Gordon H. Dixon’s trace in my personal career and the quantic jump experienced in regulatory information

ABSTRACT

Even before Rosalin Franklin had discovered the DNA double helix, in her impressive X-ray diffraction image pattern, Erwin Schröedinger, described, in his excellent book, What is Life, how the finding of aperiodic crystals in biological systems surprised him (an aperiodic crystal, which, in my opinion is the material carrier of life). In the 21st century and still far from being able to define life, we are attending to a quick acceleration of knowledge on regulatory information. With the discovery of new codes and punctuation marks, we will greatly increase our understanding in front of an impressive avalanche of genomic sequences. Trifonov et al. defined a genetic code as a widespread DNA sequence pattern that carries a message with an impact on biology. These patterns are largely captured in transcribed messages that give meaning and identity to the particular cells. In this review, I will go through my personal career in and after my years of work in the laboratory of Gordon H. Dixon, extending toward the impressive acquisition of new knowledge on regulatory information and genetic codes provided by remarkable scientists in the field.

Abbreviations: CA II: carbonic anhydridase II (chicken); Car2: carbonic anhydridase 2 (mouse); CpG islands: short (>0.5 kb) stretches of DNA with a G+C content ≥55%; DNMT1: DNA methyltransferases 1; DNMT3b: DNA methyltransferases 3B; DSB: double-strand DNA breaks; ERT: endogenous retrotransposon; ERV: endogenous retroviruses; ES cells: embryonic stem cells; GAPDH: glyceraldehide phosphate dehydrogenase; H1: histone H1; HATs: histone acetyltransferases; HDACs: histone deacetylases; H3K4me3: histone 3 trimethylated at lys 4; H3K79me2: histone 3 dimethylated at lys 79; HMG: high mobility group proteins; HMT: histone methyltransferase; HP1: heterochromatin protein 1; HR: homologous recombination; HSE: heat-shock element; ICRs: imprinted control regions; IRF: interferon regulatory factor; LDH-A/-B: lactate dehydrogenase A/B; LTR: long terminal repeats; MeCP2: methyl CpG binding protein 2; OCT4: octamer-binding transcription factor 4; PAF1: RNA Polymerase II associated factor 1; piRNA: PIWI-interacting RNA; poly(A) tails: poly-adenine tails; PRC2: polycomb repressive complex 2; PTMs: post-translational modifications; SIRT 1: sirtuin 1, silent information regulator; STAT3: signal transducer and activator of transcription; tRNAs: transfer RNA; tRFs: tRNA-derived fragments; TSS: transcription start site; TE: transposable elements; UB I: polyubiquitin I; UB II: polyubiquitin II; UBE 2N: ubiquitin conjugating enzyme E2N; 5ʹ-UTR: 5ʹ-untranslated sequences; 3ʹ-UTR: 3ʹ-untranslated sequences.

KEYWORDS:

• Chromatin code
• regulatory sequences
• tRNAs
• Piwi-piRNA

Acknowledgments

In the first place, and especially, to my family, Jordi A Blasi and my sons: Jordi, Ivan, and Diego, because they have had to endure all my scientific dreams. To Dr. Carme Martin, my adopted sister, expert physicist, who has also patiently endured my talks during full moon’s dinners; and last but not the least, to my colleagues from the research laboratory: Dr. Belen Alvarez, Dr. Michael Edel, and Dr. Jordi Requena, and from Forensic Genetics Dr. Carme Barrot and Agustina Vela. To all of them for their scientific support and encouragement, and also for the support, in so many moments, when my resilience was about to fade.

Declaration of interest

The author reports no conflicts of interest. The author is responsible for the content and writing of the article. No funding was received for this project.

Additional information

Notes on contributors

Jovita Mezquita-Pla

Wrote the manuscript, created the figures, project design, and interpretation of data: JM-P.