Additional file 3 of Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping
Quanyi ZhaoMichael DacreTrieu NguyenMilos PjanicBoxiang LiuDharini IyerPaul ChengRobert WirkaJuyong Brian KimHunter B. FraserThomas Quertermous
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Additional file 3: Table S2. The candidate CAD associated genes with TCF21 binding, chromatin accessibility and chromosomal looping QTLs loci.Keywords:
Trait
现在的学习被进行在 IR64 基因渗入线(INL ) 为叶尺寸特点识别量的特点 loci (QTL ) 。为这个目的，选择了人口从在周期性的父母 IR64 和它的导出的 INL 之间的十字导出的 F2，为叶长度和叶宽度唯一，被用来证实 QTL。八 QTL 的一个总数，在三上印射染色体，在六张 F2 人口为四个叶尺寸特点被识别。为叶长度的 QTL， qLLnpt-1，在简单顺序重复(SSR ) 附近在 HKL69 被识别染色体 1 上的标记 RM3709。为旗帜叶长度， qFLLnpt-2 和 qFLLnpt-4 的二 QTL，在 HFG39 是染色体上的 indentified 2 和 4 分别地。为旗帜叶宽度， QTL， qFLWnpt-4，在 HFG39 在染色体 4 上在 RM17483 附近被识别。当时为旗帜叶宽度的另一 QTL， qFLWnpt-1，在 HFG27 在染色体 1 上在 RM3252 附近被识别。为叶宽度的 QTL， qLWnpt-2，在 HKL75 在染色体 2 上在 RM7451 附近被识别。为叶宽度，二 QTL， qLWnpt-4a， qLWnpt-4b，在 RM7208 和 RM6909 附近在 HKL48 和 HKL99 被识别，分别地在染色体 4 上。从这研究的结果建议可能性使用帮助标记的选择并且节节上升改进米饭的这些 QTL 浇生产率。
Family-based QTL mapping
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Poor lodging resistance could limit increases in soybean yield. Previously, a considerable number of observations of quantitative trait loci (QTL) for lodging resistance have been reported by independent studies. The integration of these QTL into a consensus map will provide further evidence of their usefulness in soybean improvement. To improve informative QTL in soybean, a mapping population from a cross between the Harosoy and Clark cultivars, which inherit major U.S. soybean genetic backgrounds, was used along with previous mapping populations to identify QTL for lodging resistance. Together with 78 QTL for lodging collected from eighteen independent studies, a total of 88 QTL were projected onto the soybean consensus map. A total of 16 significant QTL clusters were observed; fourteen of them were confirmed in either two or more mapping populations or a single population subjected to different environmental conditions. Four QTL (one on chromosome 7 and three on 10) were newly identified in the present study. Further, meta-analysis was used to integrate QTL across different studies, resulting in two significant meta-QTL each on chromosomes 6 and 19. Our results provide deeper knowledge of valuable lodging resistance QTL in soybean, and these QTL could be used to increase lodging resistance.
Family-based QTL mapping
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Abstract Chromatin accessibility is essential for transcriptional activation of genomic regions. It is well established that transcription factors (TFs) and histone modifications (HMs) play critical roles in chromatin accessibility regulation. However, there is a lack of studies that quantify these relationships. Here we constructed a two-layer model to predict chromatin accessibility by integrating DNA sequence, TF binding, and HM signals. By applying the model to two human cell lines (GM12878 and HepG2), we found that DNA sequences had limited power for accessibility prediction, while both TF binding and HM signals predicted chromatin accessibility with high accuracy. According to the HM model, HM features determined chromatin accessibility in a cell line shared manner, with the prediction power attributing to five core HM types. Results from the TF model indicated that chromatin accessibility was determined by a subset of informative TFs including both cell line-specific and generic TFs. The combined model of both TF and HM signals did not further improve the prediction accuracy, indicating that they provide redundant information in terms of chromatin accessibility prediction. The TFs and HM models can also distinguish the chromatin accessibility of proximal versus distal transcription start sites with high accuracy.
Epigenomics
ChIA-PET
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Imprinting (psychology)
Genomic Imprinting
Intramuscular fat
Family-based QTL mapping
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Сазанов А.А.; Царева В.А.; Смирнов А.Ф.; Вардецка Б.; Корчак М.; Ящак К.; Романов M.Н.
