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Genetics: Probing the phenomics of noncoding RNA

  1. John S Mattick  Is a corresponding author
  1. Garvan Institute of Medical Research, Australia
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Cite this article as: eLife 2013;2:e01968 doi: 10.7554/eLife.01968


Genetic knockout experiments on mice confirm that some long noncoding RNA molecules have developmental functions.

Main text

It has been known since the late 1970s that many DNA sequences are transcribed but not translated. Moreover, most protein-coding genes in mammals are fragmented, with only a small fraction of the primary RNA transcript being spliced together to form messenger RNA. For many years it was assumed that untranslated RNA molecules served no useful purpose but, starting in the mid-1990s, a small body of researchers, including the present author (Mattick, 1994), have been arguing that these RNAs transmit regulatory information, possibly associated with the emergence of multicellular organisms. This is supported by the observation that the proportion of noncoding genomic sequences broadly correlates with developmental complexity, reaching over 98% in mammals (Liu et al., 2013), although others have argued that the increase in genome size is due to the inefficiency of selection against non-functional elements as body size goes up and population size goes down (Lynch, 2007).

High-throughput sequencing analyses over the past decade have shown that the majority of mammalian genome is transcribed, often from both strands, and have revealed an extraordinarily complex landscape of overlapping and interlacing sense and antisense, alternatively spliced, protein-coding and non-protein-coding RNAs, the latter generally referred to as long noncoding RNAs (lncRNAs). Moreover, the repertoire of these lncRNAs is different in different cells (Carninci et al., 2005; Cheng et al., 2005; Birney et al., 2007; Mercer et al., 2012). While some transcripts may encode previously unrecognized small proteins, the function or otherwise of the vast majority of lncRNAs remains to be determined.

Because many lncRNAs appear to be expressed at low levels, and many have lower sequence conservation than messenger RNAs, one interpretation has been that these RNAs represent transcriptional noise from complex genomes cluttered with evolutionary debris. However, assessments of sequence conservation rely on assumptions about the non-functionality and representative distribution of reference sequences, which are not verified and cannot be directly tested (Pheasant and Mattick, 2007). Nonetheless, many lncRNAs show patches of relative sequence conservation (Derrien et al., 2012), and even more do so at the secondary structural level (Smith et al., 2013).

Expression analyses have shown that lncRNAs originate from all over the genome and are expressed at different times during differentiation and development (Dinger et al., 2008), often exhibiting highly cell-specific patterns (Mercer et al., 2008). The precision of lncRNA expression is consistent with evidence suggesting that many are associated with chromatin-modifying complexes, thereby acting as regulators of the epigenetic control of differentiation and development (Mercer and Mattick, 2013).

A number of lncRNAs have also been linked to complex diseases like cancer (Mattick, 2009) and other complex physiological processes (see, for example, Rapicavoli et al., 2013). However, these results seem at odds with the fact that few lncRNAs have been identified in traditional genetic screens. The reason for this is likely a combination of phenotypic, technical and expectational bias: mutations in protein-coding regions of the genome generally have phenotypes that are more severe, and are easier to identify, than those in non-coding regions. By contrast, in this context, it is worth noting that ∼95% of all variants associated with complex (as opposed to monogenic) diseases in humans map to non-coding, presumably regulatory, sequences (Freedman et al., 2011).

Still, the gold standard in this field is the targeted in vivo silencing or deletion of specific genes, and since few of these have been conducted to date, some researchers have remained sceptical about the biological significance of lncRNAs. Now, in eLife, John Rinn, Paolo Arlotta and co-workers at Harvard, MIT, the Broad Institute, Rutgers and Regeneron Pharmaceuticals—including Martin Sauvageau, Loyal Goff and Simona Lodata as joint first authors—report the results of the first large-scale attack on the question (Sauvageau et al., 2013). They selected 18 lncRNA genes in the mouse genome that had been stringently assessed for lack of protein-coding capacity and that did not overlap with known protein-coding genes or other known gene annotations—hence the name long intergenic noncoding RNAs (lincRNAs)—and generated knockout mouse mutants by replacing the lncRNA gene with a lacZ reporter cassette.

