NDLI: Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles.

Please wait, while we are loading the content...

Year: 2017 Volume: 27

Year: 2016 Volume: 26

Year: 2015 Volume: 25

Year: 2014 Volume: 24

Year: 2013 Volume: 23

Year: 2012 Volume: 22

Year: 2011 Volume: 21

Year: 2011 Volume: 21 Issue: 12

Year: 2011 Volume: 21 Issue: 11

Year: 2011 Volume: 21 Issue: 10

Year: 2011 Volume: 21 Issue: 9

Cactus: Algorithms for genome multiple sequence alignment.

Genome-wide detection of novel regulatory RNAs in E. coli.

Alterations in TCF7L2 expression define its role as a key regulator of glucose metabolism.

Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles.

Unusually effective microRNA targeting within repeat-rich coding regions of mammalian mRNAs

Integrative analysis of environmental sequences using MEGAN4.

A probabilistic disease-gene finder for personal genomes.

Barcoding bias in high-throughput multiplex sequencing of miRNA.

Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features

Coactivation of GR and NFKB alters the repertoire of their binding sites and target genes.

Accurate and comprehensive sequencing of personal genomes.

Histone H3 trimethylation at lysine 36 is associated with constitutive and facultative heterochromatin.

Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity.

Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing.

Synthetic spike-in standards for RNA-seq experiments.

Year: 2011 Volume: 21 Issue: 8

Year: 2011 Volume: 21 Issue: 7

Year: 2011 Volume: 21 Issue: 6

Year: 2011 Volume: 21 Issue: 5

Year: 2011 Volume: 21 Issue: 4

Year: 2011 Volume: 21 Issue: 3

Year: 2011 Volume: 21 Issue: 2

Year: 2011 Volume: 21 Issue: 1

Year: 2010 Volume: 20

Year: 2009 Volume: 19

Year: 2008 Volume: 18

Year: 2007 Volume: 17

Year: 2006 Volume: 16

Year: 2005 Volume: 15

Year: 2004 Volume: 14

Year: 2003 Volume: 13

Year: 2002 Volume: 12

Year: 2001 Volume: 11

Year: 2000 Volume: 10

Year: 1999 Volume: 9

Year: 1998 Volume: 8

Year: 1997 Volume: 7

Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Wang, Jianbin Czech, Benjamin Crunk, Amanda Wallace, Adam Mitreva, Makedonka Hannon, Gregory J. Davis, Richard E.
Description	Country affiliation: United States Author Affiliation: Wang J ( Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.)
Abstract	Eukaryotic cells express several classes of small RNAs that regulate gene expression and ensure genome maintenance. Endogenous siRNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs) mainly control gene and transposon expression in the germline, while microRNAs (miRNAs) generally function in post-transcriptional gene silencing in both somatic and germline cells. To provide an evolutionary and developmental perspective on small RNA pathways in nematodes, we identified and characterized known and novel small RNA classes through gametogenesis and embryo development in the parasitic nematode Ascaris suum and compared them with known small RNAs of Caenorhabditis elegans. piRNAs, Piwi-clade Argonautes, and other proteins associated with the piRNA pathway have been lost in Ascaris. miRNAs are synthesized immediately after fertilization in utero, before pronuclear fusion, and before the first cleavage of the zygote. This is the earliest expression of small RNAs ever described at a developmental stage long thought to be transcriptionally quiescent. A comparison of the two classes of Ascaris endo-siRNAs, 22G-RNAs and 26G-RNAs, to those in C. elegans, suggests great diversification and plasticity in the use of small RNA pathways during spermatogenesis in different nematodes. Our data reveal conserved characteristics of nematode small RNAs as well as features unique to Ascaris that illustrate significant flexibility in the use of small RNAs pathways, some of which are likely an adaptation to Ascaris' life cycle and parasitism. The transcriptome assembly has been submitted to NCBI Transcriptome Shotgun Assembly Sequence Database(http://www.ncbi.nlm.nih.gov/genbank/TSA.html) under accession numbers JI163767JI182837 and JI210738JI257410.
File Format	HTM / HTML
ISSN	10889051
e-ISSN	15495469
DOI	10.1101/gr.121426.111
Journal	Genome Research
Issue Number	9
Volume Number	21
Language	English
Publisher	Cold Spring Harbor Laboratory Press
Publisher Date	2011-09-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Discipline Genetics Discipline Genomics Ascaris Genetics High-throughput Nucleotide Sequencing Rna, Small Interfering Metabolism Sequence Analysis, Rna Animals Cluster Analysis Conserved Sequence Embryonic Development Gametogenesis Gene Expression Gene Expression Profiling Gene Expression Regulation, Developmental Genetic Variation Inverted Repeat Sequences Molecular Sequence Data Spermatogenesis Zygote Research Support, N.i.h., Extramural Research Support, Non-u.s. Gov't
Content Type	Text
Resource Type	Article
Subject	Genetics Genetics (clinical)

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles

Sperm-borne miRNAs and endo-siRNAs are important for fertilization and preimplantation embryonic development.

Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs.

Characterization of small RNAs and their target genes in wheat seedlings using sequencing-based approaches.

Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa.

MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries.

26G endo-siRNAs regulate spermatogenic and zygotic gene expression in Caenorhabditis elegans.

Characterization of microRNAs from goat (Capra hircus) by Solexa deep-sequencing technology.

Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells.

Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles.

Similar Documents

Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles

Sperm-borne miRNAs and endo-siRNAs are important for fertilization and preimplantation embryonic development.

Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs.

Characterization of small RNAs and their target genes in wheat seedlings using sequencing-based approaches.

Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa.

MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries.

26G endo-siRNAs regulate spermatogenic and zygotic gene expression in Caenorhabditis elegans.

Characterization of microRNAs from goat (Capra hircus) by Solexa deep-sequencing technology.

Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells.

Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles.