Non-coding RNAs as regulators of embryogenesis.
Non-coding RNAs (ncRNAs) are emerging as key regulators of embryogenesis. They control embryonic gene expression by several means, ranging from microRNA-induced degradation of mRNAs to long ncRNA-mediated modification of chromatin. Many aspects of embryogenesis seem to be controlled by ncRNAs, including the maternal-zygotic transition, the maintenance of pluripotency, the patterning of the body axes, the specification and differentiation of cell types and the morphogenesis of organs. Drawing from several animal model systems, we describe two emerging themes for ncRNA function: promoting developmental transitions and maintaining developmental states. These examples also highlight the roles of ncRNAs in ensuring a robust commitment to one of two possible cell fates.
Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA. pauli@fas.harvard.edu
Andrea
A
Pauli
John L
JL
Rinn
Alexander F
AF
Schier
D000818:Animals; D047108:Embryonic Development; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism; D018628:Gene Dosage; D005786:Gene Expression Regulation; D006801:Humans; D012333:RNA, Messenger / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics*
D012333:RNA, Messenger; D022661:RNA, Untranslated
Development. 2006 Aug;133(15):2827-33
16835436
Genome Res. 2008 Sep;18(9):1433-45
18562676
RNA. 2010 Feb;16(2):349-63
20040592
Nature. 2003 Dec 18;426(6968):845-9
14685240
Science. 2007 Apr 20;316(5823):406-7
17446392
Development. 2010 Aug 1;137(15):2493-9
20573698
Science. 2008 Dec 12;322(5908):1717-20
18988810
Nat Genet. 2007 Mar;39(3):380-5
17259983
Nat Rev Mol Cell Biol. 2008 Sep;9(9):673-8
18719707
Cell. 2006 Dec 15;127(6):1209-21
17174895
Cell. 2007 Dec 28;131(7):1273-86
18155131
Genes Dev. 2008 Jan 1;22(1):26-36
18172163
Genes Dev. 2007 Mar 15;21(6):644-8
17369397
Genes Dev. 2006 Apr 1;20(7):858-70
16547172
Proc Natl Acad Sci U S A. 2009 Jul 14;106(28):11667-72
19571010
Genes Dev. 2007 Jan 1;21(1):71-84
17210790
Science. 2008 Apr 4;320(5872):97-100
18292307
Genes Dev. 2009 Aug 15;23(16):1831-42
19684108
Nature. 2002 Feb 14;415(6873):810-3
11845212
Dev Cell. 2008 Nov;15(5):668-79
18848501
Cell. 2010 Aug 6;142(3):409-19
20673990
Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):716-21
18184812
Cell. 2007 Apr 20;129(2):303-17
17397913
Mol Cell. 2010 Nov 24;40(4):558-70
21095586
Nature. 2009 Dec 10;462(7274):799-802
20010688
Genes Dev. 2008 Mar 15;22(6):756-69
18347095
Cell. 2009 Feb 20;136(4):615-28
19239884
Nat Cell Biol. 2008 Aug;10(8):987-93
18604195
Cell. 2010 Oct 1;143(1):46-58
20887892
Cell. 1992 Oct 30;71(3):527-42
1423611
Development. 2005 Dec;132(24):5451-60
16291785
Nature. 1978 Dec 7;276(5688):565-70
103000
Nat Cell Biol. 2007 Jun;9(6):660-5
17486114
EMBO J. 2002 Mar 1;21(5):1084-91
11867536
Nat Genet. 2008 Dec;40(12):1478-83
18978791
Genes Dev. 2007 Mar 15;21(6):682-93
17369401
Nature. 2010 Feb 25;463(7284):1084-8
20118916
Nat Rev Genet. 2009 Mar;10(3):155-9
