scholarly journals Noncoding Genes on Sex Chromosomes and Their Function in Sex Determination, Dosage Compensation, Male Traits, and Diseases

2021 ◽  
pp. 1-9
Author(s):  
Michelle C. Maier ◽  
Molly-Rose A. McInerney ◽  
Jennifer A. Marshall Graves ◽  
Fadi J. Charchar
Keyword(s):  
Y Chromosome ◽  
Sex Chromosomes ◽  
Sex Differentiation ◽  
Regulation Of Gene Expression ◽  
Genetic Material ◽  
Noncoding Rnas ◽  
Cellular Functions ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Sex Development

The mammalian Y chromosome has evolved in many species into a specialized chromosome that contributes to sex development among other male phenotypes. This function is well studied in terms of protein-coding genes. Less is known about the noncoding genome on the Y chromosome and its contribution to both sex development and other traits. Once considered junk genetic material, noncoding RNAs are now known to contribute to the regulation of gene expression and to play an important role in refining cellular functions. The prime examples are noncoding genes on the X chromosome, which mitigate the differential dosage of genes on sex chromosomes. Here, we discuss the evolution of noncoding RNAs on the Y chromosome and the emerging evidence of how micro, long, and circular noncoding RNAs transcribed from the Y chromosome contribute to sex differentiation. We briefly touch on emerging evidence that these noncoding RNAs also contribute to some other important clinical phenotypes in humans.

scholarly journals Massive gene amplification on a recently formed Drosophila Y chromosome

2018 ◽  
Author(s):  
Doris Bachtrog ◽  
Shivani Mahajan ◽  
Ryan Bracewell
Keyword(s):  
Y Chromosome ◽  
Sex Chromosomes ◽  
Sequence Homology ◽  
Small Rnas ◽  
Sex Chromosome ◽  
Male Fitness ◽  
Protein Coding ◽  
Chromosome Differentiation ◽  
Protein Coding Genes ◽  
Drastic Increase

Widespread loss of genes on the Y is considered a hallmark of sex chromosome differentiation. Here we show that the initial stages of Y evolution are driven by massive amplification of distinct classes of genes. The neo-Y chromosome of Drosophila miranda initially contained about 3000 protein-coding genes, but has gained over 3200 genes since its formation about 1.5 MY ago, primarily by tandem amplification of protein-coding genes ancestrally present on this chromosome. We show that distinct evolutionary processes may account for this drastic increase in gene number on the Y. Testis-specific and dosage sensitive genes appear to have amplified on the Y to increase male fitness. A distinct class of meiosis-related multi-copy Y genes independently co-amplified on the X, and their expansion is likely driven by conflicts over segregation. Co-amplified X/Y genes are highly expressed in testis, enriched for meiosis and RNAi functions, and are frequently targeted by small RNAs in testis. This suggests that their amplification is driven by X vs. Y antagonism for increased transmission, where sex chromosome drive suppression is likely mediated by sequence homology between the suppressor and distorter, through RNAi mechanism. Thus, our analysis suggests that newly emerged sex chromosomes are a battleground for sexual and meiotic conflict.

scholarly journals Chromosomal assembly of the nuclear genome of the endosymbiont-bearing trypanosomatid Angomonas deanei

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
John W Davey ◽  
Carolina M C Catta-Preta ◽  
Sally James ◽  
Sarah Forrester ◽  
Maria Cristina M Motta ◽  
...  
Keyword(s):  
Chromosome Number ◽  
Noncoding Rnas ◽  
Nuclear Genome ◽  
Supernumerary Chromosome ◽  
Ribosomal Rnas ◽  
Protein Coding ◽  
Transfer Rnas ◽  
Protein Coding Genes ◽  
Oxford Nanopore ◽  
Genome Assemblies

Abstract Angomonas deanei is an endosymbiont-bearing trypanosomatid with several highly fragmented genome assemblies and unknown chromosome number. We present an assembly of the A. deanei nuclear genome based on Oxford Nanopore sequence that resolves into 29 complete or close-to-complete chromosomes. The assembly has several previously unknown special features; it has a supernumerary chromosome, a chromosome with a 340-kb inversion, and there is a translocation between two chromosomes. We also present an updated annotation of the chromosomal genome with 10,365 protein-coding genes, 59 transfer RNAs, 26 ribosomal RNAs, and 62 noncoding RNAs.

