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Adaptive genomic evolution for expression regulation and survival strategies in vertebrates and bacteria : 척추동물 및 박테리아의 발현 조절 및 생존 전략을 위한 적응성 유전체 진화
| DC Field | Value | Language |
|---|---|---|
| dc.contributor.advisor | 김희발 | - |
| dc.contributor.author | 안현주 | - |
| dc.date.accessioned | 2021-11-30T06:14:45Z | - |
| dc.date.available | 2021-11-30T06:14:45Z | - |
| dc.date.issued | 2021-02 | - |
| dc.identifier.other | 000000164614 | - |
| dc.identifier.uri | https://hdl.handle.net/10371/176450 | - |
| dc.identifier.uri | https://dcollection.snu.ac.kr/common/orgView/000000164614 | ko_KR |
| dc.description | 학위논문 (박사) -- 서울대학교 대학원 : 농업생명과학대학 농생명공학부, 2021. 2. 김희발. | - |
| dc.description.abstract | Since the genomic sequence began to be produced in large quantities, research and efforts have been made to explain the evidence of adaptive evolution in the genomic sequence. Through RNA-seq, which identifies where transcript is located on the genome from gene expression data, it is possible to study the dosage compensation, which refers to the inactivation or upregulation of a specific sex chromosomal genes due to differences in composition of the sex chromosome. When looking at the sex chromosome dosage compensation observed in mammals, gene expression shows in slightly different profiles through dosage compensation in the X chromosome by tissues. And genes that are functionally associated with other proteins and require a uniform rate of expression between associated genes, may maintain a similar amount of expression in the X chromosome to autosomes. There are also XCI escape genes in the pseudo-autosomal region that exist both in the X and Y chromosome, as autosomal genes, so that they do not differ from autosomal genes to the amount of expression. In Chapter 2 we examined and compared the aspects of sex chromosome dosage compensation in both male and female, which had been reported in humans and other species, appeared in cows using genome sequence information and gene expression data.
In addition, the non-synonymous substitution of the protein-coding genes in the genome has a significant effect on the phenotype of the organism, so it is analyzed relative to the rate at which the synonymous (silent) substitution occurred, and the ratio means a selective pressure on the gene leading to functional change. The dN/dS ratio method, a method that explains directional evolution, neutral evolution, and purifying evolution of protein-coding genes, has been proposed and widely used. In Chapter 3 we analyzed dN/dS ratio using protein-coding genes of pufferfish that have 1:1 orthologous relationship with other fish genes, which has not yet been sufficiently studied in the evolutionary viewpoint. Based on the results, the positive selection of genes was discussed with the control mechanisms of neurotoxins called tetrodotoxin, which are the unique phenotypes of pufferfish. In addition, the result showed the accelerated evolution of protein-coding genes in pufferfish after species differentiation through the high dN/dS ratio distribution of the genes. Meanwhile, in the bacterial genome, there is a set of genes that are expressed simultaneously, called an operon. The three ribosomal RNAs of bacteria also comprise an operon like other functionally related genes generally. Based on the complete bacterial genomes and their symbiotic genomic characteristics, Chapter 4 demonstrated that ecological adaptation of certain symbiotic bacteria may result to the disruption of ribosomal RNA operon with the reduction of metabolic and transcription-regulating genes and certain RNases. The result suggested that not only copy number variation of rRNA operon sensitively responds to the bacterial lifestyle, but also structural modification can strongly reflect adaptation to the surrounding environmental condition. | - |
| dc.description.abstract | 유전체 서열이 대량으로 생산되기 시작한 이래, 유전체 서열에서 적응 진화의 증거를 설명하는 연구와 노력은 활발하게 이루어지고 있다. 유전자 발현 데이터로부터 transcript가 유전체 위 어떤 위치에 있는지를 파악하는 RNA-seq을 통하여, 성염색체상의 구성 차이로 인한 특정 성염색체의 비활성화 또는 발현량 증폭을 일컫는 발현 보상(dosage compensation)을 연구할 수 있다. 포유류에서 관찰되는 성염색체 발현 보상(sex chromosomal dosage compensation)을 살펴보면, 조직별로 X 염색체에서 보상 발현 양상에 차이를 보이며, 다른 단백질과 기능적으로 연관되어 있어 발현량 비율을 유지해야 하는 유전자의 경우 X염색체 유전자라 하더라도 상염색체와 비슷한 발현량을 유지하기도 한다. 또한 상염색체와 마찬가지로 X 염색체와 Y 염색체에 동시에 존재하여, X 염색체 비활성화(XCI)에서 벗어나 상염색체와 발현량에 차이를 보이지 않는 탈출 유전자(XCI escape gene)도 있다. Chapter 2에서는 소의 유전체 서열 정보와 유전자 발현 데이터를 이용하여 인간 및 다른 종에서 보고되었던 성염색체 발현 보상의 양상이 소에서는 어떻게 나타나는지를 살펴보고 비교하였다.
