-
[show abstract]
[hide abstract]
ABSTRACT: It is now clear that the genomes of many organisms encode thousands of large and small non-coding (nc)RNAs. However, relative to the discovery of ncRNAs the functions and mechanisms of ncRNAs remain disproportionately understood. One intriguing observation is that many ncRNAs are found to be associated with protein complexes including those involved in transcription regulation, post-transcriptional silencing, and epigentic regulation. These observations suggest that the functions and mechanisms of many of these ncRNAs may depend on their interactions with various protein complexes within the cell. In this review we discuss well known examples as well as newly emerging evidence of a widespread RNA-protein interactions in distinct biological processes in a wide range of organisms, and highlight the importance of developing new technologies to dissect these interactions. Finally, we propose that mis-regulation of ncRNAs interactions with their protein partners may contribute to human disease, and open up a novel approach to therapeutic interventions.
Seminars in Cell and Developmental Biology 02/2011; 22(4):359-65. · 6.65 Impact Factor
-
Maite Huarte,
Mitchell Guttman,
David Feldser,
Manuel Garber,
Magdalena J Koziol,
Daniela Kenzelmann-Broz, Ahmad M Khalil,
Or Zuk,
Ido Amit,
Michal Rabani,
Laura D Attardi,
Aviv Regev,
Eric S Lander,
Tyler Jacks,
John L Rinn
[show abstract]
[hide abstract]
ABSTRACT: Recently, more than 1000 large intergenic noncoding RNAs (lincRNAs) have been reported. These RNAs are evolutionarily conserved in mammalian genomes and thus presumably function in diverse biological processes. Here, we report the identification of lincRNAs that are regulated by p53. One of these lincRNAs (lincRNA-p21) serves as a repressor in p53-dependent transcriptional responses. Inhibition of lincRNA-p21 affects the expression of hundreds of gene targets enriched for genes normally repressed by p53. The observed transcriptional repression by lincRNA-p21 is mediated through the physical association with hnRNP-K. This interaction is required for proper genomic localization of hnRNP-K at repressed genes and regulation of p53 mediates apoptosis. We propose a model whereby transcription factors activate lincRNAs that serve as key repressors by physically associating with repressive complexes and modulate their localization to sets of previously active genes.
Cell 08/2010; 142(3):409-19. · 32.40 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: During meiosis, paternal and maternal homologous chromosomes recombine at specific recombination sites named hotspots. What renders 2% of the mammalian genomes permissive to meiotic recombination by allowing Spo11 endonuclease to initiate double-strand breaks is largely unknown. Work in yeast has shown that chromatin accessibility seems to be important for this activity. Here, we define nucleosome profiles and dynamics at four mouse recombination hotspots by purifying highly enriched fractions of meiotic cells. We found that nucleosome occupancy is generally stable during meiosis progression. Interestingly, the cores of recombination hotspots have largely open chromatin structure, and the localization of the few nucleosomes present in these cores correlates precisely with the crossover-free zones in recombinogenic domains. Collectively, these high-resolution studies suggest that nucleosome occupancy seems to direct, at least in part, how meiotic recombination events are processed.
EMBO Reports 07/2010; 11(7):555-60. · 7.36 Impact Factor
-
Ahmad M Khalil,
Mitchell Guttman,
Maite Huarte,
Manuel Garber,
Arjun Raj,
Dianali Rivea Morales,
Kelly Thomas,
Aviva Presser,
Bradley E Bernstein,
Alexander van Oudenaarden,
Aviv Regev,
Eric S Lander,
John L Rinn
[show abstract]
[hide abstract]
ABSTRACT: We recently showed that the mammalian genome encodes >1,000 large intergenic noncoding (linc)RNAs that are clearly conserved across mammals and, thus, functional. Gene expression patterns have implicated these lincRNAs in diverse biological processes, including cell-cycle regulation, immune surveillance, and embryonic stem cell pluripotency. However, the mechanism by which these lincRNAs function is unknown. Here, we expand the catalog of human lincRNAs to approximately 3,300 by analyzing chromatin-state maps of various human cell types. Inspired by the observation that the well-characterized lincRNA HOTAIR binds the polycomb repressive complex (PRC)2, we tested whether many lincRNAs are physically associated with PRC2. Remarkably, we observe that approximately 20% of lincRNAs expressed in various cell types are bound by PRC2, and that additional lincRNAs are bound by other chromatin-modifying complexes. Also, we show that siRNA-mediated depletion of certain lincRNAs associated with PRC2 leads to changes in gene expression, and that the up-regulated genes are enriched for those normally silenced by PRC2. We propose a model in which some lincRNAs guide chromatin-modifying complexes to specific genomic loci to regulate gene expression.
