miRNEST database: an integrative approach in microRNA search and annotation

Abstract

Despite accumulating data on animal and plant microRNAs and their functions, existing public miRNA resources usually collect miRNAs from a very limited number of species. A lot of microRNAs, including those from model organisms, remain undiscovered. As a result there is a continuous need to search for new microRNAs. We present miRNEST (http://mirnest.amu.edu.pl), a comprehensive database of animal, plant and virus microRNAs. The core part of the database is built from our miRNA predictions conducted on Expressed Sequence Tags of 225 animal and 202 plant species. The miRNA search was performed based on sequence similarity and as many as 10 004 miRNA candidates in 221 animal and 199 plant species were discovered. Out of them only 299 have already been deposited in miRBase. Additionally, miRNEST has been integrated with external miRNA data from literature and 13 databases, which includes miRNA sequences, small RNA sequencing data, expression, polymorphisms and targets data as well as links to external miRNA resources, whenever applicable. All this makes miRNEST a considerable miRNA resource in a sense of number of species (544) that integrates a scattered miRNA data into a uniform format with a user-friendly web interface.

In Vitro Replication Studies of Carboxymethylated DNA Lesions with Saccharomyces cerevisiae Polymerase η

“…In line with what we found from primer extension and steady-state kinetic measurements, N 3-CMdT and O 4 -CMdT are strong blockades to DNA replication in E. coli cells (31). From the replication study in E. coli cells, the major mutation observed for N 3-CMdT was T→A transversion at ∼65% frequency, along with T→C transition at a frequency of ∼5%, whereas O 4 -CMdT induced predominantly T→C transition at ∼85% frequency (31). Consistent with these findings, results from our steady-state kinetic measurements revealed substantial misincorporation of dGMP opposite O 4 -CMdT.…”

“…Along this line, a recent study on the mutagenic potential of these carboxymethylated lesions in E. coli cells revealed that N 6 -CMdA did not block DNA replication or induce mutations (31), which is in keeping with what we observed from the in vitro replication experiments using purified S. cerevisiae pol η. N 4 -CMdC only slightly blocked DNA replication in E. coli cells and it was not mutagenic (31), a finding distinct from steady-state kinetic measurement results showing that this lesion directs significant frequency of dCMP misincorporation. In line with what we found from primer extension and steady-state kinetic measurements, N 3-CMdT and O 4 -CMdT are strong blockades to DNA replication in E. coli cells (31). From the replication study in E. coli cells, the major mutation observed for N 3-CMdT was T→A transversion at ∼65% frequency, along with T→C transition at a frequency of ∼5%, whereas O 4 -CMdT induced predominantly T→C transition at ∼85% frequency (31).…”

Association of uterine fibroids and pregnancy outcomes after ovarian stimulation–intrauterine insemination for unexplained infertility

“…In participants with uterine fibroids, there was no difference in the mean uterine volume between African American and non-African American women with fibroids. A higher rate of early pregnancy loss in African American women (compared to Caucasian women) has been previously reported following IVF (36, 37). However, these studies analyzed pregnancy outcomes from the national assisted reproductive technologies registry, Society of Assisted Reproductive Technologies-Clinic Outcomes Reporting System, which does not specifically record data for fibroids.…”

miRNEST 2.0: a database of plant and animal microRNAs

“…Transcript sequences (cDNAs) were downloaded from Ensembl Plants (16), and mature miRNA sequences were retrieved from miRNEST (17). Using PAREsnip (18), we searched for miRNA targets evidenced by degradome reads.…”