02426nas a2200301 4500008004100000022001400041245011800055210006900173260005700242300001400299490000800313520138600321653003201707653001701739653001201756653001001768653002801778653002201806100002501828700002501853700002101878700001701899700002101916700001601937700002101953700002401974856012601998 2013 eng d a0032-093500aGenome-wide identification and characterization of microRNA genes and their targets in flax (Linum usitatissimum)0 aGenomewide identification and characterization of microRNA genes a233 SPRING ST, NEW YORK, NY 10013 USAbSPRINGERcAPR a1149-11610 v2373 a

MicroRNAs (miRNAs) are small (20-24 nucleotide long) endogenous regulatory RNAs that play important roles in plant growth and development. They regulate gene expression at the post-transcriptional level by translational repression or target degradation and gene silencing. In this study, we identified 116 conserved miRNAs belonging to 23 families from the flax (Linum usitatissimum L.) genome using a computational approach. The precursor miRNAs varied in length; while most of the mature miRNAs were 21 nucleotide long, intergenic and showed conserved signatures of RNA polymerase II transcripts in their upstream regions. Promoter region analysis of the flax miRNA genes indicated prevalence of MYB transcription factor binding sites. Four miRNA gene clusters containing members of three phylogenetic groups were identified. Further, 142 target genes were predicted for these miRNAs and most of these represent transcriptional regulators. The miRNA encoding genes were expressed in diverse tissues as determined by digital expression analysis as well as real-time PCR. The expression of fourteen miRNAs and nine target genes was independently validated using the quantitative reverse transcription PCR (qRT-PCR). This study suggests that a large number of conserved plant miRNAs are also found in flax and these may play important roles in growth and development of flax.

10aDigital expression analysis10aGene cluster10aLinseed10amiRNA10aMiRNA target transcript10aPromoter analysis1 aBarvkar, Vitthal, T.1 aPardeshi, Varsha, C.1 aKale, Sandip, M.1 aQiu, Shuqing1 aRollins, Meaghen1 aDatla, Raju1 aGupta, Vidya, S.1 aKadoo, Narendra, Y. uhttp://library.ncl.res.in/content/genome-wide-identification-and-characterization-microrna-genes-and-their-targets-flax-002926nas 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

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.

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

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.

10acombinatorial binding10amathematical model10amiRNA10apost-transcriptional regulation1 aNyayanit, Dimpal1 aGadgil, Chetan, J. uhttp://library.ncl.res.in/content/mathematical-modeling-combinatorial-regulation-suggests-apparent-positive-regulation-002548nas a2200265 4500008004100000022001400041245016000055210006900215260000800284300001400292490000700306520161000313653003601923653001201959653001001971653003101981653001602012100002002028700001802048700002602066700002402092700001802116700001902134856012902153 2020 eng d a0971-589400aTIAs pathway genes and associated miRNA identification in Vinca minor: supporting aspidosperma and eburnamine alkaloids linkage via transcriptomic analysis0 aTIAs pathway genes and associated miRNA identification in Vinca  cAUG a1695-17110 v263 a

V. minorcontains monomeric eburnamine-type of indole alkaloids having utilization as a neuro-medicinal plant. The biosynthetic pathway studies using miRNAs has been the focal point for plant genomic research in recent years and this technique is utilized to get an insight into a possible pathway level study inV. minoras understanding of genes in this prized medicinal plant is meagrely understood. The de novo transcriptomic analysis using Illumina Next gen sequencing has been performed in glasshouse shifted plant and transformed roots to elucidate the possible non confirmed steps of terpenoid indole alkaloids (TIAs) pathway inV. minor. A putative TIA pathway is elucidated in the study including twelve possible TIAs biosynthetic genes. The specific miRNA associated with TIAs pathway were identified and their roles were discussed for the first time inV. minor. The comparative analysis of transcriptomic data of glasshouse shifted plant and transformed roots showed that the raw reads of transformed roots were higher (83,740,316) compared to glasshouse shifted plant (67,733,538). The EST-SSR prediction showed the maximum common repeats among glasshouse shifted plant and transformed roots, although small variation was found in trinucleotide repeats restricted to glasshouse shifted plant. The study reveals overall 37 miRNAs which were observed to be true and can have a role in pathway as they can regulate the growth and alkaloid production. The identification of putative pathway genes plays an important role in establishing linkage between Aspidosperma and Eburnamine alkaloids.

10ade novo transcriptomic analysis10aEST-SSR10amiRNA10aTerpenoid indole alkaloids10aVinca minor1 aVerma, Priyanka1 aSingh, Noopur1 aKhan, Shamshad, Ahmad1 aMathur, Ajay, Kumar1 aSharma, Ashok1 aJamal, Farrukh uhttp://library.ncl.res.in/content/tias-pathway-genes-and-associated-mirna-identification-vinca-minor-supporting-aspidosperma