Posttranscriptional coordination of splicing and miRNA biogenesis in plants

Arabidopsis thaliana microRNA162 level is posttranscriptionally regulated via splicing and polyadenylation site selection

(2016) Maria Barciszewska-Pacak et al.   ACTA BIOCHIMICA POLONICA

Active 5′ splice sites regulate the biogenesis efficiency of Arabidopsis microRNAs derived from intron-containing genes

(2016) Katarzyna Knop et al.   NUCLEIC ACIDS RESEARCH

Salt Stress Reveals a New Role for ARGONAUTE1 in miRNA Biogenesis at the Transcriptional and Posttranscriptional Levels

(2016) Jakub Dolata et al.   PLANT PHYSIOLOGY

mirEX 2.0 - an integrated environment for expression profiling of plant microRNAs

(2015) Andrzej Zielezinski et al.   BMC PLANT BIOLOGY

Alternative splicing in plants: directing traffic at the crossroads of adaptation and environmental stress

(2015) Sergei Filichkin et al.   CURRENT OPINION IN PLANT BIOLOGY

NTR1 is required for transcription elongation checkpoints at alternative exons in Arabidopsis

(2015) J. Dolata et al.   EMBO JOURNAL

Chromatin, DNA structure and alternative splicing

(2015) Nicolás Nieto Moreno et al.   FEBS LETTERS

Microprocessor mediates transcriptional termination of long noncoding RNA transcripts hosting microRNAs

(2015) Ashish Dhir et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The RNA-binding protein HOS5 and serine/arginine-rich proteins RS40 and RS41 participate in miRNA biogenesis in Arabidopsis

(2015) Tao Chen et al.   NUCLEIC ACIDS RESEARCH

Functional mapping of the plant small RNA methyltransferase: HEN1 physically interacts with HYL1 and DICER-LIKE 1 proteins

(2015) Simona Baranauskė et al.   NUCLEIC ACIDS RESEARCH

HOS1 regulates Argonaute1 by promoting transcription of the microRNA geneMIR168bin Arabidopsis

(2015) Bangshing Wang et al.   PLANT JOURNAL

Microprocessor mediates transcriptional termination of long noncoding RNA transcripts hosting microRNAs

(2015) Ashish Dhir et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Roles of Arabidopsis CDF2 in Transcriptional and Posttranscriptional Regulation of Primary MicroRNAs

(2015) Zhenfei Sun et al.   PLoS Genetics

New insights into pri-miRNA processing and accumulation in plants

(2015) Shuxin Zhang et al.   Wiley Interdisciplinary Reviews-RNA

Arabidopsis microRNA expression regulation in a wide range of abiotic stress responses

(2015) Maria Barciszewska-Pacak et al.   Frontiers in Plant Science

Transcription and processing of primary microRNAs are coupled by Elongator complex in Arabidopsis

(2015) Xiaofeng Fang et al.   Nature Plants

Gene regulation by translational inhibition is determined by Dicer partnering proteins

(2015) Rodrigo S. Reis et al.   Nature Plants

Transcriptionally and post-transcriptionally regulated microRNAs in heat stress response in barley

(2014) Katarzyna Kruszka et al.   JOURNAL OF EXPERIMENTAL BOTANY

The liverwortPellia endiviifoliashares microtranscriptomic traits that are common to green algae and land plants

(2014) Sylwia Alaba et al.   NEW PHYTOLOGIST

Regulation of pri-miRNA processing by the hnRNP-like protein AtGRP7 in Arabidopsis

(2014) Tino Köster et al.   NUCLEIC ACIDS RESEARCH

Interplay between pre-mRNA splicing and microRNA biogenesis within the supraspliceosome

(2014) Lily Agranat-Tamir et al.   NUCLEIC ACIDS RESEARCH

Argonaute-1 binds transcriptional enhancers and controls constitutive and alternative splicing in human cells

