Denotes regulatory sequences nucleic acid. Medical search. Frequent questions

Therefore, to address the growing volumes of available genomic sequence, a number of algorithms that identify putative cis-regulatory modules and transcription factor binding sites using evolutionary comparisons, whole-genome data, and known descriptions of transcription factor binding sites, have been successfully developed. (biomedcentral.com)
Human endogenous retroviruses (HERVs) are a family of endogenous retroviruses that comprise the ~8.93% of the human genome sequence, with a high proportion being human specific. (mdpi.com)
100.000 cCREs in total), dispersed within the genome and present in cis-regulatory regions of ~81% of human genes, as calculated following gene enrichment analysis. (mdpi.com)
Understanding the regulatory landscape of the human genome is a long-standing objective of modern biology. (bvsalud.org)
Our annotations illuminate the regulatory functions of the human genome. (bvsalud.org)
Here we discuss recent and ongoing efforts to build gene regulatory maps, which aim to characterize the regulatory roles of all sequences in a genome. (bvsalud.org)
It has been increasingly recognized that other types of alterations in the genome, known as epigenetic changes, can modulate its structure and function without affecting the underlying DNA sequence. (ernolaszlo.com)
Here we report genome sequences and analyses of 44 diploid potatoes, as well as 2 species in the Etuberosum section. (nature.com)
We sequenced and assembled ~49 Mb into 15 super-scaffolds covering 92.83% of the M. phaseolina genome. (biomedcentral.com)
Whole-genome sequencing showed that historic and recent isolates of B. pertussis have substantial variation in genome organization and form separate phylogenetic clusters. (cdc.gov)
200 copies of insertion sequence 481 (IS481) in its genome ( 14 ). (cdc.gov)
ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. (umassmed.edu)
Here we provide a case study where we explore ways to integrate QTL data and microarray data for the pig, which has only a partial genome sequence. (biomedcentral.com)
Using the latest version of the draft sequence, the differentially expressed genes were mapped to the pig genome. (biomedcentral.com)
This enabled co-location of DE genes and previously studied QTL regions, but the draft genome sequence is still incomplete and will contain many errors. (biomedcentral.com)
This paper provides a case study for the integration of QTL data and microarray data for a species with limited genome sequence information and annotation. (biomedcentral.com)
Analyses of these interactions has previously been limited, obscuring their regulatory context, and the extent to which they occur throughout the genome. (elifesciences.org)
We show that stable 3D genome structure is an effective tool to guide searches for regulatory elements and, conversely, that regulatory elements in genetically diverse populations provide a means to infer 3D genome structure. (elifesciences.org)
Local regulatory mechanisms within the genome and their interaction with chromatin structure give rise to subtle variations in gene expression. (elifesciences.org)
Physical distance along a linear genome is a common metric for determining whether a putative regulatory element will affect a given gene's transcription. (elifesciences.org)
Hi-C applies high-throughput sequencing to collect fragments that are ligated due to spatial proximity within the genome. (biomedcentral.com)

The term "Histone H2A" is intentionally non-specific and refers to a variety of closely related proteins that vary often by only a few amino acids. (wikipedia.org)
Noncoding" sequences are not translated into proteins, and nucleic acids with such motifs need not deviate from the typical shape (e.g. the "B-form" DNA double helix). (wikipedia.org)
Specific sites within such regions are recognized by regulatory proteins (transcription factors), which act upon binding as transcriptional repressors or activators, controlling the rate of transcription. (biomedcentral.com)
One such important family of regulatory RBPs is the Serine-Arginine (SR) family of proteins. (molcells.org)
Examples include multiplex detection of single viruses, simultaneous detection of proteins and nucleic acid biomarkers, and front-to-back sample handling and single DNA detection on a single chip. (selectbiosciences.com)
functional" genes encoding proteins such as late embryogenesis-associated proteins, detoxification enzymes, heat shock proteins and molecular chaperones, which directly protect plants from abiotic stress, and "regulatory" genes encoding proteins such as protein kinases and transcription factors (TFs), which have roles in the perception and transduction of stress signals. (biomedcentral.com)
The predicted gene products with sequence similarity amongst the eiAU and SSL 2009a phage genomes include things like the putative small tail proteins tail tape mea certain, major tail proteins, major capsid proteins, head morphogenesis, phage terminase tiny subunit, and the phage terminase large subunit. (hivprotease-signal.com)
Interestingly, other struc tural proteins which includes the host specificity proteins, the tail assembly proteins, and specifically the tail fiber baseplate protein which has become suggested for exclusion in any sequence based mostly phage taxonomy scheme are certainly not shared in between the 2 genomes. (hivprotease-signal.com)
The amino acid sequences of one of many conserved structural pro teins likewise as among the non structural proteins have been selected for phylogenetic evaluation. (hivprotease-signal.com)
Moreover, as the word 'coding' refers to the relationship between nucleic acids and proteins, rather than the mere transcription of DNA into RNA, it is logical to call the strand with the mRNA sequence the coding strand, as in the first example. (genomicglossaries.com)

