Distinct Evolutionary Profiles and Functions of microRNA156 and microRNA529 in Land Plants

MicroRNA156 (miR156) and miR529 have high sequence similarity and recognize overlapping sites in the same target genes, SQUAMOSA promoter binding protein-like (SPL or SBP box) genes, making it difficult to accurately distinguish their roles in regulatory networks that affect numerous biological functions. Here, we collected data about miR156 and miR529 family members from representative land plants and performed sequence comparisons, phylogenetic analysis, small RNA sequencing, and parallel analysis of RNA ends (PARE) analysis to dissect their evolutionary and functional differences. Although miR156 and miR529 are highly similar, there are differences in their mismatch-sensitive regions, which are essential for target recognition. In land plants, miR156 precursors are conserved mainly within the hairpin region, whereas miR529 precursors are conserved outside the hairpin region, including both the 5’ and 3’ arms. Phylogenetic analysis showed that MIR156 and MIR529 evolved independently, through divergent evolutionary patterns. The two genes also exhibit different expression patterns, with MIR529 preferentially expressed in reproductive tissues and MIR156 in other tissues. PARE analysis revealed that miR156 and miR529 possess specific targets in addition to common targets in maize, pointing to functional differences between them. Based on our findings, we developed a method for the rapid identification of miR529 and miR156 family members and uncovered the evolutionary divergence of these families, providing insights into their different regulatory roles in plant growth and development.

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Genome-wide analysis of changes in miRNA and target gene expression reveals key roles in heterosis for Chinese cabbage biomass

Horticulture Research ◽

10.1038/s41438-021-00474-6 ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Peirong Li ◽

Tongbing Su ◽

Deshuang Zhang ◽

Weihong Wang ◽

Xiaoyun Xin ◽

...

Keyword(s):

Chinese Cabbage ◽

Leaf Development ◽

Target Genes ◽

Expression Patterns ◽

Seedling Stage ◽

Differentially Expressed ◽

Small Rna Sequencing ◽

Leaf Morphogenesis ◽

Expression Levels ◽

Parental Lines

AbstractHeterosis is a complex phenomenon in which hybrids show better phenotypic characteristics than their parents do. Chinese cabbage (Brassica rapa L. spp. pekinensis) is a popular leafy crop species, hybrids of which are widely used in commercial production; however, the molecular basis of heterosis for biomass of Chinese cabbage is poorly understood. We characterized heterosis in a Chinese cabbage F1 hybrid cultivar and its parental lines from the seedling stage to the heading stage; marked heterosis of leaf weight and biomass yield were observed. Small RNA sequencing revealed 63 and 50 differentially expressed microRNAs (DEMs) at the seedling and early-heading stages, respectively. The expression levels of the majority of miRNA clusters in the F1 hybrid were lower than the mid-parent values (MPVs). Using degradome sequencing, we identified 1,819 miRNA target genes. Gene ontology (GO) analyses demonstrated that the target genes of the MPV-DEMs and low parental expression level dominance (ELD) miRNAs were significantly enriched in leaf morphogenesis, leaf development, and leaf shaping. Transcriptome analysis revealed that the expression levels of photosynthesis and chlorophyll synthesis-related MPV-DEGs (differentially expressed genes) were significantly different in the F1 hybrid compared to the parental lines, resulting in increased photosynthesis capacity and chlorophyll content in the former. Furthermore, expression of genes known to regulate leaf development was also observed at the seedling stage. Arabidopsis plants overexpressing BrGRF4.2 and bra-miR396 presented increased and decreased leaf sizes, respectively. These results provide new insight into the regulation of target genes and miRNA expression patterns in leaf size and heterosis for biomass of B. rapa.

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The Complete Chloroplast Genome of the Vulnerable Oreocharis esquirolii (Gesneriaceae): Structural Features, Comparative and Phylogenetic Analysis

Plants ◽

10.3390/plants9121692 ◽

2020 ◽

Vol 9 (12) ◽

pp. 1692

Author(s):

Li Gu ◽

Ting Su ◽

Ming-Tai An ◽

Guo-Xiong Hu

Keyword(s):

