Related Story<\/p>\n
Because these sequences are highly repetitive and nearly identical, they\u2019ve been disregarded as \u201cjunk DNA<\/a>\u201d for decades\u2014genetic leftovers from long-extinct viruses. But in recent years, this unflattering view of these sequences has begun to change. Today, scientists believe<\/a> that TEs play a role in genome function, chromosome evolution, speciation, and diversity. However, due to their repetitive nature, TEs remain difficult to research. <\/p>\n Now, a new international study has found a novel method for analyzing these mysterious sequences, and they\u2019ve discovered hidden patterns responsible for gene expression<\/a>. The results of the study were published in the journal Science Advances<\/a>. <\/p>\n \u201cOur genome was sequenced long ago, but the function of many of its parts remain unknown,\u201d Fumitaka Inoue, a co-author of the study from Kyoto University, said in a press statement<\/a>. Understanding TEs would solve one of the biggest mysteries of the genome. <\/p>\n In an attempt to better understand TEs, the researchers developed a new method for classifying them. Eschewing standard annotation tools, this study groups TEs based on both their evolutionary relationships and their conservation quality in the primate<\/a> genome. Focusing on a family of sequences called MER11, the new method allowed scientists to divide the group into subgroups, named MER11_G1 through G4. The G1 subgroup represented the oldest evolutionary sequences, while G4 contained the youngest. <\/p>\n Related Story<\/p>\n By looking at MER11 through this new lens, researchers were able to compare these new subfamilies with epigenetic markers, and found that these groups appeared to have a regulatory function within the genome. In other words, they acted like on-off switches for gene expression\u2014particularly in early human development. <\/p>\n Of course, it\u2019s one thing to infer a pattern, and another to see it in action. So, the team used a technique known as \u201clentiviral massively parallel reporter assay,\u201d or lentiMPRA, to measure 7,000 MER11 sequences using human stem cells<\/a> and early-stage neural cells. This showed that the youngest of the group (MER11_G4) had the strongest impact on gene expression. According to the study, this group makes use of regulatory \u201cmotifs\u201d\u2014short stretches of DNA that influence gene development and response. <\/p>\n