November 18, 2019
For most of us in the Northern Hemisphere, the chill in the air and the shortening of daylight heralds autumn, a season of change. What does genomics have to do with natural and human-driven phenomena commonly associated with autumn? One area of research is called transcriptomics - the study of all the RNA molecules within a cell, otherwise known as the transcriptome. This research examines the initial product of genome expression-- a collection of RNA molecules derived from the transcriptome. Whole-transcriptome sequencing for organisms that haven’t been extensively studied and organisms without reference sequences, has become an efficient method for characterizing genes and understanding gene expression patterns. Read on for three interesting examples of how recent research is helping us understand the biology of the changing world and may someday, help us lead better lives.
Fall forests put on a dazzling display, turning the canopy into a mosaic of yellows, oranges, reds and purples. Scientists are unraveling the cellular mechanisms behind these processes using transcriptomics. Specific genes, which were dormant and unused all summer, begin to “turn on” and a flurry of activity unfolds in leaves as nutrients are digested and re-absorbed, and new pigments are produced during the process of senescence.
Harvest is a time of bounty, as farmers bring in bushels of ripe, beautiful crops. Advances in transcriptomics have allowed crop scientists to examine how genes turn off and on in crops as they ripen and have given us a better understanding of how this process works and is impacted by various climate and environmental factors. Better understanding the genetics behind how fruit ripens can help farmers deliver the most delicious and sustainable crops to the market in a changing world.
Bring on the Chill
Without food, hibernating mammals must rely on fat reserves, as heart rates slow drastically, and muscles go virtually unused for months. Very little was understood about mammal hibernation, partially because no scientific model species hibernate. But new transcriptomic technologies, like RNA-Seq, measure changes in the regulation of thousands of genes at once and give us powerful insight into the biology of the dramatic changes happening in a hibernating animal. Someday, understanding suspended animation may be useful for humans on long space missions or increased survival of certain traumatic conditions.
- Chen Z, Lu X, Xuan Y, Tang F, Wang J, Shi D, Fu S, Ren J. Transcriptome analysis based on a combination of sequencing platforms provides insights into leaf pigmentation in Acer rubrum. BMC plant biology. 2019.
- Wyatt LE, Strickler SR, Mueller LA, Mazourek M. An acorn squash (Cucurbita pepo ssp. ovifera) fruit and seed transcriptome as a resource for the study of fruit traits in Cucurbita. Horticulture research. 2015 Jan 28;2:14070.
- Hampton M, Melvin RG, Kendall AH, Kirkpatrick BR, Peterson N, Andrews MT. Deep sequencing the transcriptome reveals seasonal adaptive mechanisms in a hibernating mammal. PloS one. 2011 Oct 28;6(10):e27021.
- Schwartz C, Hampton M, Andrews MT. Seasonal and regional differences in gene expression in the brain of a hibernating mammal. PLoS One. 2013 Mar 20;8(3):e58427