Sauvageau, Goff, Lodata et al. report discernable developmental problems in five of the 18 mutants, with three exhibiting embryonic or post-natal lethality, two of which exhibited growth defects in the survivors. The phenotypes of two of the mutants were analyzed in detail: one of the mutants that died showed defects in multiple organs (including the lung, heart and gastrointestinal tract), and one of the mutants that survived with growth defects also showed defects in the cerebral cortex. Other mutants that did not exhibit overt developmental defects showed brain-specific expression patterns and may be associated with cognitive defects that are not grossly apparent at the developmental level.

Another group (Grote et al., 2013) recently generated a different knockout allele for one of the 18 lincRNAs interrogated by Sauvageau et al., and also reported an embryonic lethal phenotype, albeit with some differences. Importantly, the approach used by Grote et al. also provided strong evidence that the mutant defects were not caused by an indirect effect on an overlapping genomic element, such as an enhancer for a nearby gene.

The work of Sauvageau, Goff, Lodata et al. is a mini tour-de-force that shows that there are lncRNAs with important developmental functions in vivo, and it joins a small number of studies from other pioneering groups that show the same thing (Lewejohann et al., 2004; Gutschner et al., 2013; Li et al., 2013), although not all of the targeted lncRNAs showed a phenotype. Similarly, other knockout experiments of widely expressed lncRNAs, as well as some of the most highly conserved elements in the mammalian genome, also did not yield discernable phenotypes (Ahituv et al., 2007; Nakagawa et al., 2011), which should sound a note of caution about the interpretation of negative results.

Indeed, since most lncRNAs are expressed in the brain (Mercer et al., 2008) and many are primate-specific (Derrien et al., 2012), it may be that much of the lncRNA-mediated genetic information in humans (and in mammals generally) is devoted to brain function, and therefore not easily detectable in developmental, as opposed to cognitive, screens. A good example is a noncoding RNA called BC1 that is widely expressed in the brain: knockout of BC1 causes no visible anatomical consequences, but it leads to a behavioural phenotype that would be lethal in the wild (Lewejohann et al., 2004).

Although evidence for the hypothesis that lncRNAs have a role in mammalian development, brain function and physiology is growing, there is also a clear need for more sophisticated and comprehensive phenotypic screens, especially with respect to cognitive function.


