life inspired

"A crystal structure of two bound RNA molecules not only provides insight into how regulatory riboswitch sequences affect messenger RNA expression, but also expands our understanding of RNA structure and architecture." Full news article @ Nature

Labels: control, RNA

"Behold the latest curio in the cabinet of RNA oddities: naturally occurring circular RNA molecules that influence gene expression." News article @ Nature

Labels: genomics, RNA, transcription

"How species with similar repertoires of protein-coding genes differ so markedly at the phenotypic level is poorly understood. By comparing organ transcriptomes from vertebrate species spanning ~350 million years of evolution, we observed significant differences in alternative splicing complexity between vertebrate lineages, with the highest complexity in primates." Full Article @ Science

Labels: evolution, Phenotypic complexity, RNA, vertebrates

"Transposable genetic elements (TEs) comprise a vast array of DNA sequences, all having the ability to move to new sites in genomes either directly by a cut-and-paste mechanism (transposons) or indirectly through an RNA intermediate (retrotransposons).[...] it is precisely the elaboration of epigenetic mechanisms from their prokaryotic origins as suppressors of genetic exchanges that underlies both the genome expansion and the proliferation of TEs characteristic of higher eukaryotes. This is the inverse of the prevailing view that epigenetic mechanisms evolved to control the disruptive potential of TEs. The evidence that TEs shape eukaryotic genomes is by now incontrovertible. My thesis, then, is that TEs and the transposases they encode underlie the evolvability of higher eukaryotes' massive, messy genomes."Transposable Elements, Epigenetics, and Genome Evolution

Labels: dna, epigenetics, evolvability, RNA

This week, 30 research papers, including six in Nature and additional papers published by Science, sound the death knell for the idea that our DNA is mostly littered with useless bases. A decadelong project, the Encyclopedia of DNA Elements (ENCODE), has found that 80% of the human genome serves some purpose, biochemically speaking. “I don't think anyone would have anticipated even close to the amount of sequence that ENCODE has uncovered that looks like it has functional importance,” says John A. Stamatoyannopoulos, an ENCODE researcher at the University of Washington, Seattle. Full analysis @ Science

Labels: genome complexity, genomics, regulation, RNA

It is that RNA computational layer once again...

"Scientists and philosophers alike have long grasped for the essence that makes humans human, and one answer lies in the brain. Specifically, human brains express genes in different patterns than those of related species, but what causes those changes is unknown. Comparing gene expression in three primate species—human, chimpanzee, and the rhesus macaque—across post-natal development, researchers, publishing today (December 6) in PLoS Biology, found that the most drastic expression changes are found in genes that are controlled at a distance by trans regulators, instead of locally by cis regulators." News artcle @ The Scientist

M. Somel et al., “MicroRNA-driven developmental remodeling in the brain distinguishes humans from other primates,” PLoS Biology, 9: e1001214, 2011.

Labels: cognitive science, evolution, RNA

"Traces of genetic material from non-retroviruses have unexpectedly turned up in the genomes of several mammal species, including humans." See commentary @ The Scientist. The actual report:

Horie1, M. et al [2010]. "Endogenous non-retroviral RNA virus elements in mammalian genomes". Nature 463, 84-87.

Labels: evolution, RNA, virus

"More findings confirm that small RNAs work in mysterious ways. Nearly 20 years after its discovery, RNA interference (RNAi) is part of biology’s orthodoxy. Small RNA molecules can disrupt gene expression by degrading messenger RNAs (mRNAs) on their way to becoming proteins, or otherwise interfering with translation. But the discovery that these same small RNA molecules might be able to do just the opposite—enhance gene expression—was somewhat heretical". Full article @ The Scientist.com.

Labels: RNA, transcription

"To convert the encoded genetic information from eukaryotic DNA into proteins, base sequences of genes are first transcribed into RNA by RNA polymerase II. To produce functional RNA molecules, dozens of accessory factors are needed to define the proper locations for RNA polymerase II to begin and end transcription. Although we have some basic knowledge about how these factors work, it is still not possible to take a eukaryotic genome sequence and accurately predict what RNA species it will produce. Recent efforts to map and sequence "transcriptomes" have only increased the challenge by revealing a much more complex set of RNAs than expected, including many that do not produce proteins". Full article @ Science

Labels: gene regulation, genomics, RNA

"Almost every important gene and pathway will be regulated at multiple levels by a variety of microRNAs," predicts Deepak Srivastava of the University of California, San Francisco. "It's really an entirely new layer of biology."
See Full article @ The Scientist

Labels: RNA

"Dimmer switches that control the level of protein created from a given gene may regulate the development, function and, ultimately, the life span of cells that begin to vanish from the brain at the onset of Parkinson's disease". Full Story at Scientific American

Labels: RNA

MicroRNAs influence crucial decisions in the patterning of the early vertebrate embryo, reports a study in Nature. The study is the first example of microRNAs regulating a fundamental signaling cascade, the authors say.
Full Story @ The Scientist

Labels: genetics, RNA

"The known world of RNA is expanding faster than that of any other cellular building block. The latest additions are types of long and short non-coding RNAs formed by bidirectional transcription and unusual processing. The relationship between DNA, RNA and protein is no longer as simple as we once thought — that specific genomic sequences are transcribed into messenger RNAs, which are then translated into proteins. In recent years, a flurry of studies has reported the existence of a large and growing family of non-protein-coding RNAs (ncRNAs), describing the different mechanisms of their transcription and their role in regulating gene expression." Full article @ Nature

Labels: complexity, gene regulation, RNA