Structure and Function of 30nm Fibers Deduced From the Linear Distribution of Genetic Information. Part One: The Logical Framework Christine M. Povinelli, Ph.D. Copyright 2010 CM Povinelli, Confidential, All Rights Reserved

DNA FOLDING : Is information organized in chromatin structures, to facilitate its retrieval during gene activation? 30nm Fiber Copyright 2010 CM Povinelli, Confidential, All Rights Reserved DNA : Base pairs 10 nm Fiber Chromosome ……..and Retrieval? GENES ON GENES OFF For Information Storage…………. GCGC ATAT

How is information distributed along DNA = How is DNA folded in 30nm fibers? Are linear distributions of some types of information really describing 3D chromatin? DNA : Linear Distribution of Information Copyright 2010 CM Povinelli, Confidential, All Rights Reserved 30nm CHROMATIN : 3D Distribution of Information Locations of protein coding regions ( ) and gene control regions ( )

LINEAR ARRANGEMENT OF INFORMATION = Spacer sequences Folded Structures Complex Simple Junk sequences Copyright 2010 CM Povinelli, Confidential, All Rights Reserved Distant control region interactions Protein coding Promoter Enhancer

Complex folded chromatin Fragmented gene structure and distant control region interactions Junk / spacer sequences Suggests a possible link between chromatin structures and gene regulation ? FEATURES OF GENOMES FROM COMPLEX ORGANISMS Copyright 2010 CM Povinelli, Confidential, All Rights Reserved

Do the locations of gene control regions describe 30nm fiber diameter and structure during the early stages of gene activation? Is there any mechanical chromatin opening information associated with this process? Is there widespread organization within a predicted range of period lengths ? Are control region interactions facilitated by chromatin structure? CHROMATIN STRUCTURE AND GENE ACTIVATION Gene 1 Gene 2 OFF ON Copyright 2010 CM Povinelli, Confidential, All Rights Reserved Gene control : promoters and enhancers Mechanical sequences facilitating chromatin opening

Copyright 2010 CM Povinelli, Confidential, All Rights Reserved Identified a short sequence pattern associated with DNaseI HSS and gene control regions. A candidate for mechanical opening information (MECHO) ? Collected a set of experimentally well-characterized gene loci with multiple gene control regions for each gene. These were used as learning sets for development of the computational methods, and for preliminary hypothesis testing. PRELIMINARY STEPS Developed two different computational approaches for detecting, mapping, and modeling periodic organization of genetic information: methods based on signal processing (FFT) and methods based on graphical analysis. Confirmed both approaches gave identical results.

DNA sequence SIMPLIFIED OVERVIEW OF COMPUTATIONAL APPROACHES Power Frequency 11/10/2009 Copyright 2010 CM Povinelli, Confidential, All Rights Reserved Periodic organization? Signal Analysis Graphical Analysis Mark locations of pattern (MECHO) Locations of other information Do these methods give the same result? Detection and MappingDetection, Mapping, and Modeling

DEVELOPMENT OF LARGE-SCALE ANALYSIS Briefly, analysis of the smaller scale learning sets confirmed the hypothesis that several classes of genetic information, including gene control regions, are periodically distributed, in phase with each other, and with a repeat length equivalent to one turn of a solenoidal 30nm fiber. Appropriate methods were scaled up to handle longer genomic regions. Results of initial large scale analyses, of multiple genomic sites, incorporating gene regulatory genomic survey data, confirm the results obtained with the smaller scale learning sets. Copyright 2010 CM Povinelli, Confidential, All Rights Reserved