Phylogenetic Analysis ◽

Sequence Similarity ◽

Single Copy ◽

Structural Features ◽

Rrna Genes ◽

Trna Genes ◽

Sequencing Data ◽

High Sequence Similarity ◽

Plastid Genomes ◽

Cp Genome

Oreocharis esquirolii, a member of Gesneriaceae, is known as Thamnocharis esquirolii, which has been regarded a synonym of the former. The species is endemic to Guizhou, southwestern China, and is evaluated as vulnerable (VU) under the International Union for Conservation of Nature (IUCN) criteria. Until now, the sequence and genome information of O. esquirolii remains unknown. In this study, we assembled and characterized the complete chloroplast (cp) genome of O. esquirolii using Illumina sequencing data for the first time. The total length of the cp genome was 154,069 bp with a typical quadripartite structure consisting of a pair of inverted repeats (IRs) of 25,392 bp separated by a large single copy region (LSC) of 85,156 bp and a small single copy region (SSC) of18,129 bp. The genome comprised 114 unique genes with 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Thirty-one repeat sequences and 74 simple sequence repeats (SSRs) were identified. Genome alignment across five plastid genomes of Gesneriaceae indicated a high sequence similarity. Four highly variable sites (rps16-trnQ, trnS-trnG, ndhF-rpl32, and ycf 1) were identified. Phylogenetic analysis indicated that O. esquirolii grouped together with O. mileensis, supporting resurrection of the name Oreocharis esquirolii from Thamnocharisesquirolii. The complete cp genome sequence will contribute to further studies in molecular identification, genetic diversity, and phylogeny.

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The expression of delta opioid receptor mRNA in adult male zebra finches (Taenopygia guttata)

PLoS ONE ◽

10.1371/journal.pone.0256599 ◽

2021 ◽

Vol 16 (8) ◽

pp. e0256599

Author(s):

Pooja Parishar ◽

Neha Sehgal ◽

Soumya Iyengar

Keyword(s):

Opioid Receptors ◽

Sequence Similarity ◽

Expression Patterns ◽

Auditory Pathway ◽

Zebra Finches ◽

Endogenous Opioid System ◽

Endogenous Opioid ◽

High Sequence Similarity ◽

Brain Functions ◽

Song Control

The endogenous opioid system is evolutionarily conserved across reptiles, birds and mammals and is known to modulate varied brain functions such as learning, memory, cognition and reward. To date, most of the behavioral and anatomical studies in songbirds have mainly focused on μ-opioid receptors (ORs). Expression patterns of δ-ORs in zebra finches, a well-studied species of songbird have not yet been reported, possibly due to the high sequence similarity amongst different opioid receptors. In the present study, a specific riboprobe against the δ-OR mRNA was used to perform fluorescence in situ hybridization (FISH) on sections from the male zebra finch brain. We found that δ-OR mRNA was expressed in different parts of the pallium, basal ganglia, cerebellum and the hippocampus. Amongst the song control and auditory nuclei, HVC (abbreviation used as a formal name) and NIf (nucleus interfacialis nidopallii) strongly express δ-OR mRNA and stand out from the surrounding nidopallium. Whereas the expression of δ-OR mRNA is moderate in LMAN (lateral magnocellular nucleus of the anterior nidopallium), it is low in the MSt (medial striatum), Area X, DLM (dorsolateral nucleus of the medial thalamus), RA (robust nucleus of the arcopallium) of the song control circuit and Field L, Ov (nucleus ovoidalis) and MLd (nucleus mesencephalicus lateralis, pars dorsalis) of the auditory pathway. Our results suggest that δ-ORs may be involved in modulating singing, song learning as well as spatial learning in zebra finches.

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Distribution and Phylogenetic Analysis of Family 19 Chitinases in Actinobacteria

Applied and Environmental Microbiology ◽

10.1128/aem.70.2.1135-1144.2004 ◽

2004 ◽

Vol 70 (2) ◽

pp. 1135-1144 ◽

Cited By ~ 61

Author(s):

Tomokazu Kawase ◽

Akihiro Saito ◽

Toshiya Sato ◽

Ryo Kanai ◽

Takeshi Fujii ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Catalytic Domain ◽

