The information ‘deleted’ from the human genome may be what made us human

The information 'deleted' from the human genome may be what made us human

Human-specific deletions that remove nucleotides from regions highly conserved in other animals (hCONDEL). We evaluated 10,032 hCONDELs in diverse, biologically relevant datasets and identified tissue-specific enrichment (upper left). The regulatory effect of hCONDEL was characterized by comparing chimpanzee and human sequences in the MPRA (bottom left). The ability of hCONDEL to enhance or interfere with the activation and repression of gene regulatory elements was assessed (top right). The deleted chimpanzee sequence was re-introduced into human cells, leading to a transcriptional divergence cascade, hCONDEL, which regulates LOXL2 (bottom right). Credit: Science (2023). DOI: 10.1126/science.abn2253

According to a new study led by researchers at Yale and MIT’s Broad Institute, what’s missing from the human genome compared to the genomes of other primates may have been just as important to human development as what’s been added in our evolutionary history. Harvard.

The new findings, published April 28 in the journal Science, will fill an important gap in what is known about historical changes in the human genome. While the revolution in the ability to collect data from the genomes of different species has allowed scientists to identify additions that are characteristic of the human genome, such as a gene that was crucial for humans to develop the ability to speak, less attention has been paid to what is missing from the human genome.

In the new study, researchers used an even deeper genome dive into primate DNA to show that the loss of about 10,000 bits of genetic information, as small as a few base pairs of DNA, separates humans from chimpanzees over the course of our evolutionary history. our closest primate relative. Some of these “deleted” pieces of genetic information are closely related to genes involved in neuronal and cognitive functions, including one related to cell formation in the developing brain.

These 10,000 missing pieces of DNA, found in the genomes of other mammals, are shared by all humans, the Yale team found.

The authors say that the fact that these genetic deletions have persisted in all humans demonstrates their evolutionary importance, suggesting that they conferred some biological advantage.

“We often think that new biological functions require new pieces of DNA, but this work shows us that erasing the genetic code can have serious consequences for the traits that make us unique as a species,” said Stephen Reilly, assistant professor of genetics at the Yale School of Medicine. . Medicine and Work Senior Author.

This article was one of several that were published Science from the Zoonomia Project, an international research collaboration cataloging the diversity of mammalian genomes by comparing DNA sequences from 240 extant mammal species.

In their study, the Yale team found that some genetic sequences found in the genomes of most other mammalian species, from mice to whales, were lost in humans. But instead of disrupting human biology, they say, some of these deletions created new genetic codes that eliminated elements that normally turned genes off.

Erasing this genetic information, according to Reilly, had the effect of removing three characters – “n’t” – from the word “not” to create a new word “is”.

“[Such deletions] can slightly change the meaning of the instructions for making a human, helping to explain our larger brains and complex cognition,” he said.

The researchers used a technology called Massively Parallel Reporter Assays (MPRA), which can simultaneously screen and measure thousands of genetic changes in function between species.

“These tools can allow us to begin to identify the many small molecular building blocks that make us unique as a species,” Reilly said.

More information:
James R. Xue et al, Functional and evolutionary implications of human-specific deletions in conserved elements, Science (2023). DOI: 10.1126/science.abn2253

Provided by Yale University

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