(2014) M. Allo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

COP1 E3 ligase protects HYL1 to retain microRNA biogenesis

(2014) Seok Keun Cho et al.   Nature Communications

PRL1, an RNA-Binding Protein, Positively Regulates the Accumulation of miRNAs and siRNAs in Arabidopsis

(2014) Shuxin Zhang et al.   PLoS Genetics

Cross talk between spliceosome and microprocessor defines the fate of pre-mRNA

(2014) Chiara Mattioli et al.   Wiley Interdisciplinary Reviews-RNA

Developmentally regulated expression and complex processing of barley pri-microRNAs

(2013) Katarzyna Kruszka et al.   BMC GENOMICS

MicroRNAs Inhibit the Translation of Target mRNAs on the Endoplasmic Reticulum in Arabidopsis

(2013) Shengben Li et al.   CELL

A role for the RNA-binding protein MOS2 in microRNA maturation in Arabidopsis

(2013) Xueying Wu et al.   CELL RESEARCH

Introns of plant pri-miRNAs enhance miRNA biogenesis

(2013) Dawid Bielewicz et al.   EMBO REPORTS

Enhanced microRNA accumulation through stemloop-adjacent introns

(2013) Rebecca Schwab et al.   EMBO REPORTS

Multiple RNA recognition patterns during microRNA biogenesis in plants

(2013) N. G. Bologna et al.   GENOME RESEARCH

Identification and analysis of the proximal promoters of microRNA genes in Arabidopsis

(2013) Xin Zhao et al.   GENOMICS

Dissecting the interactions of SERRATE with RNA and DICER-LIKE 1 in Arabidopsis microRNA precursor processing

(2013) Y. Iwata et al.   NUCLEIC ACIDS RESEARCH

The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana

(2013) K. D. Raczynska et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

NOT2 Proteins Promote Polymerase II-Dependent Transcription and Interact with Multiple MicroRNA Biogenesis Factors in Arabidopsis

(2013) L. Wang et al.   PLANT CELL

Complexity of the Alternative Splicing Landscape in Plants

(2013) A. S. N. Reddy et al.   PLANT CELL

RACK1 scaffold proteins influence miRNA abundance in Arabidopsis

(2013) Corinna Speth et al.   PLANT JOURNAL

MIR846 and MIR842 comprise a cistronic MIRNA pair that is regulated by abscisic acid by alternative splicing in roots of Arabidopsis

(2013) Fan Jia et al.   PLANT MOLECULAR BIOLOGY

CDC5, a DNA binding protein, positively regulates posttranscriptional processing and/or transcription of primary microRNA transcripts

(2013) S. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biogenesis of intronic miRNAs located in clusters by independent transcription and alternative splicing

(2013) P. Ramalingam et al.   RNA

Ago1 Interacts with RNA Polymerase II and Binds to the Promoters of Actively Transcribed Genes in Human Cancer Cells

(2013) Vera Huang et al.   PLoS Genetics

A KH-Domain RNA-Binding Protein Interacts with FIERY2/CTD Phosphatase-Like 1 and Splicing Factors and Is Important for Pre-mRNA Splicing in Arabidopsis

(2013) Tao Chen et al.   PLoS Genetics

Comparative Analysis of MicroRNA Promoters in Arabidopsis and Rice

(2013) Xin Zhao et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

U1 snRNP Determines mRNA Length and Regulates Isoform Expression

(2012) Michael G. Berg et al.   CELL

Fast-Forward Genetics Identifies Plant CPL Phosphatases as Regulators of miRNA Processing Factor HYL1

(2012) Pablo A. Manavella et al.   CELL

Uridylation of miRNAs by HEN1 SUPPRESSOR1 in Arabidopsis

(2012) Guodong Ren et al.   CURRENT BIOLOGY

Transcriptome survey reveals increased complexity of the alternative splicing landscape inArabidopsis