Higher Plants ◽

Sequence Similarity ◽

Evolutionary Relationship ◽

Pcr Amplification ◽

High Sequence Similarity ◽

The Family ◽

Family 19 Chitinase ◽

Chitinase Genes

ABSTRACT In organisms other than higher plants, family 19 chitinase was first discovered in Streptomyces griseus HUT6037, and later, the general occurrence of this enzyme in Streptomyces species was demonstrated. In the present study, the distribution of family 19 chitinases in the class Actinobacteria and the phylogenetic relationship of Actinobacteria family 19 chitinases with family 19 chitinases of other organisms were investigated. Forty-nine strains were chosen to cover almost all the suborders of the class Actinobacteria, and chitinase production was examined. Of the 49 strains, 22 formed cleared zones on agar plates containing colloidal chitin and thus appeared to produce chitinases. These 22 chitinase-positive strains were subjected to Southern hybridization analysis by using a labeled DNA fragment corresponding to the catalytic domain of ChiC, and the presence of genes similar to chiC of S. griseus HUT6037 in at least 13 strains was suggested by the results. PCR amplification and sequencing of the DNA fragments corresponding to the major part of the catalytic domains of the family 19 chitinase genes confirmed the presence of family 19 chitinase genes in these 13 strains. The strains possessing family 19 chitinase genes belong to 6 of the 10 suborders in the order Actinomycetales, which account for the greatest part of the Actinobacteria. Phylogenetic analysis suggested that there is a close evolutionary relationship between family 19 chitinases found in Actinobacteria and plant class IV chitinases. The general occurrence of family 19 chitinase genes in Streptomycineae and the high sequence similarity among the genes found in Actinobacteria suggest that the family 19 chitinase gene was first acquired by an ancestor of the Streptomycineae and spread among the Actinobacteria through horizontal gene transfer.

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Genome-Wide Phylogenetic Analysis, Expression Pattern, and Transcriptional Regulatory Network of the Pig C/EBP Gene Family

Evolutionary Bioinformatics ◽

10.1177/11769343211041382 ◽

2021 ◽

Vol 17 ◽

pp. 117693432110413

Author(s):

Chaoxin Zhang ◽

Tao Wang ◽

Tongyan Cui ◽

Shengwei Liu ◽

Bing Zhang ◽

...

Keyword(s):

Gene Expression ◽

Phylogenetic Analysis ◽

Regulatory Network ◽

Target Genes ◽

Transcriptional Regulatory Network ◽

Expression Patterns ◽

Enrichment Analysis ◽

Functional Enrichment ◽

Genome Wide ◽

A Genome

The CCAAT/enhancer binding protein (C/EBP) transcription factors (TFs) regulate many important biological processes, such as energy metabolism, inflammation, cell proliferation etc. A genome-wide gene identification revealed the presence of a total of 99 C/EBP genes in pig and 19 eukaryote genomes. Phylogenetic analysis showed that all C/EBP TFs were classified into 6 subgroups named C/EBPα, C/EBPβ, C/EBPδ, C/EBPε, C/EBPγ, and C/EBPζ. Gene expression analysis showed that the C/EBPα, C/EBPβ, C/EBPδ, C/EBPγ, and C/EBPζ genes were expressed ubiquitously with inconsistent expression patterns in various pig tissues. Moreover, a pig C/EBP regulatory network was constructed, including C/EBP genes, TFs and miRNAs. A total of 27 feed-forward loop (FFL) motifs were detected in the pig C/EBP regulatory network. Based on the RNA-seq data, gene expression patterns related to FFL sub-network were analyzed in 27 adult pig tissues. Certain FFL motifs may be tissue specific. Functional enrichment analysis indicated that C/EBP and its target genes are involved in many important biological pathways. These results provide valuable information that clarifies the evolutionary relationships of the C/EBP family and contributes to the understanding of the biological function of C/EBP genes.

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Minimal functional domains of paralogues hnRNP L and hnRNP LL exhibit mechanistic differences in exonic splicing repression

Biochemical Journal ◽

10.1042/bj20130432 ◽

2013 ◽

Vol 453 (2) ◽

pp. 271-279 ◽

Cited By ~ 9

Author(s):

Ganesh Shankarling ◽

Kristen W. Lynch

Keyword(s):

Sequence Similarity ◽

Expression Patterns ◽

Rna Recognition ◽

High Sequence Similarity ◽

Rna Recognition Motifs ◽

Hnrnp Proteins ◽

Functional Consequences ◽

Recognition Motifs ◽

Nuclear Ribonucleoprotein ◽

Specific Control

Understanding functional distinctions between related splicing regulatory proteins is critical to deciphering tissue-specific control of alternative splicing. The hnRNP (heterogeneous nuclear ribonucleoprotein) L and hnRNP LL (hnRNP L-like) proteins are paralogues that have overlapping, but distinct, expression patterns and functional consequences. These two proteins share high sequence similarity in their RRMs (RNA-recognition motifs), but diverge in regions outside of the RRMs. In the present study, we use an MS2-tethering assay to delineate the minimal domains of hnRNP L and hnRNP LL which are required for repressing exon inclusion. We demonstrate that for both proteins, regions outside the RRMs, the N-terminal region, and a linker sequence between RRMs 2 and 3, are necessary for exon repression, but are only sufficient for repression in the case of hnRNP LL. In addition, both proteins require at least one RRM for maximal repression. Notably, we demonstrate that the region encompassing RRMs 1 and 2 of hnRNP LL imparts a second silencing activity not observed for hnRNP L. This additional functional component of hnRNP LL is consistent with the fact that the full-length hnRNP LL has a greater silencing activity than hnRNP L. Thus the results of the present study provide important insight into the functional and mechanistic variations that can exist between two highly related hnRNP proteins.