Though overrepresentation of TFBS motifs in regulatory DNA has been intensively exploited by many algorithms, it is still a difficult problem to distinguish regulatory from other genomic DNA. (biomedcentral.com)
The potential application of our method includes annotation of new genomic sequences and motif discovery. (biomedcentral.com)
Methods of this type assume that regulatory regions are highly conserved in cross-genomic comparison, and conserved segments can be extracted from evolutionary related genomes. (biomedcentral.com)
During the past decade, two major developments-the emergence of massively parallel, ultra-cheap DNA sequencing technologies and the use of these technologies as digital readouts for functional genomic assays-have led to a profusion of data describing various features of genomes, epigenomes, and transcriptomes 1 , 2 . (biorxiv.org)
Taxonomic classification of those E. ictaluri specific phages must rely on a synthesis of morphological and genomic details, taking into consideration that phage evolution continues to be profoundly directed by lateral gene transfer, and that a rational hierarchical technique of phage classification really should be based within the degree of DNA and protein sequence identity for several genetic loci. (hivprotease-signal.com)
The general genomic organization of the three new phages is shared by several members in the Siphoviridae loved ones of phages sequenced to date, and is supported through the previously described morphol ogy of these phages. (hivprotease-signal.com)

Transcriptional activator Islet-Brain 1 (IB1) is disclosed which is involved in the control of the GLUT2 and insulin genes by interacting with homologous cis-regulatory elements of the GLUT2 and insulin promoters, and to materials and methods deriving from this work. (justia.com)
This paper addresses the problem of recognising DNA cis-regulatory modules which are located far from genes. (biomedcentral.com)
This correlation indicates that linked genes are likely part of a shared regulatory mechanism in the cell. (frontiersin.org)
In both Gram-positive and Gram-negative bacteria, 'competence' for DNA uptake requires the coordinated action of rough-ly two dozen genes ( including some with regulatory func-tions ) organized within several operons. (asmblog.org)
The picture is si-milar in Vibrio - 'similar' refers to a great deal of protein homology among the numerous components in various species, despite vastly different regulatory circuits - for which the present model for competence involves 19+ genes, and, as core components: 1. (asmblog.org)
We detected the potential link between observed effects and insertion sequence element-induced changes in gene context only for a few genes. (cdc.gov)
integration of books with a Such translation survival from the page of observed patients is the sequence and host of genes. (naturheilpraxis-gisbert-fussek.de)
Synthetic antisense DNAs are used to hybridize to complementary sequences in target RNAs or DNAs to effect the functioning of specific genes for investigative or therapeutic purposes. (genomicglossaries.com)

Subsequent RNA sequence analysis and liquid chromatography with mass tandem spectrometry analyses showed that these variations translated into discretely separated transcriptomic and proteomic profiles. (cdc.gov)
Deep sequencing analyses of DNA associated with isolated nucleoli (NAD- seq) have shown that specific loci, termed nucleolus- associated domains (NADs) form frequent three- dimensional associations with nucleoli. (umassmed.edu)

In this work, we integrated somatic mutations, transcription, (hydroxy)methylation, histone modifications, and chromatin accessibility to reveal the complexity of the epigenetic landscape, the simultaneous presence of multiple regulatory mechanisms affecting drivers of leukemogenesis, and remodeling of the enhancer landscape as an important driver of intratumoral heterogeneity. (nature.com)
Studies are generally limited to examination of individual regions or overlapping single-nucleotide polymorphisms (SNPs) and open chromatin peaks with limited investigation into how these regulatory elements combine to affect gene transcription 1 , 2 . (elifesciences.org)

Regulatory regions of higher eukaryotes can be subdivided into proximal regulatory units - promoters - which are located close to and upstream of the gene, and distal transcription regulatory units called enhancers or cis-regulatory modules. (biomedcentral.com)
Synthetic promoters are designed by combining core promoters with different upstream regulatory sequences. (biorxiv.org)
To accomplish this, the transcriptional unit is preceded by regulatory elements, such as promoters and enhancers, that modulate production of its protein encoding transcript ( Figure 1.2 ). (ernolaszlo.com)

however the genetic sequence that encodes for this structure differs between variants. (wikipedia.org)
The recent expansion of repeated HERV sequences has offered a framework for genetic and epigenetic innovation. (mdpi.com)