Proceedings of the National Academy of Sciences 08/2009; 106(28):11667-72. · 9.68 Impact Factor
-
Ahmad M Khalil
Nature 04/2009; 458(7236):263. · 36.28 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Recent efforts have revealed that numerous protein-coding messenger RNAs have natural antisense transcript partners, most of which seem to be noncoding RNAs. Here we identify a conserved noncoding antisense transcript for beta-secretase-1 (BACE1), a crucial enzyme in Alzheimer's disease pathophysiology. The BACE1-antisense transcript (BACE1-AS) regulates BACE1 mRNA and subsequently BACE1 protein expression in vitro and in vivo. Upon exposure to various cell stressors including amyloid-beta 1-42 (Abeta 1-42), expression of BACE1-AS becomes elevated, increasing BACE1 mRNA stability and generating additional Abeta 1-42 through a post-transcriptional feed-forward mechanism. BACE1-AS concentrations were elevated in subjects with Alzheimer's disease and in amyloid precursor protein transgenic mice. These data show that BACE1 mRNA expression is under the control of a regulatory noncoding RNA that may drive Alzheimer's disease-associated pathophysiology. In summary, we report that a long noncoding RNA is directly implicated in the increased abundance of Abeta 1-42 in Alzheimer's disease.
Nature medicine 08/2008; 14(7):723-30. · 27.14 Impact Factor
-
Ge Shan,
Yujing Li,
Junliang Zhang,
Wendi Li,
Keith E Szulwach,
Ranhui Duan,
Mohammad A Faghihi, Ahmad M Khalil,
Lianghua Lu,
Zain Paroo,
Anthony W S Chan,
Zhangjie Shi,
Qinghua Liu,
Claes Wahlestedt,
Chuan He,
Peng Jin
[show abstract]
[hide abstract]
ABSTRACT: Small interfering RNAs (siRNAs) and microRNAs (miRNAs) are sequence-specific post-transcriptional regulators of gene expression. Although major components of the RNA interference (RNAi) pathway have been identified, regulatory mechanisms for this pathway remain largely unknown. Here we demonstrate that the RNAi pathway can be modulated intracellularly by small molecules. We have developed a cell-based assay to monitor the activity of the RNAi pathway and find that the small-molecule enoxacin (Penetrex) enhances siRNA-mediated mRNA degradation and promotes the biogenesis of endogenous miRNAs. We show that this RNAi-enhancing activity depends on the trans-activation-responsive region RNA-binding protein. Our results provide a proof-of-principle demonstration that small molecules can be used to modulate the activity of the RNAi pathway. RNAi enhancers may be useful in the development of research tools and therapeutics.
Nature Biotechnology 08/2008; 26(8):933-40. · 29.50 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Several genome-wide transcriptomics efforts have shown that a large percentage of the mammalian genome is transcribed into RNAs, however, only a small percentage (1-2%) of these RNAs is translated into proteins. Currently there is an intense interest in characterizing the function of the different classes of noncoding RNAs and their relevance to human disease. Using genomic approaches we discovered FMR4, a primate-specific noncoding RNA transcript (2.4 kb) that resides upstream and likely shares a bidirectional promoter with FMR1. FMR4 is a product of RNA polymerase II and has a similar half-life to FMR1. The CGG expansion in the 5' UTR of FMR1 appears to affect transcription in both directions as we found FMR4, similar to FMR1, to be silenced in fragile X patients and up-regulated in premutation carriers. Knockdown of FMR4 by several siRNAs did not affect FMR1 expression, nor vice versa, suggesting that FMR4 is not a direct regulatory transcript for FMR1. However, FMR4 markedly affected human cell proliferation in vitro; siRNAs knockdown of FMR4 resulted in alterations in the cell cycle and increased apoptosis, while the overexpression of FMR4 caused an increase in cell proliferation. Collectively, our results demonstrate an antiapoptotic function of FMR4 and provide evidence that a well-studied genomic locus can show unexpected functional complexity. It cannot be excluded that altered FMR4 expression might contribute to aspects of the clinical presentation of fragile X syndrome and/or related disorders.
