The draft of the human genome adds details to the X chromosome decoded without dead ends

  Our reporter Zhang Ye

  This is a small step in gene sequencing technology, but it may be a big step in the development of human genetic engineering.

  Recently, researchers from the National Institutes of Health (NIH) Human Genome Research Institute (NHGRI) announced that they have finally obtained complete, gap-free, end-to-end sequence information of the human X chromosome.

  This breakthrough discovery was published in the journal Nature, which indicates that it is possible to generate a precise base sequence of a human chromosome and generate a complete sequence of the human genome.

Eric Green, MD, director of NHGRI, said: "This achievement opens a new era in genomics research."

  The Human Genome Project, which cost US$3 billion and was launched in 1990, produced the first draft of the human genome in 2000 after ten years of hard work.

This is the most accurate and complete vertebrate genome sequence ever.

  However, the "secret book" carrying the human genetic code has not been completely deciphered, and there are still a large number of unknown gaps.

Why can't these gaps be filled?

What gene sequencing technology is helping scientists obtain the complete sequence of the X chromosome this time?

Can the remaining gene sequence blanks be successfully filled?

  Sequencing the human genome is like a puzzle

  If you have children in your family, or you are a puzzle lover, challenging more pieces and larger format puzzles must be your goal.

  But, have you ever thought that a group of scientists from different countries are also challenging a huge puzzle, and this "puzzle" may contain billions of pieces.

This huge "puzzle" is actually the work that many institutions and scientists around the world have been working on for many years, which is the human genome map.

  DNA (deoxyribonucleic acid) fragments store all the information of life's race, blood type, and processes of gestation, growth, and apoptosis.

All life phenomena such as the birth, growth, decline, illness, old age, and death of organisms are related to DNA.

  The human genome is very long, containing about 3 billion base pairs.

By locating the precise positions of these base pairs on the DNA strand, and then identifying and analyzing various genes and their functions, humans will eventually conquer many chronic diseases such as cancer, heart disease, and Alzheimer's disease.

  It should be noted that the human genome is not a sequencing study of an individual.

Human genes are broadly similar, whether you are a man or a woman, yellow skin or blue eyes.

However, everyone has their own "copy" of the genome, and each "copy" is slightly different.

  Therefore, in genome research, the concept of "reference genome" is usually adopted.

The reference genome is a database of nucleic acid sequences assembled by scientists as a reference template for the genome of a species.

  The Genome Reference Consortium (GRC) is responsible for updating the reference genome from time to time.

However, the current reference genome is still incomplete, and there are many gaps in the DNA sequence waiting to be filled.

  "Because the human genome is too long, no current sequencing technology can read all the sequence information at once. Therefore, scientists can only fragment the genome into small fragments for sequencing, and finally assemble it." Biology, Nanjing Medical University Professor Wang Qianghu, director of the Department of Informatics, said that to outsiders, the work these scientists have done is like a "puzzle."

  In this "puzzle", there are many repeated sequences.

Since sequencing technology can only read short fragments, repetitive sequences will cause many short fragments that look almost identical.

"This is like the blue sky and grassland in the puzzle. Each piece of it is blue or green, but there is no clue to tell us how these pieces are put together." Wang Qianghu said, this has brought many gaps.

  Why is the special X chromosome captured first

  As we all know, human cells have a nucleus, and the genetic material of the nucleus is on 23 pairs of chromosomes, one of which is a sex chromosome.

If it is a female, this pair of sex chromosomes is XX, but if it is a male, it is XY.

And everyone's sex chromosomes are half from the father and half from the mother.

  "There is a reason why scientists choose X chromosomes for complementary sequencing." Wang Qianghu said that the X chromosome is of medium length among 23 pairs of chromosomes, but it also contains a lot of genetic information. Once the X chromosome can be sequenced completely, it will be the integrity of other chromosomes in the future. Sequencing provides reference.