The IB1cDNA encodes a 714 amino acid protein with a proline-rich region and a putative basic helix-loop-helix domain (bHLH). (justia.com)

In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. (wikipedia.org)
Usually, however, the first letter is I, and both [RK] choices resolve to R. Since the last choice is so wide, the pattern IQxxxRGxxxR is sometimes equated with the IQ motif itself, but a more accurate description would be a consensus sequence for the IQ motif. (wikipedia.org)

Given the complexity of human transcriptional regulation in vivo and the multitude of potential epigenetic mechanisms cooperating to regulate transcriptional activity, questions remain about the interplay of regulatory mechanisms in patients with CMML. (nature.com)

Comparatively short sequences (several hundred to several thousand base pairs, depending on thespecies) upstream or downstream of the transcription start site often play a major role in the regulation of gene expression. (biomedcentral.com)

I will also discuss their emerging regulatory roles in mediating and connecting post-transcriptional processes from the nucleus to the cytoplasm. (molcells.org)
The systems biology approach, combining data-driven modeling and model-driven experiments, provides a systematic and comprehensive perspective on the regulatory roles of miRNAs in gene regulatory networks [ 3 - 5 ]. (hindawi.com)

I analyzed the presence of HERV sequences on consensus cis-regulatory elements (cCREs) from ENCODE data. (mdpi.com)
Using the reference-free alignment across 241 mammalian genomes produced by the Zoonomia Consortium, we charted evolutionary trajectories for 0.92 million human candidate cis-regulatory elements (cCREs) and 15.6 million human transcription factor binding sites (TFBSs). (bvsalud.org)

Some of these are believed to affect the shape of nucleic acids (see for example RNA self-splicing), but this is only sometimes the case. (wikipedia.org)
Thus it can be inferred from our findings that the alternative splicing exon IDX from H-Ras, coupled with the immediately downstream intron sequences, may contain an ncRNA. (lidsen.com)

Important cis-regulatory sequences were identified within this promoter region including a functionally responsive PDX-1 element, a cyclic AMP responsive element, and three cis elements termed GTI, GTII and GTIII (3,36,53). (justia.com)
It was previously shown that transcription of a gene in eukaryotic cells is not always initiated from the same nucleotide, but that it can be initiated from a range of positions in the core promoter region, with an individual, sequence-influenced pattern for each gene ( 3 - 6 ). (biorxiv.org)

About 20% of TFBSs are transposable element-derived and exhibit intricate patterns of gains and losses during primate evolution whereas sequence variants associated with complex traits are enriched in constrained TFBSs. (bvsalud.org)
In addition to implement iceLogo in R to visualize differential amino acid sequence pattern, dagLogo can also test and visualize significant amino acid group patterns by classifying the amino acids into groups according to charge, chemistry and hydrophobicity and etc. (umassmed.edu)

(B) Expressions of RNASET2 in human tissues were analyzed in the Human Protein Atlas database, and the resulting transcript expression values, denoted normalized expression (NX), were calculated for each gene in every sample. (frontiersin.org)
The sense strand has the same sequence as the mRNA transcript. (genomicglossaries.com)

Recognition of regulatory DNA regions based on description of known transcription factor binding sites (TFBS). (biomedcentral.com)
At the core promoter, the regulatory region containing the transcription start site (TSS), all inputs regulating transcription are integrated. (biorxiv.org)
When a signal is sent to express a specific gene, the DNA sequence encoding that gene is used as a template to produce single-stranded RNA in a process called transcription. (ernolaszlo.com)

The advances in high-throughput sequencing technologies have demonstrated that tRNAs are differentially transcribed and expressed among tissues [ 3 ]. (biomedcentral.com)

To overcome the host plant defense response, M. phaseolina encodes a significant number of P450s, MFS type membrane transporters, glycosidases, transposases, and secondary metabolites in comparison to all sequenced ascomycete species. (biomedcentral.com)
The human cytoplasmatic pool of tRNA for the 20 proteinogenic amino acids and selenocysteine is composed of 48 isoacceptor families -those tRNA with different anticodons- divided into 253 different isodecoder species -those tRNAs that share the same anticodon but present sequence variations in other positions [ 1 , 2 ]. (biomedcentral.com)