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Molecular characterization and phylogenetic analysis of ZmMCUs in maize

Biologia ◽

10.1515/biolog-2015-0077 ◽

2015 ◽

Vol 70 (5) ◽

Cited By ~ 4

Author(s):

Qingchang Meng ◽

Yuanyuan Chen ◽

Meijing Zhang ◽

Yanping Chen ◽

Jianhua Yuan ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Sequence Similarity ◽

Genomic Structure ◽

Expression Patterns ◽

Genomic Analysis ◽

Chromosome 1 ◽

Maize Genome ◽

Calcium Uniporter ◽

Digital Expression ◽

Eukaryotic Organisms

AbstractThe mitochondrial calcium uniporter (MCU), located in the organelle’s inner membrane of eukaryotic organisms, is a highly selective ion channel which plays a unique role in the calcium signaling. Six MCU-like genes (assigned as ZmMCU1∼ZmMCU6) were identified in the maize genome. Genomic analysis revealed that these six genes were located on chromosome 1, 3, 8 and 9. Sequence identity percent between ZmMCU1 and ZmMCU2, or between ZmMCU4 and ZmMCU5 was relatively high at both the nucleic acid and amino acid levels. Sequence alignment of ZmMCU indicated that for plants, there was “DVME” motif in the deduced protein sequences. Digital expression analysis showed the ZmMCU6 was strongly expressed in all of the studied organs in maize, while the other five ZmMCU genes had unique expression patterns. In the developing seeds of maize, the six ZmMCU genes had three divergent expression patterns. Finally, the phylogenetic analysis demonstrated that MCU homologs in plants could be grouped into two types and each type could be further classified into two subtypes along the monocot and dicot division. Moreover, MCU homologs in both the dicot and monocot had been independently duplicated and then those in maize had undergone an extra duplication for two subclades. Based on genomic structure, sequence similarity, digital expression profile, and phylogenetic analysis, our results clearly suggested that ZmMCU1 and ZmMCU2 as well as ZmMCU4 and ZmMCU5 are functionally redundant in maize genome.

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MiR-92 Family Members Form a Cluster Required for Notochord Tubulogenesis in Urochordate Ciona savignyi

Genes ◽

10.3390/genes12030406 ◽

2021 ◽

Vol 12 (3) ◽

pp. 406

Author(s):

Libo Yang ◽

Xiaoming Zhang ◽

Chengzhang Liu ◽

Jin Zhang ◽

Bo Dong

Keyword(s):

Signaling Pathways ◽

Planar Cell Polarity ◽

Target Genes ◽

Expression Patterns ◽

Family Members ◽

Mitogen Activated Protein Kinase ◽

Mirna Cluster ◽

Ciona Savignyi ◽

Larval Stages ◽

Regulatory Processes

MicroRNAs are frequently clustered in the genome and polycistronically transcribed, regulating targeted genes in diverse signaling pathways. The miR-17-92 cluster is a typical miRNA cluster, playing crucial roles in the organogenesis and homeostasis of physiological processes in vertebrates. Here, we identified three miRNAs (csa-miR-92a, csa-miR-92b, and csa-miR-92c) that belonged to the miR-92 family and formed a miRNA cluster in the genome of a urochordate marine ascidian Ciona savignyi. Except for miR-92a and miR-92b, other homologs of the vertebrate miR-17-92 cluster members could not be identified in the Ciona genome. We further found that the mature sequences of urochordate miR-92 family members were highly conserved compared with the vertebrate species. The expression pattern revealed that three miR-92 family members had consistent expression levels in adult tissues and were predominantly expressed in heart and muscle tissue. We further showed that, at the embryonic and larval stages, csa-miR-92c was expressed in the notochord of embryos during 18–31 h post fertilization (hpf) by in situ hybridization. Knockout of csa-miR-92c resulted in the disorganization of notochord cells and the block of lumen coalescence in the notochord. Fibroblast growth factor (FGF), mitogen-activated protein kinase (MAPK), and wingless/integrated (Wnt)/planar cell polarity (PCP) signaling pathways might be involved in the regulatory processes, since a large number of core genes of these pathways were the predicted target genes of the miR-92 family. Taken together, we identified a miR-92 cluster in urochordate Ciona and revealed the expression patterns and the regulatory roles of its members in organogenesis. Our results provide expression and phylogenetic data on the understanding of the miR-92 miRNA cluster’s function during evolution.

