplex DNA by triplex-forming oligonucleotides (TFOs) provides an attractive strategy for genetic manipulation. Alkylation of nucleobases with functionalized TFOs would have the potential for site-directed mutagenesis. Recently, we demonstrated that a T...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng031
更新日期:2003-03-15 00:00:00
abstract::To confirm the activity of an initial small molecule 'hit compound' from an activity screening, one needs to probe the structure-activity relationships by testing close analogs. The multi-fingerprint browser presented here (http://dcb-reymond23.unibe.ch:8080/MCSS/) enables one to rapidly identify such close analogs am...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku379
更新日期:2014-07-01 00:00:00
abstract::PCAF and hGCN5 are distinct human genes that encode proteins related to the yeast histone acetyltransferase and transcriptional adapter GCN5. The PCAF protein shares extensive similarity with the 439 amino acids of yGCN5, but it has an approximately 350 amino acid N-terminal extension that interacts with the transcrip...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.12.2948
更新日期:1998-06-15 00:00:00
abstract::RNA molecules play different roles in coding, decoding and gene expression regulation. Such roles are often associated to the RNA secondary or tertiary structures. The folding dynamics lead to multiple secondary structures of long RNA molecules, since an RNA molecule might fold into multiple distinct native states. De...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1249
更新日期:2014-12-16 00:00:00
abstract::Gene expression circuitries, which enable cells to detect precise levels within a morphogen concentration gradient, have a pivotal impact on biological processes such as embryonic pattern formation, paracrine and autocrine signalling, and cellular migration. We present the rational synthesis of a synthetic genetic cir...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq671
更新日期:2010-10-01 00:00:00
abstract::DNA methylation is the best-studied epigenetic modification and describes the conversion of cytosine to 5-methylcytosine. The importance of this phenomenon is that aberrant promoter hypermethylation is a common occurrence in cancer and is frequently associated with gene silencing. Various techniques are currently avai...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnj017
更新日期:2006-02-07 00:00:00
abstract::Human stem cells are promising sources for regenerative therapy. To ensure safety of future therapeutic applications, the differentiation potency of stem cells has to be tested and be widely opened to the public. The potency is generally assessed by teratoma formation comprising differentiated cells from all three ger...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1096
更新日期:2016-01-04 00:00:00
abstract::We investigate the role of water molecules in 89 protein-RNA complexes taken from the Protein Data Bank. Those with tRNA and single-stranded RNA are less hydrated than with duplex or ribosomal proteins. Protein-RNA interfaces are hydrated less than protein-DNA interfaces, but more than protein-protein interfaces. Majo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku679
更新日期:2014-09-01 00:00:00
abstract::We have analysed DNA modification in a HapII site (CCGG) present in the major intron of the discontinuous rabbit beta-globin gene. In most somatic tissues, including erythroid and non-erythroid tissues, about 50% of the DNA is resistant to cleavage at this site by HapII, though 100% cleavage is found with the isoschiz...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.12.4631
更新日期:1978-12-01 00:00:00
abstract::A restriction endonuclease, ApaI, has been partially purified from Acetobacter pasteurianus. This enzyme cleaves bacteriophage lambda DNA and Simian virus 40 DNA at one site, adenovirus-2 DNA at more than nine sites, but it does not cleave phi X174 DNA nor plasmid pBR322 DNA. This enzyme recognizes the sequence (formu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.13.4409
更新日期:1983-07-11 00:00:00
abstract::The conformations of supercoiled (sc) DNA and linear DNA bound to polylysine (PL)-coated mica were investigated by scanning force microscopy (SFM) in solution. From the polymer statistical analysis of linear DNA, we could distinguish between re-arrangements or trapping of the DNA on the surface. Conditions of re-arran...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng137
更新日期:2003-11-15 00:00:00
abstract::A cDNA clone named 1A11 was isolated in a screen for genes that are activated by both mesoderm inducing factors FGF and activin in animal explants of Xenopus laevis embryos. In undisturbed embryos, 1A11 is expressed during the gastrula stage in the entire marginal zone where mesoderm originates, and later in the somit...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.10.2375
更新日期:1993-05-25 00:00:00
abstract::Cell specific expression of the insulin gene is achieved through transcriptional mechanisms operating on 5' flanking DNA elements. In the enhancer of rat I insulin gene, two elements, the Nir and Far boxes, located at positions -104 and -233 respectively and containing the same octameric motif are essential for B cell...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.7.1595
更新日期:1993-04-11 00:00:00