scholarly journals Long noncoding RNA: a dazzling dancer in tumor immune microenvironment

2020 ◽  
Vol 39 (1) ◽  
Author(s):  
Yalu Zhang ◽  
Qiaofei Liu ◽  
Quan Liao
Keyword(s):  
Noncoding Rna ◽  
Molecular Mechanisms ◽  
Immune Escape ◽  
Noncoding Rnas ◽  
Pathological Process ◽  
Cellular Functions ◽  
Immune Microenvironment ◽  
Protein Coding ◽  
Functional Roles ◽  
Tumor Immune Microenvironment

Abstract Long noncoding RNAs (lncRNAs) are a class of endogenous, non-protein coding RNAs that are highly linked to various cellular functions and pathological process. Emerging evidence indicates that lncRNAs participate in crosstalk between tumor and stroma, and reprogramming of tumor immune microenvironment (TIME). TIME possesses distinct populations of myeloid cells and lymphocytes to influence the immune escape of cancer, the response to immunotherapy, and the survival of patients. However, hitherto, a comprehensive review aiming at relationship between lncRNAs and TIME is missing. In this review, we focus on the functional roles and molecular mechanisms of lncRNAs within the TIME. Furthermore, we discussed the potential immunotherapeutic strategies based on lncRNAs and their limitations.

Identify the critical protein‐coding genes and long noncoding RNAs in cardiac myxoma

2019 ◽  
Vol 120 (8) ◽  
pp. 13441-13452 ◽  
Author(s):  
Nan Cheng ◽  
Yuanbin Wu ◽  
Huajun Zhang ◽  
Yi Guo ◽  
Huimin Cui ◽  
...  
Keyword(s):  
Cardiac Myxoma ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Protein Coding ◽  
Protein Coding Genes

scholarly journals Chronic lymphocytic leukemia: interplay between noncoding RNAs and protein-coding genes

Blood ◽  
2009 ◽  
Vol 114 (23) ◽  
pp. 4761-4770 ◽  
Author(s):  
George A. Calin ◽  
Carlo M. Croce
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Noncoding Rnas ◽  
Malignant Potential ◽  
Lymphocytic Leukemia ◽  
Leukemic Cells ◽  
Cancer Genes ◽  
New Paradigm ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Molecular Oncology

Abstract One of the most unexpected and fascinating discoveries in oncology over the past few years is the interplay between abnormalities in protein-coding genes and noncoding RNAs (ncRNAs) that is causally involved in cancer initiation, progression, and dissemination. MicroRNAs (miRNAs), small regulatory ncRNAs, are involved in the pathogenesis of all types of human cancers, including leukemias, mainly via dysregulation of expression of cancer genes. Increasing evidence shows that miRNAs can work as tumor suppressors (inhibiting malignant potential) or oncogenes (activating malignant potential). Researchers first identified this new paradigm of molecular oncology in patients with chronic lymphocytic leukemia (CLL). Understanding the roles of miRNAs and other ncRNAs in leukemic cells is not only uncovering a new layer of gene regulation but also providing new markers for improved diagnosis and prognosis, as well as novel therapeutic options for CLL patients. Herein we focus on the roles of miRNAs and ultraconserved ncRNA genes in CLL, highlighting what is already known about their function, proposing a novel model of CLL predisposition and progression, and describing the challenges for the near future.

scholarly journals Complete Genome Sequence of Methanothermobacter sp. Strain THM-1, a Thermophilic and Hydrogenotrophic Methanogen Isolated from an Anaerobic Reactor in South Korea

2021 ◽  
Vol 10 (38) ◽  
Author(s):  
Byoung-Seung Jeon ◽  
Hyunjin Kim ◽  
Young Wook Go ◽  
Hyunook Kim ◽  
Okkyoung Choi ◽  
...  
Keyword(s):  
Complete Genome Sequence ◽  
Complete Genome ◽  
Noncoding Rnas ◽  
Gc Content ◽  
Its Sequence ◽  
Protein Coding ◽  
Content Type ◽  
Anaerobic Reactor ◽  
Hydrogenotrophic Methanogen ◽  
Protein Coding Genes

