PPT-The Chromatin and genome packaging

Dr Karzan Mohammad Chromatin Eukaryotic DNA is closely associated with proteins creating chromatin Of two types Heterochromatin Euchromatin Chromatin Euchromatin Actively transcribed. II:. Epigenetics and the histone code. Jim Noonan. GENE760. 1. TF binding. Biochemical indicators of regulatory function. 2. . Histone. modification. H3K27ac. H3K4me3. 3. Chromatin. modifiers &. February . 27 2013. Fundamental Goals. Improve comprehensiveness and accuracy of gene annotation. Define novel protein coding and . noncoding. gene products, including variants. Define . noncoding. regulatory elements, including both sequence and epigenetic features. integrated encyclopedia of DNA elements in the human . genome”. ENCODE Project Consortium. . Nature . 2012 Sep 6; 489:57-74.. Michael . M. Hoffman. University of Washington. 12 September 2012. Major results. On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE. AKA:. why the ENCODE . project is full of it. by Matthew . Oberhardt. What is ENCODE?. The Human Genome project sequenced “the human genome. ”. “the human genome” that we have labeled as such doesn’t actually . exist. What we call the human genome sequence is really just a . reference. 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. 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 . Chromatin conformation has large implications on gene expression, but is usually ignored in expression analysis.. Program for today:. 3D chromatin conformation. Hi-C method. Biases in Hi-C data analysis. Chromatin conformation has large implications on gene expression, but is usually ignored in expression analysis.. Program for today:. 3D chromatin conformation. Hi-C method. Biases in Hi-C data analysis. 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 Thimo Rohlf 1,4 , Lydia Steiner 1,2 , Jens Przybilla 1 , Sonja Prohaska 2 , Hans Binder 1,3 and Jörg Galle 1 * 1 Interdisciplinary Centre for Bioinformatics of Leipzig University, D-04107 Leipzig, Hardison. Genomics5_1. 2/17/15. 1. Types of data in genomics. Protein and DNA sequences . Protein structure and function. Comparisons of DNA and protein sequences. Between species. Among individuals within a species.