Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs

Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing

(2015) Takayuki Nojima et al.   CELL

H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency

(2014) Bérénice A. Benayoun et al.   CELL

Adenylation of Maternally Inherited MicroRNAs by Wispy

(2014) Mihye Lee et al.   MOLECULAR CELL

Two independent transcription initiation codes overlap on vertebrate core promoters

(2014) Vanja Haberle et al.   NATURE

microTSS: accurate microRNA transcription start site identification reveals a significant number of divergent pri-miRNAs

(2014) Georgios Georgakilas et al.   Nature Communications

Mammalian 5′-Capped MicroRNA Precursors that Generate a Single MicroRNA

(2013) Mingyi Xie et al.   CELL

Canonical nucleosome organization at promoters forms during genome activation

(2013) Y. Zhang et al.   GENOME RESEARCH

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

(2013) Chirag Nepal et al.   GENOME RESEARCH

miR-9: a versatile regulator of neurogenesis

(2013) Marion Coolen et al.   Frontiers in Cellular Neuroscience

PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs

(2013) Annalisa Marsico et al.   GENOME BIOLOGY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

Transcriptome-wide analysis of small RNA expression in early zebrafish development

(2012) C. Wei et al.   RNA

Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data

(2011) Chia-Hung Chien et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The role of miRNAs and endogenous siRNAs in maternal-to-zygotic reprogramming and the establishment of pluripotency

(2010) Petr Svoboda et al.   EMBO REPORTS

Tissue-specific regulation of mouse MicroRNA genes in endoderm-derived tissues

(2010) Yan Gao et al.   NUCLEIC ACIDS RESEARCH

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

Evidence for human microRNA-offset RNAs in small RNA sequencing data

(2009) D. Langenberger et al.   BIOINFORMATICS

Coupled RNA Processing and Transcription of Intergenic Primary MicroRNAs

(2009) M. Ballarino et al.   MOLECULAR AND CELLULAR BIOLOGY

Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs

(2009)   NATURE

A distinct class of small RNAs arises from pre-miRNA–proximal regions in a simple chordate

(2009) Weiyang Shi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chromatin organization marks exon-intron structure

(2009) Schraga Schwartz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Features of Mammalian microRNA Promoters Emerge from Polymerase II Chromatin Immunoprecipitation Data

(2009) David L. Corcoran et al.   PLoS One

Transcriptional features of genomic regulatory blocks

(2009) Altuna Akalin et al.   GENOME BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells

(2008) Alexander Marson et al.   CELL

Chromatin structure analyses identify miRNA promoters

(2008) F. Ozsolak et al.   GENES & DEVELOPMENT

Primary microRNA transcript retention at sites of transcription leads to enhanced microRNA production

(2008) Jan M. Pawlicki et al.   JOURNAL OF CELL BIOLOGY

MicroRNA-9 directs late organizer activity of the midbrain-hindbrain boundary

(2008) Christoph Leucht et al.   NATURE NEUROSCIENCE

Primary microRNA transcripts are processed co-transcriptionally

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

High-resolution in situ hybridization to whole-mount zebrafish embryos

(2007) Christine Thisse et al.   Nature Protocols