  1. 1
  2. 2
    Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    1. E Birney
    2. JA Stamatoyannopoulos
    3. A Dutta
    4. R Guigo
    5. TR Gingeras
    6. EH Margulies
    7. E Birney
    8. JA Stamatoyannopoulos
    9. A Dutta
    10. R Guigó
    11. TR Gingeras
    12. EH Margulies
    13. Z Weng
    14. M Snyder
    15. ET Dermitzakis
    16. RE Thurman
    17. MS Kuehn
    18. CM Taylor
    19. S Neph
    20. CM Koch
    21. S Asthana
    22. A Malhotra
    23. I Adzhubei
    24. JA Greenbaum
    25. RM Andrews
    26. P Flicek
    27. PJ Boyle
    28. H Cao
    29. NP Carter
    30. GK Clelland
    31. S Davis
    32. N Day
    33. P Dhami
    34. SC Dillon
    35. MO Dorschner
    36. H Fiegler
    37. PG Giresi
    38. J Goldy
    39. M Hawrylycz
    40. A Haydock
    41. R Humbert
    42. KD James
    43. BE Johnson
    44. EM Johnson
    45. TT Frum
    46. ER Rosenzweig
    47. N Karnani
    48. K Lee
    49. GC Lefebvre
    50. PA Navas
    51. F Neri
    52. SC Parker
    53. PJ Sabo
    54. R Sandstrom
    55. A Shafer
    56. D Vetrie
    57. M Weaver
    58. S Wilcox
    59. M Yu
    60. FS Collins
    61. J Dekker
    62. JD Lieb
    63. TD Tullius
    64. GE Crawford
    65. S Sunyaev
    66. WS Noble
    67. I Dunham
    68. F Denoeud
    69. A Reymond
    70. P Kapranov
    71. J Rozowsky
    72. D Zheng
    73. R Castelo
    74. A Frankish
    75. J Harrow
    76. S Ghosh
    77. A Sandelin
    78. IL Hofacker
    79. R Baertsch
    80. D Keefe
    81. S Dike
    82. J Cheng
    83. HA Hirsch
    84. EA Sekinger
    85. J Lagarde
    86. JF Abril
    87. A Shahab
    88. C Flamm
    89. C Fried
    90. J Hackermüller
    91. J Hertel
    92. M Lindemeyer
    93. K Missal
    94. A Tanzer
    95. S Washietl
    96. J Korbel
    97. O Emanuelsson
    98. JS Pedersen
    99. N Holroyd
    100. R Taylor
    101. D Swarbreck
    102. N Matthews
    103. MC Dickson
    104. DJ Thomas
    105. MT Weirauch
    106. J Gilbert
    107. J Drenkow
    108. I Bell
    109. X Zhao
    110. KG Srinivasan
    111. WK Sung
    112. HS Ooi
    113. KP Chiu
    114. S Foissac
    115. T Alioto
    116. M Brent
    117. L Pachter
    118. ML Tress
    119. A Valencia
    120. SW Choo
    121. CY Choo
    122. C Ucla
    123. C Manzano
    124. C Wyss
    125. E Cheung
    126. TG Clark
    127. JB Brown
    128. M Ganesh
    129. S Patel
    130. H Tammana
    131. J Chrast
    132. CN Henrichsen
    133. C Kai
    134. J Kawai
    135. U Nagalakshmi
    136. J Wu
    137. Z Lian
    138. J Lian
    139. P Newburger
    140. X Zhang
    141. P Bickel
    142. JS Mattick
    143. P Carninci
    144. Y Hayashizaki
    145. S Weissman
    146. T Hubbard
    147. RM Myers
    148. J Rogers
    149. PF Stadler
    150. TM Lowe
    151. CL Wei
    152. Y Ruan
    153. K Struhl
    154. M Gerstein
    155. SE Antonarakis
    156. Y Fu
    157. ED Green
    158. U Karaöz
    159. A Siepel
    160. J Taylor
    161. LA Liefer
    162. KA Wetterstrand
    163. PJ Good
    164. EA Feingold
    165. MS Guyer
    166. GM Cooper
    167. G Asimenos
    168. CN Dewey
    169. M Hou
    170. S Nikolaev
    171. JI Montoya-Burgos
    172. A Löytynoja
    173. S Whelan
    174. F Pardi
    175. T Massingham
    176. H Huang
    177. NR Zhang
    178. I Holmes
    179. JC Mullikin
    180. A Ureta-Vidal
    181. B Paten
    182. M Seringhaus
    183. D Church
    184. K Rosenbloom
    185. WJ Kent
    186. EA Stone
    187. S Batzoglou
    188. N Goldman
    189. RC Hardison
    190. D Haussler
    191. W Miller
    192. A Sidow
    193. ND Trinklein
    194. ZD Zhang
    195. L Barrera
