Results 11 to 20 of about 3,719 (149)

MYC Binding Near Transcriptional End Sites Regulates Basal Gene Expression, Read-Through Transcription, and Intragenic Contacts. [PDF]

Adv Sci (Weinh)
MYC is a transcription factor (TF) that binds DNA near transcriptional start sites (TSSs) and within enhancer elements. Here, unappreciated sites of MYC binding in the vicinity of transcriptional end sites (TESs) of many genes in multiple cell types in association with numerous other TFs are described previously.
Wang H, Ma B, Stevens T, Knapp J, Lu J, Prochownik EV.   +5 more
europepmc   +2 more sources

Optimized protocols for ChIP-seq and deletion mutant construction in Pseudomonas syringae

STAR Protocols, 2021
Summary: Chromatin immunoprecipitation sequencing (ChIP-seq) is an efficient technique to identify the binding sites of transcription factors (TFs) in both eukaryotes and prokaryotes. However, its application in bacteria is very heterogeneous.
Chunyan Yao, Xiaolong Shao, Jingwei Li, Xin Deng   +3 more
doaj   +1 more source

Deciphering the code for retroviral integration target site selection. [PDF]

PLoS Computational Biology, 2010
Upon cell invasion, retroviruses generate a DNA copy of their RNA genome and integrate retroviral cDNA within host chromosomal DNA. Integration occurs throughout the host cell genome, but target site selection is not random.
Federico Andrea Santoni, Oliver Hartley, Jeremy Luban   +2 more
doaj   +1 more source

#277 : Transcriptome Analysis Revealed a Delayed and Attenuated Estrogen Response in IUA Patients

Fertility & Reproduction, 2023
Background and Aims: Intrauterine adhesion (IUA) is characterized by the formation of scar tissue in the endometrium following a variety of insults such as endometrial damage, miscarriage, and infection.
Qi Guo
doaj   +1 more source

Computational workflow for integrative analyses of DNA replication timing, epigenomic, and transcriptomic data

STAR Protocols, 2022
Summary: Temporal profiling of DNA replication timing (RT) in combination with chromatin modifications, chromatin accessibility, and gene expression provides new insights into the causal relationships between chromatin and RT during cell cycle.
Fei Ji, Capucine Van Rechem, Johnathan R. Whetstine, Ruslan I. Sadreyev   +3 more
doaj   +1 more source

CSSQ: a ChIP-seq signal quantifier pipeline

Frontiers in Cell and Developmental Biology, 2023
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has revolutionized the studies of epigenomes and the massive increase in ChIP-seq datasets calls for robust and user-friendly computational tools for quantitative ChIP-seq. Quantitative ChIP-
Ashwath Kumar, Michael Y. Hu, Yajun Mei, Yajun Mei, Yuhong Fan, Yuhong Fan   +5 more
doaj   +1 more source

TOP1 CAD-seq: A protocol to map catalytically engaged topoisomerase 1 in human cells

STAR Protocols, 2022
Summary: TOP1 CAD-seq enables mapping of TOP1 sites of covalent engagement with DNA. The procedure depends upon enrichment of DNA-covalent adducts using chaotropic salts and immunoprecipitation with an antibody specific for TOP1. Here, we describe a step-
Vladislav Kuzin, Anika Wiegard, Donald P. Cameron, Laura Baranello   +3 more
doaj   +1 more source

ChIP-seq protocol for sperm cells and embryos to assess environmental impacts and epigenetic inheritance

STAR Protocols, 2021
Summary: In the field of epigenetic inheritance, delineating molecular mechanisms implicated in the transfer of paternal environmental conditions to descendants has been elusive. This protocol details how to track sperm chromatin intergenerationally.
Ariane Lismer, Romain Lambrot, Christine Lafleur, Vanessa Dumeaux, Sarah Kimmins   +4 more
doaj   +1 more source

Curcuphenol possesses an unusual histone deacetylase enhancing activity that counters immune escape in metastatic tumours

Frontiers in Pharmacology, 2023
Curcuphenol, a common component of the culinary spices, naturally found in marine invertebrates and plants, has been identified as a novel candidate for reversing immune escape by restoring expression of the antigen presentation machinery (APM) in ...
Samantha L. S. Ellis, Samantha L. S. Ellis, Samantha L. S. Ellis, Samantha L. S. Ellis, Sarah Dada, Sarah Dada, Sarah Dada, Sarah Dada, Sarah Dada, Sarah Dada, Lilian L. Nohara, Lilian L. Nohara, Lilian L. Nohara, Iryna Saranchova, Iryna Saranchova, Iryna Saranchova, Iryna Saranchova, Iryna Saranchova, Iryna Saranchova, Lonna Munro, Lonna Munro, Lonna Munro, Lonna Munro, Cheryl G. Pfeifer, Cheryl G. Pfeifer, Cheryl G. Pfeifer, Cheryl G. Pfeifer, Brett A. Eyford, Brett A. Eyford, Brett A. Eyford, Tunc Morova, David E. Williams, Ping Cheng, Nathan A. Lack, Nathan A. Lack, Raymond J. Andersen, Wilfred A. Jefferies, Wilfred A. Jefferies, Wilfred A. Jefferies, Wilfred A. Jefferies, Wilfred A. Jefferies, Wilfred A. Jefferies   +41 more
doaj   +1 more source

Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression

Nature Communications, 2017
Polycomb repressive complexes modify histones but it is unclear how changes in chromatin states alter kinetics of transcription. Here, the authors use single-cell RNAseq and ChIPseq to find that actively transcribed genes with Polycomb marks have greater
Gozde Kar, Jong Kyoung Kim, Aleksandra A. Kolodziejczyk, Kedar Nath Natarajan, Elena Torlai Triglia, Borbala Mifsud, Sarah Elderkin, John C. Marioni, Ana Pombo, Sarah A. Teichmann   +9 more
doaj   +1 more source