Большинство хозяйственно ценных признаков домашних животных имеют сложный полигенный тип наследования и контролируются многими генами, расположенными в локусах QTL (quantitative trait loci). Изучение комплексной молекулярной архитектуры QTL представляет интерес с точки зрения общей генетики. Кроме того, данные о нуклеотидных последовательностях из районов QTL могут быть использованы в практическом животноводстве для селекции с помощью молекулярных маркеров (marker assisted selection, MAS).
В настоящее время нами проведен ряд экспериментов по позиционному клонированию двух районов хромосомы 4 домашней курицы, содержащие QTL толщины скорлупы на 53 недели жизни (ST53) и массы белка в яйце на 33 неделе (AW33). Указанные признаки различаются у двух линий кур (польская зеленоногая и род-айленд) на 3,3% и 7,5%, соответственно. Показано сцепление признака AW33 с микросателлитным маркером MCW170 (генетическое расстояние 1сМ) и практически полное сцепление QTL ST53 с микросателлитным маркером MCW114. С использованием баз данных компьютерной сети Интернет показана локализация количественного признака AW33 в пределах интервала, ограниченного микросателлитными локусами MCW0170 и LEI0081, и QTL ST53 внутри района с границами MCW0114 и ADL0241. Проведен скрининг гридированной геномной BAC-библиотеки курицы 031-JF256-BI (http://hbz.tamu.edu) с использованием в качестве ДНК-зондов меченых -32P-dCTP последовательностей микросателлитов MCW0170, LEI0081, MCW0114 и ADL0241. Графическая обработка результатов скрининга проведена при помощи сканера FX-scan и пакета компьютерных программ Quantity One. Определены координаты двадцати клонов, имеющих гомологию последовательностей ДНК вставки с микросателлитными локусами MCW0170, LEI0081, MCW0114 и ADL0241.
Полученные данные позволят «заякорить» районы QTL на детально разработанных сравнительных генетических картах «человек-мышь» на основе гомологии и, возможно, выявить гены, ответственные за QTL толщины скорлупы и массы белка в яйце. ( Кандидатские проекты.)
Family-based QTL mapping
Marker-Assisted Selection
Positional cloning
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イネ系統「北海PL9」（穂ばらみ期耐冷性が極強）と「北海287号」（やや強）の組換え自殖系統群を用いて，穂ばらみ期耐冷性に関する量的形質遺伝子座（quantitative trait locus: QTL）解析を行った．穂ばらみ期耐冷性は冷水深水処理後の稔実率の逆正弦変換値（稔実指数）で評価した．その結果，既報の穂ばらみ期耐冷性QTL， qCTB8と同じ第8染色体短腕領域にqCTB8.1を検出したのに加えて，新たに第1染色体に2種類のQTL， qCTB1.1およびqCTB1.2を検出した．いずれのQTLにおいても「北海PL9」の対立遺伝子が稔実指数を増加させ，組換え自殖系統群の全変異に対する寄与率はそれぞれ14.2（ qCTB8.1），18.8（qCTB1.1）および11.8%（qCTB1.2）であった．さらに，穂ばらみ期の耐冷性評価に大きく影響を与える形質である出穂期および稈長についてもQTL解析を行い，出穂期に関しては第2および第3染色体に，稈長については第1，第2，第3（3ヶ所），第8，第9（2ヶ所）および第11染色体にQTLsを検出した．出穂期および稈長に関するQTLの染色体上での位置は，穂ばらみ期耐冷性QTLとは一致しなかった．検出された穂ばらみ期耐冷性QTLsの集積効果を明らかにするために，3種類のQTLsの遺伝子型別に稔実指数を比較したところ，「北海PL9」型対立遺伝子に稔実指数を相加的に向上させる効果が認められた．
Family-based QTL mapping
Trait
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Regulation of chromatin composition and structure is crucial for maintaining genome integrity and execution of the wide array of functions related to gene regulation and downstream cell signaling. Chemical modifications of chromatin are at the core of these processes and include methylation of the primary sequence of DNA, as well as various modifications of the proteinaceous chromatin packaging units - the histones. Recent genome-wide mapping approaches have been instrumental for characterization of the location and distribution of these marks relative to the different functional domains and gene regulatory elements in chromatin. The majority of the characterized chromatin modifications function as signaling platforms for recruitment of various protein complexes. Therefore, it is of equal importance to describe these sets of proteins for dissection of the functional consequence of their binding. More importantly, global analysis of the interactomes of functionally associated chromatin modifications might shed light on the proteins required for establishment and operation of specific chromatin domains. In this study, a novel approach for identification of chromatin modification-dependent protein binding was established. In vitro reconstituted oligonucleosomal templates with homogeneous and defined modification status were used for affinity purification from SILAC-labeled nuclear extracts. The interactomes of ten individual chromatin species were investigated and the results provided valuable insight into chromatin biology on several levels. Investigation of the nature of the subproteomes recruited by single modifications provided evidence for their functional role. Additionally, the results offer a comprehensive catalogue of candidate proteins for further dissection of specific chromatin modification molecular readout. This was exemplified here with the demonstration of the recruitment of the SWI/SNF complex to monoubiquitylated H2B-containing chromatin for regulation of transcription of a specific set of genes. Investigation of the interactome of doubly modified chromatin identified a large number of factors whose recruitment presumably depends on the cooperative action of two modifications. Furthermore, the comparative analysis of individual datasets revealed novel relationships between the different modifications. On a global scale, this resulted in the identification of a limited set of proteins that likely play an important role for the function of heterochromatin domains. Lastly, the chromatin affinity purification approach was used for developing a SILAC internal standard method for direct quantitative comparison of recruitment to different chromatin modifications and combinations thereof.