    196. R Stuart
    197. DC King
    198. A Ameur
    199. S Enroth
    200. MC Bieda
    201. J Kim
    202. AA Bhinge
    203. N Jiang
    204. J Liu
    205. F Yao
    206. VB Vega
    207. CW Lee
    208. P Ng
    209. A Shahab
    210. A Yang
    211. Z Moqtaderi
    212. Z Zhu
    213. X Xu
    214. S Squazzo
    215. MJ Oberley
    216. D Inman
    217. MA Singer
    218. TA Richmond
    219. KJ Munn
    220. A Rada-Iglesias
    221. O Wallerman
    222. J Komorowski
    223. JC Fowler
    224. P Couttet
    225. AW Bruce
    226. OM Dovey
    227. PD Ellis
    228. CF Langford
    229. DA Nix
    230. G Euskirchen
    231. S Hartman
    232. AE Urban
    233. P Kraus
    234. S Van Calcar
    235. N Heintzman
    236. TH Kim
    237. K Wang
    238. C Qu
    239. G Hon
    240. R Luna
    241. CK Glass
    242. MG Rosenfeld
    243. SF Aldred
    244. SJ Cooper
    245. A Halees
    246. JM Lin
    247. HP Shulha
    248. X Zhang
    249. M Xu
    250. JN Haidar
    251. Y Yu
    252. Y Ruan
    253. VR Iyer
    254. RD Green
    255. C Wadelius
    256. PJ Farnham
    257. B Ren
    258. RA Harte
    259. AS Hinrichs
    260. H Trumbower
    261. H Clawson
    262. J Hillman-Jackson
    263. AS Zweig
    264. K Smith
    265. A Thakkapallayil
    266. G Barber
    267. RM Kuhn
    268. D Karolchik
    269. L Armengol
    270. CP Bird
    271. PI de Bakker
    272. AD Kern
    273. N Lopez-Bigas
    274. JD Martin
    275. BE Stranger
    276. A Woodroffe
    277. E Davydov
    278. A Dimas
    279. E Eyras
    280. IB Hallgrímsdóttir
    281. J Huppert
    282. MC Zody
    283. GR Abecasis
    284. X Estivill
    285. GG Bouffard
    286. X Guan
    287. NF Hansen
    288. JR Idol
    289. VV Maduro
    290. B Maskeri
    291. JC McDowell
    292. M Park
    293. PJ Thomas
    294. AC Young
    295. RW Blakesley
    296. DM Muzny
    297. E Sodergren
    298. DA Wheeler
    299. KC Worley
    300. H Jiang
    301. GM Weinstock
    302. RA Gibbs
    303. T Graves
    304. R Fulton
    305. ER Mardis
    306. RK Wilson
    307. M Clamp
    308. J Cuff
    309. S Gnerre
    310. DB Jaffe
    311. JL Chang
    312. K Lindblad-Toh
    313. ES Lander
    314. M Koriabine
    315. M Nefedov
    316. K Osoegawa
    317. Y Yoshinaga
    318. B Zhu
    319. PJ de Jong
    Nature 447:799–816.
  3. 3
    The transcriptional landscape of the mammalian genome
    1. P Carninci
    2. T Kasukawa
    3. S Katayama
    4. J Gough
    5. MC Frith
    6. N Maeda
    7. P Carninci
    8. T Kasukawa
    9. S Katayama
    10. J Gough
    11. MC Frith
    12. N Maeda
    13. R Oyama
    14. T Ravasi
    15. B Lenhard
    16. C Wells
    17. R Kodzius
    18. K Shimokawa
    19. VB Bajic
    20. SE Brenner
    21. S Batalov
    22. AR Forrest
    23. M Zavolan
    24. MJ Davis
    25. LG Wilming
    26. V Aidinis
    27. JE Allen
    28. A Ambesi-Impiombato
    29. R Apweiler
    30. RN Aturaliya
    31. TL Bailey
    32. M Bansal
    33. L Baxter
    34. KW Beisel
    35. T Bersano
    36. H Bono
    37. AM Chalk
    38. KP Chiu
    39. V Choudhary
    40. A Christoffels
    41. DR Clutterbuck
    42. ML Crowe
    43. E Dalla
    44. BP Dalrymple
    45. B de Bono
    46. G Della Gatta
    47. D di Bernardo
    48. T Down
    49. P Engstrom
    50. M Fagiolini
    51. G Faulkner
    52. CF Fletcher
    53. T Fukushima
    54. M Furuno
    55. S Futaki
    56. M Gariboldi
    57. P Georgii-Hemming
    58. TR Gingeras
    59. T Gojobori
    60. RE Green
    61. S Gustincich
    62. M Harbers
    63. Y Hayashi
    64. TK Hensch
    65. N Hirokawa
    66. D Hill
    67. L Huminiecki
    68. M Iacono
    69. K Ikeo