The fundamental idea behind all these notations is the matching principle, which assigns a meaning to a sequence of elements of the pattern notation: a sequence of elements of the pattern notation matches a sequence of amino acids if and only if the latter sequence can be partitioned into subsequences in such a way that each pattern element matches the corresponding subsequence in turn. (wikipedia.org)
PROSITE allows the following pattern elements in addition to those described previously: The lower case letter 'x' can be used as a pattern element to denote any amino acid. (wikipedia.org)
In the current report, a systematic approach is implemented to catalogue regulatory elements within HERVs, as a roadmap to potential functions of HERV sequences in gene networks. (mdpi.com)
Compared with conventional conservation scores, fitCons scores show considerably improved prediction power for cis -regulatory elements. (biorxiv.org)

Within a sequence or database of sequences, researchers search and find motifs using computer-based techniques of sequence analysis, such as BLAST. (wikipedia.org)

3 Catabolite view как расшифровать of group nucleic E. construct cannot estimate produced into the site in the knowledge of type, because the parameter construct, LacY, is individual in the disease of exhibit( Winkler and Wilson, 1967). (scoutconnection.com)
We first construct a p21 regulatory network based on data from the literature and further expand it using algorithms that predict molecular interactions. (hindawi.com)

Currently, an increasing number of studies are being carried out to deepen our understanding of miRNA regulatory mechanisms and functions. (hindawi.com)

See also consensus sequence. (wikipedia.org)
We sequenced 264 LR-RNA-seq PacBio libraries totaling over 1 billion circular consensus reads (CCS) for 81 unique human and mouse samples. (bvsalud.org)

For view как расшифровать почерк рафология, short-term marginal alleles of structural h0tis as molecules, obstimevariable, or the temperature of Purification after using the medicine have made to baculovirus convergence and life of theory of Non-limiting optional parameters( 8, 11) and they can help better sites of the composite enhancers than the equal class of the sequence. (scoutconnection.com)

Phylogenetic analysis primarily based to the significant terminase subunit amino acid sequence plus the DNA polymerase I amino acid sequence of eiAU reveal that phages eiAU, eiDWS, and eiMSLS were most much like phage that infect other enterobacteria and Sodalis glossinidius. (hivprotease-signal.com)

We also discuss new techniques the field can leverage and emerging challenges it will face while striving to build gene regulatory maps of ever-increasing resolution and comprehensiveness. (bvsalud.org)
MicroRNAs (miRNAs) are potent effectors in gene regulatory networks where aberrant miRNA expression can contribute to human diseases such as cancer. (hindawi.com)
To investigate a gene regulatory network, an iterative process of four steps is needed. (hindawi.com)
In turn, these hypotheses, which provide reasonable explanations for the biological phenomenon, lead to an enhanced understanding of the gene regulatory network. (hindawi.com)
The application of the systems biology approach to the analysis of a gene regulatory network is demonstrated with a case study of the regulation of p21 by multiple miRNAs [ 4 ]. (hindawi.com)

An underexplored way of analyzing the rich data obtained from sequencing liquid biopsy-derived cfRNA liquid biopsy is weighted gene co-expression network analysis (WGCNA). (frontiersin.org)
To date, many studies have focused on WGCNA analysis of bulk or single-cell RNA (scRNA) sequencing data from tissue samples. (frontiersin.org)
Evolutionary turnover may cause inconsistencies between sequence orthology and functional homology that substantially limit this type of analysis. (biorxiv.org)

Non-coding RNAs (ncRNAs) have emerged as one of the most abundant regulatory molecules. (lidsen.com)
For many years, tRNAs have been considered as housekeeping molecules without any additional regulatory function, but compelling recent evidence of the intricacy of tRNA biology have proven that this initial misconception was far from reality. (biomedcentral.com)

For a better understanding of the regulatory role of miRNAs in coordinating gene expression, we here present a systems biology approach combining data-driven modeling and model-driven experiments. (hindawi.com)

However, such an approach offers little information as to the specific function of the conserved sequences. (biomedcentral.com)
The 'VirION' (Viral, long-read metagenomics via MinION sequencing) approach was first validated using mock communities where it was found to be as relatively quantitative as short-read methods and provided significant improvements in recovery of viral genomes. (peerj.com)

We show that, in the data used, our method is able to distinguish cis-regulatory modules by exploiting statistical differences between the probability distributions of similar words in regulatory and other DNA. (biomedcentral.com)
We have generated fitCons scores for three human cell types based on public data from EN-CODE. (biorxiv.org)
Many computational methods for gaining functional insights from sequence data are based on the simple, but powerful, observation that functionally important nucleotides tend to remain unchanged over evolutionary time, because mutations at these sites generally reduce fitness and are therefore eliminated by natural selection 7 - 15 . (biorxiv.org)

Direct DNA damage can induce changes to the sequence variants. (wikipedia.org)

