Symmetry In DNA And Analysis Of Eukaryotic Cis-Regulatory Module

The work is consist of two parts.First, we finded a little of symmetry in DNA and discussed why they happen. Second, based on those facts , we builded the CRMSS( Cis-Regulatory Module Search System) and applied it to HLA regulatory regions, the result proved that CRMSS is reliable hi data processing correction and database management.Symmetry in DNABackgroundSymmetry is a intrinsic character in DNA. There are A=T G = C between double strands, and also A=T, G=C inside single strand. A few reports have indicated that this first-order parity rule extends at higher orders to oligonucleotide composition.Seuoka suggested a hypothesis to explain the symmetry: if select press and nature mutation were equal between double strands , there would appear the result of AT, GC in single strand after long time. But many experiences have been designed to answer those question, a few results show that genes located in complementary strands suffered varied effects in the course of copy, transcription and repair, many authors assume that the bases composition in coding regions are diversity.MotivationsFirst, this paper compare base and ammo acid composition of coding region, codon position among two strands , explore whether selection press and nature mutation are balanced between double strands.Second, according to three concise oligos forms , [AT]-[GC], [AG]-[CT], [AC]-[GT], we discover if there also be symmetry along the side of yeast gene and whether the character is valueble to predict regulatory regions.Methods1. Using the regular expression of Perl, split the coding regions in two part according to which strand it locate, and throw off the annotation lines.2. Count the bases composition of coding regions and three codon position among two strands.3. Compare the amino acids composition between double strands.4. Analyse concise 6-oligosnucleotide distributions in coding region and non-coding regions in yeast genome.5. Cluster 5'UTR , coding region, 3'UTR according to concise oligos composition.6. Discriminate each sequence from different regions by distribution of concise oligosResultsl.The frequencies of four bases in coding regions almost equal to those in complementary strand.2.The four bases composition in each codon position of Watson strand is approximately same as the Crick strand's. Each base composition of each codon position is correlative to others, specially, A% is significant positive correlation to T %, the G% is positive correlate to C%. but two bonding bases(A + T) and three bonding bases(G + C) is significant negative correlation to opposite set.3. Each amino acid distribution is similar to complementary strand.4. Three forms concise oligosnucleotide is symmetry along the axis of gene.5. In non-coding regions , [AG]-[CT], [AC]-[GT] forms concise oligos are equal to their complementary segment.6. Clustering with concise oligos compostion, untranslated regions always cluster together first, coding region and non-coding region gathered last.7. Concise oligos composition is valueble to discrimate coding region from non-coding regions.Analysis of Eukaryotic Control Region ModuleBackgroundA major challenge in interpreting genome sequences is understanding how the genome encodes the information that specifies when and where a gene will be expressed. The first step in this process is the identification ofregions of the genome that contain regulatory information. In higher eukaryotes, this cis-regulatory module information is organized into modular units [ cis-regulatory modules(CRM)] of a few hundred base pairs. A common feature of these cis-regulatory modules is the presence of multiple binding sites for multiple transcription factors.Motivations1. Pickuping and selecting the characters of control regions ,such as sequence similarity, oligos composition, transcription factor binding sites, repeat sequences.2. Identifying which regions contain regulatory information.MethodsWe establi...