    70. A Iwama
    71. T Ishikawa
    72. M Jakt
    73. A Kanapin
    74. M Katoh
    75. Y Kawasawa
    76. J Kelso
    77. H Kitamura
    78. H Kitano
    79. G Kollias
    80. SP Krishnan
    81. A Kruger
    82. SK Kummerfeld
    83. IV Kurochkin
    84. LF Lareau
    85. D Lazarevic
    86. L Lipovich
    87. J Liu
    88. S Liuni
    89. S McWilliam
    90. M Madan Babu
    91. M Madera
    92. L Marchionni
    93. H Matsuda
    94. S Matsuzawa
    95. H Miki
    96. F Mignone
    97. S Miyake
    98. K Morris
    99. S Mottagui-Tabar
    100. N Mulder
    101. N Nakano
    102. H Nakauchi
    103. P Ng
    104. R Nilsson
    105. S Nishiguchi
    106. S Nishikawa
    107. F Nori
    108. O Ohara
    109. Y Okazaki
    110. V Orlando
    111. KC Pang
    112. WJ Pavan
    113. G Pavesi
    114. G Pesole
    115. N Petrovsky
    116. S Piazza
    117. J Reed
    118. JF Reid
    119. BZ Ring
    120. M Ringwald
    121. B Rost
    122. Y Ruan
    123. SL Salzberg
    124. A Sandelin
    125. C Schneider
    126. C Schönbach
    127. K Sekiguchi
    128. CA Semple
    129. S Seno
    130. L Sessa
    131. Y Sheng
    132. Y Shibata
    133. H Shimada
    134. K Shimada
    135. D Silva
    136. B Sinclair
    137. S Sperling
    138. E Stupka
    139. K Sugiura
    140. R Sultana
    141. Y Takenaka
    142. K Taki
    143. K Tammoja
    144. SL Tan
    145. S Tang
    146. MS Taylor
    147. J Tegner
    148. SA Teichmann
    149. HR Ueda
    150. E van Nimwegen
    151. R Verardo
    152. CL Wei
    153. K Yagi
    154. H Yamanishi
    155. E Zabarovsky
    156. S Zhu
    157. A Zimmer
    158. W Hide
    159. C Bult
    160. SM Grimmond
    161. RD Teasdale
    162. ET Liu
    163. V Brusic
    164. J Quackenbush
    165. C Wahlestedt
    166. JS Mattick
    167. DA Hume
    168. C Kai
    169. D Sasaki
    170. Y Tomaru
    171. S Fukuda
    172. M Kanamori-Katayama
    173. M Suzuki
    174. J Aoki
    175. T Arakawa
    176. J Iida
    177. K Imamura
    178. M Itoh
    179. T Kato
    180. H Kawaji
    181. N Kawagashira
    182. T Kawashima
    183. M Kojima
    184. S Kondo
    185. H Konno
    186. K Nakano
    187. N Ninomiya
    188. T Nishio
    189. M Okada
    190. C Plessy
    191. K Shibata
    192. T Shiraki
    193. S Suzuki
    194. M Tagami
    195. K Waki
    196. A Watahiki
    197. Y Okamura-Oho
    198. H Suzuki
    199. J Kawai
    200. Y Hayashizaki
    201. FANTOM Consortium
    202. Genome Network Project Core Group
    Science 309:1559–1563.
  4. 4
  5. 5
  6. 6
  7. 7
  8. 8
  9. 9
  10. 10
  11. 11
  12. 12
  13. 13
    The origins of genome architecture
    1. M Lynch
    Sunderland, MA: Sinauer Associates.
  14. 14
    Introns: evolution and function
    1. JS Mattick
    Current Opinion in Genetics & Development 4:823–831.
  15. 15
  16. 16
    Specific expression of long noncoding RNAs in the mouse brain
    1. TR Mercer
    2. ME Dinger
    3. SM Sunkin
    4. MF Mehler
    5. JS Mattick
    Proceedings of the National Academy of Sciences of the United States of America 105:716–721.
  17. 17
  18. 18
  19. 19
  20. 20
  21. 21
  22. 22
  23. 23

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Author details

  1. John S Mattick, Reviewing Editor

    St Vincent’s Clinical School and the School of Biotechnology and Biomolecular Sciences, Garvan Institute of Medical Research, Sydney, Australia
    For correspondence
    Competing interests
    The author declares that no competing interests exist.

Publication history

  1. Version of Record published: December 31, 2013 (version 1)


© 2013, Mattick

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