Простое начало. Как четыре закона физики формируют живой мир - Партасарати Рагувир

12 Folding@home – боремся с болезнями с помощью глобально распределенного суперкомпьютера. https://foldingathome.org/; Greene K. Folding@home takes to the lab. Science. 2002; October 21 (https://www.sciencemag.org/news/2002/10/foldinghome-takes-lab).

13 Cooper S. et al. Predicting protein structures with a multiplayer online game. Nature. 2010; 466: 756–760.

14 Service R. F. «The game has changed.» AI triumphs at protein folding. Science. 2020; 370: 1144–1145.

Глава 3. Гены и механика ДНК

1 Deeb S. S. The molecular basis of variation in human color vision. Clin. Genet. 2005; 67: 369–377; Color vision deficiency. MedlinePlus. 2020 (https://medlineplus.gov/genetics/condition/color-vision-deficiency/).

2 Kino T. et al. Noncoding RNA gas5 is a growth arrest– and starvation-associated repressor of the glucocorticoid receptor. Sci. Signal. 2010; 3: ra8; Guttman M., Rinn J. L. Modular regulatory principles of large non-coding RNAs. Nature. 2012; 482: 339–346.

3 Kyoto Encyclopedia of Genes and Genomes (KEGG), https://www.genome.jp/kegg/ (Mycobacterium tuberculosis, https://www.genome.jp/kegg-bin/show_organism?org=mtu; Vibrio cholerae, http://www.genome.jp/kegg-bin/show_organism?org=vch).

4 National Center for Biotechnology Information, https://www.ncbi.nlm.nih.gov/genome/?term=Lactobacillus%20delbrueckii /Organism/.

5 Ezkurdia I. et al. Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes. Hum. Mol. Genet. 2014; 23: 5866–5878; Willyard C. New human gene tally reignites debate. Nature. 2018; 558: 354–355.

6 Church D. M. et al. Lineage-specific biology revealed by a finished genome assembly of the mouse. PLOS Biology. 2009; 7: e1000112; Wade C. M. et al. Genome sequence, comparative analysis, and population genetics of the domestic horse. Science. 2009; 326: 865–867; Zhan X. et al. Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle. Nature Genetics. 2013; 45: 563–566; Ohm R. A. et al. Genome sequence of the model mushroom Schizophyllum commune. Nature Biotechnology. 2010; 28: 957–963; Colbourne J. K. et al. The ecoresponsive genome of Daphnia pulex. Science. 2011; 331: 555–561; Rice Annotation Project database (RAP-DB): 2008 update. Nucleic Acids Res. 2008; 36: D1028 – D1033; Gramene database (http://ensembl.gramene.org/Zea_mays/Info/Annotation/); Wang H. et al. Analysis of non-coding transcriptome in rice and maize uncovers roles of conserved lncRNAs associated with agriculture traits. Plant J. 2015; 84: 404–416.

7 В базе данных BioNumbers, http://bionumbers.hms.harvard.edu/search.aspx, есть информация о размере геномов, включая геномы хлебной плесени Neurospora crassa и почвенной амебы Dictyostelium discoideum; вводите в строку поиска «number of genes» или название вида.

8 Schiessel H. The physics of chromatin. J. Phys. Condens. Matter. 2003; 15: R699 – R774; Tremethick D. J. Higher-order structures of chromatin: The elusive 30 nm fiber. Cell. 2007; 128: 651–654. Изображение ДНК, намотанной на гистонный комплекс, основано на структуре 1AOI из Protein Data Bank: https://www.rcsb.org/structure/1AOI; Luger K. et al. Nature. 1997; 389: 251–260.

9 Ou H. D. et al. ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells. Science. 2017; 357: eaag0025.

10 Mirabella C. et al. Chromatin deregulation in disease. Chromosoma. 2016; 125: 75–93; DeLaurier A. et al. Histone deacetylase-4 is required during early cranial neural crest development for generation of the zebrafish palatal skeleton. BMC Developmental Biology. 2012; 12: 16.