  "This is not to say that the Y chromosome is not important." Wang Qianghu said that the Y chromosome has 27 special coding genes, which the X chromosome does not have. From this point of view, boys have 27 more coding genes from their fathers than girls.

  The murder case of a female student at Nanjing Medical University 28 years ago, which was broken in February this year, relied on Y-STR family investigation technology to find the family through Y-chromosome analysis, and then took oral swabs from 11 males in the suspect’s family and performed DAN comparison. Yes, confirm the culprit.

  "The Y chromosome is unique to men and can only come from the inheritance of the father. It is a bit like the ancients said that it is'in the same line.'" Wang Qianghu told reporters that the grandfather passed it on to the father and the father passed it on to the son.

Therefore, as long as the Y chromosome of a male in a family is tested, it is basically known what the Y chromosomes of other males in the family are.

  Women inherit two X chromosomes, one from the mother and one from the father.

However, the two X chromosomes are not the same, and their DNA sequences contain many differences.

  In this study, the researchers did not sequence the X chromosomes of normal human cells.

Instead, a special type of female cell is used-with two X chromosomes from the same source.

Compared with male cells with only a single copy of the X chromosome, this cell can provide more DNA for sequencing.

It also avoids the sequence differences encountered when analyzing the two X chromosomes of a typical female cell.

  Nanopore technology is the biggest contributor to X chromosome sequencing

  Compared with the human genome draft obtained 20 years ago, this time the scientists sequenced the X chromosome completely, and the biggest contribution is the nanopore sequencing technology.

  "This is a third-generation sequencing technology." According to Wang Qianghu, in 1996, Daniel Brandon of Harvard University, David Demer of the University of California, and colleagues, published in the journal Proceedings of the National Academy of Sciences. The first published article pointed out that membrane channels can be used to detect multiple nucleic acid sequences, which became the origin of nanopore sequencing technology.

  The study used a special nanopore sequencer, which sequenced DNA by detecting changes in current when a single DNA molecule passes through a small hole (nanopore) in the membrane.

  "Nanopore sequencing technology can obtain'ultra-long reads' containing hundreds of thousands of base pairs. Such lengths can span the entire repetitive region, thereby bypassing some complex challenges." Wang Qianghu told reporters that the first generation of genes Sequencing technology can only read a few hundred base pairs at a time. In the past two decades, sequencing technology has made great progress, making it relatively easy to sequence repetitive sequences that were once considered very difficult.

  "This achievement is undoubtedly a milestone." Wang Qianghu said that by analyzing the genetic information of the X chromosome, scientists may soon overcome some complex and difficult diseases.

  For example, there are famous genes F8 (coagulation factor 8) and F9 (coagulation factor 9) on the X chromosome. Deficiency of coagulation factors 8 and 9 can lead to hemophilia.

  Because men have only one X chromosome, once a problem occurs, they cannot produce clotting factors 8 and 9.

This is why hemophilia usually occurs in men: women have two X chromosomes. If one chromosome has a problem and the other is normal, the symptoms of hemophilia usually do not appear, but it will be passed on to the next generation. .

  Wang Qianghu believes that the new human genome sequence fills many gaps in the current human reference genome and opens up new areas for genome research.

But potential challenges remain. For example, the repetitive DNA fragments on chromosomes 1 and 9 are much longer than those on the X chromosome.

Scientists next plan to continue their efforts to bridge more unknown gaps.

  At the same time, multiple genome projects for the Chinese are also being implemented. Wang Qianghu said: "The current human reference genome is based on European and American populations, but there are subtle differences in genes between European and American populations and Chinese. For example, the Chinese Academy of Engineering Academician and Professor Hongbing Shen's group of Nanjing Medical University have found 19 susceptibility genes related to lung cancer in Chinese through genome-wide association studies, which can be used as a polygenic genetic risk assessment index for lung cancer in the Chinese population and can achieve prospective prevention."