Methanothermobacter sp. strain THM-1, a thermophilic and hydrogenotrophic methanogen, was isolated from an anaerobic reactor enriched with thermophilic methanogens. The genome of THM-1 shares 98.81% of its sequence with Methanothermobacter wolfeii isolate SIV6 and consists of 1,724,502 bp with 1,665 protein-coding genes, 50 noncoding RNAs, and a GC content of 48.6%.

scholarly journals Genome Sequence of Lactobacillus fermentum 47-7, a Good In Vitro Probiotic Strain Isolated from a Healthy Thai Infant

2019 ◽  
Vol 8 (39) ◽  
Author(s):  
Atthaphon Konyanee ◽  
Panjamaporn Yotpanya ◽  
Marutpong Panya ◽  
Chulapan Engchanil ◽  
Namfon Suebwongsa ◽  
...  
Keyword(s):  
Genome Size ◽  
Genome Sequence ◽  
Noncoding Rnas ◽  
Probiotic Strain ◽  
Lactobacillus Fermentum ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes

We report the genome sequence of Lactobacillus fermentum 47-7, a good in vitro probiotic strain isolated from an infant. Its genome size is 1.83 Mb, it is assembled from 180 contigs, and it consists of 1,636 protein-coding genes, 15 rRNAs, 57 tRNAs, and 4 noncoding RNAs. This genome sequence will be useful for a variety of applications.

scholarly journals On the discovery of ADRAM, an experience-dependent long noncoding RNA that drives fear extinction through a direct interaction with the chaperone protein 14-3-3

2021 ◽  
Author(s):  
XIang Li ◽  
Qiongyi Zhao ◽  
Ziqi Wang ◽  
Wei-Siang Liau ◽  
Dean Basic ◽  
...  
Keyword(s):  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Large Population ◽  
Regulation Of Gene Expression ◽  
Fear Extinction ◽  
Early Gene ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Chaperone Protein ◽  
The Brain

Long-noncoding RNA (lncRNA) comprise a new class of genes that have been assigned key roles in development and disease. Many lncRNAs are specifically transcribed in the brain where they regulate the expression of protein-coding genes that underpin neuronal function; however, their role in learning and memory remains largely unexplored. We used RNA Capture-Seq to identify a large population of lncRNAs that are expressed in the infralimbic cortex of adult male mice in response to fear-related learning, with 14.5% of these annotated in the GENCODE database as lncRNAs with no known function. We combined these data with cell-type-specific ATAC-seq on neurons that had been selectively activated by fear-extinction learning, and revealed 434 lncRNAs derived from enhancer regions in the vicinity of protein-coding genes. In particular, we discovered an experience-induced lncRNA called ADRAM that acts as both a scaffold and a combinatorial guide to recruit the brain-enriched chaperone protein 14-3-3 to the promoter of the memory-associated immediate early gene Nr4a2. This leads to the expulsion of histone deactylases 3 and 4, and the recruitment of the histone acetyltransferase creb binding protein, which drives learning-induced Nr4a2 expression. Knockdown of ADRAM disrupts this interaction, blocks the expression of Nr4a2, and ultimately impairs the formation of fear-extinction memory. This study expands the lexicon of experience-dependent lncRNA activity in the brain, highlights enhancer-derived RNAs (eRNAs) as key players in the epigenetic regulation of gene expression associated with fear extinction, and suggests eRNAs, such as ADRAM, may constitute viable targets in developing novel treatments for fear-related anxiety disorders.

scholarly journals Bacterial Noncoding RNAs Excised from within Protein-Coding Transcripts

mBio ◽  
2018 ◽  
Vol 9 (5) ◽  
Author(s):  
Daniel Dar ◽  
Rotem Sorek
Keyword(s):  
Expression Patterns ◽  
Noncoding Rnas ◽  
Large Set ◽  
Rna Structures ◽  
Protein Coding ◽  
Small Noncoding Rnas ◽  
Coding Regions ◽  
Protein Coding Genes ◽  
Evolutionarily Conserved ◽  
Intergenic Regions

