...Paul Bump; Kaitlyn Loubet-Senear; Sarah Arnold; Mansi Srivastava ABSTRACT Chromatin profiling data can generate and corroborate hypotheses for regulatory events that underlie the control of gene expression in biological processes. Here, we have profiled chromatin accessibility to build a catalog...

... effectors of extracellular signals, allowed us to determine the interactions of these signaling pathways at the chromatin level. Here, we focused on the FL, as a great wealth of data concerning the underlying gene regulatory networks exists for this tissue (Andrey et al., 2017 ; Zuniga and Zeller, 2020...

... response is mostly mediated by repression of transcriptional targets that occur in tandem with reductions in chromatin accessibility at regulatory regions. Furthermore, immediate early ERK responses are largely shared by different cell types but produce cell-specific programmes as these responses interface...

... for the transcription pre-initiation complex and chromatin remodeling complexes (Vermeulen et al., 2007 ; Wysocka et al., 2006). In yeast, Set1 catalyzes all methylation forms of H3K4 (i.e. H3K4me1/2/3) and its catalytic activity is modulated via a multi-subunit protein complex known as the Complex of proteins...

... of DNA into chromatin prevents the binding of many transcription factors. Pioneer factors overcome this barrier owing to unique properties that enable them to bind closed chromatin, promote accessibility and, in so doing, mediate binding of additional factors that activate gene expression. Because...

...Fanju W. Meng; Kristin E. Murphy; Claire E. Makowski; Benjamin Delatte; Patrick J. Murphy ABSTRACT The histone variant H2A.Z is central to early embryonic development, determining transcriptional competency through chromatin regulation of gene promoters and enhancers. In addition to genic loci, we...

...Patrick J. Murphy; Frédéric Berger ABSTRACT We propose that several chromatin-mediated regulatory processes are dominated by source-sink relationships in which factors operate as ‘sources’ to produce or provide a resource and compete with each other to occupy separate ‘sinks’. In this model, large...

... dedifferentiation following injury (Jopling et al., 2010 ; Kikuchi et al., 2010). Chromatin modifications are likely involved in this process, as EZH2 is upregulated following cardiac injury in zebrafish. H3K27me3 correspondingly increased over sarcomeric and cytoskeletal genes that were downregulated in response...

...: Amino acid substitutions in a histone deacetylase demonstrate catalytic-dependent gene activation and non-enzymatic gene repression as crucial for Drosophila embryo development. HDAC3 Histone deacetylase Chromatin Transcription Embryo development Drosophila Cancerfonden http...

... 15.5 and 19.5 rat uterine-placental interface tissues, and integrated the data with single-cell RNA-seq data generated at the same stages. We determined the chromatin accessibility profiles of invasive trophoblast, natural killer, macrophage, endothelial and smooth muscle cells, and compared invasive...

...-confidence autism spectrum disorder (ASD) risk genes highlight chromatin regulation and synaptic function as major contributors to pathobiology. Our recent functional work in vivo has additionally implicated tubulin biology and cellular proliferation. As many chromatin regulators, including the ASD risk...

...Olesya Sokolova; Valeriya Morgunova; Tatyana V. Sizova; Pavel A. Komarov; Oxana M. Olenkina; Dmitry S. Babaev; Elena A. Mikhaleva; Dmitry A. Kwon; Maksim Erokhin; Alla Kalmykova ABSTRACT Insulators are architectural elements implicated in the organization of higher-order chromatin structures...

...Aushaq B. Malla; Shannon R. Rainsford; Zachary D. Smith; Bluma J. Lesch ABSTRACT Unique chromatin remodeling factors orchestrate dramatic changes in nuclear morphology during differentiation of the mature sperm head. A crucial step in this process is histone-to-protamine exchange, which must...

...Anna Török; Martin J. G. Browne; Jordina C. Vilar; Indu Patwal; Timothy Q. DuBuc; Febrimarsa; Erwan Atcheson; Uri Frank; Sebastian G. Gornik; Andrew Flaus ABSTRACT Many animals achieve sperm chromatin compaction and stabilisation by replacing canonical histones with sperm nuclear basic proteins...

... tissues. CUT&RUN-LoV-U outperforms original CUT&RUN when targeting co-factors that do not bind the DNA, can profile all classes of chromatin regulators and is well suited for simultaneous processing of several samples. We believe that the application of our protocol will allow the detection...

... cases in which perturbed eRNA function contributes to disease. eRNA Non-coding RNA Enhancers Chromatin Transcription Gene expression Wellcome Trust http://dx.doi.org/10.13039/100010269 213501/Z/18/Z Royal Society http://dx.doi.org/10.13039/501100000288 213501/Z/18/Z...

... Article: A context-specific requirement of Vsx2 enhancer elements during retinogeneis. VSX2 Chromatin Super-enhancers Retina Neurogenesis Bipolar cells Cell fate PAX6 University of Pittsburgh http://dx.doi.org/10.13039/100007921 Washington University in St Louis...

... genes repressed by Dlx1/2 , including Olig2 . Consequently, heterozygosity of Dlx1/2 and Rbbp4 leads to an increase in the production of OLIG2 + cells. These findings highlight the importance of the interplay between transcription factors and chromatin remodelers in regulating cell-fate decisions...

... zygotic genome activation. ZGA Chromatin Reprogramming HDAC1/2 Preimplantation Embryo National Natural Science Foundation of China http://dx.doi.org/10.13039/501100001809 31672416 32072939 31941007 32072731 31872348 Zhejiang Provincial Natural Science Foundation http...

... embryo serves as a sophisticated mechanism for maintaining a genome-wide network of gene regulatory elements in an inaccessible chromatin structure throughout the body. As development progresses, programmed demethylation in each cell type then provides the specificity for maintaining select elements...