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Distinct miRNA Signatures and Networks Discern Fetal from Adult Erythroid Differentiation and Primary from Immortalized Erythroid Cells

International Journal of Molecular Sciences ◽

10.3390/ijms22073626 ◽

2021 ◽

Vol 22 (7) ◽

pp. 3626

Author(s):

Panayiota L. Papasavva ◽

Nikoletta Y. Papaioannou ◽

Petros Patsali ◽

Ryo Kurita ◽

Yukio Nakamura ◽

...

Keyword(s):

Mirna Expression ◽

Regulatory Networks ◽

Target Genes ◽

Human Peripheral Blood ◽

Expression Patterns ◽

Erythroid Differentiation ◽

Erythroid Cell ◽

Small Rna Sequencing ◽

Erythroid Cells ◽

Mirna Regulation

MicroRNAs (miRNAs) are small non-coding RNAs crucial for post-transcriptional and translational regulation of cellular and developmental pathways. The study of miRNAs in erythropoiesis elucidates underlying regulatory mechanisms and facilitates related diagnostic and therapy development. Here, we used DNA Nanoball (DNB) small RNA sequencing to comprehensively characterize miRNAs in human erythroid cell cultures. Based on primary human peripheral-blood-derived CD34+ (hCD34+) cells and two influential erythroid cell lines with adult and fetal hemoglobin expression patterns, HUDEP-2 and HUDEP-1, respectively, our study links differential miRNA expression to erythroid differentiation, cell type, and hemoglobin expression profile. Sequencing results validated by reverse-transcription quantitative PCR (RT-qPCR) of selected miRNAs indicate shared differentiation signatures in primary and immortalized cells, characterized by reduced overall miRNA expression and reciprocal expression increases for individual lineage-specific miRNAs in late-stage erythropoiesis. Despite the high similarity of same-stage hCD34+ and HUDEP-2 cells, differential expression of several miRNAs highlighted informative discrepancies between both cell types. Moreover, a comparison between HUDEP-2 and HUDEP-1 cells displayed changes in miRNAs, transcription factors (TFs), target genes, and pathways associated with globin switching. In resulting TF-miRNA co-regulatory networks, major therapeutically relevant regulators of globin expression were targeted by many co-expressed miRNAs, outlining intricate combinatorial miRNA regulation of globin expression in erythroid cells.

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Duplicated Proteasome Subunit Genes in Drosophila melanogaster Encoding Testes-Specific Isoforms

Genetics ◽

10.1093/genetics/144.1.147 ◽

1996 ◽

Vol 144 (1) ◽

pp. 147-157 ◽

Cited By ~ 3

Author(s):

Xiaoqing Yuan ◽

Mary Miller ◽

John M Belote

Keyword(s):

Drosophila Melanogaster ◽

Genomic Library ◽

Sequence Similarity ◽

Expression Patterns ◽

Primary Spermatocyte ◽

Amino Acid Identity ◽

High Sequence Similarity ◽

New Genes ◽

Cell Type Specific ◽

Elongation Phase

Abstract Using the previously cloned proteasome α-type subunit gene Pros28.1, we screened a Drosophila melanogaster genomic library using reduced stringency conditions to identify closely related genes. Two new genes, Pros28.1A (map position 92F) and Pros28.IB (map position 60D7), showing high sequence similarity to Pros28.1, were identified and characterized. Pros28.1A encodes a protein with 74% amino acid identity to PROS28.1, while the Pros28.1B gene product is 58% identical. The Pros28.1B gene has two introns, located in exactly analogous positions as the two introns in Pros28.1, while the Pros28.IA gene lacks introns. Northern blot analysis reveals that the two new genes are expressed only in males, during the pupal and adult stages. Tissue-specific patterns of expression were examined using transgenic flies carrying Zacz-fusion reporter genes. This analysis revealed that both genes are expressed in germline cells during spermatogenesis, although their expression patterns differed. Pros28.1A expression is first detected at the primary spermatocyte stage and persists into the spermatid elongation phase of spermiogenesis, while Pros28. IB expression is prominent only during spermatid elongation. These genes represent the most striking example of cell-type-specific proteasome gene expression reported to date in any system and support the notion that there is structural and functional heterogeneity among proteasomes in metazoans.

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