Neanderthals, Denisovans or chimpanzees: who does the genome of modern humans look like?

Human genome

This is a collection of hereditary material enclosed in a human cell. Human

the genome consists of 23 pairs of chromosomes found in the nucleus, as well as mitochondrial DNA.

Twenty-two autosomes, two sex chromosomes X and Y, and human mitochondrial DNA contain together approximately 3.1 billion base pairs.

During the implementation of the Human Genome Project,determined the DNA sequence of all chromosomes and mitochondrial DNA. Currently, these data are actively used all over the world in biomedical research.

Complete sequencing revealed that humanthe genome contains 20-25 thousand active genes, which is significantly less than expected at the beginning of the project (about 100 thousand) - that is, only 1.5% of all genetic material encodes proteins or functional RNA.

The rest is non-coding DNA, often referred to as junk DNA, but which has proven to play an important role in regulating gene activity.

Features of the human gene

  • Chromosomes

There are 23 pairs of chromosomes in the genome:22 pairs of autosomal chromosomes, as well as a pair of sex chromosomes X and Y. In humans, male sex is heterogametic and is determined by the presence of a Y chromosome. Normal diploid somatic cells have 46 chromosomes.

  • Genes

Preliminary estimates suggested the presence ofthe human genome has more than 100 thousand genes. According to the results of the Human Genome project, the number of genes, or rather open reading frames, amounted to about 28,000 genes. In connection with the improvement of methods for searching (predicting) genes, a further decrease in the number of genes is expected.

The number of genes in humans is only slightly larger than that of simpler organisms, such as the roundworm Caenorhabditis elegans or flies Drosophila melanogaster... This is due to the fact that alternative splicing is widely represented in the human genome. Alternative splicing produces several different protein chains from a single gene.

As a result, the human proteome turns out to bemuch larger than the proteome of the considered organisms. Most human genes have multiple exons, and introns are often significantly longer than the border exons in a gene.

  • Regulatory sequences

The human genome contains many differentsequences responsible for the regulation of genes. Regulation refers to the control of gene expression (the process of constructing messenger RNA along a portion of the DNA molecule).

These are usually short sequences,located either next to the gene or within the gene. Sometimes they are located at a considerable distance from the gene (enhancers). Systematization of these sequences, understanding of the mechanisms of work, as well as issues of mutual regulation of a group of genes by a group of corresponding enzymes are currently only at the initial stage of study.

Mutual regulation of gene groups is described withusing gene regulation networks. The study of these issues is at the intersection of several disciplines: applied mathematics, high performance computing and molecular biology. Knowledge comes from comparisons of genomes of different organisms and from advances in the organization of artificial gene transcription in the laboratory.

Identification of regulatory sequences inthe human genome was partially produced on the basis of evolutionary conservatism (the property of preserving important fragments of the chromosomal sequence that correspond to approximately the same function).

According to the molecular clock, evolutionarythe human and mouse lines split about 100 million years ago. For two genomes, computer methods have revealed conservative sequences (sequences that are identical or very slightly different in the compared genomes) in the noncoding part and it turned out that they are actively involved in the mechanisms of gene regulation in both organisms.

Another approach to obtaining regulatoryThe sequences are based on a comparison of the genes of humans and puffer fish. The gene sequences and regulatory sequences in humans and puffer fish are substantially similar, but the puffer fish genome contains 8 times less "junk DNA". This "compactness" of the fish genome makes it much easier to search for regulatory sequences for genes.

  • Other objects in the genome

Protein coding sequences (setsequences composing exons) make up less than 1.5% of the genome. Leaving aside known regulatory sequences, the human genome contains a host of objects that look important, but whose function, if any, has not yet been elucidated.

These objects occupy up to 97% of the total volume of the human genome. Such objects include:

  • Viruses

About 1% of the human genome is occupied by embeddedgenes of retroviruses (endogenous retroviruses). These genes usually do not benefit the host, but there are exceptions. So, about 43 million years ago, retroviral genes, which served to build the envelope of the virus, entered the genome of the ancestors of monkeys and humans. In humans and monkeys, these genes are involved in the work of the placenta.

Most retroviruses were incorporated into the genome of human ancestors over 25 million years ago. Among younger human endogenous retroviruses, no beneficial ones have been found so far.

Decoding the genome of the Neanderthal

The genome of the Neanderthal is similar in size to the genome of modern humans. Preliminary results show that the DNA of modern humans and Neanderthals is approximately 99.5% identical.

Researchers have extracted fossil DNANeanderthal man from the thigh bone of a Neanderthal skeleton 38,000 years ago from Vindia Cave in Croatia, as well as from other bones found in Spain, Russia and Germany. Using the chimpanzee and human mitochondrial DNA sequences as reference points, the scientists calculated that the date of the discrepancy between the human and Neanderthal mtDNA is 660,000 ± 140,000 years.

In the genomes of the last European Neanderthals fromcaves Vindia, Mezmaiskaya 2, Goye and Le Cotte, who lived approx. 45-39 thousand liters. n. after the arrival of the Sapiens in Europe, no admixture of Cro-Magnon genes was found.

Comparison of genomes of late Neanderthals withthe genome of an older Neanderthal man from the Caucasus (Mezmaiskaya 1) showed that at the end of the history of the Neanderthals, the turnover of the Neanderthal population probably took place either in the Caucasus or throughout Europe.