ABSTRACT Prokaryotic genomes encode a plethora of small noncoding RNAs (ncRNAs) that fine-tune the expression of specific genes. The vast majority of known bacterial ncRNAs are encoded from within intergenic regions, where their expression is controlled by promoter and terminator elements, similarly to protein-coding genes. In addition, recent studies have shown that functional ncRNAs can also be derived from gene 3′ untranslated regions (3′UTRs) via an alternative biogenesis pathway, in which the ncRNA segment is separated from the mRNA via RNase cleavage. Here, we report the detection of a large set of decay-generated noncoding RNAs (decRNAs), many of which are completely embedded within protein-coding mRNA regions rather than in the UTRs. We show that these decRNAs are “carved out” of the mRNA through the action of RNase E and that they are predicted to fold into highly stable RNA structures, similar to those of known ncRNAs. A subset of these decRNAs is predicted to interact with Hfq or ProQ or both, which act as ncRNA chaperones, and some decRNAs display evolutionarily conserved sequences and conserved expression patterns between different species. These results suggest that mRNA protein-coding regions may harbor a large set of potentially functional small RNAs. IMPORTANCE Bacteria and archaea utilize regulatory small noncoding RNAs (ncRNAs) to control the expression of specific genetic programs. These ncRNAs are almost exclusively encoded within intergenic regions and are independently transcribed. Here, we report on a large set ncRNAs that are “carved out” from within the protein-coding regions of Escherichia coli mRNAs by cellular RNases. These protected mRNA fragments fold into energetically stable RNA structures, reminiscent of those of intergenic regulatory ncRNAs. In addition, a subset of these ncRNAs coprecipitate with the major ncRNA chaperones Hfq and ProQ and display evolutionarily conserved sequences and conserved expression patterns between different bacterial species. Our data suggest that protein-coding genes can potentially act as a reservoir of regulatory ncRNAs.

scholarly journals An integrative proteogenomics approach reveals peptides encoded by annotated lincRNA in the mouse kidney inner medulla

2020 ◽  
Vol 52 (10) ◽  
pp. 485-491
Author(s):  
Cameron T. Flower ◽  
Lihe Chen ◽  
Hyun Jun Jung ◽  
Viswanathan Raghuram ◽  
Mark A. Knepper ◽  
...  
Keyword(s):  
Noncoding Rnas ◽  
Peptide Identification ◽  
Mouse Kidney ◽  
Open Reading Frames ◽  
Specific Expression ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Peptide Database ◽  
Liquid Chromatography Tandem Mass ◽  
Spectrum Matching

Long noncoding RNAs (lncRNAs) are intracellular transcripts longer than 200 nucleotides and lack protein-coding information. A subclass of lncRNA known as long intergenic noncoding RNAs (lincRNAs) are transcribed from genomic regions that share no overlap with annotated protein-coding genes. Increasing evidence has shown that some annotated lincRNA transcripts do in fact contain open reading frames (ORFs) encoding functional short peptides in the cell. Few robust methods for lincRNA-encoded peptide identification have been reported, and the tissue-specific expression of these peptides has been largely unexplored. Here we propose an integrative workflow for lincRNA-encoded peptide discovery and test it on the mouse kidney inner medulla (IM). In brief, low molecular weight protein fractions were enriched from homogenate of IMs and trypsinized into shorter peptides, which were sequenced by high resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS). To curate a hypothetical lincRNA-encoded peptide database for peptide-spectrum matching following LC-MS/MS, we performed RNA-Seq on IMs, computationally removed reads overlapping with annotated protein-coding genes, and remapped the remaining reads to a database of mouse noncoding transcripts to infer lincRNA expression. Expressed lincRNAs were searched for ORFs by an existing rule-based algorithm, and translated ORFs were used for peptide-spectrum matching. Peptides identified by LC-MS/MS were further evaluated by using several quality control criteria and bioinformatics methods. We discovered three novel lincRNA-encoded peptides, which are conserved in mouse, rat, and human. The workflow can be adapted for discovery of small protein-coding genes in any species or tissue where noncoding transcriptome information is available.

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