Sentences with phrase «transcription start»

Host proteins, including specific transcription factors with binding sites near transcription start sites, are necessary for this specificity (32 - 33).

However, it is still unknown where exactly transcription starts and which regularly recurring DNA segments, DNA modifications or structural modifications of the DNA are required to determine the start of transcription.

When mapped to the genome, they tell us not only about the level of expression for various genes, but also which transcription start sites were used.

Further studies are needed to determine whether the specific use of transcription starting points is a widely disseminated mechanism for gene regulation.

The data indicate that the epigenetic response to maternal care involves not only single candidate gene promoters but includes transcriptional and intragenic sequences, as well as those residing distantly from transcription start sites.

The approach was pioneered at RIKEN and is useful for determining transcription start sites (i.e., the regions of the genome corresponding to the capped 5 ′ end of RNAs).

The authors developed a method called decomposition - based peak identification (DPI) to cluster CAGE tags and identify the peaks, which should represent transcription start sites (TSSs).

A, schematic representation of serial p21waf1 / cip1 promoter — driven luciferase reporters used in transactivation assay: p21 - Luc contains the 2.3 - kb full - length of p21waf1 / cip1 promoter (from − 2,326 to +10 nucleotide related transcription start site); its derivatives (− 159 / +8) p21 - Luc, (− 123 / +8) p21 - Luc, (− 84 / +8) p21 - Luc, (− 76 / +8) p21 - Luc, (− 63 / +8) p21 - Luc, and (− 56 / +8) p21 - Luc contain a series of deleted promoters of p21waf1 / cip1.

First, the authors assigned lncRNAs to an epigenomic class based on the overlap between their strongest transcription start site (TSS) with DNase I hypersensitive regulatory regions defined by the RoadMap Epigenomics Consortium:

An imprinting mark region characterized by paternal allele specific methylation has been suggested to reside in a GC - rich region of 400 bp direct repeats starting at -2 kb relative to the H19 transcription start and extending upstream.

Numbering indicates the location of the major enhancer clusters relative to the MYC transcription start site.

The current project iteration, FANTOM5, has mapped enhancers and transcription start sites in hundreds of primary human cell types.

Exchange with components of a Saccharomyces cerevisiae system was undertaken to reveal the factor or factors responsible for the difference in location of the transcription start site, about 30 base pairs and 40 to 120 base pairs downstream of the TATA box in S. pombe and S. cerevisiae, respectively.

Transcription start site — associated RNAs (TSSa - RNAs) nonrandomly flank active promoters, with peaks of antisense and sense short RNAs at 250 nucleotides upstream and 50 nucleotides downstream of TSSs, respectively.

The transcriptional repressor (CRISPRi) library contains 10 sgRNAs for each transcription start site in those 15,977 human genes.

The activator (CRISPRa) sgRNA library uses the sunCas9 system and contains 10 sgRNAs for each transcription start site in 15,977 human genes.

Supporting this notion is the fact that the DDX3 - induced activation level of serial 5 ′ - deleted p21waf1 / cip1 promoter — directed reporters that lack two p53 responsive elements (at the − 2,301 and − 1,394 nucleotide region upstream of the transcription start site; ref.

Plasmid p21 - Luc was constructed by insertion of a 2.3 - kb HindIII fragment (spanning the promoter region − 2,325 to +8 related to transcription start site of human p21waf1 / cip1 gene) from pWWP - Luc (16) into HindIII - treated GL2 vector (Promega Corp., Madison, WI).

Moreover, DDX3 exerted its transactivation function on p21waf1 / cip1 promoter through an ATPase - dependent but helicase - independent mechanism, and the four Sp1 sites located within the − 123 to − 63 region, relative to the transcription start site of p21waf1 / cip1 promoter, were essential for the response to DDX3.

That being said, we generally pick guides by putting the promoter of the gene into a gRNA finder such as WU - CRISPR (6) or our lab's sgRNA scorer 1.0 (7) and picking whichever guides are closest to the transcription start site (TSS).

This observation suggested that the DDX3 responsive region within the p21waf1 / cip1 promoter was located between − 123 to − 63 upstream of the transcription start site.

Multiple Sp1 sites (Sp1 - 1, Sp1 - 2, Sp1 - 3, and Sp1 - 4) located at − 123 to − 63 related to transcription start site are essential for the transactivation of DDX3 on p21waf1 / cip1 promoter.

CAGE isolates the 5 ′ end of long RNA molecules, providing high - resolution mapping of the transcription start sites and core promoters of genes.

Transcription of the HMOX1 gene is controlled, in part, through the binding of either Nrf2 or Bach1 to an ARE, termed HMOX1 E2, located approximately 9 kbp from the transcription start site.

The analysis of 6.6 kb of newly generated upstream H19 sequence determined in this study identified a series of the direct 400 bp repeats that extends to approximately -5.3 kb relative to the transcription start.

(B) Most genes with a high number of isoforms arise from multiple combinations of slight variations in the (a) transcription start site, (b) the differential inclusion of specific exons and (c) the difference in splice sites, which produces exons that differ in length by a few nucleotides.

They helped reveal the transcription start sites and antisense transcripts of microbial species, improving the microbial genome annotation.

Numbers for the nucleotides are relative to the transcription start site (+1) of MELK.

Shortly after initiation of transcription, Pol II pauses near the transcription start site largely due to the actions of two negative transcription elongation factors NELF and DSIF (Peterlin and Price, 2006).

CpG islands are small regions with unusually high CpG densities that are typically unmethylated [82], particularly when found near the transcription start sites of genes [82].

We mapped the methylation state of the promoters of nearly 20 000 genes and 400 microRNAs in triplicate using custom designed 244 K promoter tiling arrays (Agilent technologies) containing probes selected to tile ∼ 1000 bp upstream to ∼ 250 bp downstream of the transcription start site.

A map of the sites relative to the transcription start site is shown above the bar graph.