PLoS ONE 02/2008; 3(1):e1486. · 4.09 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Based on the formation of the XY body at pachytene and expression studies of a few X-linked genes, the X and Y chromosomes seem to undergo transcriptional inactivation during mammalian spermatogenesis. However, the extent and the mechanism of X and Y inactivation are not known. Here, we show that both the X and Y chromosomes undergo sequential changes in their histone modifications beginning at the pachytene stage of meiosis. These changes usually are associated with transcriptional inactivation in somatic cells, and they coincide with the exclusion of the phosphorylated (active) form of RNA polymerase II from the XY body. Both sex chromosomes undergo extensive deacetylation at histones H3 and H4 and (di)methylation of lysine (K)9 on histone H3; however, there are no changes in H3-K4 methylation. These changes persist even when the XY body disappears in late pachytene, and the X and Y chromosomes segregate from one another after the first meiotic division. By the spermatid stage, histone modifications of the X and Y chromosomes revert to those of active chromatin and RNA polymerase II reengages with both chromosomes. Our observations indicate that X and Y inactivation is extensive and persists even when the X and Y chromosomes are separated in secondary spermatocytes. These findings provide insights into epigenetic programming and chromatin dynamics in the male germ line.
Proceedings of the National Academy of Sciences 11/2004; 101(47):16583-7. · 9.68 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: The process of spermatogenesis is a unique form of cellular differentiation and is regulated by genetic and epigenetic factors. Recent studies have shown that some epigenetic factors (histone variants and histone modifying enzymes) are exclusively expressed during spermatogenesis; the disruption of these factors leads to spermatogenic defects. Also, during spermatogenesis a key epigenetic process termed meiotic sex chromosomes inactivation (MSCI) occurs; MSCI leads to the inactivation of most genes on the X and Y chromosomes; however, the mechanism of MSCI is distinct from X inactivation in female somatic cells. Furthermore, a new class of non-coding RNAs (i.e., piRNAs) has recently been identified which is exclusively expressed during spermatogenesis. This review discusses recent advances in our understanding of epigenetic mechanisms that operate during spermatogenesis with specific emphasis on histone modifications, MSCI and non-coding RNAs. Finally, we propose that spermatogenesis can be a powerful experimental system to dissect epigenetic mechanisms of gene regulation.
Epigenetics: official journal of the DNA Methylation Society 3(1):21-8. · 4.58 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: It is now estimated that 150-200 genes clustered in several discrete regions escape X inactivation in somatic cells of human females by unknown mechanisms. Here, we show that although the human female inactive X chromosome is largely devoid of histone 3 lysine 4 trimethylation (H3K4me3), regions that are known to escape X inactivation, including the pseudoautosomal regions, are enriched with this modification. Also, H3K4me3, unlike H3K4me2 and H4 and H3 acetylation, is restricted to discrete regions on metaphase chromosomes. In contrast to humans, there are only a few genes that are known to escape X inactivation in the mouse. Therefore, we examined mouse female somatic cells with H3K4me3 to identify candidate regions with genes that escape X inactivation. We found the mouse female inactive X in somatic cells and the male inactive X in meiosis to have seven discrete regions that are enriched with H3K4me3. Furthermore, RNA polymerase II is largely excluded from the XY body at male pachytene except for several discrete regions on the X and Y suggesting the presence of regions that also escape sex chromosome inactivation during male meiosis.
Epigenetics: official journal of the DNA Methylation Society 2(2):114-8. · 4.58 Impact Factor
