PPT-DNA:chromatin

interactions Exploring transcription factor binding and the epigenomic landscape Lisa Stubbs Eukaryotic genomes are complex structures comprised of modified and unmodified DNA RNA and many types of interacting proteins. Part II. DNA Regulatory . Elements. BNFO 602/691. Biological Sequence Analysis. Mark Reimers, VIPBG. Epigenetic Marks . (as per current use). Any stable modification of DNA or chromatin. DNA modifications. Exploring transcription factor binding and the . epigenomic. landscape. Saurabh. Sinha. (several slides here are courtesy of . Lisa . Stubbs). Eukaryotic genomes . are. complex structures comprised of modified and unmodified DNA, RNA and many types of interacting proteins. CpG. Island landscape. Héctor. Corrada Bravo. CMSC702 . Spring . 2013. (many slides courtesy of Rafael Irizarry). Genetics: the alphabet of life. Letters of DNA sequence carry the . information. How is this information read and parsed.. Domain in . Drosophila. :. Investigating the Strange . Dot Chromosome. Sarah C R Elgin . January 2012. . A collaborative investigation involving:. - former members of the Elgin Lab: . Lee Silver, Carl Wu, TC James, Joel Eissenberg, Lori Wallrath, Fang Lin Sun, Karmella Haynes. Waddington, 1942. “The study of any potentially stable, and ideally, heritable change in gene expression or cellular phenotype that occurs without changes in Watson-Crick base-pairing of . DNA” . Features: . (. i. ) Provides standardised ‘. DeepSEA. score’ for noncoding variants. (ii) Provides info on chromatin feature(s) and cell type(s) to concentrate on. (iii) Identify base-resolution sequence features by . Most DNA is wrapped around a “histone core”, to form nucleosomes. The classical histone protein complexes bind very tightly to DNA and prevent association with other proteins. Modifications of the classical histones, or their replacement with unusual histone types under certain conditions, can “loosen” the interaction with DNA, allowing access to transcription factors, RNA polymerase, and other proteins . By. Dr. . Walaa. . Bayoumie. El . Gazzar. Chromatin. The simplest form of chromatin is . present . in non dividing eukaryotic cells, when chromosomes are not sufficiently condensed to be visible by light microscope.. Introduction. Genetic . material DNA. . in . . eukaryotic . cells never . found as a naked molecule but always found in association . with:. i. . . Histon. . proteins. , . i. i. HMG . proteins. ,. Stephen Clark – . Reik. Lab, . Babraham. Institute. Background. Bulk analyses mask intercellular differences . vs.. Background. Bulk analyses mask intercellular differences . Silva . J, Smith . A, . 3D . genome organisation. Vladimir Teif. BS222 – Genome Science Lecture 6. Module structure. Genomes, sequencing projects and genomic databases (VT. ). Sequencing . technologies (VT. ). What is a gene? . Chromatin-binding factorshistone macromolecules that bind either directly or indirectly to DNA.Transcription factorhistone protein that directly binds to DNA.Architectural proteinsProteins that have a histones. (50%). Five major . histones. ; H2A, H2B, H3, H4 and H1 highly basic (. Arg. and Lys >25%). Roger Kornberg in 1974; . Chromatin. is made up of repeating units called . nucleosomes. , each containing 200 . . phase. . separation. (LLPS) under . physiologic. . conditions. Linker. DNA . length. and . patterning. , . histone. H1, and . acetylation. modulate . chromatin. LLPS. Acetylated. . chromatin.