Darwin's - Impact personified

Future lies in Junk DNA

Scientific progress ever since Mendel’s laws of heredity were rediscovered is phenomenal. In due course the world witnessed significant advancements in the field of molecular biology, from understanding the 3-D structure of DNA to the decryption of human genome sequence. Human genome holds precious information about our evolution, development, and physiology. International Human Genome Sequencing Consortium revealed the presence of 3 billion base pairs in our genome1. New data suggests the presence of 25,000 - 30,000 protein coding genes in human; Compare it with the genes encoded by 1,000-cell roundworm C.elegans which is 19,500. Structural and developmental complexity of organisms does not parallel their numbers of protein-coding genes but non coding sequences of DNA rise with the complexity of Organism2. This shows that they must be doing something indispensible otherwise, they would have got lost under evolution and selective pressures. Geneticists have long focused only on 1.5 % of DNA that contains the blueprint for proteins. Genes are fragmented into chunks of protein-coding sequences separated by extensive tracts of non-protein coding sequences. This 98.5% of the remainder DNA – was often dismissed as junk. What is the significance of these Introns and long stretches of Intergenic DNA between genes? Why have they been conserved in Evolution? It was too hasty for earlier geneticists to assume that Introns, which do not code for proteins as non-functional and junk. Present era’s groundbreaking discoveries are overturning the above assumption.

The central dogma of biology holds that genetic information normally flows from DNA to RNA to proteins. The dogma is itself being challenged by some startling observations. Conventionally, a gene must get transcribed to produce proteins. But, studies of several genes show that they are clearly functional even though they do not code for any protein but produce only RNA. According to Claes wahlestedt of Karolinska Institute the term “gene” is always loosely defined, “we tend not to talk about ‘genes’ any more, we just refer to any segment that is transcribed to RNA as a ‘transcriptional unit’”. Well, if this is the case there are about 70,000 to 100,000 such elements. More than half of it would certainly not fit into classical “gene”. These non-coding RNA [ncRNA] dominates the genomic output of the higher organisms2. They have been shown to control chromosomal architecture, mRNA turnover, and developmental timing of protein expression.

These RNA-only encoding genes give rise to intricate structures. One such is Antisense RNA made from the complementary DNA strand that sits opposite to the protein-coding gene on the double helix. Antisense RNAs can intercept the messenger RNA transcribed from the gene, preventing the mRNA from being translated into protein.

Analogously, MicroRNAs are evolutionarily conserved, small, ncRNA molecules that regulate gene expression at the level of translation. RNA interference machinery processes the microRNA (miRNAs) and uses it to destroy mRNA made by particular genes, effectively suppressing them. Humans are estimated to encode for +1000 unique miRNAs. They are predicted to directly regulate the expression of at least 30% of all human protein-encoding genes3. miRNAs play big roles in neural development and analysis of their perturbed expressional patterns in diseased state may serve our quest to understand Oncogenesis profoundly .

Probably the most intriguing form of RNA yet discovered is the Riboswitch, isolated in 2002 by Ronald R. Breaker’s lab at Yale. Riboswitches, Produced in many cases from noncoding DNA between known genes. These are complex folded RNA domains which serve as receptors for specific metabolites. When one part of the folded RNA binds to the specific target protein or chemical, another part containing the RNA decodes for a protein product. The riboswitch is precisely turned “on” and protein is translated only in the presence of its target. Breaker’s Lab is underway engineering this hybrid digital-analog molecule to do useful things, such as killing germs.4

Are introns ancient genomic elements or were they acquired only recently in the evolution of eukaryotes? This remains controversial but they play vital role in genome of complex organisms. They are also the source of non-coding snoRNAs [small nucleolar RNA], which acts in precise chemical modification of various RNAs. These novel snoRNA-like molecules are reported to be specifically expressed in mammalian brain e.g. HBII-52 snoRNA processes the serotonin 2C receptor gene.5 Introns also regulate gene expression e.g. the second intron of human apolipoprotein B gene is required for expression of this gene in liver. They also act in alternative splicing, exon-shuffling and gene evolution.

Non-coding RNAs are proving their indispensible role in regulating cell circuitry. Why were ncRNAs not identified earlier? “The failure to recognize the importance of Introns may well go down as one of the biggest mistakes in the history of molecular biology” says John S Mattick of University of Queensland. “What was damned as junk because it was not understood may, in fact, turn out to be the very basis of human complexity” states Wayne gibbs.

In the end the orthodoxy of central dogma that proteins alone regulate the genes of humans and other complex organisms must be reassessed. As biologists sift more and more novel kinds of active RNA genes out of the long-neglected introns and Intergenic stretches of DNA, we are poised to understand the very basis of genomic programming and developmental regulation. New roles of RNA are waiting to be discovered which would surely revolutionize the field of molecular genetics. For me the most exciting era in genetics has begun……

REFERENCES:
1. Initial sequencing and analysis of human genome Nature 2001
2. Mattick JS, Gagen MJ. The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms. Mol Biol Evol. 2001
3. Lewis et al 2003
4. Barrick, J. E. et al. New motifs suggest an expanded scope for riboswitches in bacterial genetic control USA. PNAS 2004
5. Cavaille, et al Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization. PNAS 1997