The bulk of the flow of Neanderthal genes in the early Homo sapiens came from one or more originalpopulations of Neanderthals, which diverged from the last Neanderthals at least 90 thousand years. BC, but after they split off from the previously sequenced Neanderthal from Siberia (Altai Neandertal) about 150 thousand years ago.

Whose genes have we inherited?

  • Denisovites

People of the modern type interbred with Denisovans twice, American genetics found out, who analyzed the DNA of 5639 inhabitants of Eurasia and Oceania.

As stated in an article published in the magazine Cell, scientists have found that the ancestors of the inhabitants of modern China and Japan interbred with Denisovans from two populations - the Altai and the unknown second.

Neanderthals and Denisovans are considered separatespecies (according to another version - subspecies) of ancient people. Neanderthals lived in Europe and Central Asia and became extinct about 30 thousand years ago, leaving numerous remains and artifacts.

Much less is known about Denisovans.There are practically no traces of them (so far only three molars and a phalanx of a finger have been discovered), which were found in one place - Denisova Cave in Altai. Actually, a new kind of people was discovered by genetics, sequencing DNA from the phalanx of a finger and finding significant differences in the mitochondrial and nuclear genomes from the genomes of modern humans and Neanderthals.

  • Neanderthals

The genome of Neanderthals and modern humansdiffers by 0.16%. On the one hand, the differences are small. On the other hand, you can see which genes are present in modern humans, but absent in both chimpanzees and Neanderthals.

These are hypothetical elements that are notinherited from a common ancestor and appeared only after the divergence of the branches of modern man and the Neanderthal. There were 78 such purely modern elements - nucleotide substitutions in genes. Some of these nucleotide substitutions may be neutral (they could have become entrenched as a result of normal demographic processes, bottlenecks, etc.), while others may have adaptive significance.

So, there were 5 such genes that carried alongseveral of these nucleotide substitutions. These genes and, accordingly, these mutations are obviously adaptive for modern people, otherwise evolution would not have paid such close attention to them. These are genes associated with skin functions, mental activity, energy metabolism /

How did the gene pool affect the human population?

In 2010 Neanderthal nuclear genome was first fully studied. The genetic footprint of this species is recalculated very often. Population genetics from the University of Washington Benjamin Vernott and Joshua Ecky engaged in research and the new approach allowed the authors to "pull out" all the sequences of Neanderthal DNA hidden in modern genomes.

They came to the conclusion that in the gene pool of modernEuropean and Asian populations in total circulate about 20% of the Neanderthal genome. Neanderthal sequences in the genome of modern humans are rather short - this is due to the fact that a lot of time has passed since the time of hybridization with Neanderthals, and long sequences were broken recombinations (exchange of sites between different chromosomes).

26% of all coding proteins also contain Neanderthal alleles.

Genes in keratinocytes (skin cells): they are needed for improved pigmentation or adaptation. And the region on the seventh chromosome containing the gene helped develop human speech.

Latest scientific advances

  • The oldest European genome has been recreated

Scientists from the genetic laboratory of the Max Planck Institute for the History of Humanity in Germany have reconstructed the oldest European genome.

For the study, material was taken from a skull about 45 thousand years old, found in the town of Zlata Kun in the Czech Republic. It belonged to a woman.

It turned out that the genome from Zlata Kun containsabout the same amount of Neanderthal DNA as in other modern people, about 2-3%, but the segments of Neanderthal genes in it are much longer than in all.

According to the authors of the work, the DNA of this woman is notoccurs in people who later lived in Europe or Asia. This suggests that modern people met in Southeast Europe as early as 47–43 thousand years ago.

  • New mechanism of gene regulation

A group of scientists from Russia studied the role of double-stranded fragments of maturing RNA and showed that interactions between its distant parts can regulate gene expression.

RNA has two structures - primary and secondary.The primary structure of nucleic acids is understood as the order, the sequence of the arrangement of mononucleotides in the polynucleotide chain of RNA. This chain is stabilized by 3 ', 5'-phosphodiester bonds. In turn, the secondary structure is the conformational arrangement of the main chain of a macromolecule (for example, a polypeptide chain of a protein or a chain of nucleic acids), regardless of the conformation of the side chains or relation to other segments.

In describing the secondary structure, it is important to determine the hydrogen bonds that stabilize individual fragments of macromolecules.

Thanks to the new work, it turned out that the secondarystructure plays an important role in the maturation of information-carrying RNA molecules, and especially in splicing. This is a process in which the non-coding regions are excised and the coding regions are stitched together (as in the maturation of RNA molecules). Scientists have shown that RNA secondary structures can regulate splicing and thus contribute more to gene regulation than previously thought.

  • CRISPR / Cas9 system

The biggest breakthrough of the decade was the CRISPR / Cas9 system, for which its creators, Jennifer Doudna and Emmanuelle Charpentier, received the Nobel Prize in Chemistry in 2020.

CRISPR / Cas9 is a genome editing methodhigh accuracy, allowing you to change the genes of living microorganisms, including humans. And with its help there are chances to create methods of combating HIV and other diseases, which today sound like a sentence.

  • Genetically modified children

In 2018 were borngenetically modified children - girls Lulu and Nana. The zygote was obtained using IVF (in vitro fertilization), genetically altered with CRISPR / Cas9 and implanted into the uterus of the woman who gave birth to the girls.

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