(2012) Yamile Marquez et al.   GENOME RESEARCH

Role of microRNAs and other sRNAs of plants in their changing environments

(2012) Katarzyna Kruszka et al.   JOURNAL OF PLANT PHYSIOLOGY

Stress-Induced Alternative Splicing Provides a Mechanism for the Regulation of MicroRNA Processing in Arabidopsis thaliana

(2012) Kang Yan et al.   MOLECULAR CELL

Cytoplasmic Assembly and Selective Nuclear Import of Arabidopsis ARGONAUTE4/siRNA Complexes

(2012) Ruiqiang Ye et al.   MOLECULAR CELL

Argonaute proteins couple chromatin silencing to alternative splicing

(2012) Maya Ameyar-Zazoua et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

STA1, an Arabidopsis pre-mRNA processing factor 6 homolog, is a new player involved in miRNA biogenesis

(2012) Samir Ben Chaabane et al.   NUCLEIC ACIDS RESEARCH

Mutation ofArabidopsis SPLICEOSOMAL TIMEKEEPER LOCUS1Causes Circadian Clock Defects

(2012) Matthew A. Jones et al.   PLANT CELL

Suppression of Arabidopsis ARGONAUTE1-Mediated Slicing, Transgene-Induced RNA Silencing, and DNA Methylation by Distinct Domains of the Cucumber mosaic virus 2b Protein

(2012) C.-G. Duan et al.   PLANT CELL

CDKF;1 and CDKD Protein Kinases Regulate Phosphorylation of Serine Residues in the C-Terminal Domain ofArabidopsisRNA Polymerase II

(2012) Mohsen Hajheidari et al.   PLANT CELL

The Helicase and RNaseIIIa Domains of Arabidopsis Dicer-Like1 Modulate Catalytic Parameters during MicroRNA Biogenesis

(2012) C. Liu et al.   PLANT PHYSIOLOGY

Expression-Based Functional Investigation of the Organ-Specific MicroRNAs in Arabidopsis

(2012) Yijun Meng et al.   PLoS One

Regulation of miRNA abundance by RNA binding protein TOUGH in Arabidopsis

(2012) G. Ren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Arabidopsis proline-rich protein important for development and abiotic stress tolerance is involved in microRNA biogenesis

(2012) X. Zhan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential GC Content between Exons and Introns Establishes Distinct Strategies of Splice-Site Recognition

(2012) Maayan Amit et al.   Cell Reports

Non-Canonical Processing of Arabidopsis pri-miR319a/b/c Generates Additional microRNAs to Target One RAP2.12 mRNA Isoform

(2012) Lukasz Sobkowiak et al.   Frontiers in Plant Science

The Role of Polypyrimidine Tract-Binding Proteins and Other hnRNP Proteins in Plant Splicing Regulation

(2012) Andreas Wachter et al.   Frontiers in Plant Science

The Spliceosome-Activating Complex: Molecular Mechanisms Underlying the Function of a Pleiotropic Regulator

(2012) Csaba Koncz et al.   Frontiers in Plant Science

Cyclophilin 40 facilitates HSP90-mediated RISC assembly in plants

(2011) Taichiro Iki et al.   EMBO JOURNAL

Global analysis of gene-level microRNA expression in Arabidopsis using deep sequencing data

(2011) Xiaozeng Yang et al.   GENOMICS

Molecular insights into miRNA processing by Arabidopsis thaliana SERRATE

(2011) Satoru Machida et al.   NUCLEIC ACIDS RESEARCH

Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation

(2011) X. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Feed-Forward Microprocessing and Splicing Activities at a MicroRNA–Containing Intron

(2011) Maja M. Janas et al.   PLoS Genetics

Regulation of mRNA Translation and Stability by microRNAs

(2010) Marc Robert Fabian et al.   Annual Review of Biochemistry

In Vitro Assembly of Plant RNA-Induced Silencing Complexes Facilitated by Molecular Chaperone HSP90