또한 유전체 상에서 단백질을 코딩하는 유전자의 유의미한 서열 변이(non-synonymous substitution)는 유기체의 표현형에 미치는 영향이 크므로, 조용한 서열 변이(synonymous substitution)가 일어난 비율과 비교 분석하여 방향성 진화(directional selection), 중립 진화(neutral selection), 정제 진화(purifying selection)를 설명하는 분석 방법(dN/dS ratio)이 고안되어 널리 쓰이고 있다. Chapter 3에서는 아직 진화 연구가 충분히 이루어지지 않은 복어 공개 유전체 정보에서, 다른 물고기와 1:1 ortholog 관계를 이루고 있는 단백질 코딩 유전자를 이용하여 dN/dS ratio를 분석하였다. 그리고 그 결과를 토대로 복어의 특이적인 표현형인 신경독과 관련된 유전자 진화 선택을 추정하고, 진화 선택을 받은 유전자의 높은 dN/dS ratio 분포를 통해 종 분화(diversification) 이후 복어 단백질 코딩 유전자의 진화 가속을 논의하였다. 한편 박테리아의 유전체에서는 함께 동시에 발현되는 유전체 묶음인 오페론이 존재한다. ribosomal RNA 또한 오페론 형태로 존재하며, 서로 다른 세 가지 rRNA가 오페론 내에 포함되어 있다. Chapter 4에서는 다양한 박테리아 유전체 정보를 이용하여, ribosomal RNA 오페론 형태가 깨진 존재하지 않는 박테리아들의 유전체에서 공생 박테리아의 유전체 특징이 강하게 나타나는 것을 관찰하였고, 동시에 이러한 박테리아에서 메타볼리즘에 관련된 유전자 및 전사 조절에 관련된 유전자가 줄어들고 특정 RNase 또한 소실되는 것을 확인하였다. 이로부터 박테리아의 라이프스타일에 따른 적응에는 rRNA 오페론의 copy number 뿐 아니라 구조적인 변형 또한 유도될 수 있다는 가능성을 제시하였다. | - |
| dc.description.tableofcontents | Contents
ABSTRACT ii CONTENTS v LIST OF TABLES vii LIST OF FIGURES viii CHAPTER 1. LITERATURE REVIEW １ 1.1. THE ADAPTIVE EVOLUTION IN THE CHROMOSOME STRUCTURE ２ 1.2. THE ADAPTIVE EVOLUTION IN THE PROTEIN-CODING GENE OF THE GENOME SEQUENCE ５ 1.3. THE ADAPTIVE EVOLUTION IN THE RIBOSOMAL RNA OF BACTERIA ８ CHAPTER 2. STATUS OF DOSAGE COMPENSATION OF X CHROMOSOME IN BOVINE GENOME １０ 2.1. ABSTRACT １１ 2.2. INTRODUCTION １３ 2.3. MATERIALS AND METHODS １９ 2.4. RESULTS AND DISCUSSION ３１ CHAPTER 3. SELECTIVE PRESSURE ON THE PROTEIN CODING GENES OF THE PUFFERFISH IS CORRELATED WITH PHENOTYPIC TRAITS ５７ 3.1. ABSTRACT ５８ 3.2. INTRODUCTION ６０ 3.3. MATERIALS AND METHODS ６３ 3.4. RESULTS ６９ 3.5. DISCUSSION ８７ CHAPTER 4. ENHANCED SYMBIOTIC CHARACTERISTICS IN BACTERIAL GENOMES WITH THE DISRUPTION OF RRNA OPERON ９５ 4.1. ABSTRACT ９６ 4.2. INTRODUCTION ９７ 4.3. MATERIALS AND METHODS １００ 4.3. RESULTS １０７ 4.4. DISCUSSION １４８ 4.5. CONCLUSIONS １５５ GENERAL DISCUSSION １５６ REFERENCES １５９ 요약(국문초록) １７９ List of Tables TABLE 2.1. FUNCTIONAL GENES FOUND IN PAR OF CATTLE GENOME. ２４ TABLE 2.2. XCI ESCAPE GENES FOR MAMMAL SPECIES. ２６ TABLE 2.3. PHRED (Q) SCORES FOR 40 SAMPLES. ３３ TABLE 2.4. MAPPING RATE. ３５ TABLE 2.5. STATISTICS OF EXPRESSED DATA. ３８ TABLE 2.6. X-LINKED