Special Cis-regulatory Elements And Chromatin Three-dimensional Structure

Chromatin,the largest single biological macromolecule of eukaryotes is the common carrier of genetic and epigenetic information and stored in the nucleus as the basic existence form of genome.Relative to each other and radial nuclear positions,peach chromatin is confined to a discrete region during the mitotic phase.This discrete but relative stable region is called chromosome territory.Each chromatin is folded into complex three dimensional structure at different level.These stable high-order structure play important roles in DNA replication,recombinant and transcription.As previously reported,many regulatory factors function dependent on the three dimensional space of chromatin structure.3C(Chromosome Conformation Capture),developed in 2002 by Job Dekker,is the main molecular biology technique for analyzing the spatial organization of chromatin in a cell..In recent years,with the development of DNA-FISH and 3C derivative technologies such as 4C,5C,Hi-C,Capture-C and ChIA-PET,we learn much more about the chromatin folding.It is generally believed that mitosis interphase chromatin is hhierarchically folded at the level of chromatin territory,topological associated domain(TAD),chromatin loop and other structural unit.As the carrier,responder or moderator of genome sequence,histone modification and regulatory proteins' binding,the genome 3D folding is closely related with one-dimensional omics characteristics such as DNA methylation,DNase I high sensitive sites and genome function features such as replication,transcription etc.Cis-regulatory elements(CREs)are regions of non-coding DNA which regulate the transcription of nearby or faraway genes.According to the characters of sequence features,the CREs can be classified into promoter,terminator,enhancer,insulator,boundary elements,locus control region and repetitive elements,MARs(Matrix attachment regions)etc.Repetitive elements(also known as repeated sequence,or repeats)are a series of DNA or RNA elements occurred many times throughout the genome and contained many different structures and sources.Repetitive DNA was first detected because of its rapid re-association kinetics.Repetitive elements can reach more than half in eukaryotic genomes.In human,over two-thirds of the genome sequence consisting of repetitive elements.According to repeated fragment length and biological characteristics,repetitive elements can be further divided into tandem repeats,transposable elements,etc.Due to the limitation of read length of sequencing and mapping,the genome functions and mechanism of repetitive elements remain elusive and need further exploration.MARs(Matrix Attachment Regions)is a kind of widespread DNA elements,rich of AT sequences and closely interacted with nuclear matrix.It is believed that MARs can function both as the structure units to involve chromatins folding and as function units to regulate gene expression.Mainly basing on the chromatin three-dimensional datasets and in combination with multi-omics integrative analysis,our research focused on the potential roles of some special CREs,MARs and repetitive elements,during chromatin folding and the effects of chromatin folding on the evolution processes of CREs.The established approaches and the primary results will be helpful for the further studying of other different CREs' s functions during the establishment,maintenance and inheritance of 3D genome folding.The main results of this work are as follows:The Hi-C data processing software HBP was developed.We established the method to study roles played by special CREs,and presented HBP(Hi-C BED file analysis Pipeline)to analyze interactions involved by these CREs.The freely available HBP is an optimized and flexible pipeline for analyzing the folding of whole chromosome and interactions between some special sequence sites from the Hi-C raw sequencing reads to the partially processed datasets.The other complex genetic and epigenetic datasets from public sources can also easily be integrated into HBP,hence the final output results of HBP could provide a comprehensive in-depth understanding for the specific chromatin interactions,potential molecular mechanisms and biological significance.We believe that HBP is a reliable tool for the rapidly analysis of Hi-C data and will be very useful for a wide range of researchers.The effects of repetitive elements on chromatin folding were investigated.Repetitive elements are widely distributed among the genomes of different species.The classes and functions of these elements are diverse.On the one hand,we found that a few sub-families of repetitive elements that are highly associated with genome structure,such as Alu,are indeed extensively involved in the genome folding.On the other hand,we systematically examined the evolution process of repetitive elements basing on their 3D spatial distance in the genome.By comparison with the classical phylogenetic data,we revealed that 3D chromatin interaction strength of some repetitive elements is positively correlated with their 1D sequence evolutionary relationship.These results suggested that evolution processed of some repetitive elements might strongly correlated with the formation of genome 3D structure.The involvement of MARs in chromatin folding was examined.The MARs(Matrix Associated Regions)are widely exists among diverse species.Except the AT sequence enrichment,MARs do not have common sequence conservation and other characteristics.The function and mechanism of matrix associated regions were largely unknown.In this study,the frequency distribution,network topological structure and biological functions of MARs were examined.The interaction frequency analysis revealed that MARs is widely involvement in chromatin interactions.Among those extensively interacted sequences,the proportion MARs is high.These results strongly suggested that MARs really have important effect on the genome folding.Further topological structure analysis revealed MARs can be divided into different classes,including the structure units to maintain the chromatin territory and high-order structure and functional units to regulate gene expression.In summary,for the study of special CREs roles during chromatin folding,a Hi-C dataset processing software HBP and integrative multi-omics analysis approaches were developed.The relationship of some repetitive elements and MARs to chromatin folding were examined.The primary results indicated that repetitive elements and MARs are widely involvement in chromatin folding,which established foundation for the further study of chromatin folding and function.