11 Segal E. et al. A genomic code for nucleosome positioning. Nature. 2006; 442: 772–778; Brunet F. G. et al. Evidence for DNA sequence encoding of an accessible nucleosomal array across vertebrates. Biophysical Journal. 2018; 114: 2308–2316.

12 Evilevitch A. et al. Osmotic pressure inhibition of DNA ejection from phage. Proc. Natl. Acad. Sci. 2003; 100: 9292–9295; Gelbart W. M., Knobler C. M. Virology: Pressurized viruses. Science. 2009; 323: 1682–1683.

Глава 4. Хореография генов

1 Изображение lac-репрессора, прикрепленного к ДНК, основано на структуре белков 1EFA и 1TLF из Protein Data Bank и на комбинированной иллюстрации Дэвида Гудселла: https://www.rcsb.org/structure/1EFA; https://www.rcsb.org/structure/TLF; Goodsell D. Molecule of the Month: lac Repressor. PDB-101. 2003 (http://pdb101.rcsb.org/motm/39); Bell C. E., Lewis M. A closer view of the conformation of the lac repressor bound to operator. Nat. Struct. Biol. 2000; 7: 209–214.

2 Schleif R. DNA Looping. Annual Review of Biochemistry. 1992; 61: 199–223.

3 Vörös Z. et al. Proteins mediating DNA loops effectively block transcription. Protein Sci. 2017; 26: 1427–1438; Becker N. A. et al. Mechanism of promoter repression by lac repressor-DNA loops. Nucleic Acids Res. 2013; 41: 156–166.

4 История изучения генетической регуляции описана в Morange M. A History of Molecular Biology. Cambridge, MA: Harvard University Press, 2000.

5 Lambert S. A., et al. The human transcription factors. Cell. 2018; 172: 650–665.

6 Schoenfelder S., Fraser P. Long-range enhancer – promoter contacts in gene expression control. Nature Reviews Genetics. 2019; 20: 437–455.

7 Cronin C. A. et al. The lac operator-repressor system is functional in the mouse. Genes Dev. 2001; 15: 1506–1517.

8 О памяти, часах и других генетических схемах: Nelson P. C. Physical Models of Living Systems. W. H. Freeman, 2015; Alon U. An Introduction to Systems Biology: Design Principles of Biological Circuits. Boca Raton, FL: CRC Press, 2007. О циркадном ритме и его клеточных часах: Brown S. A. et al. (Re)inventing the circadian feedback loop. Dev. Cell. 2012; 22: 477–487; Maywood E. S. et al. Analysis of core circadian feedback loop in suprachiasmatic nucleus of mCry1-luc transgenic reporter mouse. Proc. Natl. Acad. Sci. 2013; 110: 9547–9552; Pett J. P. et al. Feedback loops of the mammalian circadian clock constitute repressilator. PLOS Comput. Biol. 2016; 12: e1005266.

9 Elowitz M. B., Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature. 2000; 403: 335–338.

10 Stricker J. et al. A fast, robust and tunable synthetic gene oscillator. Nature. 2008; 456: 516–519.

11 Lawrence M. et al. Lateral thinking: How histone modifications regulate gene expression. Trends in Genetics. 2016; 32: 42–56; Ho L., Crabtree G. R. Chromatin remodelling during development. Nature. 2010; 463: 474–484.

12 Allis C. D., Jenuwein T. The molecular hallmarks of epigenetic control. Nature Reviews Genetics. 2016; 17: 487–500; Boškoviс A., Rando O. J. Transgenerational epigenetic inheritance. Annual Review of Genetics. 2018; 52: 21–41; Heijmans B. T. et al. Persistent epigenetic differences associated with prenatal exposure to famine in humans. PNAS. 2008; 105: 17046–17049.

13 Painter R. C. et al. Transgenerational effects of prenatal exposure to the Dutch famine on neonatal adiposity and health in later life. BJOG: An International Journal of Obstetrics & Gynaecology. 2008; 115: 1243–1249; Veenendaal M. V. E. et al. Transgenerational effects of prenatal exposure to the 1944–45 Dutch famine. BJOG: An International Journal of Obstetrics & Gynaecology. 2013; 120: 548–554.