02926nas a2200265   4500008004100000022001400041245007400055210006900129260008000198300000700278490000600285520204200291653003102333653001102364653001002375653001902385653001002404100002402414700002302438700002902461700002202490700002302512700001802535856010702553       2014                        eng d  a1662-510200aNon-coding RNA interact to regulate neuronal development and function0 aNoncoding RNA interact to regulate neuronal development and func  aPO BOX 110, LAUSANNE, 1015, SWITZERLANDbFRONTIERS RESEARCH FOUNDATIONcFEB  a470 v83 a<p>The human brain is one of the most complex biological systems, and the cognitive abilities have greatly expanded compared to invertebrates without much expansion in the number of protein coding genes. This suggests that gene regulation plays a very important role in the development and function of nervous system, by acting at multiple levels such as transcription and translation. In this article we discuss the regulatory roles of three classes of non-protein coding RNAs (ncRNAs)-microRNAs (miRNAs), piwi-interacting RNA (piRNAs) and long-non-coding RNA (lncRNA), in the process of neurogenesis and nervous function including control of synaptic plasticity and potential roles in neurodegenerative diseases. miRNAs are involved in diverse processes including neurogenesis where they channelize the cellular physiology toward neuronal differentiation. miRNAs can also indirectly influence neurogenesis by regulating the proliferation and self renewal of neural stem cells and are dysregulated in several neurodegenerative diseases. miRNAs are also known to regulate synaptic plasticity and are usually found to be co-expressed with their targets. The dynamics of gene regulation is thus dependent on the local architecture of the gene regulatory network (GRN) around the miRNA and its targets. piRNAs had been classically known to regulate transposons in the germ cells. However, piRNAs have been, recently, found to be expressed in the brain and possibly function by imparting epigenetic changes by DNA methylation. piRNAs are known to be maternally inherited and we assume that they may play a role in early development. We also explore the possible function of piRNAs in regulating the expansion of transposons in the brain. Brain is known to express several lncRNA but functional roles in brain development are attributed to a few lncRNA while functions of most of the them remain unknown. We review the roles of some known lncRNA and explore the other possible functions of lncRNAs including their interaction with miRNAs.</p>10agene expression regulation10alncRNA10amiRNA10anetwork-motifs10apiRNA1 aIyengar, Bharat, R.1 aChoudhary, Ashwani1 aSarangdhar, Mayuresh, A.1 aVenkatesh, K., V.1 aGadgil, Chetan, J.1 aPillai, Beena  uhttp://library.ncl.res.in/content/non-coding-rna-interact-regulate-neuronal-development-and-function-002509nas a2200205   4500008004100000022001400041245017400055210006900229260010600298300001200404490000700416520161600423653002602039653002302065653001002088653003602098100002102134700002302155856012502178       2015                        eng d  a1355-838200aMathematical modeling of combinatorial regulation suggests that apparent positive regulation of targets by miRNA could be an artifact resulting from competition for mRNA0 aMathematical modeling of combinatorial regulation suggests that   a1 BUNGTOWN RD, COLD SPRING HARBOR, NY 11724 USAbCOLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPTcMAR  a307-3190 v213 a<p>MicroRNAs bind to and regulate the abundance and activity of target messenger RNA through sequestration, enhanced degradation, and suppression of translation. Although miRNA have a predominantly negative effect on the target protein concentration, several reports have demonstrated a positive effect of miRNA, i.e., increase in target protein concentration on miRNA overexpression and decrease in target concentration on miRNA repression. miRNA-target pair-specific effects such as protection of mRNA degradation owing to miRNA binding can explain some of these effects. However, considering such pairs in isolation might be an oversimplification of the RNA biology, as it is known that one miRNA interacts with several targets, and conversely target mRNA are subject to regulation by several miRNAs. We formulate a mathematical model of this combinatorial regulation of targets by multiple miRNA. Through mathematical analysis and numerical simulations of this model, we show that miRNA that individually have a negative effect on their targets may exhibit an apparently positive net effect when the concentration of one miRNA is experimentally perturbed by repression/overexpression in such a multi-miRNA multitarget situation. We show that this apparent unexpected effect is due to competition and will not be observed when miRNA interact noncompetitively with the target mRNA. This result suggests that some of the observed unusual positive effects of miRNA may be due to the combinatorial complexity of the system rather than due to any inherently unusual positive effect of the miRNA on its target.</p>10acombinatorial binding10amathematical model10amiRNA10apost-transcriptional regulation1 aNyayanit, Dimpal1 aGadgil, Chetan, J.  uhttp://library.ncl.res.in/content/mathematical-modeling-combinatorial-regulation-suggests-apparent-positive-regulation-0