Significant fraction (98.5% in humans) of most animal genomes is non- coding dark matter. Its largely unknown function (1-5) is related to programming (rather than to spontaneous mutations) of accurate adaptation to rapidly changing environment. Programmed adaptation to the same universal law for non-competing animals from anaerobic yeast to human is revealed in the study of their extensively quantified mortality (6-21). Adaptation of animals with removed non-coding DNA fractions may specify their contribution to genomic programming. Emergence of new adaptation programs and their (non-Mendelian) heredity may be studied in antibiotic mini-extinctions (22-24). On a large evolutionary scale rapid universal adaptation was vital for survival, and evolved, in otherwise lethal for diverse species major mass extinctions (25-28). Evolutionary and experimental data corroborate these conclusions (6-21, 29-32). Universal law implies certain biological universality of diverse species, thus quantifies applicability of animal models to humans). Genomic adaptation programming calls for unusual approach to its study and implies unanticipated perspectives, in particular, directed biological changes.
Identification of possible differences in coding and non-coding fragments of DNA sequences by using the method of the Recurrence Quantification Analysis
Increasing biological complexity is positively correlated with the relative genome-wide expansion of non-protein-coding DNA sequences
背景资料：在当前的基因组时代之前，有人认为生物体所使用的蛋白质编码基因的数量是衡量其复杂性的有效指标。然而，现在很清楚的是，主要的不一致性存在，生物复杂性和蛋白质编码基因的数量之间只有微弱的关系。例如，使用蛋白质编码基因数量作为评估生物复杂性的基础，将使尾索动物和昆虫的复杂性低于线虫，而人类的复杂性低于水稻。结果如下：我们分析了85个测序物种的非编码基因组DNA与总基因组DNA的比率（ncDNA/tgDNA），发现这个比率与生物学复杂性的增加密切相关。对于原核生物，ncDNA/tgDNA比率通常包含在0.05-0.24的带宽内，但在单细胞真核生物中上升到0.26-0.52，并且对于发育复杂的多细胞生物体上升到0.62-0.985。值得注意的是，原核生物物种的物种分布不均匀，接近平均值0.1177 ncDNA/tgDNA（p=1.58 x 10^-13），ncDNA/tgDNA与基因组大小呈非线性关系（r=0.15）。重要的是，ncDNA/tgDNA比率校正倍性，并且基本上不受重复序列的可变负荷的影响。结论：我们认为，所观察到的非编码DNA的增加和组成模式主要是增加的信息含量的函数。因此，内含子、基因间序列、重复元件和基因组DNA可能对复杂生物的进化和功能库比以前认识到的要重要得多。
Identification and characterization of unique to human regulatory sequences in embryonic stem cells reveal associations with transposable elements, distal enhancers, non-coding RNA, and DNA methylation-driven mechanisms of genome editing
The Stanford University School of Medicine（斯坦福大学医学院）；Sanford-Burnham Medical Research Institute（桑福德-伯纳姆医学研究所）；Genlight Technology Corporation（Genlight科技有限公司）
Facultad de Ciencias, Universidad Nacional Autónoma de México（墨西哥国立自治大学理学院）；Centro de Investigación y Estudios Avanzados（高级研究与调查中心）；International Max Planck Research School for Computational Biology and Scientific Computing（国际马克斯·普朗克计算生物学与科学计算研究学院）；Freie Universität Berlin（柏林自由大学）；Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México（墨西哥国立自治大学复杂性科学中心）
GRAPE: Heterogeneous Graph Representation Learning for Genetic Perturbation with Coding and Non-Coding Biotype
Zhejiang University（浙江大学）；AI Lab, Research Center for Industries of the Future, Westlake University（西交大人工智能实验室，未来产业研究中心，西湖大学）；Department of Automation, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University（自动化系，电子信息与电气工程学院，上海交通大学）
DeepVRegulome: DNABERT-based deep-learning framework for predicting the functional impact of short genomic variants on the human regulome
Stony Brook University（石溪大学）；Renaissance School of Medicine, Stony Brook University（石溪大学文艺复兴医学院）；Northwestern University Feinberg School of Medicine（西北大学范伯格医学院）；Northwestern University（西北大学）