abstract::Gene duplications are a major source of evolutionary innovations. Understanding the functional divergence of duplicates and their role in genetic robustness is an important challenge in biology. Previously, analyses of genetic robustness were primarily focused on duplicates essentiality and epistasis in several labora...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1200
更新日期:2014-02-01 00:00:00
abstract::Antisense oligodeoxynucleotides (ODNs) have biological activity in treating various forms of cancer. The antisense effects of two types of 20mer ODNs, phosphorothioate-modified ODNs (S-ODNs) and S-ODNs with 12 2'-O-methyl groups (Me-S-ODNs), targeted to sites 109 and 277 of bcl-2 mRNA, were compared. Both types were a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh516
更新日期:2004-04-02 00:00:00
abstract::A correlation between histone acetylation and transcription has been noted for a long time, but little is known about what step(s) in the transcription cycle is influenced by acetylation. We have examined the immediate transcriptional response to histone deacetylase (HDAC) inhibition, and find that release of promoter...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa234
更新日期:2020-05-21 00:00:00
abstract::Allostery is comprehensively studied for natural macromolecules, such as proteins and nucleic acids. Here, we present controllable allostery of synthetic DNA nanostructure-enzyme systems. Rational designs of the synthetic allosteric systems are based on an in-depth understanding of allosteric sites with several types ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa488
更新日期:2020-07-27 00:00:00
abstract::Mycobacterium tuberculosis (Mtb) Cmr (Rv1675c) is a CRP/FNR family transcription factor known to be responsive to cAMP levels and during macrophage infections. However, Cmr's DNA binding properties, cellular targets and overall role in tuberculosis (TB) complex bacteria have not been characterized. In this study, we u...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv889
更新日期:2016-01-08 00:00:00
abstract::N-nitrosation of glycine and its derivatives generates potent alkylating agents that can lead to the formation of O(6)-carboxymethylguanine (O(6)-CMG) in DNA. O(6)-CMG has been identified in DNA derived from human colon tissue, and its occurrence has been linked to diets high in red and processed meats. By analogy to ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt198
更新日期:2013-05-01 00:00:00
abstract::Ribosomal RNA (rRNA) in intact ribosomes is cleaved into discrete products on incubation of reticulocyte lysates or L-cell extracts with ppp(A2'p)3A. Cleavage of rRNA may, therefore, provide a useful assay for 2-5A (ppp)A2'p)nA; n = 2 to 4) or for the presence of a 2-5A-dependent nuclease. The results with reticulocyt...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.7.1571
更新日期:1981-04-10 00:00:00
abstract::NetMHC-3.0 is trained on a large number of quantitative peptide data using both affinity data from the Immune Epitope Database and Analysis Resource (IEDB) and elution data from SYFPEITHI. The method generates high-accuracy predictions of major histocompatibility complex (MHC): peptide binding. The predictions are bas...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn202
更新日期:2008-07-01 00:00:00
abstract::The circadian clock comprises transcriptional feedback loops of clock genes. Cryptochromes are essential components of the negative feedback loop in mammals as they inhibit CLOCK-BMAL1-mediated transcription. We purified mouse CRY1 (mCRY1) protein complexes from Sarcoma 180 cells to determine their roles in circadian ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn1013
更新日期:2009-03-01 00:00:00
abstract::A minizyme is a hammerhead ribozyme with short oligonucleotide linkers instead of stem-loop II. In a previous study we demonstrated that a minizyme with high activity forms a dimeric structure with a common stem II. Because of their dimeric structure, minizymes are potentially capable of cleaving a substrate at two di...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.12.2302
更新日期:1996-06-15 00:00:00
abstract::Type II CRISPR-Cas9 RNA-guided nucleases are widely used for genome engineering. Type II-A SpCas9 protein from Streptococcus pyogenes is the most investigated and highly used enzyme of its class. Nevertheless, it has some drawbacks, including a relatively big size, imperfect specificity and restriction to DNA targets ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz1225
更新日期:2020-02-28 00:00:00
abstract::Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. The CORUM (http://mips.gsf.de/genre/proj/corum/index.html) database is a collection of experimentally verified mammalian protein complexes. Information is manually derived by critical reading of the scient...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm936
更新日期:2008-01-01 00:00:00
abstract::Module identification is a frequently used approach for mining local structures with more significance in global networks. Recently, a wide variety of bilayer networks are emerging to characterize the more complex biological processes. In the light of special topological properties of bilayer networks and the accompan...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw679
更新日期:2016-11-16 00:00:00