19188922
Cold Spring Harb Symp Quant Biol. 2006;71:217-24
17381300
Nat Biotechnol. 2008 Jan;26(1):101-6
18059259
Development. 2002 Nov;129(21):4923-30
12397101
Nature. 2010 Sep 23;467(7314):415-9
20864994
RNA. 2008 Aug;14(8):1539-49
18566191
Trends Cell Biol. 2008 Aug;18(8):357-9
18585040
Nat Genet. 2010 Dec;42(12):1113-7
21057500
Nature. 1996 Jan 11;379(6561):131-7
8538762
Neuron. 2009 Sep 24;63(6):803-17
19778509
Mol Cell. 2008 Oct 24;32(2):232-46
18951091
Nat Struct Mol Biol. 2009 Apr;16(4):365-71
19330006
Cell. 2008 Aug 22;134(4):599-609
18724933
Science. 2004 Apr 23;304(5670):594-6
15105502
Nature. 2008 Feb 7;451(7179):730-3
18200011
Dev Cell. 2009 Apr;16(4):517-27
19386261
Curr Biol. 2008 Apr 8;18(7):501-6
18394895
Mol Cell. 2006 Mar 3;21(5):617-28
16507360
Cell. 2009 May 15;137(4):647-58
19409607
Nature. 2010 Oct 28;467(7319):1128-32
20953170
Proc Natl Acad Sci U S A. 2006 Feb 14;103(7):2422-7
16461918
Science. 2006 Feb 24;311(5764):1118-23
16497925
Nat Neurosci. 2009 Apr;12(4):399-408
19287386
J Mol Biol. 1961 Jun;3:318-56
13718526
Genetics. 2003 Jul;164(3):1003-14
12871910
Nature. 2007 Sep 13;449(7159):183-8
17728715
Cell. 1993 Dec 3;75(5):843-54
8252621
PLoS Genet. 2007 Dec;3(12):e215
18085825
Genes Dev. 2005 Dec 15;19(24):2947-52
16357215
Nat Cell Biol. 2009 Dec;11(12):1411-20
19898466
Nat Rev Genet. 2009 Feb;10(2):94-108
19148191
Oncogene. 2008 Apr 3;27(15):2128-36
17968323
Dev Cell. 2005 Sep;9(3):403-14
16139228
Cell. 2007 Jun 29;129(7):1311-23
17604720
Cell. 1993 Dec 3;75(5):855-62
8252622
Nat Cell Biol. 2008 Sep;10(9):1098-105
19160491
Nature. 2010 Apr 15;464(7291):1071-6
20393566
Nat Biotechnol. 2009 May;27(5):459-61
19363475
Cell. 2009 Aug 7;138(3):592-603
19665978
Genes Dev. 2005 May 1;19(9):1067-80
15833912
Mol Cell. 2010 Sep 10;39(5):761-72
20832727
Nature. 2006 Jan 19;439(7074):283-9
16421561
Mamm Genome. 2008 Aug;19(7-8):454-92
18839252
Nature. 2007 Feb 8;445(7128):666-70
17237763
Proc Natl Acad Sci U S A. 2009 Jan 27;106(4):1122-7
19164542
Mol Cell. 2008 Oct 24;32(2):276-84
18951094
Mol Cell. 2000 Feb;5(2):367-75
10882077
Mol Cell. 2007 Aug 3;27(3):435-48
17679093
EMBO Rep. 2008 Jun;9(6):582-9
18483486
Nature. 2009 Jul 30;460(7255):642-6
19561591
Nat Rev Genet. 2010 Sep;11(9):597-610
20661255
Mech Dev. 2005 Oct;122(10):1094-105
16125915
Genes Dev. 2008 Apr 1;22(7):894-907
18381893
Nat Cell Biol. 2009 Dec;11(12):1487-95
19935649
Nature. 2010 Feb 4;463(7281):621-6
20054295
Genes Dev. 2008 Jan 1;22(1):8-13
18172160
Nat Genet. 2002 Feb;30(2):167-74
11780141
Nature. 2007 May 24;447(7143):418-24
17522675
Cancer Res. 2007 Aug 15;67(16):7713-22
17699775
Eur J Cell Biol. 2010 Feb-Mar;89(2-3):250-7
20031253
Development. 2002 Nov;129(21):4915-22
12397100
Genes Dev. 2006 Oct 15;20(20):2793-805
17015424
Proc Natl Acad Sci U S A. 1999 Aug 17;96(17):9733-8
10449763
Nature. 1991 May 23;351(6324):325-9
2034278
Genes Dev. 1987 May;1(3):307-22
3119423
Science. 1969 Jul 25;165(3891):349-57
5789433
