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Identifying Ortholog Selective Fragment Molecules for Bacterial Glutaredoxins by NMR and Affinity Enhancement by Modification with an Acrylamide Warhead

Ram B. Khattri, Daniel L. Morris, Stephanie M. Bilinovich, Erendra Manandhar, Kahlilah R. Napper, Jacob W. Sweet, David A. Modarelli, Thomas C. Leeper
2019 Molecules  
well for future work to identify potent, species specific drug molecules targeted against proteins heretofore deemed undruggable.  ...  Reactivity of the top warhead-fragment lead suggests that the ortholog selectivity observed for a fragment hit can translate into a substantial kinetic advantage in the mature warhead lead, which bodes  ...  Figure 1 depicts these three methods used in congress to identify an exemplary fragment, RK246. 3 evolutionarily related protein orthologs using the exact same conditions and panel of fragments to identify  ... 
doi:10.3390/molecules25010147 pmid:31905878 pmcid:PMC6983068 fatcat:h7e33rruyvfuzm7qx2w6xs7ilm

An Egg Apparatus-Specific Enhancer of Arabidopsis, Identified by Enhancer Detection

W. Yang
2005 Plant Physiology  
Using the Ds-based enhancer-detector line ET253, we have cloned an egg apparatus-specific enhancer (EASE) from Arabidopsis (Arabidopsis thaliana).  ...  Our data showed that this enhancer is unique in the Arabidopsis genome, is conserved among different accessions, and shows an unusual pattern of sequence variation.  ...  RESULTS Egg Apparatus-Specific GUS Expression in the Enhancer-Detector Line ET253 To identify genes expressed in the female gametophyte, a collection of enhancer-detector lines was screened for GUS activity  ... 
doi:10.1104/pp.105.068262 pmid:16258010 pmcid:PMC1283777 fatcat:f7tmnccsoncmzhrg23zippmrpm

Chromatin profiling ofDrosophilaCNS subpopulations identifies active transcriptional enhancers

Joseph C. Pearson, Daniel J. McKay, Jason D. Lieb, Stephen T. Crews
2016 Development  
Midline enhancer fragments with a midline FAIRE peak tend to be near midline-expressed genes, whereas midline enhancers without a midline FAIRE peak were often distant from midline-expressed genes and  ...  In a complementary analysis, we compared a large dataset of fragments that drive midline expression in vivo with the FAIRE data.  ...  Through cloning of thousands of genomic fragments for transgenic reporter analysis, the Janelia Research Campus (JRC) FlyLight project identified 438 fragments with enhancer activity associated with 253  ... 
doi:10.1242/dev.136895 pmid:27802137 pmcid:PMC5087646 fatcat:m7mue75zb5er7hyzyvk4irdqvq

Start from Scratch: Precisely Identify Massive Active Enhancers by Sequencing [article]

Xiusheng Zhu, Lei Huang, Qing Li, Yubo Zhang
2019 bioRxiv   pre-print
Enhancer loci identified by ChIP-Seq or other experimental methods occupy hundreds of base pairs on the genome.  ...  With the results, we successfully identify hundreds known accurate active enhancer sequences as expected.  ...  In the study, we develop a new technology termed as MAE-Seq (Massive Active enhancers by sequencing) to identify the precise position of enhancers.  ... 
doi:10.1101/604686 fatcat:pjorlpegx5hnhejot6mf6kxqde

Analysis of vertebrate SCL loci identifies conserved enhancers

Berthold Göttgens, Linda M. Barton, James G.R. Gilbert, Anthony J. Bench, Maria-José Sanchez, Sabine Bahn, Shailesh Mistry, Darren Grafham, Amanda McMurray, Mark Vaudin, Enrique Amaya, David R. Bentley (+1 others)
2000 Nature Biotechnology  
Comparisons between mammalian and chicken sequences identified some, but not all, SCL enhancers.  ...  This combination of long-range comparative sequence analysis with a high-throughput transgenic bioassay provides a powerful strategy for identifying and characterizing developmentally important enhancers  ...  SCL enhancers have been identified in a region of ∼40 kb in the mouse 23 .  ... 
doi:10.1038/72635 pmid:10657125 fatcat:gb3hntcsrfgffnkokggvdenr7a