Well-established procedures can aggregate and transform sequenced reads into a Hi-C matrix (called contact map ) at a specific resolution. (biomedcentral.com)

Liquid biopsy represents a promising alternative to invasive tissue biopsies in particular for cancer diagnosis as it enables the study of cell-free (cf) nucleic acids in the blood, which includes cfDNA and various cfRNAs (e.g., protein-coding, lncRNA, microRNA, etc. (frontiersin.org)
The substantial terminase subunit which is a structural protein is together with the portal protein viewed as essentially the most universally conserved gene sequence in phages, consequently they are good possibilities to assist in phage classification. (hivprotease-signal.com)

(A) Amino acid sequence of RNases T2 from human, mouse, rabbit, fruit fly, and classical swine fever virus showing the wide evolutionary conservation of these enzymes. (frontiersin.org)

This has led to the concept of a "local area" in which most regulatory interactions take place. (elifesciences.org)

There are many superfamilies of Znf motifs, varying in both sequence and structure. (embl-heidelberg.de)
The likelihood of interaction was most strongly defined by the three-dimensional (3D) domain structure rather than linear DNA sequence. (elifesciences.org)

This is an actively progressing area, as more and more sequenced genomes appear. (biomedcentral.com)

Extracting clustered recognition motifs is one of the most reliable techniques, but is limited to the recognition of similarly regulated cis-regulatory regions. (biomedcentral.com)

Understanding these regulatory processes is therefore essential for understanding cellular responses to changes in environmental conditions. (biorxiv.org)

The select agent regulations provision for the exclusion of attenuated select agents or modified toxins that no longer have the potential to pose a severe threat to public health and safety is an important mechanism for reducing the regulatory burden on entities that do not need to work with the fully virulent or toxic forms of the agent or toxin. (cdc.gov)

This rat insulin promoter element 3 (RIPE3) is an important enhancer sequence sufficient to confer .beta. (justia.com)

The term "epigenetics" was initially defined by Conrad Waddington in the 1940s, but in the modern context, it was formally defined in the 1990s by Wolffe and Matzkeset as "the study of heritable changes in gene expression that occur without a change in DNA sequence" (Alokail 2015). (ernolaszlo.com)

Here, we highlight that an important RNA sequence region, encompassing an exon-intron hairpin loop (also called IDX-rasISS1), of the H-Ras pre-mRNA may encode an ncRNA that regulates p68 RNA helicase. (lidsen.com)

In particular, the use of IB1 nucleic acid, IB1 polypeptides and anti-IB1 antibodies in the diagnosis, and prophylactic and therapeutic treatment of conditions such as diabetes and neurological diseases such as dementia and/or parkinsonism is disclosed. (justia.com)
In particular, the present invention relates to the uses of IB1 nucleic acid, IB1 polypeptides and anti-IB1antibodies in the diagnosis, and prophylactic and therapeutic treatment of conditions such as diabetes and neurological diseases such as dementia and/or parkinsonism. (justia.com)

view как расшифровать acids within or near the results. (scoutconnection.com)

The invention also relates to nucleic acid constructs, vectors, and host cells comprising the nucleic acid sequences as well as methods for producing the trichodiene synthases. (justia.com)

When tested in vitro, IB1 bound specifically to the GTII cis element of the GLUT2 gene and to an homologous regulatory sequence of the insulin promoter termed RIPE3. (justia.com)

Here we established a low-cost, low-input, high throughput alternative sequencing and informatics workflow to improve viral metagenomic assemblies using short-read and long-read technology. (peerj.com)

Anatomy10

Organisms17

Diseases2

Chemicals and Drugs83

Analytical, Diagnostic and Therapeutic Techniques and Equipment35

Phenomena and Processes114

Disciplines and Occupations3

Technology, Industry, Agriculture1

Information Science10

Health Care2

Genome21

Proteins10

Genomic6

Genes8

Analyses2

Chromatin2

Promoters3

Genetic2

Putative1

Motif2

Epigenetic1

Upstream1

Roles2

CCREs2

Splicing2

Promoter region2

Patterns2

Transcript2

Transcription3

Differentially1

Species2

Elements4

Researchers1

Construct2

Mechanisms1

Consensus2

Enhancers1

Phylogenetic1

Gene regulatory5

Analysis3

Molecules2

Systems Biology Approach1

Approach2

Data3

Variants1

Specific1

Protein2

Evolutionary1

Interactions1

Structure2

Genomes1

Recognition1

Understanding1

Mechanism1

Sufficient1

Expression1

Important1

Diagnosis2

Results1

Methods1

Element1

Alternative1