DEGS FROM THE RNA-SEQ ANALYSIS. ４６ TABLE 2.7. CURRENT STATUS OF DOSAGE COMPENSATION IN MAMMALS. ５６ TABLE 3.1. P-VALUES FROM ANOVA TEST FOR DN/DS VALUES AMONG TETRAODONTIFORMES, TAKIFUGU RUBRIPES AND TETRAODON NIGROVIRIDIS ７１ TABLE 3.2. P-VALUES OF TUKEYS HSD TEST FOR ANOVA TEST (SUPP. TABLE 1) BETWEEN TETRAODONTIFORMES, TAKIFUGU RUBRIPES AND TETRAODON NIGROVIRIDIS ７２ TABLE 3.3. MEDIAN OF DN/DS VALUES OF ALL ORTHOLOGOUS GENES IN THREE DIFFERENT SETTING OF THE FOREGROUND BRANCHES. ７３ TABLE 3.4. MEDIAN OF DN/DS VALUES OF ALL ORTHOLOGOUS GENES IN POECILIA FORMOSA AND XIPHOPHORUS MACULATUS ９１ TABLE 4.1. RRNA OPERON STATUS IN REFSEQ COMPLETE GENOME. １１０ TABLE 4.2. LIST OF GENERA WITH THE CONSERVATION OF RRNA OPERON DISRUPTION. １３４ List of Figures FIGURE 2.1. PHYLOGENETIC TREE OF MAMMALIAN EVOLUTION. １８ FIGURE 2.2. IDENTIFICATION OF PAR GENES AND XCI ESCAPE CANDIDATES. ２３ FIGURE 2.3. EXPRESSION OF AUTOSOMAL AND X-LINKED GENES IN CATTLE GENOME. ３７ FIGURE 2.4. X:A MEDIAN EXPRESSION RATIOS. ４１ FIGURE 2.6. X:A EXPRESSION RATIO WITH GENES INVOLVED IN PROTEIN COMPLEXES IN CATTLE. ５２ FIGURE 2.7. DISTRIBUTION OF X:A RATIO FOR EACH OF TISSUES AND COMPLEX CATEGORIES. ５３ FIGURE 3.1. PHYLOGENETIC LINEAGES OF SEVEN FISHES USED IN THIS STUDY. DIVERGENCE OF SPECIES IS MARKED BY DIFFERENT COLORS. ６４ FIGURE 3.2. DIAGRAMS OF PHYLOGENETIC TREES DISPLAYING FOREGROUND BRANCHES DIFFERENTLY SET IN BRANCH-SITE MODELS. ６７ FIGURE 3.3. DISTRIBUTION OF DN/DS OF TOTAL GENES OF THE THREE DIFFERENT PUFFERFISH BRANCHES. ７４ FIGURE 3.4. GO ENRICHMENT HIERARCHY OF GENES UNDER POSITIVE SELECTION ON TETRAODONTIFORMES LINEAGE USING A TAKIFUGU RUBRIPES GO BACKGROUND (BIOLOGICAL PROCESSES, CELLULAR COMPONENTS, MOLECULAR FUNCTIONS IN ORDER). ７９ FIGURE 3.5. GO ENRICHMENT HIERARCHY OF GENES UNDER POSITIVE SELECTION ON TETRAODONTIFORMES LINEAGE USING A TETRAODON NIGROVIRIDIS GO BACKGROUND (BIOLOGICAL PROCESSES, CELLULAR COMPONENTS, MOLECULAR FUNCTIONS IN ORDER). ８１ FIGURE 3.6. GO ENRICHMENT OF PSGS USING TWO DIFFERENT GO BACKGROUNDS. ８２ FIGURE 3.7. GO ENRICHMENT HIERARCHY OF GENES UNDER POSITIVE SELECTION ON TAKIFUGU RUBRIPES LINEAGE USING A TAKIFUGU RUBRIPES GO BACKGROUND (CELLULAR COMPONENTS, MOLECULAR FUNCTIONS IN ORDER). ８４ FIGURE 3.8. GO ENRICHMENT HIERARCHY OF GENES UNDER POSITIVE SELECTION ON TETRAODON NIGROVIRIDIS LINEAGE USING A TETRAODON NIGROVIRIDIS GO BACKGROUND (BIOLOGICAL PROCESSES, CELLULAR COMPONENTS, MOLECULAR FUNCTIONS IN ORDER). ８６ FIGURE 4.1. FLOW CHART OF OPERON STATUS IDENTIFICATION FROM THE COMPLETE GENOME SEQUENCE. １０３ FIGURE 4.2. SCHEMATIC DIAGRAM OF RRNA OPERON IDENTIFICATION IN THE GENOME SEQUENCE. １０４ FIGURE 4.3. RESULTS OF GENOME SCREENING. １３０ FIGURE 4.4. FEATURES OF EACH UNLINKED GENOME WITH PHYLOGENETIC TREE. １３６ FIGURE 4.5. PCA PLOT OF GENOMIC FEATURES OF SYMBIOTIC BACTERIA. １３７ FIGURE 4.6. THE DISTRIBUTION OF GENOMIC FEATURES OF SYMBIOTIC BACTERIAL GENOMES WITH THE LINKAGE STATUS OF RRNA OPERONS. １３８ FIGURE 4.7. COMPARISONS OF GENOMIC FEATURES BETWEEN SYMBIOTIC BACTERIA AND NON-SYMBIOTIC BACTERIA WITH UNLINKED RRNA OPERONS. １４０ FIGURE 4.8. QUANTITATIVE ABUNDANCE OF COG CATEGORIES BETWEEN LINKED AND UNLINKED GENOMES. １４５ FIGURE 4.9. HEATMAP DRAWN BASED ON THE NUMBER OF RNASES IN THE 30 GENERA. １４６ | - |
| dc.format.extent | ix, 181 | - |
| dc.language.iso | eng | - |
| dc.publisher | 서울대학교 대학원 | - |
| dc.subject | Adaptive genomic evolution | - |
| dc.subject | Sex chromosomal dosage compensation | - |
| dc.subject | Non-synonymous substitution | - |
| dc.subject | Protein-coding gene | - |
| dc.subject | Bacterial rRNA operon | - |
| dc.subject | 적응성 유전체 진화 | - |
| dc.subject | 성염색체 발현 보상 | - |
| dc.subject | 비동의 염기 치환 | - |
| dc.subject | 단백질 코딩 유전자 | - |
| dc.subject | 박테리아 rRNA 오페론 | - |
| dc.subject.ddc | 630 | - |
| dc.title | Adaptive genomic evolution for expression regulation and survival strategies in vertebrates and bacteria | - |
| dc.title.alternative | 척추동물 및 박테리아의 발현 조절 및 생존 전략을 위한 적응성 유전체 진화 | - |
| dc.type | Thesis | - |
| dc.type | Dissertation | - |
| dc.contributor.AlternativeAuthor | Hyeonju Ahn | - |
| dc.contributor.department | 농업생명과학대학 농생명공학부 | - |
| dc.description.degree | Doctor | - |
| dc.date.awarded | 2021-02 | - |
| dc.contributor.major | 동물생명공학전공 | - |
| dc.identifier.uci | I804:11032-000000164614 | - |
| dc.identifier.holdings | 000000000044▲000000000050▲000000164614▲ | - |
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