ChIA-PET
Histone-modifying enzymes
Bivalent chromatin
Interactome
Scaffold/matrix attachment region
Epigenomics
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Data from an F 2 cross between breeds of livestock are typically analysed by least squares line-cross or half-sib models to detect quantitative trait loci (QTL) that differ between or segregate within breeds. These models can also be combined to increase power to detect QTL, while maintaining the computational efficiency of least squares. Tests between models allow QTL to be characterized into those that are fixed (LC QTL), or segregating at similar (HS QTL) or different (CB QTL) frequencies in parental breeds. To evaluate power of the combined model, data wih various differences in QTL allele frequencies (FD) between parental breeds were simulated. Use of all models increased power to detect QTL. The line-cross model was the most powerful model to detect QTL for FD>0·6. The combined and half-sib models had similar power for FD<0·4. The proportion of detected QTL declared as LC QTL decreased with FD. The opposite was observed for HS QTL. The proportion of CB QTL decreased as FD deviated from 0·5. Accuracy of map position tended to be greatest for CB QTL. Models were applied to a cross of Berkshire and Yorkshire pig breeds and revealed 160 (40) QTL at the 5% chromosome (genome)-wise level for the 39 growth, carcass composition and quality traits, of which 72, 54, and 34 were declared as LC, HS and CB QTL. Fourteen CB QTL were detected only by the combined model. Thus, the combined model can increase power to detect QTL and mapping accuracy and enable characterization of QTL that segregate within breeds.
Family-based QTL mapping
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Quantitative trait loci(QTL) analysis for some important agronomic traits(plant height,ear height and leaf angle) were carried out,using SSR markers and three F2:3 populations(H21×Mo17,Zi330×K36 and B73×L050) in order to understand the genetic and molecular mechanisms of these traits.Eighteen QTL were detected for plant height,twelve QTL for ear height and nine QTL for leaf angle.Some of these QTL were located within the same chromosome regions,and the peaks of some QTL regions overlaid.In addition,it was found that some QTL were located in the same regions with known qualitative genetic loci affecting these traits.
Trait
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Abstract Chromatin accessibility is essential for transcriptional activation of genomic regions. It is well established that transcription factors (TFs) and histone modifications (HMs) play critical roles in chromatin accessibility regulation. However, there is a lack of studies that quantify these relationships. Here we constructed a two-layer model to predict chromatin accessibility by integrating DNA sequence, TF binding, and HM signals. By applying the model to two human cell lines (GM12878 and HepG2), we found that DNA sequences had limited power for accessibility prediction, while both TF binding and HM signals predicted chromatin accessibility with high accuracy. According to the HM model, HM features determined chromatin accessibility in a cell line shared manner, with the prediction power attributing to five core HM types. Results from the TF model indicated that chromatin accessibility was determined by a subset of informative TFs including both cell line-specific and generic TFs. The combined model of both TF and HM signals did not further improve the prediction accuracy, indicating that they provide redundant information in terms of chromatin accessibility prediction. The TFs and HM models can also distinguish the chromatin accessibility of proximal versus distal transcription start sites with high accuracy.
Epigenomics
ChIA-PET
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