An enhancer trap in the ascidian Ciona intestinalis identifies enhancers of its Musashi orthologous gene

Satoko Awazu, Akane Sasaki, Terumi Matsuoka, Nori Satoh, Yasunori Sasakura
2004 Developmental Biology  
These results clearly demonstrate that an enhancer trap event that entrapped enhancers of Ci-Musashi occurred in C. intestinalis. D  ...  The enhancer trap technique, established in Drosophila melanogaster, is a very sophisticated tool.  ...  Enhancer trapping is a useful technique to identify genes with a novel expression pattern and enhancers responsible for the specific expression.  ... 
doi:10.1016/j.ydbio.2004.08.029 pmid:15501231 fatcat:af34lg5l3zfxvdf7bnpdpdkhiq

A DNA Contact Map for the Mouse Runx1 Gene Identifies Novel Hematopoietic Enhancers [article]

Judith Marsman, Amarni Thomas, Motomi Osato, Justin M. O'Sullivan, Julia A. Horsfield
2017 bioRxiv   pre-print
Here we use circular chromosome conformation capture sequencing to identify DNA interactions with the P1 and P2 promoters of Runx1, and the previously identified +24 enhancer, in the mouse multipotent  ...  The Runx1 DNA contact map identifies connections with multiple novel hematopoietic enhancers that are likely to be involved in regulating Runx1 expression in hematopoietic progenitor cells.  ...  One previously identified Runx1 enhancer is located 24 kb downstream of the P1 transcriptional start site 11, 12 .  ... 
doi:10.1101/147793 fatcat:7vvsxex6tvdtjb4mve6xwpj2pe

Enhanced Approaches for Identifying Amadori Products: Application to Peanut Allergens

Katina L. Johnson, Jason G. Williams, Soheila J. Maleki, Barry K. Hurlburt, Robert E. London, Geoffrey A. Mueller
2016 Journal of Agricultural and Food Chemistry  
Identifying AGEs is technically challenging.  ...  Amadori product ions matched to expected peptides and yielded fragments that included a loss of three waters and HCHO.  ...  Qualitatively, this confirmed that a low value of the Shannon entropy would be able to identify the type of spectra containing the typical Amadori product fragmentation pattern seen in Figure 1A .  ... 
doi:10.1021/acs.jafc.5b05492 pmid:26811263 pmcid:PMC4813809 fatcat:zihfsbmglrbydabnnesahtm4w4

Enhancing Notation-based Code Cloning Method With An External-based Identifier Model

Ngoc-Tu Chau, Souhwan Jung
2020 IEEE Access  
of code fragments with change in identifier names and literal values (Type-2) • Identical code fragment modifications at statement level (Type-3) • Code fragment that contain syntactically dissimilar  ...  McGraw published his research on enhancing automated code review with lexical analysis [19] .  ... 
doi:10.1109/access.2020.3016943 fatcat:5yb6z5h7yndbjf3aam7sp7qtiq

An enhancer trap line identifies the Drosophila homolog of the L37a ribosomal protein

Peter Gaines, Craig T Woodard, John R Carlson
1999 Gene  
A gene identified from an enhancer trap screen is shown to encode the Drosophila melanogaster homolog of the L37a ribosomal protein.  ...  This screen produced 38 positively hybridizing clones, one of which (a 2.5 kb clone, J4) was isolated In an attempt to identify cDNAs located near the P element insertion site of the P( lacZ ) enhancer  ...  A full viously identified Minute mutations.  ... 
doi:10.1016/s0378-1119(99)00363-7 pmid:10571043 fatcat:ujlwfw4navdwheuc636u23nfju

Clusters of nuclear factor I binding sites identify enhancers of several papillomaviruses but alone are not sufficient for enhancer function