Nature. 2009 Feb 19;457(7232):974-5
19225515
J Biol Chem. 2008 Jan 11;283(2):1026-33
17991735
Nat Biotechnol. 2010 May;28(5):503-10
20436462
Neural Dev. 2010 Oct 01;5:25
20920300
Cell. 2007 Jun 29;129(7):1401-14
17604727
Cell. 2009 Jan 23;136(2):215-33
19167326
Cell. 2009 Nov 25;139(5):871-90
19945376
Genes Dev. 2007 Aug 15;21(16):2030-40
17699750
Cell. 2010 Oct 29;143(3):390-403
21029862
Development. 2009 May;136(9):1399-410
19363150
Curr Opin Genet Dev. 2010 Apr;20(2):142-8
20362426
Development. 2009 Sep;136(18):3033-42
19700615
Nature. 2005 Jul 14;436(7048):214-20
15951802
Science. 2006 Apr 7;312(5770):75-9
16484454
Nucleic Acids Res. 2010 Jun;38(11):3780-93
20176573
Nat Genet. 2007 Feb;39(2):259-63
17220889
Science. 2010 Aug 6;329(5992):689-93
20616235
Mol Cell. 2010 Aug 13;39(3):373-84
20705240
Curr Biol. 2010 Feb 9;20(3):271-7
20116247
Science. 2008 Oct 31;322(5902):750-6
18974356
Mol Cell. 2010 Jun 11;38(5):675-88
20542000
Nat Cell Biol. 2008 May;10(5):593-601
18376396
Annu Rev Cell Dev Biol. 2007;23:175-205
17506695
Nat Neurosci. 2008 Jun;11(6):641-8
18454145
Cold Spring Harb Perspect Biol. 2010 Sep;2(9):a003749
20739414
Trends Genet. 2010 Jan;26(1):21-8
19944475
Nature. 2008 Jul 3;454(7200):56-61
18548003
Cold Spring Harb Perspect Biol. 2009 Nov;1(5):a003459
20066122
J Biol Chem. 2008 May 30;283(22):14910-4
18411277
Nature. 2009 Aug 13;460(7257):909-13
19578360
Nature. 2009 Mar 12;458(7235):223-7
19182780
Development. 2010 Sep 1;137(17):2951-60
20667912
Science. 2007 Oct 12;318(5848):271-4
17761850
Nat Genet. 2003 Nov;35(3):215-7
14528307
Genes Dev. 2006 Jun 1;20(11):1470-84
16705037
PLoS One. 2009 Oct 19;4(10):e7513
19838299
Nat Neurosci. 2009 Aug;12(8):1020-7
19620975
Science. 2005 May 6;308(5723):833-8
15774722
J Cell Physiol. 2009 Feb;218(2):251-5
18821562
Nat Genet. 2006 Feb;38(2):228-33
16380711
Genes Dev. 2008 Jan 1;22(1):14-9
18172161
Nat Genet. 2006 Jul;38(7):813-8
16751773
Nat Genet. 2004 Dec;36(12):1296-300
15516932
Genes Dev. 2006 May 15;20(10):1268-82
16702402
Cell. 2008 Aug 8;134(3):521-33
18692474
Cell. 1992 Oct 30;71(3):515-26
1423610
Science. 2010 Jul 16;329(5989):336-9
20647469
Curr Biol. 2010 Jul 27;20(14):1321-5
20579881
Nat Genet. 2004 Oct;36(10):1079-83
15361871
Nature. 2008 Oct 30;455(7217):1193-7
18830242
Curr Biol. 2005 Mar 29;15(6):501-12
15797018
Nat Rev Genet. 2009 Dec;10(12):833-44
19920851
PLoS Genet. 2009 Aug;5(8):e1000617
19696892
Curr Biol. 2010 Feb 23;20(4):367-73
20096582
RNA. 2009 Dec;15(12):2351-63
19854872
Genes Dev. 2007 Apr 1;21(7):744-9
17403776
Nature. 2009 Nov 12;462(7270):222-5
19865085
Genes Dev. 2006 Oct 15;20(20):2787-92
17043308
Annu Rev Genet. 2004;38:553-85
15568986
Development. 2009 Jun;136(11):1771-83
19429783
Genes Dev. 2005 Feb 15;19(4):489-501
15713842
Proc Natl Acad Sci U S A. 2005 Aug 23;102(34):12135-40
16099834
Curr Biol. 2006 Nov 7;16(21):2135-42
17084698
Science. 2008 Jun 6;320(5881):1336-41
18535243
RNA. 2010 Feb;16(2):324-37
20026622