(2010) Taichiro Iki et al.   MOLECULAR CELL

Splicing-Dependent RNA Polymerase Pausing in Yeast

(2010) Ross D. Alexander et al.   MOLECULAR CELL

Global Analysis of Nascent RNA Reveals Transcriptional Pausing in Terminal Exons

(2010) Fernando Carrillo Oesterreich et al.   MOLECULAR CELL

U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation

(2010) Daisuke Kaida et al.   NATURE

Genome-wide computational identification of WG/GW Argonaute-binding proteins in Arabidopsis

(2010) Wojciech M. Karlowski et al.   NUCLEIC ACIDS RESEARCH

MicroRNA402 Affects Seed Germination of Arabidopsis thaliana Under Stress Conditions via Targeting DEMETER-LIKE Protein3 mRNA

(2010) J. Y. Kim et al.   PLANT AND CELL PHYSIOLOGY

Implementing a Rational and Consistent Nomenclature for Serine/Arginine-Rich Protein Splicing Factors (SR Proteins) in Plants

(2010) Andrea Barta et al.   PLANT CELL

Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein-protein interaction

(2010) H. Qin et al.   RNA

Structure of Arabidopsis HYPONASTIC LEAVES1 and Its Molecular Implications for miRNA Processing

(2010) Seong Wook Yang et al.   STRUCTURE

Spliceosome Structure and Function

(2010) C. L. Will et al.   Cold Spring Harbor Perspectives in Biology

An active role for splicing in 3′-end formation

(2010) Harold G. Martinson   Wiley Interdisciplinary Reviews-RNA

Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells

(2009) Christine Mayr et al.   CELL

A loop-to-base processing mechanism underlies the biogenesis of plant microRNAs miR319 and miR159

(2009) Nicolás G Bologna et al.   EMBO JOURNAL

Rates of in situ transcription and splicing in large human genes

(2009) Jarnail Singh et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Gene structures and processing of Arabidopsis thaliana HYL1-dependent pri-miRNAs

(2009) Bogna Szarzynska et al.   NUCLEIC ACIDS RESEARCH

Involvement of the nuclear cap-binding protein complex in alternative splicing in Arabidopsis thaliana

(2009) Katarzyna Dorota Raczynska et al.   NUCLEIC ACIDS RESEARCH

Biochemical Evidence for Translational Repression by Arabidopsis MicroRNAs

(2009) E. Lanet et al.   PLANT CELL

The Arabidopsis Tandem Zinc Finger Protein AtTZF1 Traffics between the Nucleus and Cytoplasmic Foci and Binds Both DNA and RNA

(2009) M. C. Pomeranz et al.   PLANT PHYSIOLOGY

AGO1 Homeostasis Involves Differential Production of 21-nt and 22-nt miR168 Species by MIR168a and MIR168b

(2009) Hervé Vaucheret   PLoS One

A dominant mutation in DCL1 suppresses the hyl1 mutant phenotype by promoting the processing of miRNA

(2009) Y. Tagami et al.   RNA

Co-transcriptional splicing of constitutive and alternative exons

(2009) A. Pandya-Jones et al.   RNA

Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome

(2009) C. Addo-Quaye et al.   RNA

A Genome-Wide Characterization of MicroRNA Genes in Maize

(2009) Lifang Zhang et al.   PLoS Genetics

Plant polycistronic precursors containing non-homologous microRNAs target transcripts encoding functionally related proteins

(2009) Francisco Merchan et al.   GENOME BIOLOGY

In silico identification of conserved microRNAs in large number of diverse plant species

(2008) Ramanjulu Sunkar et al.   BMC PLANT BIOLOGY

Primary microRNA transcripts are processed co-transcriptionally

(2008) Mariangela Morlando et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis

(2008) B. Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs)

(2008) C. Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana

(2008) S. Laubinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1

(2008) Z. Dong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Widespread Translational Inhibition by Plant miRNAs and siRNAs

(2008) P. Brodersen et al.   SCIENCE

Intronic noncoding RNAs and splicing

(2008) John W.S. Brown et al.   TRENDS IN PLANT SCIENCE