Bernd Gloss, Michele Yeo-Gloss, Michael Meisterernst, Lars Rogge, Ernst L. Winnacker, Hans-Ulrich Bernard
1989 Nucleic Acids Research  
enhancers.  ...  NFI seems to be necessary but not sufficient for HPV enhancer activation.  ...  Possibly, a factor not present in HeLa cells may have to contribute for HPV-8 enhancer activation, or the enhancer requires sites outside the tested restriction fragment.  ... 
doi:10.1093/nar/17.9.3519 pmid:2542901 pmcid:PMC317793 fatcat:k2rc3drmjje4fps5qogrkum24q

Identifying Novel Enhancer Elements with CRISPR-Based Screens

Jason C. Klein, Wei Chen, Molly Gasperini, Jay Shendure
2018 ACS Chemical Biology  
While traditional MPRAs are episomal assays, CRISPR-based screens identify enhancer elements directly in their endogenous genomic loci.  ...  In the context of this review, ChIP-seq has been used to identify regions of DNA bound by proteins and modified-histones associated with enhancer activity, such as P300, H3K27ac, and H3K4me1.  ...  Korkmaz et al. focused on identifying enhancers regulated by p53 and ERα and selected based on oncogene-induced senescence and ERα expression. 29 Sanjana et al. focused on identifying enhancers surrounding  ... 
doi:10.1021/acschembio.7b00778 pmid:29300083 pmcid:PMC6218247 fatcat:74ydykbdnjaitkoclgaxemkaqm

Identifying causal regulatory SNPs in ChIP-seq enhancers

Di Huang, Ivan Ovcharenko
2014 Nucleic Acids Research  
We applied this model to HepG2 enhancers and detected 4796 enhancer SNPs capable of disrupting enhancer activity upon allelic change.  ...  Our model is directly applicable to any enhancer set for mapping causal regulatory SNPs.  ...  To capture sequence features of given enhancers, we used k-mer sequences, i.e. all DNA fragments of k-bps long.  ... 
doi:10.1093/nar/gku1318 pmid:25520196 pmcid:PMC4288203 fatcat:x6s5eugwkrgmrhksv2piaeqina

DNA methylation at enhancers identifies distinct breast cancer lineages

Thomas Fleischer, Xavier Tekpli, Anthony Mathelier, Shixiong Wang, Daniel Nebdal, Hari P. Dhakal, Kristine Kleivi Sahlberg, Ellen Schlichting, Anne-Lise Børresen-Dale, Elin Borgen, Bjørn Naume, Ragnhild Eskeland (+4 others)
2017 Nature Communications  
manner by DNA methylation at enhancers.  ...  In the estrogen related cluster, using ChromHMM segmentation and transcription factor chromatin immunoprecipitation sequencing data, we identify transcriptional networks regulated in a cell lineage-specific  ...  Total RNA was extracted with TRIzol Reagent (Life Technologies) and fragmented with RNA Fragmentation Reagent (Life Technologies).  ... 
doi:10.1038/s41467-017-00510-x pmid:29123100 pmcid:PMC5680222 fatcat:ewrsjn6yyjfhhhofxipbdkzcnq

WT1 Activates a Glomerular-Specific Enhancer Identified from the Human Nephrin Gene

G. Guo
2004 Journal of the American Society of Nephrology  
Mutations in the nephrin gene (NPHS1) lead to congenital Finnish nephropathy, whereas alterations in the level of nephrin expression have been identified in a wide range of acquired glomerular diseases  ...  A 186-bp fragment from the human NPHS1 promoter is capable of directing podocyte-specific expression of a ␤-galactosidase transgene when placed in front of a heterologous minimal promoter in transgenic  ...  Results Identification of a Podocyte-Specific Enhancer To identify a putative glomerular enhancer element, the human and murine promoters that have been shown to direct podocyte-specific expression within  ... 
doi:10.1097/01.asn.0000143474.91362.c4 pmid:15504938 fatcat:zlapqkmi7rhfthxemy7ilngjh4
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